A Novel Characterization of Amalgamated Networks in Natural Systems

PubMed Central

Barranca, Victor J.; Zhou, Douglas; Cai, David

2015-01-01

Densely-connected networks are prominent among natural systems, exhibiting structural characteristics often optimized for biological function. To reveal such features in highly-connected networks, we introduce a new network characterization determined by a decomposition of network-connectivity into low-rank and sparse components. Based on these components, we discover a new class of networks we define as amalgamated networks, which exhibit large functional groups and dense connectivity. Analyzing recent experimental findings on cerebral cortex, food-web, and gene regulatory networks, we establish the unique importance of amalgamated networks in fostering biologically advantageous properties, including rapid communication among nodes, structural stability under attacks, and separation of network activity into distinct functional modules. We further observe that our network characterization is scalable with network size and connectivity, thereby identifying robust features significant to diverse physical systems, which are typically undetectable by conventional characterizations of connectivity. We expect that studying the amalgamation properties of biological networks may offer new insights into understanding their structure-function relationships. PMID:26035066

Concerted Interconversion between Ionic Lock Substates of the β2 Adrenergic Receptor Revealed by Microsecond Timescale Molecular Dynamics

PubMed Central

Romo, Tod D.; Grossfield, Alan; Pitman, Michael C.

2010-01-01

Abstract The recently solved crystallographic structures for the A2A adenosine receptor and the β1 and β2 adrenergic receptors have shown important differences between members of the class-A G-protein-coupled receptors and their archetypal model, rhodopsin, such as the apparent breaking of the ionic lock that stabilizes the inactive structure. Here, we characterize a 1.02 μs all-atom simulation of an apo-β2 adrenergic receptor that is missing the third intracellular loop to better understand the inactive structure. Although we find that the structure is remarkably rigid, there is a rapid influx of water into the core of the protein, as well as a slight expansion of the molecule relative to the crystal structure. In contrast to the x-ray crystal structures, the ionic lock rapidly reforms, although we see an activation-precursor-like event wherein the ionic lock opens for ∼200 ns, accompanied by movements in the transmembrane helices associated with activation. When the lock reforms, we see the structure return to its inactive conformation. We also find that the ionic lock exists in three states: closed (or locked), semi-open with a bridging water molecule, and open. The interconversion of these states involves the concerted motion of the entire protein. We characterize these states and the concerted motion underlying their interconversion. These findings may help elucidate the connection between key local events and the associated global structural changes during activation. PMID:20074514

Perovskite-Inspired Photovoltaic Materials: Toward Best Practices in Materials Characterization and Calculations

DOE PAGES

Hoye, Robert L. Z.; Schulz, Philip; Schelhas, Laura T.; ...

2017-02-28

Recently, there has been an explosive growth in research based on hybrid lead-halide perovskites for photovoltaics owing to rapid improvements in efficiency. The advent of these materials for solar applications has led to widespread interest in understanding the key enabling properties of these materials. This has resulted in renewed interest in related compounds and a search for materials that may replicate the defect-tolerant properties and long lifetimes of the hybrid lead-halide perovskites. Given the rapid pace of development of the field, the rises in efficiencies of these systems have outpaced the more basic understanding of these materials. Measuring or calculatingmore » the basic properties, such as crystal/electronic structure and composition, can be challenging because some of these materials have anisotropic structures, and/or are composed of both heavy metal cations and volatile, mobile, light elements. Some consequences are beam damage during characterization, composition change under vacuum, or compound effects, such as the alteration of the electronic structure through the influence of the substrate. These effects make it challenging to understand the basic properties integral to optoelectronic operation. Compounding these difficulties is the rapid pace with which the field progresses. This has created an ongoing need to continually evaluate best practices with respect to characterization and calculations, as well as to identify inconsistencies in reported values to determine if those inconsistencies are rooted in characterization methodology or materials synthesis. This article describes the difficulties in characterizing hybrid lead-halide perovskites and new materials and how these challenges may be overcome. The topic was discussed at a seminar at the 2015 Materials Research Society Fall Meeting & Exhibit. This article highlights the lessons learned from the seminar and the insights of some of the attendees, with reference to both recent literature and controlled experiments to illustrate the challenges discussed. The focus in this article is on crystallography, composition measurements, photoemission spectroscopy, and calculations on perovskites and new, related absorbers. We suggest how the reporting of the important artifacts could be streamlined between groups to ensure reproducibility as the field progresses.« less

Perovskite-Inspired Photovoltaic Materials: Toward Best Practices in Materials Characterization and Calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hoye, Robert L. Z.; Schulz, Philip; Schelhas, Laura T.

Recently, there has been an explosive growth in research based on hybrid lead-halide perovskites for photovoltaics owing to rapid improvements in efficiency. The advent of these materials for solar applications has led to widespread interest in understanding the key enabling properties of these materials. This has resulted in renewed interest in related compounds and a search for materials that may replicate the defect-tolerant properties and long lifetimes of the hybrid lead-halide perovskites. Given the rapid pace of development of the field, the rises in efficiencies of these systems have outpaced the more basic understanding of these materials. Measuring or calculatingmore » the basic properties, such as crystal/electronic structure and composition, can be challenging because some of these materials have anisotropic structures, and/or are composed of both heavy metal cations and volatile, mobile, light elements. Some consequences are beam damage during characterization, composition change under vacuum, or compound effects, such as the alteration of the electronic structure through the influence of the substrate. These effects make it challenging to understand the basic properties integral to optoelectronic operation. Compounding these difficulties is the rapid pace with which the field progresses. This has created an ongoing need to continually evaluate best practices with respect to characterization and calculations, as well as to identify inconsistencies in reported values to determine if those inconsistencies are rooted in characterization methodology or materials synthesis. This article describes the difficulties in characterizing hybrid lead-halide perovskites and new materials and how these challenges may be overcome. The topic was discussed at a seminar at the 2015 Materials Research Society Fall Meeting & Exhibit. This article highlights the lessons learned from the seminar and the insights of some of the attendees, with reference to both recent literature and controlled experiments to illustrate the challenges discussed. The focus in this article is on crystallography, composition measurements, photoemission spectroscopy, and calculations on perovskites and new, related absorbers. We suggest how the reporting of the important artifacts could be streamlined between groups to ensure reproducibility as the field progresses.« less

Rapid Characterization of Constituents in Tribulus terrestris from Different Habitats by UHPLC/Q-TOF MS.

PubMed

Zheng, Wei; Wang, Fangxu; Zhao, Yang; Sun, Xinguang; Kang, Liping; Fan, Ziquan; Qiao, Lirui; Yan, Renyi; Liu, Shuchen; Ma, Baiping

2017-11-01

A strategy for rapid identification of the chemical constituents from crude extracts of Tribulus terrestris was proposed using an informatics platform for the UHPLC/Q-TOF MS E data analyses. This strategy mainly utilizes neutral losses, characteristic fragments, and in-house library to rapidly identify the structure of the compounds. With this strategy, rapid characterization of the chemical components of T. terrestris from Beijing, China was successfully achieved. A total of 82 steroidal saponins and nine flavonoids were identified or tentatively identified from T. terrestris. Among them, 15 new components were deduced based on retention times and characteristic MS fragmentation patterns. Furthermore, the chemical components of T. terrestris, including the other two samples from Xinjiang Uygur Autonomous region, China, and Rome, Italy, were also identified with this strategy. Altogether, 141 chemical components were identified from these three samples, of which 39 components were identified or tentatively identified as new compounds, including 35 groups of isomers. It demonstrated that this strategy provided an efficient protocol for the rapid identification of chemical constituents in complex samples such as traditional Chinese medicines (TCMs) by UHPLC/Q-TOF MS E with informatics platform. Graphical Abstract ᅟ.

Rapid Characterization of Constituents in Tribulus terrestris from Different Habitats by UHPLC/Q-TOF MS

NASA Astrophysics Data System (ADS)

Zheng, Wei; Wang, Fangxu; Zhao, Yang; Sun, Xinguang; Kang, Liping; Fan, Ziquan; Qiao, Lirui; Yan, Renyi; Liu, Shuchen; Ma, Baiping

2017-08-01

A strategy for rapid identification of the chemical constituents from crude extracts of Tribulus terrestris was proposed using an informatics platform for the UHPLC/Q-TOF MSE data analyses. This strategy mainly utilizes neutral losses, characteristic fragments, and in-house library to rapidly identify the structure of the compounds. With this strategy, rapid characterization of the chemical components of T. terrestris from Beijing, China was successfully achieved. A total of 82 steroidal saponins and nine flavonoids were identified or tentatively identified from T. terrestris. Among them, 15 new components were deduced based on retention times and characteristic MS fragmentation patterns. Furthermore, the chemical components of T. terrestris, including the other two samples from Xinjiang Uygur Autonomous region, China, and Rome, Italy, were also identified with this strategy. Altogether, 141 chemical components were identified from these three samples, of which 39 components were identified or tentatively identified as new compounds, including 35 groups of isomers. It demonstrated that this strategy provided an efficient protocol for the rapid identification of chemical constituents in complex samples such as traditional Chinese medicines (TCMs) by UHPLC/Q-TOF MSE with informatics platform. [Figure not available: see fulltext.

Formation mechanism of atomic cluster structures in Al-Mg alloy during rapid solidification processes

NASA Astrophysics Data System (ADS)

Liu, Feng-xiang; Liu, Rang-su; Hou, Zhao-yang; Liu, Hai-Rong; Tian, Ze-an; Zhou, Li-li

2009-02-01

The rapid solidification processes of Al 50Mg 50 liquid alloy consisting of 50,000 atoms have been simulated by using molecular dynamics method based on the effective pair potential derived from the pseudopotential theory. The formation mechanisms of atomic clusters during the rapid solidification processes have been investigated adopting a new cluster description method—cluster-type index method (CTIM). The simulated partial structure factors are in good agreement with the experimental results. And Al-Mg amorphous structure characterized with Al-centered icosahedral topological short-range order (SRO) is found to form during the rapid solidification processes. The icosahedral cluster plays a key role in the microstructure transition. Besides, it is also found that the size distribution of various clusters in the system presents a magic number sequence of 13, 19, 23, 25, 29, 31, 33, 37, …. The magic clusters are more stable and mainly correspond to the incompact arrangements of linked icosahedra in the form of rings, chains or dendrites. And each magic number point stands correspondingly for one certain combining form of icosahedra. This magic number sequence is different from that generated in the solidification structure of liquid Al and those obtained by methods of gaseous deposition and ionic spray, etc.

Rapid characterizing of ferromagnetic materials using spin rectification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fan, Xiaolong, E-mail: fanxiaolong@lzu.edu.cn; Wang, Wei; Wang, Yutian

2014-12-29

Spin rectification is a powerful tool for dc electric detections of spin dynamics and electromagnetic waves. Technically, elaborately designed on-chip microwave devices are needed in order to realize that effect. In this letter, we propose a rapid characterizing approach based on spin rectification. By directly sending dynamic current into ferromagnetic films with stripe shape, resonant dc voltages can be detected along the longitudinal or transversal directions. As an example, Fe (010) films with precise crystalline structure and magnetic parameters were used to testify the reliability of such method. We investigated not only the dynamic parameters and the precise anisotropy constantsmore » of the Fe crystals but also the principle of spin rectification in this method.« less

Rapid Reconstitution Packages (RRPs) implemented by integration of computational fluid dynamics (CFD) and 3D printed microfluidics.

PubMed

Chi, Albert; Curi, Sebastian; Clayton, Kevin; Luciano, David; Klauber, Kameron; Alexander-Katz, Alfredo; D'hers, Sebastian; Elman, Noel M

2014-08-01

Rapid Reconstitution Packages (RRPs) are portable platforms that integrate microfluidics for rapid reconstitution of lyophilized drugs. Rapid reconstitution of lyophilized drugs using standard vials and syringes is an error-prone process. RRPs were designed using computational fluid dynamics (CFD) techniques to optimize fluidic structures for rapid mixing and integrating physical properties of targeted drugs and diluents. Devices were manufactured using stereo lithography 3D printing for micrometer structural precision and rapid prototyping. Tissue plasminogen activator (tPA) was selected as the initial model drug to test the RRPs as it is unstable in solution. tPA is a thrombolytic drug, stored in lyophilized form, required in emergency settings for which rapid reconstitution is of critical importance. RRP performance and drug stability were evaluated by high-performance liquid chromatography (HPLC) to characterize release kinetics. In addition, enzyme-linked immunosorbent assays (ELISAs) were performed to test for drug activity after the RRPs were exposed to various controlled temperature conditions. Experimental results showed that RRPs provided effective reconstitution of tPA that strongly correlated with CFD results. Simulation and experimental results show that release kinetics can be adjusted by tuning the device structural dimensions and diluent drug physical parameters. The design of RRPs can be tailored for a number of applications by taking into account physical parameters of the active pharmaceutical ingredients (APIs), excipients, and diluents. RRPs are portable platforms that can be utilized for reconstitution of emergency drugs in time-critical therapies.

Comparison of dissimilarity measures for cluster analysis of X-ray diffraction data from combinatorial libraries

NASA Astrophysics Data System (ADS)

Iwasaki, Yuma; Kusne, A. Gilad; Takeuchi, Ichiro

2017-12-01

Machine learning techniques have proven invaluable to manage the ever growing volume of materials research data produced as developments continue in high-throughput materials simulation, fabrication, and characterization. In particular, machine learning techniques have been demonstrated for their utility in rapidly and automatically identifying potential composition-phase maps from structural data characterization of composition spread libraries, enabling rapid materials fabrication-structure-property analysis and functional materials discovery. A key issue in development of an automated phase-diagram determination method is the choice of dissimilarity measure, or kernel function. The desired measure reduces the impact of confounding structural data issues on analysis performance. The issues include peak height changes and peak shifting due to lattice constant change as a function of composition. In this work, we investigate the choice of dissimilarity measure in X-ray diffraction-based structure analysis and the choice of measure's performance impact on automatic composition-phase map determination. Nine dissimilarity measures are investigated for their impact in analyzing X-ray diffraction patterns for a Fe-Co-Ni ternary alloy composition spread. The cosine, Pearson correlation coefficient, and Jensen-Shannon divergence measures are shown to provide the best performance in the presence of peak height change and peak shifting (due to lattice constant change) when the magnitude of peak shifting is unknown. With prior knowledge of the maximum peak shifting, dynamic time warping in a normalized constrained mode provides the best performance. This work also serves to demonstrate a strategy for rapid analysis of a large number of X-ray diffraction patterns in general beyond data from combinatorial libraries.

Structural analysis of cell wall polysaccharides using PACE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mortimer, Jennifer C.

The plant cell wall is composed of many complex polysaccharides. The composition and structure of the polysaccharides affect various cell properties including cell shape, cell function and cell adhesion. Many techniques to characterize polysaccharide structure are complicated, requiring expensive equipment and specialized operators e.g. NMR, MALDI-MS. PACE (Polysaccharide Analysis using Carbohydrate gel Electrophoresis) uses a simple, rapid technique to analyze polysaccharide quantity and structure (Goubet et al. 2002). Whilst the method here describes xylan analysis, it can be applied (by use of the appropriate glycosyl hydrolase) to any cell wall polysaccharide.

Characterization of Novel Thin-Films and Structures for Integrated Circuit and Photovoltaic Applications

NASA Astrophysics Data System (ADS)

Zhao, Zhao

Thin films have been widely used in various applications. This research focuses on the characterization of novel thin films in the integrated circuits and photovoltaic techniques. The ion implanted layer in silicon can be treated as ion implanted thin film, which plays an essential role in the integrated circuits fabrication. Novel rapid annealing methods, i.e. microwave annealing and laser annealing, are conducted to activate ion dopants and repair the damages, and then are compared with the conventional rapid thermal annealing (RTA). In terms of As+ and P+ implanted Si, the electrical and structural characterization confirms that the microwave and laser annealing can achieve more efficient dopant activation and recrystallization than conventional RTA. The efficient dopant activation in microwave annealing is attributed to ion hopping under microwave field, while the liquid phase growth in laser annealing provides its efficient dopant activation. The characterization of dopants diffusion shows no visible diffusion after microwave annealing, some extent of end range of diffusion after RTA, and significant dopant diffusion after laser annealing. For photovoltaic applications, an indium-free novel three-layer thin-film structure (transparent composited electrode (TCE)) is demonstrated as a promising transparent conductive electrode for solar cells. The characterization of TCE mainly focuses on its optical and electrical properties. Transfer matrix method for optical transmittance calculation is validated and proved to be a desirable method for predicting transmittance of TCE containing continuous metal layer, and can estimate the trend of transmittance as the layer thickness changes. TiO2/Ag/TiO2 (TAgT) electrode for organic solar cells (OSCs) is then designed using numerical simulation and shows much higher Haacke figure of merit than indium tin oxide (ITO). In addition, TAgT based OSC shows better performance than ITO based OSC when compatible hole transfer layer is employed. The electrical and structural characterization of hole transfer layers (HTLs) in OSCs reveals MoO3 is the compatible HTL for TAgT anode. In the end, the reactive ink printed Ag film for solar cell contact application is studied by characterizing its electromigration lifetime. A percolative model is proposed and validated for predicting the resistivity and lifetime of printed Ag thin films containing porous structure.

Towards High-Throughput, Simultaneous Characterization of Thermal and Thermoelectric Properties

NASA Astrophysics Data System (ADS)

Miers, Collier Stephen

The extension of thermoelectric generators to more general markets requires that the devices be affordable and practical (low $/Watt) to implement. A key challenge in this pursuit is the quick and accurate characterization of thermoelectric materials, which will allow researchers to tune and modify the material properties quickly. The goal of this thesis is to design and fabricate a high-throughput characterization system for the simultaneous characterization of thermal, electrical, and thermoelectric properties for device scale material samples. The measurement methodology presented in this thesis combines a custom designed measurement system created specifically for high-throughput testing with a novel device structure that permits simultaneous characterization of the material properties. The measurement system is based upon the 3o method for thermal conductivity measurements, with the addition of electrodes and voltage probes to measure the electrical conductivity and Seebeck coefficient. A device designed and optimized to permit the rapid characterization of thermoelectric materials is also presented. This structure is optimized to ensure 1D heat transfer within the sample, thus permitting rapid data analysis and fitting using a MATLAB script. Verification of the thermal portion of the system is presented using fused silica and sapphire materials for benchmarking. The fused silica samples yielded a thermal conductivity of 1.21 W/(m K), while a thermal conductivity of 31.2 W/(m K) was measured for the sapphire samples. The device and measurement system designed and developed in this thesis provide insight and serve as a foundation for the development of high throughput, simultaneous measurement platforms.

Characterization of the geometry and topology of DNA pictured as a discrete collection of atoms

PubMed Central

Olson, Wilma K.

2014-01-01

The structural and physical properties of DNA are closely related to its geometry and topology. The classical mathematical treatment of DNA geometry and topology in terms of ideal smooth space curves was not designed to characterize the spatial arrangements of atoms found in high-resolution and simulated double-helical structures. We present here new and rigorous numerical methods for the rapid and accurate assessment of the geometry and topology of double-helical DNA structures in terms of the constituent atoms. These methods are well designed for large DNA datasets obtained in detailed numerical simulations or determined experimentally at high-resolution. We illustrate the usefulness of our methodology by applying it to the analysis of three canonical double-helical DNA chains, a 65-bp minicircle obtained in recent molecular dynamics simulations, and a crystallographic array of protein-bound DNA duplexes. Although we focus on fully base-paired DNA structures, our methods can be extended to treat the geometry and topology of melted DNA structures as well as to characterize the folding of arbitrary molecules such as RNA and cyclic peptides. PMID:24791158

Identification and characterization of functional aquaporin water channel protein from alimentary tract of whitefly, Bemisia tabaci

USDA-ARS?s Scientific Manuscript database

Some hemipteran xylem and phloem feeding insects have evolved specialized alimentary structures or filter chambers that rapidly transport water for excretion or osmoregulation. In the whitefly, Bemisia tabaci, mass movement of water through opposing alimentary tract tissues within the filter chamber...

Rapid Characterization of Bacterial Electrogenicity Using a Single-Sheet Paper-Based Electrofluidic Array

PubMed Central

Gao, Yang; Hassett, Daniel J.; Choi, Seokheun

2017-01-01

Electrogenicity, or bacterial electron transfer capacity, is an important application which offers environmentally sustainable advances in the fields of biofuels, wastewater treatment, bioremediation, desalination, and biosensing. Significant boosts in this technology can be achieved with the growth of synthetic biology that manipulates microbial electron transfer pathways, thereby potentially significantly improving their electrogenic potential. There is currently a need for a high-throughput, rapid, and highly sensitive test array to evaluate the electrogenic properties of newly discovered and/or genetically engineered bacterial species. In this work, we report a single-sheet, paper-based electrofluidic (incorporating both electronic and fluidic structure) screening platform for rapid, sensitive, and potentially high-throughput characterization of bacterial electrogenicity. This novel screening array uses (i) a commercially available wax printer for hydrophobic wax patterning on a single sheet of paper and (ii) water-dispersed electrically conducting polymer mixture, poly(3,4-ethylenedioxythiophene):polystyrene sulfonate, for full integration of electronic and fluidic components into the paper substrate. The engineered 3-D, microporous, hydrophilic, and conductive paper structure provides a large surface area for efficient electron transfer. This results in rapid and sensitive power assessment of electrogenic bacteria from a microliter sample volume. We validated the effectiveness of the sensor array using hypothesis-driven genetically modified Pseudomonas aeruginosa mutant strains. Within 20 min, we observed that the sensor platform successfully measured the electricity-generating capacities of five isogenic mutants of P. aeruginosa while distinguishing their differences from genetically unmodified bacteria. PMID:28798914

A rapid approach for characterization of thiol-conjugated antibody-drug conjugates and calculation of drug-antibody ratio by liquid chromatography mass spectrometry.

PubMed

Firth, David; Bell, Leonard; Squires, Martin; Estdale, Sian; McKee, Colin

2015-09-15

We present the demonstration of a rapid "middle-up" liquid chromatography mass spectrometry (LC-MS)-based workflow for use in the characterization of thiol-conjugated maleimidocaproyl-monomethyl auristatin F (mcMMAF) and valine-citrulline-monomethyl auristatin E (vcMMAE) antibody-drug conjugates. Deconvoluted spectra were generated following a combination of deglycosylation, IdeS (immunoglobulin-degrading enzyme from Streptococcus pyogenes) digestion, and reduction steps that provide a visual representation of the product for rapid lot-to-lot comparison-a means to quickly assess the integrity of the antibody structure and the applied conjugation chemistry by mass. The relative abundance of the detected ions also offer information regarding differences in drug conjugation levels between samples, and the average drug-antibody ratio can be calculated. The approach requires little material (<100 μg) and, thus, is amenable to small-scale process development testing or as an early component of a complete characterization project facilitating informed decision making regarding which aspects of a molecule might need to be examined in more detail by orthogonal methodologies. Copyright © 2015 Elsevier Inc. All rights reserved.

Rapid identification of triterpenoid sulfates and hydroxy fatty acids including two new constituents from Tydemania expeditionis by LC-MS

PubMed Central

Zhang, Jian-Long; Kubanek, Julia; Hay, Mark E.; Aalbersberg, William; Ye, Wen-Cai; Jiang, Ren-Wang

2011-01-01

Tydemania expeditionis Weber-van Bosse (Udoteaceae) is a weakly calcified green alga. In the present paper, liquid chromatography coupled with photodiode array detection and electrospray mass spectrometry was developed to identify the fingerprint components. A total of four triterpenoid sulfates and three hydroxy fatty acids in the ethyl acetate fraction of the crude extract were structurally characterized on the basis of retention time, online UV spectrum and mass fragmentation pattern. Furthermore, detailed LC-MS analysis revealed two new hydroxy fatty acids, which were then prepared and characterized by extensive NMR analyses. The proposed method provides a scientific and technical platform for the rapid identification of triterpenoid sulfates and hydroxy fatty acids in similar marine algae and terrestrial plants. PMID:21915955

Preparation, structural characterization, and catalytic performance of Pd(II) and Pt(II) complexes derived from cellulose Schiff base

NASA Astrophysics Data System (ADS)

Baran, Talat; Yılmaz Baran, Nuray; Menteş, Ayfer

2018-05-01

In this study, we reported production, characterization, and catalytic behavior of two novel heterogeneous palladium(II) and platinum(II) catalysts derived from cellulose biopolymer. In order to eliminate the use of toxic organic or inorganic solvents and to reduce the use of excess energy in the coupling reactions, we have developed a very simple, rapid, and eco-friendly microwave irradiation protocol. The developed microwave-assisted method of Suzuki cross coupling reactions produced excellent reaction yields in the presence of cellulose supported palladium and platinum (II) catalysts. Moreover, the catalysts easily regenerated after simple filtration, and they gave good reusability. This study revealed that the designed catalysts and method provide clean, simple, rapid, and impressive catalytic performance for Suzuki coupling reactions.

Structural Characterization of Ginsenosides from Flower Buds of Panax ginseng by RRLC-Q-TOF MS.

PubMed

Wu, Wei; Lu, Ziyan; Teng, Yaran; Guo, Yingying; Liu, Shuying

2016-02-01

Ginseng flower bud as a part of Panax ginseng has received much attention as a valuable functional food with medicinal potential. A few studies focused on systematic and comprehensive studies on its major ingredients. This study aims to rapidly characterize ginsenosides in ginseng flower buds and provide scientific basis for developing functional food, exploiting pharmaceutical effects and making full use of ginseng resources. A rapid resolution liquid chromatography coupled with quadrupole-time-of-flight mass spectrometry (RRLC-Q-TOF-MS) method was developed for rapid qualitative and quantitative analysis of ginsenosides in ginseng flower buds. The compounds were identified by comparing retention time of the reference standards, accurate mass measurement and the fragment ions obtained from RRLC-Q-TOF-MS/MS analyses. A total of 14 kinds of ginsenosides were identified and 5 kinds of malonyl-ginsenosides were first tentatively identified in ginseng flower buds. Ten kinds of main ginsenosides were quantitatively analyzed. The developed RRLC-Q-TOF-MS method was demonstrated as an effective analytical means for rapid characterization of the ginsenosides in flower buds of P. ginseng. The research result is valuable for quality control, assessment of authenticity and stability evaluation of ginseng flower buds. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Thermal Analysis by Structural Characterization as a Method for Assessing Heterogeneity in Complex Solid Pharmaceutical Dosage Forms.

PubMed

Alhijjaj, Muqdad; Reading, Mike; Belton, Peter; Qi, Sheng

2015-11-03

Characterizing inter- and intrasample heterogeneity of solid and semisolid pharmaceutical products is important both for rational design of dosage forms and subsequent quality control during manufacture; however, most pharmaceutical products are multicomponent formulations that are challenging in this regard. Thermal analysis, in particular differential scanning calorimetry, is commonly used to obtain structural information, such as degree of crystallinity, or identify the presence of a particular polymorph, but the results are an average over the whole sample; it cannot directly provide information about the spatial distribution of phases. This study demonstrates the use of a new thermo-optical technique, thermal analysis by structural characterization (TASC), that can provide spatially resolved information on thermal transitions by applying a novel algorithm to images acquired by hot stage microscopy. We determined that TASC can be a low cost, relatively rapid method of characterizing heterogeneity and other aspects of structure. In the examples studied, it was found that high heating rates enabled screening times of 3-5 min per sample. In addition, this study demonstrated the higher sensitivity of TASC for detecting the metastable form of polyethylene glycol (PEG) compared to conventional differential scanning calorimetry (DSC). This preliminary work suggests that TASC will be a worthwhile additional tool for characterizing a broad range of materials.

Preparative isolation and characterization of some minor impurities of astaxanthin by high-performance liquid chromatography.

PubMed

Rao, R Nageswara; Alvi, S Naseeruddin; Rao, B Nageswara

2005-05-27

A simple and rapid preparative high-performance liquid chromatography (HPLC) method has been developed to isolate and characterize some minor impurities of astaxanthin using a normal-phase Lichrosorb silica column with n-hexane-acetone-tetrahydrofuran (90:2:8, v/v/v) as mobile-phase and detection at 475 nm. The isolated impurities were characterized as astacene, dehydro astacene and apoastaxanthinal by UV-vis, ESI-MS, 1H and 13C NMR spectroscopy and the molecular structures were assigned. The impurities collected using the developed conditions were over 98% pure.

Solid-State NMR Spectroscopy of Metal–Organic Framework Compounds (MOFs)

PubMed Central

Hoffmann, Herbert C.; Debowski, Marta; Müller, Philipp; Paasch, Silvia; Senkovska, Irena; Kaskel, Stefan; Brunner, Eike

2012-01-01

Nuclear Magnetic Resonance (NMR) spectroscopy is a well-established method for the investigation of various types of porous materials. During the past decade, metal–organic frameworks have attracted increasing research interest. Solid-state NMR spectroscopy has rapidly evolved into an important tool for the study of the structure, dynamics and flexibility of these materials, as well as for the characterization of host–guest interactions with adsorbed species such as xenon, carbon dioxide, water, and many others. The present review introduces and highlights recent developments in this rapidly growing field.

[Socio-demographic aspects of the rural household in Iran (author's transl)].

PubMed

Mohseni, M

1980-01-01

Explores the dynamics of sociodemographic aspects of rural Iranian households and the effects on economic, demographic and social structures of rural areas where there has been rapid development. The rural population is characterized by early and high fertility and rapid population growth. The patrilinear kinship system contributes to the high birth rate, while judicial, economic and social factors limit women's rights to birth control. Rights and duties towards children, and their rights and duties towards their parents, have a strong influence on decisions concerning fertility. (author's modified)

Perspective: Composition–structure–property mapping in high-throughput experiments: Turning data into knowledge

DOE PAGES

Hattrick-Simpers, Jason R.; Gregoire, John M.; Kusne, A. Gilad

2016-05-26

With their ability to rapidly elucidate composition-structure-property relationships, high-throughput experimental studies have revolutionized how materials are discovered, optimized, and commercialized. It is now possible to synthesize and characterize high-throughput libraries that systematically address thousands of individual cuts of fabrication parameter space. An unresolved issue remains transforming structural characterization data into phase mappings. This difficulty is related to the complex information present in diffraction and spectroscopic data and its variation with composition and processing. Here, we review the field of automated phase diagram attribution and discuss the impact that emerging computational approaches will have in the generation of phase diagrams andmore » beyond.« less

Flow structures and sandbar dynamics in a canyon river during a controlled flood, Colorado River, Arizona

USGS Publications Warehouse

Wright, S.A.; Kaplinski, M.

2011-01-01

In canyon rivers, debris fan constrictions create rapids and downstream pools characterized by secondary flow structures that are closely linked to channel morphology. In this paper we describe detailed measurements of the three-dimensional flow structure and sandbar dynamics of two pools along the Colorado River in the Grand Canyon during a controlled flood release from Glen Canyon Dam. Results indicate that the pools are characterized by large lateral recirculation zones (eddies) resulting from flow separation downstream from the channel constrictions, as well as helical flow structures in the main channel and eddy. The lateral recirculation zones are low-velocity areas conducive to fine sediment deposition, particularly in the vicinity of the separation and reattachment points and are thus the dominant flow structures controlling sandbar dynamics. The helical flow structures also affect morphology but appear secondary in importance to the lateral eddies. During the controlled flood, sandbars in the separation and reattachment zones at both sites tended to build gradually during the rising limb and peak flow. Deposition in shallow water on the sandbars was accompanied by erosion in deeper water along the sandbar slope at the interface with the main channel. Erosion occurred via rapid mass failures as well as by gradual boundary shear stress driven processes. The flow structures and morphologic links at our study sites are similar to those identified in other river environments, in particular sharply curved meanders and channel confluences where the coexistence of lateral recirculation and helical flows has been documented. Copyright 2011 by the American Geophysical Union.

Characterization of nanoscale oxide and oxyhydroxide powders using EXAFS spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Darab, J.G.; Linehan, J.C.; Matson, D.W.

1993-06-01

Extended x-ray absorption fine structure (EXAFS) spectroscopy has been used to determine the structural environment local to iron(HI) and zircorium(IV) cations in respectively, nanoscale iron oxyhydroxide and nanoscale zirconium oxide powders. The iron oxyhydroxide powder, produced by the modified reverse micelle (MRM) technology, was found to have a short-range structure most similar to that of goethite ([alpha]-FeOOH). The short-range structure of the zirconium oxide powder, produced using the rapid thermal decomposition of solutes (RTDS) technology, was found to be a mixture of monoclinic zirconia and cubic zirconia environments.

Characterization of nanoscale oxide and oxyhydroxide powders using EXAFS spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Darab, J.G.; Linehan, J.C.; Matson, D.W.

1993-06-01

Extended x-ray absorption fine structure (EXAFS) spectroscopy has been used to determine the structural environment local to iron(HI) and zircorium(IV) cations in respectively, nanoscale iron oxyhydroxide and nanoscale zirconium oxide powders. The iron oxyhydroxide powder, produced by the modified reverse micelle (MRM) technology, was found to have a short-range structure most similar to that of goethite ({alpha}-FeOOH). The short-range structure of the zirconium oxide powder, produced using the rapid thermal decomposition of solutes (RTDS) technology, was found to be a mixture of monoclinic zirconia and cubic zirconia environments.

Corrosion Inhibition on SAE 1010 Steel by Nanoscale Exopolysaccharides Coatings Determined by Electrochemical and Surface Characterization

USDA-ARS?s Scientific Manuscript database

Plating, painting and the application of enamel are the most common anti-corrosion treatments. They are effective by providing a barrier of corrosion resistant material between the damaging environment and the structural material. Coatings start failing rapidly if scratched or damaged because a co...

Too many chemicals, too little time: Rapid in silico methods to characterize and predict ADME properties for chemical toxicity and exposure potential

EPA Science Inventory

Evaluating proposed alternative chemical structures to support the design of safer chemicals and products is an important component of EPA's Green Chemistry and Design for the Environment (DfE) Programs. As such, science-based alternatives assessment is essential to support EPA's...

Chemical Characterization and Determination of the Anti-Oxidant Capacity of Two Brown Algae with Respect to Sampling Season and Morphological Structures Using Infrared Spectroscopy and Multivariate Analyses.

PubMed

Beratto, Angelo; Agurto, Cristian; Freer, Juanita; Peña-Farfal, Carlos; Troncoso, Nicolás; Agurto, Andrés; Castillo, Rosario Del P

2017-10-01

Brown algae biomass has been shown to be a highly important industrial source for the production of alginates and different nutraceutical products. The characterization of this biomass is necessary in order to allocate its use to specific applications according to the chemical and biological characteristics of this highly variable resource. The methods commonly used for algae characterization require a long time for the analysis and rigorous pretreatments of samples. In this work, nondestructive and fast analyses of different morphological structures from Lessonia spicata and Macrocystis pyrifera, which were collected during different seasons, were performed using Fourier transform infrared (FT-IR) techniques in combination with chemometric methods. Mid-infrared (IR) and near-infrared (NIR) spectral ranges were tested to evaluate the spectral differences between the species, seasons, and morphological structures of algae using a principal component analysis (PCA). Quantitative analyses of the polyphenol and alginate contents and the anti-oxidant capacity of the samples were performed using partial least squares (PLS) with both spectral ranges in order to build a predictive model for the rapid quantification of these parameters with industrial purposes. The PCA mainly showed differences in the samples based on seasonal sampling, where changes were observed in the bands corresponding to polysaccharides, proteins, and lipids. The obtained PLS models had high correlation coefficients (r) for the polyphenol content and anti-oxidant capacity (r > 0.9) and lower values for the alginate determination (0.7 < r < 0.8). Fourier transform infrared-based techniques were suitable tools for the rapid characterization of algae biomass, in which high variability in the samples was incorporated for the qualitative and quantitative analyses, and have the potential to be used on an industrial scale.

Positron annihilation lifetime spectroscopy (PALS) as a characterization technique for nanostructured self-assembled amphiphile systems.

PubMed

Dong, Aurelia W; Pascual-Izarra, Carlos; Pas, Steven J; Hill, Anita J; Boyd, Ben J; Drummond, Calum J

2009-01-08

Positron annihilation lifetime spectroscopy (PALS) has potential as a novel rapid characterization method for self-assembly amphiphile systems; however, a lack of systematic correlation of PALS parameters with structural attributes has limited its more widespread application. In this study, using the well-characterized phytantriol/water and the phytantriol/vitamin E acetate/water self-assembly amphiphile systems, the impact of systematic structural changes controlled by changes in composition and temperature on PALS parameters has been studied. The PALS parameters (orthopositronium (oPs) lifetime and intensity signatures) were shown to be sensitive to the molecular packing and mobility of the self-assembled lipid molecules in various lyotropic liquid crystalline phases, enabling differentiation between liquid crystalline structures. The oPs lifetime, related to the molecular packing and mobility, is correlated with rheological properties of the individual mesophases. The oPs lifetime links the lipid chain packing and mobility in the various mesophases to resultant macroscopic properties, such as permeability, which is critical for the use of these mesophase structures as diffusion-controlled release matrices for active liposoluble compounds.

Propulsion Systems Panel

NASA Technical Reports Server (NTRS)

Bianca, Carmelo J.; Miner, Robert; Johnston, Lawrence M.; Bruce, R.; Dennies, Daniel P.; Dickenson, W.; Dreshfield, Robert; Karakulko, Walt; Mcgaw, Mike; Munafo, Paul M.

1993-01-01

Topics addressed are: (1) cryogenic tankage; (2) launch vehicle TPS/insulation; (3) durable passive thermal control devices and/or coatings; (4) development and characterization of processing methods to reduce anisotropy of material properties in Al-Li; (5) durable thermal protection system (TPS); (6) unpressurized Al-Li structures (interstages, thrust structures); (7) near net shape sections; (8) pressurized structures; (9) welding and joining; (10) micrometeoroid and debris hypervelocity shields; (11) state-of-the-art shell buckling structure optimizer program to serve as a rapid design tool; (12) test philosophy; (13) reduced load cycle time; (14) structural analysis methods; (15) optimization of structural criteria; and (16) develop an engineering approach to properly trade material and structural concepts selection, fabrication, facilities, and cost.

Propulsion Systems Panel

NASA Astrophysics Data System (ADS)

Bianca, Carmelo J.; Miner, Robert; Johnston, Lawrence M.; Bruce, R.; Dennies, Daniel P.; Dickenson, W.; Dreshfield, Robert; Karakulko, Walt; McGaw, Mike; Munafo, Paul M.

1993-02-01

Topics addressed are: (1) cryogenic tankage; (2) launch vehicle TPS/insulation; (3) durable passive thermal control devices and/or coatings; (4) development and characterization of processing methods to reduce anisotropy of material properties in Al-Li; (5) durable thermal protection system (TPS); (6) unpressurized Al-Li structures (interstages, thrust structures); (7) near net shape sections; (8) pressurized structures; (9) welding and joining; (10) micrometeoroid and debris hypervelocity shields; (11) state-of-the-art shell buckling structure optimizer program to serve as a rapid design tool; (12) test philosophy; (13) reduced load cycle time; (14) structural analysis methods; (15) optimization of structural criteria; and (16) develop an engineering approach to properly trade material and structural concepts selection, fabrication, facilities, and cost.

Seismological properties of intermediate-mass stars

NASA Astrophysics Data System (ADS)

Audard, N.; Provost, J.

1994-02-01

Stars more massive than about 1.2 solar mass are characterized by a convective core, which induces at its frontier a rapid variation of the density, sound speed and Brunt-Vaisala frequency, close to a discontinuity. For three stars of 1, 1.5 and 2 solar mass we have studied the properties of p-mode frequencies of high radial order and low degree, and we present results on the effects on p-mode oscillations of some rapid variations of the internal structure. We first point out the difficulties of the classical asymptotic theory to represent with accuracy the p-mode spectrum of the stars considered. We compare the numerical frequencies with asymptotic and polynomial approximations obtained from fits. The variation of the derived global coefficients characterizing the p-mode spectrum along the evolutionary tracks has been estimated; it would help to separate the effects of age and mass of intermediate-mass stars. The sensitivity of these coefficients to stellar parameters substantially depends on the stellar mass and must be considered for asteroseismic calibration. The effects of rapid variations in the stellar internal structure are finally considered. An asymptotic formula taking into account the rapid variation of the sound speed at the convective core boundary of the 1.5 and 2 solar mass stars predicts an oscillatory behavior of the frequencies with a very large period. We also show that the second frequency difference delta2nu = nun, l - 2nun-1, l + nun-2, l exhibits a substantial oscillation which corresponds to the region of the He II ionization of the 1, 1.5 and 2 solar mass stars.

Application of Natural Isotopic Abundance ¹H-¹³C- and ¹H-¹⁵N-Correlated Two-Dimensional NMR for Evaluation of the Structure of Protein Therapeutics.

PubMed

Arbogast, Luke W; Brinson, Robert G; Marino, John P

2016-01-01

Methods for characterizing the higher-order structure of protein therapeutics are in great demand for establishing consistency in drug manufacturing, for detecting drug product variations resulting from modifications in the manufacturing process, and for comparing a biosimilar to an innovator reference product. In principle, solution NMR can provide a robust approach for characterization of the conformation(s) of protein therapeutics in formulation at atomic resolution. However, molecular weight limitations and the perceived need for stable isotope labeling have to date limited its practical applications in the biopharmaceutical industry. Advances in NMR magnet and console technologies, cryogenically cooled probes, and new rapid acquisition methodologies, particularly selective optimized flip-angle short transient pulse schemes and nonuniform sampling, have greatly ameliorated these limitations. Here, we describe experimental methods for the collection and analysis of 2D (1)H(N)-(15)N-amide- and (1)H-(13)C-methyl-correlated spectra applied to protein drug products at natural isotopic abundance, including representatives from the rapidly growing class of monoclonal antibody (mAb) therapeutics. Practical aspects of experimental setup and data acquisition for both standard and rapid acquisition NMR techniques are described. Furthermore, strategies for the statistical comparison of 2D (1)H(N)-(15)N-amide- and (1)H-(13)C-methyl-correlated spectra are detailed. 2016 Published by Elsevier Inc.

Research Developments in Nondestructive Evaluation and Structural Health Monitoring for the Sustainment of Composite Aerospace Structures at NASA

NASA Technical Reports Server (NTRS)

Cramer, K. Elliott

2016-01-01

The use of composite materials continues to increase in the aerospace community due to the potential benefits of reduced weight, increased strength, and manufacturability. Ongoing work at NASA involves the use of the large-scale composite structures for spacecraft (payload shrouds, cryotanks, crew modules, etc). NASA is also working to enable both the use and sustainment of composites in commercial aircraft structures. One key to the sustainment of these large composite structures is the rapid, in-situ characterization of a wide range of potential defects that may occur during the vehicle's life. Additionally, in many applications it is necessary to monitor changes in these materials over their lifetime. Quantitative characterization through Nondestructive Evaluation (NDE) of defects such as reduced bond strength, microcracking, and delamination damage due to impact, are of particular interest. This paper will present an overview of NASA's applications of NDE technologies being developed for the characterization and sustainment of advanced aerospace composites. The approaches presented include investigation of conventional, guided wave, and phase sensitive ultrasonic methods and infrared thermography techniques for NDE. Finally, the use of simulation tools for optimizing and validating these techniques will also be discussed.

Complementary MS Methods Assist Conformational Characterization of Antibodies with Altered S-S Bonding Networks

NASA Astrophysics Data System (ADS)

Jones, Lisa M.; Zhang, Hao; Cui, Weidong; Kumar, Sandeep; Sperry, Justin B.; Carroll, James A.; Gross, Michael L.

2013-06-01

As therapeutic monoclonal antibodies (mAbs) become a major focus in biotechnology and a source of the next-generation drugs, new analytical methods or combination methods are needed for monitoring changes in higher order structure and effects of post-translational modifications. The complexity of these molecules and their vulnerability to structural change provide a serious challenge. We describe here the use of complementary mass spectrometry methods that not only characterize mutant mAbs but also may provide a general framework for characterizing higher order structure of other protein therapeutics and biosimilars. To frame the challenge, we selected members of the IgG2 subclass that have distinct disulfide isomeric structures as a model to evaluate an overall approach that uses ion mobility, top-down MS sequencing, and protein footprinting in the form of fast photochemical oxidation of proteins (FPOP). These three methods are rapid, sensitive, respond to subtle changes in conformation of Cys → Ser mutants of an IgG2, each representing a single disulfide isoform, and may be used in series to probe higher order structure. The outcome suggests that this approach of using various methods in combination can assist the development and quality control of protein therapeutics.

31P NMR Characterization of Tricin and Its Structurally Similar Flavonoids

DOE PAGES

Li, Mi; Pu, Yunqiao; Tschaplinski, Timothy J.; ...

2017-04-24

Tricin, a flavonoid metabolite, has been recently identified as a component of lignin in select monocot plants. This finding has initiated consideration on updating the lignin biosynthesis pathway. Here, we report a rapid method of determination of tricin in corn stover lignin, based on 31P nuclear magnetic resonance (NMR) spectroscopy by phosphitylating with 2-chloro-4,4,5,5-tetramethyl-1,3,2-dioxaphospholane (TMDP). Nine other flavonoids, with similar structure to tricin, have also been examined using the current method. The application of 31P NMR enables rapid identification of tricin-like flavonoids in the heterogeneous lignin polymer. The well resolved spectroscopic peaks from these derivatized flavonoids and lignin functional groupsmore » provide important information for the determination of flavonoids individually or their association with lignin.« less

31P NMR Characterization of Tricin and Its Structurally Similar Flavonoids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Mi; Pu, Yunqiao; Tschaplinski, Timothy J.

Tricin, a flavonoid metabolite, has been recently identified as a component of lignin in select monocot plants. This finding has initiated consideration on updating the lignin biosynthesis pathway. Here, we report a rapid method of determination of tricin in corn stover lignin, based on 31P nuclear magnetic resonance (NMR) spectroscopy by phosphitylating with 2-chloro-4,4,5,5-tetramethyl-1,3,2-dioxaphospholane (TMDP). Nine other flavonoids, with similar structure to tricin, have also been examined using the current method. The application of 31P NMR enables rapid identification of tricin-like flavonoids in the heterogeneous lignin polymer. The well resolved spectroscopic peaks from these derivatized flavonoids and lignin functional groupsmore » provide important information for the determination of flavonoids individually or their association with lignin.« less

Rapid analysis of drug dissolution by paper spray ionization mass spectrometry.

PubMed

Liu, Yang; Liu, Ning; Zhou, Ya-Nan; Lin, Lan; He, Lan

2017-03-20

With a great quantity of solid dosage tested by dissolution technology, developing a rapid and sensitive method to access the content of drug within dissolution media is highly desired by analysts and scientists. Traditionally, dissolution media is not compatible with mass spectrometry since the inorganic salts in the media might damage the mass spectrometer. Here, paper spray ionization mass spectrometry (PSI-MS), one of the ambient mass spectrometry technologies, is developed to characterize the content of drugs in dissolution media. The porous structure of paper can effectively retain salts from entering mass spectrometer. This makes the measurement of drug content within dissolution media by mass spectrometer possible. After the experimental parameters were optimized, calibration curves of model drugs - enalapril, quinapril and benazepril were established by using corresponding deuterated internal standards. PSI-MS was then deployed to characterize the content of enalapril from the dissolution testing of enalapril tablets. The results from PSI-MS are comparable to those from HPLC characterization. More importantly, the analysis time of 6 samples is shortened from 90min to 6min. Detection limit of enalapril maleate tablets by PSI-MS is 1/300 of LC. PSI-MS is rapid, sensitive and accurate in analyzing drug content from dissolution tests. Copyright © 2016 Elsevier B.V. All rights reserved.

Molecular genetics of lignin-degrading fungi and their applications in organopollutant degradation

Treesearch

Daniel Cullen

2002-01-01

This chapter provides an overview of the physiology and associated molecular genetics of wood- decaying fungi as they relate to organopollutant degradation. White-rot fungi are characterized by an ability to fragment all major structural polymers of wood including lignin. More poorly understood are the brown-rot fungi, which rapidly depolymerize cellulosic materials...

Electrical Characterization of Amorphous Silicon MIS-Based Structures for HIT Solar Cell Applications.

PubMed

García, Héctor; Castán, Helena; Dueñas, Salvador; Bailón, Luis; García-Hernansanz, Rodrigo; Olea, Javier; Del Prado, Álvaro; Mártil, Ignacio

2016-12-01

A complete electrical characterization of hydrogenated amorphous silicon layers (a-Si:H) deposited on crystalline silicon (c-Si) substrates by electron cyclotron resonance chemical vapor deposition (ECR-CVD) was carried out. These structures are of interest for photovoltaic applications. Different growth temperatures between 30 and 200 °C were used. A rapid thermal annealing in forming gas atmosphere at 200 °C during 10 min was applied after the metallization process. The evolution of interfacial state density with the deposition temperature indicates a better interface passivation at higher growth temperatures. However, in these cases, an important contribution of slow states is detected as well. Thus, using intermediate growth temperatures (100-150 °C) might be the best choice.

Electrical Characterization of Amorphous Silicon MIS-Based Structures for HIT Solar Cell Applications

NASA Astrophysics Data System (ADS)

García, Héctor; Castán, Helena; Dueñas, Salvador; Bailón, Luis; García-Hernansanz, Rodrigo; Olea, Javier; del Prado, Álvaro; Mártil, Ignacio

2016-07-01

A complete electrical characterization of hydrogenated amorphous silicon layers (a-Si:H) deposited on crystalline silicon (c-Si) substrates by electron cyclotron resonance chemical vapor deposition (ECR-CVD) was carried out. These structures are of interest for photovoltaic applications. Different growth temperatures between 30 and 200 °C were used. A rapid thermal annealing in forming gas atmosphere at 200 °C during 10 min was applied after the metallization process. The evolution of interfacial state density with the deposition temperature indicates a better interface passivation at higher growth temperatures. However, in these cases, an important contribution of slow states is detected as well. Thus, using intermediate growth temperatures (100-150 °C) might be the best choice.

Structural Characterization of Sm(III)(EDTMP).

PubMed

Yang, Y; Pushie, M J; Cooper, D M L; Doschak, M R

2015-11-02

Samarium-153 ethylenediamine-N,N,N',N'-tetrakis(methylenephosphonic acid) ((153)Sm-EDTMP, or samarium lexidronam), also known by its registered trademark name Quadramet, is an approved therapeutic radiopharmaceutical used in the palliative treatment of painful bone metastases. Typically, patients with prostate, breast, or lung cancer are most likely to go on to require bone pain palliation treatment due to bone metastases. Sm(EDTMP) is a bone-seeking drug which accumulates on rapidly growing bone, thereby delivering a highly region-specific dose of radiation, chiefly through β particle emission. Even with its widespread clinical use, the structure of Sm(EDTMP) has not yet been characterized at atomic resolution, despite attempts to crystallize the complex. Herein, we prepared a 1:1 complex of the cold (stable isotope) of Sm(EDTMP) under alkaline conditions and then isolated and characterized the complex using conventional spectroscopic techniques, as well as with extended X-ray absorption fine structure (EXAFS) spectroscopy and density functional structure calculations, using natural abundance Sm. We present the atomic resolution structure of [Sm(III)(EDTMP)-8H](5-) for the first time, supported by the EXAFS data and complementary spectroscopic techniques, which demonstrate that the samarium coordination environment in solution is in agreement with the structure that has long been conjectured.

Structural characterization of constituents with molecular diversity in fractions from Lysidice brevicalyx by liquid chromatography/diode-array detection/electrospray ionization tandem mass spectrometry and liquid chromatography/nuclear magnetic resonance.

PubMed

Qu, Jing; Hu, You-cai; Li, Jian-bei; Wang, Ying-hong; Zhang, Jin-lan; Abliz, Zeper; Yu, Shi-shan; Liu, Yun-bao

2008-01-01

A combination of electrospray ionization tandem mass spectrometry with high-performance liquid chromatography (HPLC/ESI-MSn), and hyphenation of liquid chromatography to nuclear magnetic resonance spectroscopy (HPLC/NMR), have been extensively utilized for on-line analysis of natural products, analyzing metabolite and drug impurity. In our last paper, we reported an on-line analytical method for structural identification of trace alkaloids in the same class. However, the structural types of the constituents in plants were various, such as flavanoids, terpenoids and steroids. It is important to establish an effective analytical method for on-line structural identification of constituents with molecular diversity in extracts of plants. So, in the present study, the fragmentation patterns of some isolated stilbenes, phloroglucinols and flavanoids from Lysidice rhodostegia were investigated by ESI-MSn. Their fragmentation rules and UV characteristics are summarized, and the relationship between the spectral characteristics, rules and the structures is described. According to the fragmentation rules, NMR and UV spectral characteristics, 24 constituents of different types in the fractions from L. brevicalyx of the same genus were structurally characterized on the basis of HPLC/HRMS, HPLC-UV/ESI-MSn, HPLC/1H NMR and HPLC/1H-1H COSY rapidly. Of these, six (10, 13, 14, 16, 17 and 23) are new compounds and all of them are reported from L. brevicalyx for the first time. The aim is to develop an effective analytical method for on-line structural identification of natural products with molecular diversity in plants, and to guide the rapid and direct isolation of novel compounds by chemical screening.

Spotting the differences in two-dimensional materials - the Raman scattering perspective.

PubMed

Zhang, Shishu; Zhang, Na; Zhao, Yan; Cheng, Ting; Li, Xiaobo; Feng, Rui; Xu, Hua; Liu, Zhirong; Zhang, Jin; Tong, Lianming

2018-05-08

Two-dimensional (2D) layered materials have attracted tremendous attention and led to a prosperous development in both fundamental investigation and device applications in various fields, such as nanoelectronics, flexible devices, sustainable energy and catalysts. The precise characterization of the structure and properties of 2D materials is in urgent need. Raman scattering spectroscopy is one of the most popular characterization tools that is convenient, rapid and non-invasive. It provides information on both the lattice structure from the frequency of phonon modes and the electronic band structure through the intensity due to electronic resonance Raman scattering. Although a few morphological characterization tools can image 2D materials with atomic resolution, Raman scattering measurements are more tolerant to the conditions of sample preparation such as the substrate and less technically demanding, and have been one of the routine tools for the characterization of 2D materials. In this review, we focus on the characterization of 2D materials using Raman scattering spectroscopy, in particular, the revealing of differences from primitive 2D materials, such as defects, doping effects, van der Waals heterostructures and the interaction with molecules. The characteristic Raman features of such differences and the corresponding interpretation will be discussed. We hope that this review will be useful for wide research communities of materials, physics, chemistry and engineering.

Rapid Characterization of Insulin Modifications and Sequence Variations by Proteinase K Digestion and UHPLC-ESI-MS

NASA Astrophysics Data System (ADS)

Yang, Rong-Sheng; Tang, Weijuan; Sheng, Huaming; Meng, Fanyu

2018-01-01

Discovery of novel insulin analogs as therapeutics has remained an active area of research. Compared with native human insulin, insulin analog molecules normally incorporate either covalent modifications or amino acid sequence variations. From the drug discovery and development perspective, methods for efficient and detailed characterization of these primary structural changes are very important. In this report, we demonstrate that proteinase K digestion coupled with UPLC-ESI-MS analysis provides a simple and rapid approach to characterize the modifications and sequence variations of insulin molecules. A commercially available proteinase K digestion kit was used to process recombinant human insulin (RHI), insulin glargine, and fluorescein isothiocynate-labeled recombinant human insulin (FITC-RHI) samples. The LC-MS data clearly showed that RHI and insulin glargine samples can be differentiated, and the FITC modifications in all three amine sites of the RHI molecule are well characterized. The end-to-end experiment and data interpretation was achieved within 60 min. This approach is fast and simple, and can be easily implemented in early drug discovery laboratories to facilitate research on more advanced insulin therapeutics. [Figure not available: see fulltext.

Rapid Characterization of Insulin Modifications and Sequence Variations by Proteinase K Digestion and UHPLC-ESI-MS

NASA Astrophysics Data System (ADS)

Yang, Rong-Sheng; Tang, Weijuan; Sheng, Huaming; Meng, Fanyu

2018-05-01

Discovery of novel insulin analogs as therapeutics has remained an active area of research. Compared with native human insulin, insulin analog molecules normally incorporate either covalent modifications or amino acid sequence variations. From the drug discovery and development perspective, methods for efficient and detailed characterization of these primary structural changes are very important. In this report, we demonstrate that proteinase K digestion coupled with UPLC-ESI-MS analysis provides a simple and rapid approach to characterize the modifications and sequence variations of insulin molecules. A commercially available proteinase K digestion kit was used to process recombinant human insulin (RHI), insulin glargine, and fluorescein isothiocynate-labeled recombinant human insulin (FITC-RHI) samples. The LC-MS data clearly showed that RHI and insulin glargine samples can be differentiated, and the FITC modifications in all three amine sites of the RHI molecule are well characterized. The end-to-end experiment and data interpretation was achieved within 60 min. This approach is fast and simple, and can be easily implemented in early drug discovery laboratories to facilitate research on more advanced insulin therapeutics. [Figure not available: see fulltext.

Novel characterization method for fibrous materials using non-contact acoustics: material properties revealed by ultrasonic perturbations.

PubMed

Periyaswamy, Thamizhisai; Balasubramanian, Karthikeyan; Pastore, Christopher

2015-02-01

Fibrous materials are unique hierarchical complex structures exhibiting a range of mechanical, thermal, optical and electrical properties. The inherent discontinuity at micro and macro levels, heterogeneity and multi-scale porosity differentiates fibrous materials from other engineering materials that are typically continuum in nature. These structural complexities greatly influence the techniques and modalities that can be applied to characterize fibrous materials. Typically, the material response to an applied external force is measured and used as a characteristic number of the specimen. In general, a range of equipment is in use to obtain these numbers to signify the material properties. Nevertheless, obtaining these numbers for materials like fiber ensembles is often time consuming, destructive, and requires multiple modalities. It is hypothesized that the material response to an applied acoustic frequency would provide a robust alternative characterization mode for rapid and non-destructive material analysis. This research proposes applying air-coupled ultrasonic acoustics to characterize fibrous materials. Ultrasonic frequency waves transmitted through fibrous assemblies were feature extracted to understand the correlation between the applied frequency and the material properties. Mechanical and thermal characteristics were analyzed using ultrasonic features such as time of flight, signal velocity, power and the rate of attenuation of signal amplitude. Subsequently, these temporal and spectral characteristics were mapped with the standard low-stress mechanical and thermal properties via an empirical artificial intelligence engine. A high correlation of >0.92 (S.D. 0.06) was observed between the ultrasonic features and the standard measurements. The proposed ultrasonic technique can be used toward rapid characterization of dynamic behavior of flexible fibrous assemblies. Copyright © 2014 Elsevier B.V. All rights reserved.

Rapid identification of triterpenoid sulfates and hydroxy fatty acids including two new constituents from Tydemania expeditionis by liquid chromatography-mass spectrometry.

PubMed

Zhang, Jian-Long; Kubanek, Julia; Hay, Mark E; Aalbersberg, William; Ye, Wen-Cai; Jiang, Ren-Wang

2011-09-01

Tydemania expeditionis Weber-van Bosse (Udoteaceae) is a weakly calcified green alga. In the present paper, liquid chromatography coupled with photodiode array detection and electrospray mass spectrometry was developed to identify the fingerprint components. A total of four triterpenoid sulfates and three hydroxy fatty acids in the ethyl acetate fraction of the crude extract were structurally characterized on the basis of retention time, online UV spectrum, and mass fragmentation pattern. Furthermore, a detailed liquid chromatography-mass spectrometry analysis revealed two new hydroxy fatty acids, which were then prepared and characterized by extensive nuclear magnetic resonance (NMR) analyses. The proposed method provides a scientific and technical platform for the rapid identification of triterpenoid sulfates and hydroxy fatty acids in similar marine algae and terrestrial plants. Copyright © 2011 John Wiley & Sons, Ltd.

Rapid and solvent-free solid-state synthesis and characterization of Zn3V2O8 nanostructures and their phenol red aqueous solution photodegradation

NASA Astrophysics Data System (ADS)

Mazloom, Fatemeh; Masjedi-Arani, Maryam; Salavati-Niasari, Masoud

2017-08-01

Zinc vanadate (Zn3V2O8) nanostructures have been successfully synthesized via simple, rapid and solvent-free solid-state method by using different complex precursors of Zn and NH4VO3 as novel starting materials. Effects of various zinc (II) Schiff base complex precursors and calcination temperatures were investigated to reach optimum condition. It was found that particle size and optical property of the as-prepared products could be greatly influenced via these parameters. The products were characterized by X-ray diffraction (XRD), Fourier transform infrared (FT-IR) spectra, energy dispersive X-ray microanalysis (EDX), scanning electron microscopy (SEM), transmission electron microscopy (TEM), Photoluminescence and ultraviolet-visible (UV-Vis) spectroscopy. The photocatalytic activity of zinc vanadate nano and bulk structures were compared by degradation of phenol red aqueous solution.

Synthesis, characterization and catalytic activity of silver nanoparticles using Tribulus terrestris leaf extract.

PubMed

Ashokkumar, S; Ravi, S; Kathiravan, V; Velmurugan, S

2014-01-01

Biomediated silver nanoparticles were synthesized with the aid of an eco-friendly biomaterial, namely, aqueous Tribulus terrestris extract. Silver nanoparticles were synthesized using a rapid, single step, and completely green biosynthetic method employing aqueous T. terrestris leaf extracts as both the reducing and capping agent. Silver ions were rapidly reduced by aqueous T. terrestris leaf extracts, leading to the formation of highly crystalline silver nanoparticles. An attempt has been made and formation of the silver nanoparticles was verified by surface plasmon spectra using an UV-vis (Ultra violet), spectrophotometer. Morphology and crystalline structure of the prepared silver nanoparticles were characterized by TEM (Transmission Electron Microscope) and XRD (X-ray Diffraction), techniques, respectively. FT-IR (Fourier Transform Infrared), analysis suggests that the obtained silver nanoparticles might be stabilized through the interactions of carboxylic groups, carbonyl groups and the flavonoids present in the T. terrestris extract. Copyright © 2013 Elsevier B.V. All rights reserved.

Characterizing the graded structure of false killer whale (Pseudorca crassidens) vocalizations.

PubMed

Murray, S O; Mercado, E; Roitblat, H L

1998-09-01

The vocalizations from two, captive false killer whales (Pseudorca crassidens) were analyzed. The structure of the vocalizations was best modeled as lying along a continuum with trains of discrete, exponentially damped sinusoidal pulses at one end and continuous sinusoidal signals at the other end. Pulse trains were graded as a function of the interval between pulses where the minimum interval between pulses could be zero milliseconds. The transition from a pulse train with no inter-pulse interval to a whistle could be modeled by gradations in the degree of damping. There were many examples of vocalizations that were gradually modulated from pulse trains to whistles. There were also vocalizations that showed rapid shifts in signal type--for example, switching immediately from a whistle to a pulse train. These data have implications when considering both the possible function(s) of the vocalizations and the potential sound production mechanism(s). A short-time duty cycle measure was developed to characterize the graded structure of the vocalizations. A random sample of 500 vocalizations was characterized by combining the duty cycle measure with peak frequency measurements. The analysis method proved to be an effective metric for describing the graded structure of false killer whale vocalizations.

Rapid and sensitive screening and characterization of phenolic acids, phthalides, saponins and isoflavonoids in Danggui Buxue Tang by rapid resolution liquid chromatography/diode-array detection coupled with time-of-flight mass spectrometry.

PubMed

Qi, Lian-Wen; Wen, Xiao-Dong; Cao, Jun; Li, Chang-Yin; Li, Ping; Yi, Ling; Wang, Yu-Xia; Cheng, Xiao-Lan; Ge, Xiao-Xiao

2008-08-01

A novel rapid resolution liquid chromatography (RRLC) method coupled with diode-array detection (DAD) and time-of-flight mass spectrometry (TOFMS) in both positive and negative modes has been developed for quick and sensitive identification of the major compounds in Danggui Buxue Tang (DBT) preparation. Significant advantages of the use of RRLC with 1.8-microm porous particles include the much higher speed of chromatographic separation and great enhancement in sensitivity, compared with the conventional high-performance liquid chromatography (HPLC). With dynamic adjustment of the key role as fragmentor voltage in TOFMS, an efficient transmission of the ions was achieved to obtain the best sensitivity for providing the molecular formula for each analyte, and abundant fragment ions for structural information. The structural characterization of the major compounds in DBT was elucidated with authentic standards by DAD-TOF/MS, including phenolic acids, phthalides, saponins and isoflavonoids. The targets were rapidly screened from the complicated DBT matrix using a narrow mass window of 0.01 Da to restructure extracted ion chromatograms. By accurate mass measurements within 3 ppm error for each molecular ion and subsequent fragment ions, ten phenolic acids and phthalides including three groups of isomers, thirteen major saponins with a 20,24-epoxy-9,19-cyclolanostane-3,6,16,25-tetrol skeleton, sixteen isoflavonoids, corresponding glycosides, malonylglycosides, and acetylglycosides were identified in DBT preparation. The appropriate fragmentation pathways for them were also proposed based on definite elemental composition of the fragment ions. Copyright (c) 2008 John Wiley & Sons, Ltd.

Structural genomics: keeping up with expanding knowledge of the protein universe.

PubMed

Grabowski, Marek; Joachimiak, Andrzej; Otwinowski, Zbyszek; Minor, Wladek

2007-06-01

Structural characterization of the protein universe is the main mission of Structural Genomics (SG) programs. However, progress in gene sequencing technology, set in motion in the 1990s, has resulted in rapid expansion of protein sequence space--a twelvefold increase in the past seven years. For the SG field, this creates new challenges and necessitates a re-assessment of its strategies. Nevertheless, despite the growth of sequence space, at present nearly half of the content of the Swiss-Prot database and over 40% of Pfam protein families can be structurally modeled based on structures determined so far, with SG projects making an increasingly significant contribution. The SG contribution of new Pfam structures nearly doubled from 27.2% in 2003 to 51.6% in 2006.

Final Report: Hot Carrier Collection in Thin Film Silicon with Tailored Nanocrystalline/Amorphous Structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Collins, Reuben T.

This project developed, characterized, and perfected a new type of highly tunable nanocrystalline silicon (nc-Si:H) incorporating quantum confined silicon nanoparticles (SiNPs). A dual zone deposition process and system were developed and demonstrated. The depositions of SiNPs, the amorphous phase, and co-deposited material were characterized and optimized. Material design and interpretation of results were guided by new theoretical tools that examined both the electronic structure and carrier dynamics of this hybrid material. Heterojunction and p-i-n solar cells were demonstrated and characterized. Photo-thin-film-transistors allowed mobility to be studied as a function SiNP density in the films. Rapid (hot) transfer of carriers frommore » the amorphous matrix to the quantum confined SiNPs was observed and connected to reduced photo-degradation. The results carry quantum confined Si dots from a novelty to materials that can be harnessed for PV and optoelectronic applications. The growth process is broadly extendable with alternative amorphous matrices, novel layered structures, and alternative NPs easily accessible. The hot carrier effects hold the potential for third generation photovoltaics.« less

Genomic characterization and phylogenetic analysis of Zika virus circulating in the Americas.

PubMed

Ye, Qing; Liu, Zhong-Yu; Han, Jian-Feng; Jiang, Tao; Li, Xiao-Feng; Qin, Cheng-Feng

2016-09-01

The rapid spread and potential link with birth defects have made Zika virus (ZIKV) a global public health problem. The virus was discovered 70years ago, yet the knowledge about its genomic structure and the genetic variations associated with current ZIKV explosive epidemics remains not fully understood. In this review, the genome organization, especially conserved terminal structures of ZIKV genome were characterized and compared with other mosquito-borne flaviviruses. It is suggested that major viral proteins of ZIKV share high structural and functional similarity with other known flaviviruses as shown by sequence comparison and prediction of functional motifs in viral proteins. Phylogenetic analysis demonstrated that all ZIKV strains circulating in the America form a unique clade within the Asian lineage. Furthermore, we identified a series of conserved amino acid residues that differentiate the Asian strains including the current circulating American strains from the ancient African strains. Overall, our findings provide an overview of ZIKV genome characterization and evolutionary dynamics in the Americas and point out critical clues for future virological and epidemiological studies. Copyright © 2016 Elsevier B.V. All rights reserved.

A novel image-based quantitative method for the characterization of NETosis

PubMed Central

Zhao, Wenpu; Fogg, Darin K.; Kaplan, Mariana J.

2015-01-01

NETosis is a newly recognized mechanism of programmed neutrophil death. It is characterized by a stepwise progression of chromatin decondensation, membrane rupture, and release of bactericidal DNA-based structures called neutrophil extracellular traps (NETs). Conventional ‘suicidal’ NETosis has been described in pathogenic models of systemic autoimmune disorders. Recent in vivo studies suggest that a process of ‘vital’ NETosis also exists, in which chromatin is condensed and membrane integrity is preserved. Techniques to assess ‘suicidal’ or ‘vital’ NET formation in a specific, quantitative, rapid and semiautomated way have been lacking, hindering the characterization of this process. Here we have developed a new method to simultaneously assess both ‘suicidal’ and ‘vital’ NETosis, using high-speed multi-spectral imaging coupled to morphometric image analysis, to quantify spontaneous NET formation observed ex-vivo or stimulus-induced NET formation triggered in vitro. Use of imaging flow cytometry allows automated, quantitative and rapid analysis of subcellular morphology and texture, and introduces the potential for further investigation using NETosis as a biomarker in pre-clinical and clinical studies. PMID:26003624

Dermatoxin and phylloxin from the waxy monkey frog, Phyllomedusa sauvagei: cloning of precursor cDNAs and structural characterization from lyophilized skin secretion.

PubMed

Chen, Tianbao; Walker, Brian; Zhou, Mei; Shaw, Chris

2005-07-15

Amphibian skin is a morphologically, biochemically and physiologically complex organ that performs the wide range of functions necessary for amphibian survival. Here we describe the primary structures of representatives of two novel classes of amphibian skin antimicrobials, dermatoxin and phylloxin, from the skin secretion of Phyllomedusa sauvagei, deduced from their respective precursor encoding cDNAs cloned from a lyophilized skin secretion library. A degenerate primer, designed to a highly conserved domain in the 5'-untranslated region of analogous peptide precursor cDNAs from Phyllomedusa bicolor, was employed in a 3'-RACE reaction. Peptides with molecular masses coincident with precursor-deduced mature toxin peptides were identified in LC/MS fractions of skin secretion and primary structures were confirmed by MS/MS fragmentation. This integrated experimental approach can thus rapidly expedite the primary structural characterization of amphibian skin peptides in a manner that circumvents specimen sacrifice whilst preserving robustness of scientific data.

Assessing Structure and Condition of Temperate And Tropical Forests: Fusion of Terrestrial Lidar and Airborne Multi-Angle and Lidar Remote Sensing

NASA Astrophysics Data System (ADS)

Saenz, Edward J.

Forests provide vital ecosystem functions and services that maintain the integrity of our natural and human environment. Understanding the structural components of forests (extent, tree density, heights of multi-story canopies, biomass, etc.) provides necessary information to preserve ecosystem services. Increasingly, remote sensing resources have been used to map and monitor forests globally. However, traditional satellite and airborne multi-angle imagery only provide information about the top of the canopy and little about the forest structure and understory. In this research, we investigative the use of rapidly evolving lidar technology, and how the fusion of aerial and terrestrial lidar data can be utilized to better characterize forest stand information. We further apply a novel terrestrial lidar methodology to characterize a Hemlock Woolly Adelgid infestation in Harvard Forest, Massachusetts, and adapt a dynamic terrestrial lidar sampling scheme to identify key structural vegetation profiles of tropical rainforests in La Selva, Costa Rica.

Conformational Dynamics of Thermus aquaticus DNA Polymerase I during Catalysis

PubMed Central

Suo, Zucai

2014-01-01

Despite the fact that DNA polymerases have been investigated for many years and are commonly used as tools in a number of molecular biology assays, many details of the kinetic mechanism they use to catalyze DNA synthesis remain unclear. Structural and kinetic studies have characterized a rapid, pre-catalytic open-to-close conformational change of the Finger domain during nucleotide binding for many DNA polymerases including Thermus aquaticus DNA polymerase I (Taq Pol), a thermostable enzyme commonly used for DNA amplification in PCR. However, little has been done to characterize the motions of other structural domains of Taq Pol or any other DNA polymerase during catalysis. Here, we used stopped-flow Förster resonance energy transfer (FRET) to investigate the conformational dynamics of all five structural domains of the full-length Taq Pol relative to the DNA substrate during nucleotide binding and incorporation. Our study provides evidence for a rapid conformational change step induced by dNTP binding and a subsequent global conformational transition involving all domains of Taq Pol during catalysis. Additionally, our study shows that the rate of the global transition was greatly increased with the truncated form of Taq Pol lacking the N-terminal domain. Finally, we utilized a mutant of Taq Pol containing a de novo disulfide bond to demonstrate that limiting protein conformational flexibility greatly reduced the polymerization activity of Taq Pol. PMID:24931550

Structural Characterization of N-Alkylated Twisted Amides: Consequences for Amide Bond Resonance and N-C Cleavage.

PubMed

Hu, Feng; Lalancette, Roger; Szostak, Michal

2016-04-11

Herein, we describe the first structural characterization of N-alkylated twisted amides prepared directly by N-alkylation of the corresponding non-planar lactams. This study provides the first experimental evidence that N-alkylation results in a dramatic increase of non-planarity around the amide N-C(O) bond. Moreover, we report a rare example of a molecular wire supported by the same amide C=O-Ag bonds. Reactivity studies demonstrate rapid nucleophilic addition to the N-C(O) moiety of N-alkylated amides, indicating the lack of n(N) to π*(C=O) conjugation. Most crucially, we demonstrate that N-alkylation activates the otherwise unreactive amide bond towards σ N-C cleavage by switchable coordination. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A perspective on extracellular vesicles proteomics

NASA Astrophysics Data System (ADS)

Rosa-Fernandes, Livia; Rocha, Victória Bombarda; Carregari, Victor Corasolla; Urbani, Andrea; Palmisano, Giuseppe

2017-11-01

Increasing attention has been given to secreted extracellular vesicles (EVs) in the past decades, especially in the portrayal of their molecular cargo and role as messengers in both homeostasis and pathophysiological conditions. This review presents the state-of-the-art proteomic technologies to identify and quantify EVs proteins along with their PTMs, interacting partners and structural details. The rapid growth of mass spectrometry-based analytical strategies for protein sequencing, PTMs and structural characterization has improved the level of molecular details that can be achieve from limited amount of EVs isolated from different biological sources. Here we will provide a perspective view on the achievements and challenges on EVs proteome characterization using mass spectrometry. A detailed bioinformatics approach will help us to picture the molecular fingerprint of EVs and understand better their pathophysiological function.

Audiovisual Simultaneity Judgment and Rapid Recalibration throughout the Lifespan.

PubMed

Noel, Jean-Paul; De Niear, Matthew; Van der Burg, Erik; Wallace, Mark T

2016-01-01

Multisensory interactions are well established to convey an array of perceptual and behavioral benefits. One of the key features of multisensory interactions is the temporal structure of the stimuli combined. In an effort to better characterize how temporal factors influence multisensory interactions across the lifespan, we examined audiovisual simultaneity judgment and the degree of rapid recalibration to paired audiovisual stimuli (Flash-Beep and Speech) in a sample of 220 participants ranging from 7 to 86 years of age. Results demonstrate a surprisingly protracted developmental time-course for both audiovisual simultaneity judgment and rapid recalibration, with neither reaching maturity until well into adolescence. Interestingly, correlational analyses revealed that audiovisual simultaneity judgments (i.e., the size of the audiovisual temporal window of simultaneity) and rapid recalibration significantly co-varied as a function of age. Together, our results represent the most complete description of age-related changes in audiovisual simultaneity judgments to date, as well as being the first to describe changes in the degree of rapid recalibration as a function of age. We propose that the developmental time-course of rapid recalibration scaffolds the maturation of more durable audiovisual temporal representations.

Developing advanced X-ray scattering methods combined with crystallography and computation.

PubMed

Perry, J Jefferson P; Tainer, John A

2013-03-01

The extensive use of small angle X-ray scattering (SAXS) over the last few years is rapidly providing new insights into protein interactions, complex formation and conformational states in solution. This SAXS methodology allows for detailed biophysical quantification of samples of interest. Initial analyses provide a judgment of sample quality, revealing the potential presence of aggregation, the overall extent of folding or disorder, the radius of gyration, maximum particle dimensions and oligomerization state. Structural characterizations include ab initio approaches from SAXS data alone, and when combined with previously determined crystal/NMR, atomistic modeling can further enhance structural solutions and assess validity. This combination can provide definitions of architectures, spatial organizations of protein domains within a complex, including those not determined by crystallography or NMR, as well as defining key conformational states of a protein interaction. SAXS is not generally constrained by macromolecule size, and the rapid collection of data in a 96-well plate format provides methods to screen sample conditions. This includes screening for co-factors, substrates, differing protein or nucleotide partners or small molecule inhibitors, to more fully characterize the variations within assembly states and key conformational changes. Such analyses may be useful for screening constructs and conditions to determine those most likely to promote crystal growth of a complex under study. Moreover, these high throughput structural determinations can be leveraged to define how polymorphisms affect assembly formations and activities. This is in addition to potentially providing architectural characterizations of complexes and interactions for systems biology-based research, and distinctions in assemblies and interactions in comparative genomics. Thus, SAXS combined with crystallography/NMR and computation provides a unique set of tools that should be considered as being part of one's repertoire of biophysical analyses, when conducting characterizations of protein and other macromolecular interactions. Copyright © 2013 Elsevier Inc. All rights reserved.

Rapid Sintering of Li₂O-Nb₂O₅-TiO₂ Solid Solution by Air Pressure Control and Clarification of Its Mechanism.

PubMed

Nakano, Hiromi; Kamimoto, Konatsu; Yamamoto, Takahisa; Furuta, Yoshio

2018-06-11

We first successfully synthesized Li 1+ x − y Nb 1− x −3 y Ti x +4 y O₃ (LNT) solid solutions (0.13 ≤ x ≤ 0.18, 0 ≤ y ≤ 0.06) rapidly at 1373 K for one hour under 0.35 MPa by the controlling of air pressure using an air-pressure control atmosphere furnace. The composition is a formation area of a superstructure for LNT, in which the periodical intergrowth layer was formed in the matrix, and where it can be controlled by Ti content. Therefore, the sintering time depended on Ti content, and annealing was repeated for over 24 h until a homogeneous structure was formed using a conventional electric furnace. We clarified the mechanism of the rapid sintering using various microscale to nanoscale characterization techniques: X-ray diffraction, a scanning electron microscope, a transmission electron microscope (TEM), a Cs-corrected scanning TEM equipped with electron energy-loss spectroscopy, and X-ray absorption fine structure spectroscopy.

Effects of Rapid Thermal Annealing on the Structural, Electrical, and Optical Properties of Zr-Doped ZnO Thin Films Grown by Atomic Layer Deposition.

PubMed

Wu, Jingjin; Zhao, Yinchao; Zhao, Ce Zhou; Yang, Li; Lu, Qifeng; Zhang, Qian; Smith, Jeremy; Zhao, Yongming

2016-08-13

The 4 at. % zirconium-doped zinc oxide (ZnO:Zr) films grown by atomic layer deposition (ALD) were annealed at various temperatures ranging from 350 to 950 °C. The structural, electrical, and optical properties of rapid thermal annealing (RTA) treated ZnO:Zr films have been evaluated to find out the stability limit. It was found that the grain size increased at 350 °C and decreased between 350 and 850 °C, while creeping up again at 850 °C. UV-vis characterization shows that the optical band gap shifts towards larger wavelengths. The Hall measurement shows that the resistivity almost keeps constant at low annealing temperatures, and increases rapidly after treatment at 750 °C due to the effect of both the carrier concentration and the Hall mobility. The best annealing temperature is found in the range of 350-550 °C. The ZnO:Zr film-coated glass substrates show good optical and electrical performance up to 550 °C during superstrate thin film solar cell deposition.

Effects of Rapid Thermal Annealing on the Structural, Electrical, and Optical Properties of Zr-Doped ZnO Thin Films Grown by Atomic Layer Deposition

PubMed Central

Wu, Jingjin; Zhao, Yinchao; Zhao, Ce Zhou; Yang, Li; Lu, Qifeng; Zhang, Qian; Smith, Jeremy; Zhao, Yongming

2016-01-01

The 4 at. % zirconium-doped zinc oxide (ZnO:Zr) films grown by atomic layer deposition (ALD) were annealed at various temperatures ranging from 350 to 950 °C. The structural, electrical, and optical properties of rapid thermal annealing (RTA) treated ZnO:Zr films have been evaluated to find out the stability limit. It was found that the grain size increased at 350 °C and decreased between 350 and 850 °C, while creeping up again at 850 °C. UV–vis characterization shows that the optical band gap shifts towards larger wavelengths. The Hall measurement shows that the resistivity almost keeps constant at low annealing temperatures, and increases rapidly after treatment at 750 °C due to the effect of both the carrier concentration and the Hall mobility. The best annealing temperature is found in the range of 350–550 °C. The ZnO:Zr film-coated glass substrates show good optical and electrical performance up to 550 °C during superstrate thin film solar cell deposition. PMID:28773816

Structural genomics: keeping up with expanding knowledge of the protein universe

PubMed Central

Grabowski, Marek; Joachimiak, Andrzej; Otwinowski, Zbyszek; Minor, Wladek

2010-01-01

Structural characterization of the protein universe is the main mission of Structural Genomics (SG) programs. However, progress in gene sequencing technology, set in motion in the 1990s, has resulted in rapid expansion of protein sequence space — a twelvefold increase in the past seven years. For the SG field, this creates new challenges and necessitates a reassessment of its strategies. Nevertheless, despite the growth of sequence space, at present nearly half of the content of the Swiss-Prot database and over 40% of Pfam protein families can be structurally modeled based on structures determined so far, with SG projects making an increasingly significant contribution. The SG contribution of new Pfam structures nearly doubled from 27.2% in 2003 to 51.6% in 2006. PMID:17587562

Database on Performance of Neutron Irradiated FeCrAl Alloys

DOE Office of Scientific and Technical Information (OSTI.GOV)

Field, Kevin G.; Briggs, Samuel A.; Littrell, Ken

The present report summarizes and discusses the database on radiation tolerance for Generation I, Generation II, and commercial FeCrAl alloys. This database has been built upon mechanical testing and microstructural characterization on selected alloys irradiated within the High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory (ORNL) up to doses of 13.8 dpa at temperatures ranging from 200°C to 550°C. The structure and performance of these irradiated alloys were characterized using advanced microstructural characterization techniques and mechanical testing. The primary objective of developing this database is to enhance the rapid development of a mechanistic understanding on the radiation tolerancemore » of FeCrAl alloys, thereby enabling informed decisions on the optimization of composition and microstructure of FeCrAl alloys for application as an accident tolerant fuel (ATF) cladding. This report is structured to provide a brief summary of critical results related to the database on radiation tolerance of FeCrAl alloys.« less

Simple method for the characterization of intense Laguerre-Gauss vector vortex beams

NASA Astrophysics Data System (ADS)

Allahyari, E.; JJ Nivas, J.; Cardano, F.; Bruzzese, R.; Fittipaldi, R.; Marrucci, L.; Paparo, D.; Rubano, A.; Vecchione, A.; Amoruso, S.

2018-05-01

We report on a method for the characterization of intense, structured optical fields through the analysis of the size and surface structures formed inside the annular ablation crater created on the target surface. In particular, we apply the technique to laser ablation of crystalline silicon induced by femtosecond vector vortex beams. We show that a rapid direct estimate of the beam waist parameter is obtained through a measure of the crater radii. The variation of the internal and external radii of the annular crater as a function of the laser pulse energy, at fixed number of pulses, provides another way to evaluate the beam spot size through numerical fitting of the obtained experimental data points. A reliable estimate of the spot size is of paramount importance to investigate pulsed laser-induced effects on the target material. Our experimental findings offer a facile way to characterize focused, high intensity complex optical vector beams which are more and more applied in laser-matter interaction experiments.

Humans Rapidly Learn Grammatical Structure in a New Musical Scale

PubMed Central

Loui, Psyche; Wessel, David L.; Hudson Kam, Carla L.

2010-01-01

Knowledge of musical rules and structures has been reliably demonstrated in humans of different ages, cultures, and levels of music training, and has been linked to our musical preferences. However, how humans acquire knowledge of and develop preferences for music remains unknown. The present study shows that humans rapidly develop knowledge and preferences when given limited exposure to a new musical system. Using a non-traditional, unfamiliar musical scale (Bohlen-Pierce scale), we created finite-state musical grammars from which we composed sets of melodies. After 25–30 min of passive exposure to the melodies, participants showed extensive learning as characterized by recognition, generalization, and sensitivity to the event frequencies in their given grammar, as well as increased preference for repeated melodies in the new musical system. Results provide evidence that a domain-general statistical learning mechanism may account for much of the human appreciation for music. PMID:20740059

Humans Rapidly Learn Grammatical Structure in a New Musical Scale.

PubMed

Loui, Psyche; Wessel, David L; Hudson Kam, Carla L

2010-06-01

Knowledge of musical rules and structures has been reliably demonstrated in humans of different ages, cultures, and levels of music training, and has been linked to our musical preferences. However, how humans acquire knowledge of and develop preferences for music remains unknown. The present study shows that humans rapidly develop knowledge and preferences when given limited exposure to a new musical system. Using a non-traditional, unfamiliar musical scale (Bohlen-Pierce scale), we created finite-state musical grammars from which we composed sets of melodies. After 25-30 min of passive exposure to the melodies, participants showed extensive learning as characterized by recognition, generalization, and sensitivity to the event frequencies in their given grammar, as well as increased preference for repeated melodies in the new musical system. Results provide evidence that a domain-general statistical learning mechanism may account for much of the human appreciation for music.

Nontargeted diagnostic ion network analysis (NINA): A software to streamline the analytical workflow for untargeted characterization of natural medicines.

PubMed

Ye, Hui; Zhu, Lin; Sun, Di; Luo, Xiaozhuo; Lu, Gaoyuan; Wang, Hong; Wang, Jing; Cao, Guoxiu; Xiao, Wei; Wang, Zhenzhong; Wang, Guangji; Hao, Haiping

2016-11-30

The characterization of herbal prescriptions serves as a foundation for quality control and regulation of herbal medicines. Previously, the characterization of herbal chemicals from natural medicines often relied on the analysis of signature fragment ions from the acquired tandem mass spectrometry (MS/MS) spectra with prior knowledge of the herbal species present in the herbal prescriptions of interest. Nevertheless, such an approach is often limited to target components, and it risks missing the critical components that we have no prior knowledge of. We previously reported a "diagnostic ion-guided network bridging" strategy. It is a generally applicable and robust approach to analyze unknown substances from complex mixtures in an untargeted manner. In this study, we have developed a standalone software named "Nontargeted Diagnostic Ion Network Analysis (NINA)" with a graphical user interface based on a strategy for post-acquisition data analysis. NINA allows one to rapidly determine the nontargeted diagnostic ions (NIs) by summarizing all of the fragment ions shared by the precursors from the acquired MS/MS spectra. A NI-guided network using bridging components that possess two or more NIs can then be established via NINA. With such a network, we could sequentially identify the structures of all the NIs once a single compound has been identified de novo. The structures of NIs can then be used as "priori" knowledge to narrow the candidates containing the sub-structure of the corresponding NI from the database hits. Subsequently, we applied the NINA software to the characterization of a model herbal prescription, Re-Du-Ning injection, and rapidly identified 56 herbal chemicals from the prescription using an ultra-performance liquid chromatography quadrupole time-of-flight system in the negative mode with no knowledge of the herbal species or herbal chemicals in the mixture. Therefore, we believe the applications of NINA will greatly facilitate the characterization of complex mixtures, such as natural medicines, especially when no advance information is available. In addition to herbal medicines, the NINA-based workflow will also benefit many other fields, such as environmental analysis, nutritional science, and forensic analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

Ultra(high)-pressure liquid chromatography-electrospray ionization-time-of-flight-ion mobility-high definition mass spectrometry for the rapid identification and structural characterization of flavonoid glycosides from cauliflower waste.

PubMed

Gonzales, Gerard Bryan; Raes, Katleen; Coelus, Sofie; Struijs, Karin; Smagghe, Guy; Van Camp, John

2014-01-03

In this paper, a strategy for the detection and structural elucidation of flavonoid glycosides from a complex matrix in a single chromatographic run using U(H)PLC-ESI-IMS-HDMS/MS(E) is presented. This system operates using alternative low and high energy voltages that is able to perform the task of conventional MS/MS in a data-independent way without re-injection of the sample, which saves analytical time. Also, ion mobility separation (IMS) was employed as an additional separation technique for compounds that are co-eluting after U(H)PLC separation. First, the fragmentation of flavonoid standards were analyzed and criteria was set for structural elucidation of flavonoids in a plant extract. Based on retention times, UV spectra, exact mass, and MS fragment characteristics, such as abundances of daughter ions and the presence of radical ions ([Y0-H](-)), a total 19 flavonoid glycosides, of which 8 non-acylated and 11 acylated, were detected and structurally characterized in a cauliflower waste extract. Kaempferol and quercetin were the main aglycones detected while sinapic and ferulic acid were the main phenolic acids. C-glycosides were also found although their structure could not be elucidated. The proposed method can be used as a rapid screening test for flavonoid identification and for routine analysis of plant extracts, such as these derived from cauliflower waste. The study also confirms that agroindustrial wastes, such as cauliflower leaves, could be seen as a valuable source of different bioactive phenolic compounds. Copyright © 2013 Elsevier B.V. All rights reserved.

NMR experiments for the rapid identification of P=O···H-X type hydrogen bonds in nucleic acids.

PubMed

Duchardt-Ferner, Elke; Wöhnert, Jens

2017-10-01

Hydrogen bonds involving the backbone phosphate groups occur with high frequency in functional RNA molecules. They are often found in well-characterized tertiary structural motifs presenting powerful probes for the rapid identification of these motifs for structure elucidation purposes. We have shown recently that stable hydrogen bonds to the phosphate backbone can in principle be detected by relatively simple NMR-experiments, providing the identity of both the donor hydrogen and the acceptor phosphorous within the same experiment (Duchardt-Ferner et al., Angew Chem Int Ed Engl 50:7927-7930, 2011). However, for imino and hydroxyl hydrogen bond donor groups rapidly exchanging with the solvent as well as amino groups broadened by conformational exchange experimental sensitivity is severely hampered by extensive line broadening. Here, we present improved methods for the rapid identification of hydrogen bonds to phosphate groups in nucleic acids by NMR. The introduction of the SOFAST technique into 1 H, 31 P-correlation experiments as well as a BEST-HNP experiment exploiting 3h J N,P rather than 2h J H,P coupling constants enables the rapid and sensitive identification of these hydrogen bonds in RNA. The experiments are applicable for larger RNAs (up to ~ 100-nt), for donor groups influenced by conformational exchange processes such as amino groups and for hydrogen bonds with rather labile hydrogens such as 2'-OH groups as well as for moderate sample concentrations. Interestingly, the size of the through-hydrogen bond scalar coupling constants depends not only on the type of the donor group but also on the structural context. The largest coupling constants were measured for hydrogen bonds involving the imino groups of protonated cytosine nucleotides as donors.

Quantitative assessment of biophotonic imaging system performance with phantoms fabricated by rapid prototyping

NASA Astrophysics Data System (ADS)

Wang, Jianting; Coburn, James; Woolsey, Nicholas; Liang, Chia-Pin; Ramella-Roman, Jessica; Chen, Yu; Pfefer, Joshua

2014-03-01

In biophotonic imaging, turbid phantoms that are low-cost, biologically-relevant, and durable are desired for standardized performance assessment. Such phantoms often contain inclusions of varying depths and sizes in order to quantify key image quality characteristics such as penetration depth, sensitivity and contrast detectability. The emerging technique of rapid prototyping with three-dimensional (3D) printers provides a potentially revolutionary way to fabricate these structures. Towards this goal, we have characterized the optical properties and morphology of phantoms fabricated by two 3D printing approaches: thermosoftening and photopolymerization. Material optical properties were measured by spectrophotometry while the morphology of phantoms incorporating 0.2-1.0 mm diameter channels was studied by μCT, optical coherence tomography (OCT) and optical microscopy. A near-infrared absorbing dye and nanorods at several concentrations were injected into channels to evaluate detectability with a near-infrared hyperspectral reflectance imaging (HRI) system (650-1100 nm). Phantoms exhibited biologically-relevant scattering and low absorption across visible and near-infrared wavelengths. Although limitations in resolution were noted, channels with diameters of 0.4 mm or more could be reliably fabricated. The most significant problem noted was the porosity of phantoms generated with the thermosoftening-based printer. The aforementioned three imaging methods provided a valuable mix of insights into phantom morphology and may also be useful for detailed structural inspection of medical devices fabricated by rapid prototyping, such as customized implants. Overall, our findings indicate that 3D printing has significant potential as a method for fabricating well-characterized, standard phantoms for medical imaging modalities such as HRI.

Mode extraction on wind turbine blades via phase-based video motion estimation

NASA Astrophysics Data System (ADS)

Sarrafi, Aral; Poozesh, Peyman; Niezrecki, Christopher; Mao, Zhu

2017-04-01

In recent years, image processing techniques are being applied more often for structural dynamics identification, characterization, and structural health monitoring. Although as a non-contact and full-field measurement method, image processing still has a long way to go to outperform other conventional sensing instruments (i.e. accelerometers, strain gauges, laser vibrometers, etc.,). However, the technologies associated with image processing are developing rapidly and gaining more attention in a variety of engineering applications including structural dynamics identification and modal analysis. Among numerous motion estimation and image-processing methods, phase-based video motion estimation is considered as one of the most efficient methods regarding computation consumption and noise robustness. In this paper, phase-based video motion estimation is adopted for structural dynamics characterization on a 2.3-meter long Skystream wind turbine blade, and the modal parameters (natural frequencies, operating deflection shapes) are extracted. Phase-based video processing adopted in this paper provides reliable full-field 2-D motion information, which is beneficial for manufacturing certification and model updating at the design stage. The phase-based video motion estimation approach is demonstrated through processing data on a full-scale commercial structure (i.e. a wind turbine blade) with complex geometry and properties, and the results obtained have a good correlation with the modal parameters extracted from accelerometer measurements, especially for the first four bending modes, which have significant importance in blade characterization.

Single-shot characterization of enzymatic reaction constants Km and kcat by an acoustic-driven, bubble-based fast micromixer.

PubMed

Xie, Yuliang; Ahmed, Daniel; Lapsley, Michael Ian; Lin, Sz-Chin Steven; Nawaz, Ahmad Ahsan; Wang, Lin; Huang, Tony Jun

2012-09-04

In this work we present an acoustofluidic approach for rapid, single-shot characterization of enzymatic reaction constants K(m) and k(cat). The acoustofluidic design involves a bubble anchored in a horseshoe structure which can be stimulated by a piezoelectric transducer to generate vortices in the fluid. The enzyme and substrate can thus be mixed rapidly, within 100 ms, by the vortices to yield the product. Enzymatic reaction constants K(m) and k(cat) can then be obtained from the reaction rate curves for different concentrations of substrate while holding the enzyme concentration constant. We studied the enzymatic reaction for β-galactosidase and its substrate (resorufin-β-D-galactopyranoside) and found K(m) and k(cat) to be 333 ± 130 μM and 64 ± 8 s(-1), respectively, which are in agreement with published data. Our approach is valuable for studying the kinetics of high-speed enzymatic reactions and other chemical reactions.

Facile characterization of polymer fractions from waste electrical and electronic equipment (WEEE) for mechanical recycling.

PubMed

Taurino, Rosa; Pozzi, Paolo; Zanasi, Tania

2010-12-01

In view of the environmental problem involved in the management of WEEE, and then in the recycling of post-consumer plastic of WEEE there is a pressing need for rapid measurement technologies for simple identification of the various commercial plastic materials and of the several contaminants, to improve the recycling of such wastes. This research is focused on the characterization and recycling of two types of plastics, namely plastic from personal computer (grey plastic) and plastic from television (black plastic). Various analytical techniques were used to monitor the compositions of WEEE. Initially, the chemical structure of each plastic material was identified by Fourier transform infrared (FTIR) spectroscopy and differential scanning calorimetry (DSC). Polymeric contaminants of these plastics, in particular brominated flame retardants (BFRs) were detected in grey plastics only using different techniques. These techniques are useful for a rapid, correct and economics identification of a large volumes of WEEE plastics. Copyright © 2010 Elsevier Ltd. All rights reserved.

Structural Characterization of Sputtered Silicon Thin Films after Rapid Thermal Annealing for Active-Matrix Organic Light Emitting Diode

NASA Astrophysics Data System (ADS)

de Dieu Mugiraneza, Jean; Miyahira, Tomoyuki; Sakamoto, Akinori; Chen, Yi; Okada, Tatsuya; Noguchi, Takashi; Itoh, Taketsugu

2010-12-01

The microcrystalline phase obtained by adopting a two-step rapid thermal annealing (RTA) process for rf-sputtered silicon films deposited on thermally durable glass was characterized. The optical properties, surface morphology, and internal stress of the annealed Si films are investigated. As the thermally durable glass substrate allows heating of the deposited films at high temperatures, micro-polycrystalline silicon (micro-poly-Si) films of uniform grain size with a smooth surface and a low internal stress could be obtained after annealing at 750 °C. The thermal stress in the Si films was 100 times lower than that found in the films deposited on conventional glass. Uniform grains with an average grain size of 30 nm were observed by transmission electron microscopy (TEM) in the films annealed at 800 °C. These micro-poly-Si films have potential application for fabrication of uniform and reliable thin film transistors (TFTs) for large scale active-matrix organic light emitting diode (AMOLED) displays.

Characterization of iron-phosphate-silicate chemical garden structures.

PubMed

Barge, Laura M; Doloboff, Ivria J; White, Lauren M; Stucky, Galen D; Russell, Michael J; Kanik, Isik

2012-02-28

Chemical gardens form when ferrous chloride hydrate seed crystals are added or concentrated solutions are injected into solutions of sodium silicate and potassium phosphate. Various precipitation morphologies are observed depending on silicate and phosphate concentrations, including hollow plumes, bulbs, and tubes. The growth of precipitates is controlled by the internal osmotic pressure, fluid buoyancy, and membrane strength. Additionally, rapid bubble-led growth is observed when silicate concentrations are high. ESEM/EDX analysis confirms compositional gradients within the membranes, and voltage measurements across the membranes during growth show a final potential of around 150-200 mV, indicating that electrochemical gradients are maintained across the membranes as growth proceeds. The characterization of chemical gardens formed with iron, silicate, and phosphate, three important components of an early earth prebiotic hydrothermal system, can help us understand the properties of analogous structures that likely formed at submarine alkaline hydrothermal vents in the Hadean-structures offering themselves as the hatchery of life. © 2011 American Chemical Society

Sensitive clay landslide detection and characterization in and around Lakelse Lake, British Columbia, Canada

NASA Astrophysics Data System (ADS)

Geertsema, Marten; Blais-Stevens, Andrée; Kwoll, Eva; Menounos, Brian; Venditti, Jeremy G.; Grenier, Alain; Wiebe, Kelsey

2018-02-01

The Lakelse Lake area in northwestern British Columbia, Canada, has a long history, and prehistory, of rapid sensitive clay landslides moving on very low gradients. However, until now, many landslides have gone undetected. We use an array of modern tools to identify hitherto unknown or poorly known landslide deposits, including acoustic subbottom profiles, multibeam sonar, and LiDAR. The combination of these methods reveals not only landslide deposits, but also geomorphic and sedimentologic structures that give clues about landslide type and mode of emplacement. LiDAR and bathymetric data reveal the areal extent of landslide deposits as well as the orientation of ridges that differentiate between spreading and flowing kinematics. The subbottom profiles show two-dimensional structures of disturbed landslide deposits, including horst and grabens indicative of landslides classified as spreads. A preliminary computer tomography (CT) scan of a sediment core confirms the structures of one subbottom profile. We also use archival data from the Ministry of Transportation and Infrastructure and resident interviews to better characterize historic landslides.

Effects of rapid thermal annealing on the optical properties of strain-free quantum ring solar cells

PubMed Central

2013-01-01

Strain-free GaAs/Al0.33Ga0.67As quantum rings are fabricated by droplet epitaxy. Both photoresponse and photoluminescence spectra confirm optical transitions in quantum rings, suggesting that droplet epitaxial nanomaterials are applicable to intermediate band solar cells. The effects of post-growth annealing on the quantum ring solar cells are investigated, and the optical properties of the solar cells with and without thermal treatment are characterized by photoluminescence technique. Rapid thermal annealing treatment has resulted in the significant improvement of material quality, which can be served as a standard process for quantum structure solar cells grown by droplet epitaxy. PMID:23281811

Rapid lead discovery through iterative screening of one bead one compound libraries.

PubMed

Gao, Yu; Amar, Sabrina; Pahwa, Sonia; Fields, Gregg; Kodadek, Thomas

2015-01-12

Primary hits that arise from screening one bead one compound (OBOC) libraries against a target of interest rarely have high potency. However, there has been little work focused on the development of an efficient workflow for primary hit improvement. In this study, we show that by characterizing the binding constants for all of the hits that arise from a screen, structure-activity relationship (SAR) data can be obtained to inform the design of "derivative libraries" of a primary hit that can then be screened under more demanding conditions to obtain improved compounds. Here, we demonstrate the rapid improvement of a primary hit against matrix metalloproteinase-14 using this approach.

Early stage structural development of prototypical zeolitic imidazolate framework (ZIF) in solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Terban, Maxwell W.; Banerjee, Debasis; Ghose, Sanjit

Given the wide-ranging potential applications of metal organic frameworks (MOFs), an emerging imperative is to understand their formation with atomic scale precision. This will aid in designing syntheses for next-generation MOFs with enhanced properties and functionalities. Major challenges are to characterize the early-stage seeds, and the pathways to framework growth, which require synthesis coupled with in situ structural characterization sensitive to nanoscale structures in solution. Here we report measurements of an in situ synthesis of a prototypical MOF, ZIF-8, utilizing synchrotron X-ray atomic pair distribution function (PDF) analysis optimized for sensitivity to dilute species, complemented by mass spectrometry, electron microscopy,more » and density functional theory calculations. We observe that despite rapid formation of the crystalline product, a high concentration of Zn(2-MeIm) 4(2-MeIm=2-methylimidazolate) initially forms and persists as stable clusters over long times. A secondary, amorphous phase also pervades during the synthesis, which has a structural similarity to the final ZIF-8 and may act as an intermediate to the final product.« less

Early stage structural development of prototypical zeolitic imidazolate framework (ZIF) in solution

DOE PAGES

Terban, Maxwell W.; Banerjee, Debasis; Ghose, Sanjit; ...

2018-02-05

Given the wide-ranging potential applications of metal organic frameworks (MOFs), an emerging imperative is to understand their formation with atomic scale precision. This will aid in designing syntheses for next-generation MOFs with enhanced properties and functionalities. Major challenges are to characterize the early-stage seeds, and the pathways to framework growth, which require synthesis coupled with in situ structural characterization sensitive to nanoscale structures in solution. Here we report measurements of an in situ synthesis of a prototypical MOF, ZIF-8, utilizing synchrotron X-ray atomic pair distribution function (PDF) analysis optimized for sensitivity to dilute species, complemented by mass spectrometry, electron microscopy,more » and density functional theory calculations. We observe that despite rapid formation of the crystalline product, a high concentration of Zn(2-MeIm) 4(2-MeIm=2-methylimidazolate) initially forms and persists as stable clusters over long times. A secondary, amorphous phase also pervades during the synthesis, which has a structural similarity to the final ZIF-8 and may act as an intermediate to the final product.« less

Growth and form of planetary seedlings: results from a microgravity aggregation experiment.

PubMed

Blum, J; Wurm, G; Kempf, S; Poppe, T; Klahr, H; Kozasa, T; Rott, M; Henning, T; Dorschner, J; Schräpler, R; Keller, H U; Markiewicz, W J; Mann, I; Gustafson, B A; Giovane, F; Neuhaus, D; Fechtig, H; Grün, E; Feuerbacher, B; Kochan, H; Ratke, L; El Goresy, A; Morfill, G; Weidenschilling, S J; Schwehm, G; Metzler, K; Ip, W H

2000-09-18

The outcome of the first stage of planetary formation, which is characterized by ballistic agglomeration of preplanetary dust grains due to Brownian motion in the free molecular flow regime of the solar nebula, is still somewhat speculative. We performed a microgravity experiment flown onboard the space shuttle in which we simulated, for the first time, the onset of free preplanetary dust accumulation and revealed the structures and growth rates of the first dust agglomerates in the young solar system. We find that a thermally aggregating swarm of dust particles evolves very rapidly and forms unexpected open-structured agglomerates.

In-situ Polymerization of Polyaniline/Polypyrrole Copolymer using Different Techniques

NASA Astrophysics Data System (ADS)

Hammad, A. S.; Noby, H.; Elkady, M. F.; El-Shazly, A. H.

2018-01-01

The morphology and surface area of the poly(aniline-co-pyrrole) copolymer (PANPY) are important properties which improve the efficiency of the copolymer in various applications. In this investigation, different techniques were employed to produce PANPY in different morphologies. Aniline and pyrrole were used as monomers, and ammonium peroxydisulfate (APS) was used as an oxidizer with uniform molar ratio. Rapid mixing, drop-wise mixing, and supercritical carbon dioxide (ScCO2) polymerization techniques were appointed. The chemical structure, crystallinity, porosity, and morphology of the composite were distinguished by Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), Brunauer, Emmett and Teller (BET) analysis, and transmission electron microscopy (TEM) respectively. The characterization tests indicated that the polyaniline/polypyrrole copolymer was successfully prepared with different morphologies. Based on the obtained TEM, hollow nanospheres were formed using rapid mixing technique with acetic acid that have a diameter of 75 nm and thickness 26 nm approximately. Also, according to the XRD, the produced structures have a semi- crystalline structure. The synthesized copolymer with ScCO2-assisted polymerization technique showed improved surface area (38.1 m2/g) with HCl as dopant.

Preparation and characterization of core-shell structured LiFePO4/C composite using a novel carbon source for lithium-ion battery cathode

NASA Astrophysics Data System (ADS)

Huang, Zan; Luo, Peifang; Wang, Daxiang

2017-03-01

Core-shell structured LiFePO4/C1 cathode material is synthesized via a rapid microwave irradiation route using ethylene diamine tetraacetic acid (EDTA) as the novel carbon source. XRD results reveal that all the patterns can be indexed as the olivine-type structured LiFePO4 with the space group of Pnma. TEM images show that the obtained carbon is an amorphous layer with a thickness of about 3-4 nm. When the LiFePO4/C1 used as cathode material for lithium-ion battery, it delivers an initial discharge capacity of 163.1 mAh g-1 at 0.1 C which is about 96% of the theoretical capacity. Moreover, it also shows excellent rate performance and good cycle stability due to the enhanced electronic conductivity as proved by the electrochemical impedance spectroscopy (EIS). Thus, this carbon decorated LiFePO4 composite synthesized via the rapid microwave irradiation method is a promising cathode material for high-performance lithium-ion battery.

Structural insights into the evolution of a sexy protein: novel topology and restricted backbone flexibility in a hypervariable pheromone from the red-legged salamander, Plethodon shermani.

PubMed

Wilburn, Damien B; Bowen, Kathleen E; Doty, Kari A; Arumugam, Sengodagounder; Lane, Andrew N; Feldhoff, Pamela W; Feldhoff, Richard C

2014-01-01

In response to pervasive sexual selection, protein sex pheromones often display rapid mutation and accelerated evolution of corresponding gene sequences. For proteins, the general dogma is that structure is maintained even as sequence or function may rapidly change. This phenomenon is well exemplified by the three-finger protein (TFP) superfamily: a diverse class of vertebrate proteins co-opted for many biological functions - such as components of snake venoms, regulators of the complement system, and coordinators of amphibian limb regeneration. All of the >200 structurally characterized TFPs adopt the namesake "three-finger" topology. In male red-legged salamanders, the TFP pheromone Plethodontid Modulating Factor (PMF) is a hypervariable protein such that, through extensive gene duplication and pervasive sexual selection, individual male salamanders express more than 30 unique isoforms. However, it remained unclear how this accelerated evolution affected the protein structure of PMF. Using LC/MS-MS and multidimensional NMR, we report the 3D structure of the most abundant PMF isoform, PMF-G. The high resolution structural ensemble revealed a highly modified TFP structure, including a unique disulfide bonding pattern and loss of secondary structure, that define a novel protein topology with greater backbone flexibility in the third peptide finger. Sequence comparison, models of molecular evolution, and homology modeling together support that this flexible third finger is the most rapidly evolving segment of PMF. Combined with PMF sequence hypervariability, this structural flexibility may enhance the plasticity of PMF as a chemical signal by permitting potentially thousands of structural conformers. We propose that the flexible third finger plays a critical role in PMF:receptor interactions. As female receptors co-evolve, this flexibility may allow PMF to still bind its receptor(s) without the immediate need for complementary mutations. Consequently, this unique adaptation may establish new paradigms for how receptor:ligand pairs co-evolve, in particular with respect to sexual conflict.

Characterization and optimization of polycrystalline Si70%Ge30% for surface micromachined thermopiles in human body applications

NASA Astrophysics Data System (ADS)

Wang, Ziyang; Fiorini, Paolo; Leonov, Vladimir; Van Hoof, Chris

2009-09-01

This paper presents the material characterization methods, characterization results and the optimization scheme for polycrystalline Si70%Ge30% (poly-SiGe) from the perspective of its application in a surface micromachined thermopile. Due to its comparative advantages, such as lower thermal conductivity and ease of processing, over other materials, poly-SiGe is chosen to fabricate a surface micromachined thermopile and eventually a wearable thermoelectric generator (TEG) to be used on a human body. To enable optimal design of advanced thermocouple microstructures, poly-SiGe sample materials prepared by two different techniques, namely low-pressure chemical vapor deposition (LPCVD) with in situ doping and rapid thermal chemical vapor deposition (RTCVD) with ion implantation, have been characterized. Relevant material properties, including electrical resistivity, Seebeck coefficient, thermal conductivity and specific contact resistance, have been reported. For the determination of thermal conductivity, a novel surface-micromachined test structure based on the Seebeck effect is designed, fabricated and measured. Compared to the traditional test structures, it is more advantageous for sample materials with a relatively large Seebeck coefficient, such as poly-SiGe. Based on the characterization results, a further optimization scheme is suggested to allow independent respective optimization of the figure of merit and the specific contact resistance.

Rapid crystallization and morphological adjustment of zeolite ZSM-5 in nonionic emulsions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang Ying, E-mail: yingzh1977@163.co; Jin Chao; Research Institute of Petroleum Processing, Beijing 100083

2011-01-15

Zeolite ZSM-5 was synthesized for the first time in a nonionic emulsion composed of polyoxyethylated alkylphenol, butanol, cyclohexane and tetraethylammonium hydroxide (TEAOH)-containing zeolite synthesis mixture. The crystallization kinetics in the emulsion was investigated and the ZSM-5 product was characterized in detail by XRD, SEM, FT-IR, TG, N{sub 2} adsorption and CHN analysis techniques. Compared with the conventionally hydrothermal synthesis with the same structure directing agent TEAOH, the emulsion system allows rapid crystallization of ZSM-5. The ZSM-5 product exhibits unusual agglomerated structure and possesses larger specific surface area. The FT-IR, TG results plus CHN analysis show the encapsulation of a tracemore » of emulsion components in the emulsion ZSM-5. Control experiments show the emulsion system exerts the crystallization induction and morphological adjustment effects mainly during the aging period. The effects are tentatively attributed to the confined space domains, surfactant-water interaction as well as surfactant-growing crystals interaction existing in the emulsion. -- Graphical abstract: The nonionic emulsion synthesis allows rapid crystallization and morphological adjustment of zeolite ZSM-5 compared with the conventional hydrothermal synthesis. Display Omitted« less

Microstructure and corrosion resistance of nitrogen-rich surface layers on AISI 304 stainless steel by rapid nitriding in a hollow cathode discharge

NASA Astrophysics Data System (ADS)

Li, Yang; He, Yongyong; Zhang, Shangzhou; Wang, Wei; Zhu, Yijie

2018-01-01

Nitriding treatments have been successfully applied to austenitic stainless steels to improve their hardness and tribological properties. However, at temperatures above 450 °C, conventional plasma nitriding processes decrease the corrosion resistance due to the formation of CrN phases within the modified layer. In this work, AISI 304 austenitic stainless steels were efficiently treated by rapid plasma nitriding at a high temperature of 530 °C in a hollow cathode discharge. The enhanced ionization obtained in the hollow cathode configuration provided a high current density and, consequently, a high temperature could be attained in a short time. The nitrided layers were characterized by X-ray diffraction, scanning electron microscopy, atomic force microscopy, transmission electron microscopy and X-ray photoelectron spectroscopy. The results indicated that the dual-layer structure of the nitrided layer consists of a high-N face-centered cubic structure with a free CrN precipitate outer (top) layer and a nitrogen-expanded austenite S-phase bottom layer. The rapid nitriding-assisted hollow cathode discharge technique permits the use of high temperatures, as high as 530 °C, without promoting degradation in the corrosion resistance of stainless steel.

Characterization of ionic currents of cells of the subfornical organ that project to the supraoptic nuclei

NASA Technical Reports Server (NTRS)

Johnson, R. F.; Beltz, T. G.; Jurzak, M.; Wachtel, R. E.; Johnson, A. K.

1999-01-01

The subfornical organ (SFO) is a forebrain structure that converts peripheral blood-borne signals reflecting the hydrational state of the body to neural signals and then through efferent fibers conveys this information to several central nervous system structures. One of the forebrain areas receiving input from the SFO is the supraoptic nucleus (SON), a source of vasopressin synthesis and control of release from the posterior pituitary. Little is known of the transduction and transmission processes by which this conversion of systemic information to brain input occurs. As a step in elucidating these mechanisms, the present study characterized the ionic currents of dissociated cells of the SFO that were identified as neurons that send efferents to the SON. A retrograde tracer was injected into the SON area in eleven-day-old rats. After three days for retrograde transport of the label, the SFOs of these animals were dissociated and plated for tissue culture. The retrograde tracer was used to identify the soma of SFO cells projecting to the SON so that voltage-dependent ionic currents using whole-cell voltage clamp methods could be studied. The three types of currents in labeled SFO neurons were characterized as a 1) rapid, transient inward current that can be blocked by tetrodotoxin (TTX) characteristic of a sodium current; 2) slow-onset sustained outward current that can be blocked by tetraethylammonium (TEA) characteristic of a delayed rectifier potassium current; and 3) remaining outward current that has a rapid-onset and transient characteristic of a potassium A-type current. Copyright 1999 Elsevier Science B.V.

Nonequilibrium Phase Chemistry in High Temperature Structure Alloys

NASA Technical Reports Server (NTRS)

Wang, R.

1991-01-01

Titanium and nickel aluminides of nonequilibrium microstructures and in thin gauge thickness were identified, characterized and produced for potential high temperature applications. A high rate sputter deposition technique for rapid surveillance of the microstructures and nonequilibrium phase is demonstrated. Alloys with specific compositions were synthesized with extended solid solutions, stable dispersoids, and specific phase boundaries associated with different heat treatments. Phase stability and mechanical behavior of these nonequilibrium alloys were investigated and compared.

Structural properties of medium-range order in CuNiZr alloy

NASA Astrophysics Data System (ADS)

Gao, Tinghong; Hu, Xuechen; Xie, Quan; Li, Yidan; Ren, Lei

2017-10-01

The evolution characteristics of icosahedral clusters during the rapid solidification of Cu50Ni10Zr40 alloy at cooling rate of 1011 K s-1 are investigated based on molecular dynamics simulations. The structural properties of the short-range order and medium-range order of Cu50Ni10Zr40 alloy are analyzed by several structural characterization methods. The results reveal that the icosahedral clusters are the dominant short-range order structure, and that they assemble themselves into medium-range order by interpenetrating connections. The different morphologies of medium-range order are found in the system and include chain, triangle, tetrahedral, and their combination structures. The tetrahedral morphologies of medium-range order have excellent structural stability with decreasing temperature. The Zr atoms are favorable to form longer chains, while the Cu atoms are favorable to form shorter chains in the system. Those chains interlocked with each other to improve the structural stability.

Characterization and chromosomal localization of the gene for human rhodopsin kinase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khani, S.C.; Yamamoto, S.; Dryja, T.P.

1996-08-01

G-protein-dependent receptor kinases (GRKs) play a key role in the adapatation of receptors to persistent stimuli. In rod photoreceptors rhodopsin kinase (RK) mediates rapid densensitization of rod photoreceptors to light by catalyzing phosphorylation of the visual pigment rhodopsin. To study the structure and mechanism of FRKs in human photoreceptors, we have isolated and characterized cDNA and genomic clones derived from the human RK locus using a bovine rhodopsin kinase cDNA fragment as a probe. The RK locus, assigned to chromosome 13 band q34, is composed of seven exons that encode a protein 92% identical in amino acid sequence to bovinemore » rhodopsin kinase. The marked difference between the structure of this gene and that of another recently clone human GRK gene suggests the existence of a wide evolutionary gap between members of the GRK gene family. 39 refs., 3 figs.« less

New structure of diamine curing agent for epoxy resins with self-restoration ability: Synthesis and spectroscopy characterization

NASA Astrophysics Data System (ADS)

Raimondo, Marialuigia; Guadagno, Liberata; Naddeo, Carlo; Longo, Pasquale; Mariconda, Annaluisa; Agovino, Anna

2017-02-01

The development of smart materials in aeronautical structures consisting of compounds based on epoxy resins having self-repair capability has been hampered by some criticalities. One of the main critical points is related to the impossibility to use primary amines (e.g.: 4,4‧-diaminodiphenyl sulfone, DDS) as hardeners, because they can poison the catalyst responsible for the healing mechanisms. In this paper, the synthesis, characterization and some tests of applicability of a new hardener, the tetramethylated diaminodiphenyl sulfone (tm-DDS), are shown. The tm-DDS is able to rapidly react with epoxy resin, giving a composite material having some characteristics significantly better than composites hardened with different tertiary amines. The new hardener is able to increase the glass transition temperature (Tg) of about 90 °C with respect to the more common hardener, ancamine K54, already used in self-healing epoxy formulations.

Accelerating the design of biomimetic materials by integrating RNA-seq with proteomics and materials science.

PubMed

Guerette, Paul A; Hoon, Shawn; Seow, Yiqi; Raida, Manfred; Masic, Admir; Wong, Fong T; Ho, Vincent H B; Kong, Kiat Whye; Demirel, Melik C; Pena-Francesch, Abdon; Amini, Shahrouz; Tay, Gavin Z; Ding, Dawei; Miserez, Ali

2013-10-01

Efforts to engineer new materials inspired by biological structures are hampered by the lack of genomic data from many model organisms studied in biomimetic research. Here we show that biomimetic engineering can be accelerated by integrating high-throughput RNA-seq with proteomics and advanced materials characterization. This approach can be applied to a broad range of systems, as we illustrate by investigating diverse high-performance biological materials involved in embryo protection, adhesion and predation. In one example, we rapidly engineer recombinant squid sucker ring teeth proteins into a range of structural and functional materials, including nanopatterned surfaces and photo-cross-linked films that exceed the mechanical properties of most natural and synthetic polymers. Integrating RNA-seq with proteomics and materials science facilitates the molecular characterization of natural materials and the effective translation of their molecular designs into a wide range of bio-inspired materials.

Depth estimation of laser glass drilling based on optical differential measurements of acoustic response

NASA Astrophysics Data System (ADS)

Gorodesky, Niv; Ozana, Nisan; Berg, Yuval; Dolev, Omer; Danan, Yossef; Kotler, Zvi; Zalevsky, Zeev

2016-09-01

We present the first steps of a device suitable for characterization of complex 3D micro-structures. This method is based on an optical approach allowing extraction and separation of high frequency ultrasonic sound waves induced to the analyzed samples. Rapid, non-destructive characterization of 3D micro-structures are limited in terms of geometrical features and optical properties of the sample. We suggest a method which is based on temporal tracking of secondary speckle patterns generated when illuminating a sample with a laser probe while applying known periodic vibration using an ultrasound transmitter. In this paper we investigated lasers drilled through glass vias. The large aspect ratios of the vias possess a challenge for traditional microscopy techniques in analyzing depth and taper profiles of the vias. The correlation of the amplitude vibrations to the vias depths is experimentally demonstrated.

Unambiguous identification and discovery of bacterial siderophores by direct injection 21 Tesla Fourier transform ion cyclotron resonance mass spectrometry.

PubMed

Walker, Lawrence R; Tfaily, Malak M; Shaw, Jared B; Hess, Nancy J; Paša-Tolić, Ljiljana; Koppenaal, David W

2017-01-25

Under iron-limiting conditions, bacteria produce low molecular mass Fe(iii) binding molecules known as siderophores to sequester the Fe(iii), along with other elements, increasing their bioavailability. Siderophores are thought to influence iron cycling and biogeochemistry in both marine and terrestrial ecosystems and hence the need for rapid, confident characterization of these compounds has increased. In this study, the type of siderophores produced by two marine bacterial species, Synechococcus sp. PCC 7002 and Vibrio cyclitrophicus 1F53, were characterized by use of a newly developed 21 T Fourier Transform Ion Cyclotron Resonance Mass Spectrometer (FTICR MS) with direct injection electrospray ionization. This technique allowed for the rapid detection of synechobactins from Synechococcus sp. PCC 7002 as well as amphibactins from Vibrio cyclitrophicus 1F53 based on high mass accuracy and resolution allowing for observation of specific Fe isotopes and isotopic fine structure enabling highly confident identification of these siderophores. When combined with molecular network analysis two new amphibactins were discovered and verified by tandem MS. These results show that high-field FTICR MS is a powerful technique that will greatly improve the ability to rapidly identify and discover metal binding species in the environment.

Oxidation of SiC/BN/SiC Composites in Reduced Oxygen Partial Pressures

NASA Technical Reports Server (NTRS)

Opila, Elizabeth J.; Boyd, Meredith

2010-01-01

SiC fiber-reinforced SiC composites with a BN interphase are proposed for use as leading edge structures of hypersonic vehicles. The durability of these materials under hypersonic flight conditions is therefore of interest. Thermogravimetric analysis was used to characterize the oxidation kinetics of both the constituent fibers and composite coupons at four temperatures: 816, 1149, 1343, and 1538 C (1500, 2100, 2450, and 2800 F) and in oxygen partial pressures between 5% and 0.1% (balance argon) at 1 atm total pressure. One edge of the coupons was ground off so the effects of oxygen ingress into the composite could be monitored by post-test SEM and EDS. Additional characterization of the oxidation products was conducted by XPS and TOF-SIMS. Under most conditions, the BN oxidized rapidly, leading to the formation of borosilicate glass. Rapid initial oxidation followed by volatilization of boria lead to protective oxide formation and further oxidation was slow. At 1538C in 5% oxygen, both the fibers and coupons exhibited borosilicate glass formation and bubbling. At 1538C in 0.1% oxygen, active oxidation of both the fibers and the composites was observed leading to rapid SiC degradation. BN oxidation at 1538C in 0.1% oxygen was not significant.

Unambiguous identification and discovery of bacterial siderophores by direct injection 21 Tesla Fourier transform ion cyclotron resonance mass spectrometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Walker, Lawrence R.; Tfaily, Malak M.; Shaw, Jared B.

Under iron-limiting conditions, bacteria produce low molecular mass Fe(III) binding molecules known as siderophores to sequester the Fe(III), along with other elements, increasing their bioavailibility. Siderophores are thought to influence iron cycling and biogeochemistry in both marine and terrestrial ecosystems and hence the need for rapid, confident characterization of these compounds has increased. In this study, the type of siderophores produced by two marine bacterial species, Synechococcus sp. PCC 7002 and Vibrio cyclitrophicus 1F53, were characterized using a newly developed 21T Fourier Transform Ion Cyclotron Resonance Mass Spectrometer (FTICR MS) with direct injection electrospray ionization. This technique allowed for themore » rapid detection of synechobactins from Synechococcus sp. PCC 7002 as well as amphibactins from Vibrio cyclitrophicus 1F53 based on high mass accuracy and resolution allowing for observation of specific Fe isotopic peaks and fine isotopic structure enables highly confident identification of these sideropohores. When combined with molecular network analysis two new amphibactins were discovered and verified by tandem MS. These results show that high-field FTICR MS is a powerful technique that will greatly improve the ability to rapidly identify and discover metal binding species in the environment.« less

High-field FT-ICR-MS and aromaticity equivalent approach for structural identification of water soluble organic compounds (WSOC)

NASA Astrophysics Data System (ADS)

Harir, Mourad; Yassine, Mahmoud M.; Dabek-Zlotorzynska, Ewa; Hertkorn, Norbert; Schmitt-Kopplin, Philippe

2015-04-01

Organic aerosol (OA) makes up a large and often dominant fraction, (20 to 90%) of the submicron atmospheric particulate mass, and its effects are becoming increasingly important in determining climatic and health effects of atmospheric aerosols. Despite the abundance of OA, our understanding of the sources, formation processes and atmospheric properties of OA is limited. Atmospheric OA has both primary (directly emitted) and secondary (formed in the atmosphere from precursor gases) sources, which can be natural (e.g. vegetation) and/or anthropogenic (e.g. fossil-based vehicle exhaust or biomass burning). A significant fraction of OA contains as much as 20-70% of water soluble organic compounds (WSOC). The WSOC fraction is a very complex mixture of low volatility, polyfunctional aliphatic and aromatic compounds containing carboxyl, alcohol, carbonyl, sulfo, nitro, and other functionalities. This high degree of chemical complexity of atmospheric organics has inspired a number of sophisticated approaches that are capable of identifying and detecting a variety of different analytes in OA. Accordingly, one of the most challenging areas of atmospheric particulate matter (PM) analysis is to comprehend the molecular complexity of the OA, especially WSOC fraction, a significant component of atmospheric fine PM (PM2.5). The sources of WSOC are not well understood, especially the relative contributions of primary vs. secondary organic aerosol. Therefore, the molecular characterization of WSOC is important because it allows gaining insight into aerosol sources and underlying mechanisms of secondary organic aerosols (SOA) formation and transformation. In this abstract, molecular characterization of WSOC was achieved using high-field mass spectrometry FT-ICR-MS and aromaticity equivalent approach. Aromaticity equivalent (Xc), defined recently as a new parameter calculated from the assigned molecular formulas (complementary to the aromaticity index [1]), is introduced to improve identification and characterization of aromatic and condensed aromatic compounds in WSOC [2]. We proposed threshold values of Xc≥ 2.5000 and Xc≥ 2.7143 as ambiguous minimum criteria for the presence of aromatic structure and condensed aromatic compounds, respectively. The advantage of employing this parameter is that Xc would have a constant value for each proposed core structure regardless the degree of alkylation, and thus visual representation and structural interpretations of the spectra become advantageous for characterizing and comparing complex samples. Diesel particulate matter (DPM) and two atmospheric aerosols collected in the industrial area affected by biomass burning events were used to study the applicability of the proposed criteria for the improved identification of aromatic and condensed aromatic structures in complex mixtures in the FT-ICR mass spectra. References [1] Koch.BP, Dittmar.T. From mass to structure: an aromaticity index for high-resolution mass data of natural organic matter. Rapid Commun. Mass Spectrom. 2006, 20, 926-932 [2] Yassine.MM, Harir.M, Dabek-Zlotorzynska.E, Schmitt-Kopplin.Ph. Structural characterization of organic aerosol using Fourier transform ion cyclotron resonance mass spectrometry: Aromaticity equivalent approach. Rapid Commun. Mass Spectrom. 2014. 28. 2445-2454

3' rapid amplification of cDNA ends (RACE) walking for rapid structural analysis of large transcripts.

PubMed

Ozawa, Tatsuhiko; Kondo, Masato; Isobe, Masaharu

2004-01-01

The 3' rapid amplification of cDNA ends (3' RACE) is widely used to isolate the cDNA of unknown 3' flanking sequences. However, the conventional 3' RACE often fails to amplify cDNA from a large transcript if there is a long distance between the 5' gene-specific primer and poly(A) stretch, since the conventional 3' RACE utilizes 3' oligo-dT-containing primer complementary to the poly(A) tail of mRNA at the first strand cDNA synthesis. To overcome this problem, we have developed an improved 3' RACE method suitable for the isolation of cDNA derived from very large transcripts. By using the oligonucleotide-containing random 9mer together with the GC-rich sequence for the suppression PCR technology at the first strand of cDNA synthesis, we have been able to amplify the cDNA from a very large transcript, such as the microtubule-actin crosslinking factor 1 (MACF1) gene, which codes a transcript of 20 kb in size. When there is no splicing variant, our highly specific amplification allows us to perform the direct sequencing of 3' RACE products without requiring cloning in bacterial hosts. Thus, this stepwise 3' RACE walking will help rapid characterization of the 3' structure of a gene, even when it encodes a very large transcript.

Structure and Mechanical Properties of Al-Cu-Fe-X Alloys with Excellent Thermal Stability.

PubMed

Školáková, Andrea; Novák, Pavel; Mejzlíková, Lucie; Průša, Filip; Salvetr, Pavel; Vojtěch, Dalibor

2017-11-05

In this work, the structure and mechanical properties of innovative Al-Cu-Fe based alloys were studied. We focused on preparation and characterization of rapidly solidified and hot extruded Al-Cu-Fe, Al-Cu-Fe-Ni and Al-Cu-Fe-Cr alloys. The content of transition metals affects mechanical properties and structure. For this reason, microstructure, phase composition, hardness and thermal stability have been investigated in this study. The results showed exceptional thermal stability of these alloys and very good values of mechanical properties. Alloying by chromium ensured the highest thermal stability, while nickel addition refined the structure of the consolidated alloy. High thermal stability of all tested alloys was described in context with the transformation of the quasicrystalline phases to other types of intermetallics.

Structure and Mechanical Properties of Al-Cu-Fe-X Alloys with Excellent Thermal Stability

PubMed Central

Školáková, Andrea; Novák, Pavel; Mejzlíková, Lucie; Průša, Filip; Salvetr, Pavel; Vojtěch, Dalibor

2017-01-01

In this work, the structure and mechanical properties of innovative Al-Cu-Fe based alloys were studied. We focused on preparation and characterization of rapidly solidified and hot extruded Al-Cu-Fe, Al-Cu-Fe-Ni and Al-Cu-Fe-Cr alloys. The content of transition metals affects mechanical properties and structure. For this reason, microstructure, phase composition, hardness and thermal stability have been investigated in this study. The results showed exceptional thermal stability of these alloys and very good values of mechanical properties. Alloying by chromium ensured the highest thermal stability, while nickel addition refined the structure of the consolidated alloy. High thermal stability of all tested alloys was described in context with the transformation of the quasicrystalline phases to other types of intermetallics. PMID:29113096

Picosecond Pulsed Laser Ablation for the Surface Preparation of Epoxy Composites

NASA Technical Reports Server (NTRS)

Palmieri, Frank; Ledesma, Rodolfo; Fulton, Tayler; Arthur, Alexandria; Eldridge, Keishara; Thibeault, Sheila; Lin, Yi; Wohl, Chris; Connell, John

2017-01-01

As part of a technical challenge under the Advanced Composites Program, methods for improving pre-bond process control for aerospace composite surface treatments and inspections, in conjunction with Federal Aviation Administration guidelines, are under investigation. The overall goal is to demonstrate high fidelity, rapid and reproducible surface treatment and surface characterization methods to reduce uncertainty associated with the bonding process. The desired outcomes are reliable bonded airframe structure, and reduced timeline to certification. In this work, laser ablation was conducted using a q-switched Nd:YVO4 laser capable of nominal pulse durations of 8 picoseconds (ps). Aerospace structural carbon fiber reinforced composites with an epoxy resin matrix were laser treated, characterized, processed into bonded assemblies and mechanically tested. The characterization of ablated surfaces were conducted using scanning electron microscopy (SEM), water contact angle (WCA) goniometry, micro laser induced breakdown spectroscopy (uLIBS), and electron spin resonance (ESR). The bond performance was assessed using a double cantilever beam (DCB) test with an epoxy adhesive. The surface characteristics and bond performance obtained from picosecond ablated carbon fiber reinforced plastics (CFRPs) are presented herein.

Premature terminator analysis sheds light on a hidden world of bacterial transcriptional attenuation.

PubMed

Naville, Magali; Gautheret, Daniel

2010-01-01

Bacterial transcription attenuation occurs through a variety of cis-regulatory elements that control gene expression in response to a wide range of signals. The signal-sensing structures in attenuators are so diverse and rapidly evolving that only a small fraction have been properly annotated and characterized to date. Here we apply a broad-spectrum detection tool in order to achieve a more complete view of the transcriptional attenuation complement of key bacterial species. Our protocol seeks gene families with an unusual frequency of 5' terminators found across multiple species. Many of the detected attenuators are part of annotated elements, such as riboswitches or T-boxes, which often operate through transcriptional attenuation. However, a significant fraction of candidates were not previously characterized in spite of their unmistakable footprint. We further characterized some of these new elements using sequence and secondary structure analysis. We also present elements that may control the expression of several non-homologous genes, suggesting co-transcription and response to common signals. An important class of such elements, which we called mobile attenuators, is provided by 3' terminators of insertion sequences or prophages that may be exapted as 5' regulators when inserted directly upstream of a cellular gene. We show here that attenuators involve a complex landscape of signal-detection structures spanning the entire bacterial domain. We discuss possible scenarios through which these diverse 5' regulatory structures may arise or evolve.

X-ray solution scattering combined with computation characterizing protein folds and multiple conformational states : computation and application.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, S.; Park, S.; Makowski, L.

Small angle X-ray scattering (SAXS) is an increasingly powerful technique to characterize the structure of biomolecules in solution. We present a computational method for accurately and efficiently computing the solution scattering curve from a protein with dynamical fluctuations. The method is built upon a coarse-grained (CG) representation of the protein. This CG approach takes advantage of the low-resolution character of solution scattering. It allows rapid determination of the scattering pattern from conformations extracted from CG simulations to obtain scattering characterization of the protein conformational landscapes. Important elements incorporated in the method include an effective residue-based structure factor for each aminomore » acid, an explicit treatment of the hydration layer at the surface of the protein, and an ensemble average of scattering from all accessible conformations to account for macromolecular flexibility. The CG model is calibrated and illustrated to accurately reproduce the experimental scattering curve of Hen egg white lysozyme. We then illustrate the computational method by calculating the solution scattering pattern of several representative protein folds and multiple conformational states. The results suggest that solution scattering data, when combined with a reliable computational method, have great potential for a better structural description of multi-domain complexes in different functional states, and for recognizing structural folds when sequence similarity to a protein of known structure is low. Possible applications of the method are discussed.« less

Structural characterization of agonist and antagonist-bound acetylcholine-binding protein from Aplysia californica.

PubMed

Hansen, Scott B; Sulzenbacher, Gerlind; Huxford, Tom; Marchot, Pascale; Bourne, Yves; Taylor, Palmer

2006-01-01

Nicotinic acetylcholine receptors (nAChRs) are well-characterized allosteric transmembrane proteins involved in the rapid gating of ions elicited by ACh. These receptors belong to the Cys-loop superfamily of ligand-gated ion channels, which also includes GABAA and GABAC, 5-HT3, and glycine receptors. The nAChRs are homo- or heteromeric pentamers of structurally related subunits that encompass an extracellular N-terminal ligand-binding domain, four transmembrane-spanning regions that form the ion channel, and an extended intracellular region between spans 3 and 4. Ligand binding triggers conformational changes that are transmitted to the transmembrane-spanning region, leading to gating and changes in membrane potential. The four transmembrane spans on each of the five subunits create a substantial region of hydrophobicity that precludes facile crystallization of this protein. However the freshwater snail, Lymnaea stagnalis, produces a soluble homopentameric protein, termed the ACh-binding protein (AChBP), which binds ACh (Smit et al., 2001). Its structure was determined recently (Brejc et al., 2001) at high resolution, revealing the structural scaffold for nAChR, and has become a functional and structural surrogate of the nAChR ligand-binding domain. We have characterized an AChBP from Aplysia californica and determined distinct ligand-binding properties when compared to those of L. stagnalis, including ligand specificity for the nAChR alpha7 subtype-specific alpha-conotoxin ImI (Hansen et al., 2004).

Light scattering techniques for the characterization of optical components

NASA Astrophysics Data System (ADS)

Hauptvogel, M.; Schröder, S.; Herffurth, T.; Trost, M.; von Finck, A.; Duparré, A.; Weigel, T.

2017-11-01

The rapid developments in optical technologies generate increasingly higher and sometimes completely new demands on the quality of materials, surfaces, components, and systems. Examples for such driving applications are the steadily shrinking feature sizes in semiconductor lithography, nanostructured functional surfaces for consumer optics, and advanced optical systems for astronomy and space applications. The reduction of surface defects as well as the minimization of roughness and other scatter-relevant irregularities are essential factors in all these areas of application. Quality-monitoring for analysing and improving those properties must ensure that even minimal defects and roughness values can be detected reliably. Light scattering methods have a high potential for a non-contact, rapid, efficient, and sensitive determination of roughness, surface structures, and defects.

A Hybrid Approach for the Automated Finishing of Bacterial Genomes

PubMed Central

Robins, William P.; Chin, Chen-Shan; Webster, Dale; Paxinos, Ellen; Hsu, David; Ashby, Meredith; Wang, Susana; Peluso, Paul; Sebra, Robert; Sorenson, Jon; Bullard, James; Yen, Jackie; Valdovino, Marie; Mollova, Emilia; Luong, Khai; Lin, Steven; LaMay, Brianna; Joshi, Amruta; Rowe, Lori; Frace, Michael; Tarr, Cheryl L.; Turnsek, Maryann; Davis, Brigid M; Kasarskis, Andrew; Mekalanos, John J.; Waldor, Matthew K.; Schadt, Eric E.

2013-01-01

Dramatic improvements in DNA sequencing technology have revolutionized our ability to characterize most genomic diversity. However, accurate resolution of large structural events has remained challenging due to the comparatively shorter read lengths of second-generation technologies. Emerging third-generation sequencing technologies, which yield markedly increased read length on rapid time scales and for low cost, have the potential to address assembly limitations. Here we combine sequencing data from second- and third-generation DNA sequencing technologies to assemble the two-chromosome genome of a recent Haitian cholera outbreak strain into two nearly finished contigs at > 99.9% accuracy. Complex regions with clinically significant structure were completely resolved. In separate control assemblies on experimental and simulated data for the canonical N16961 reference we obtain 14 and 8 scaffolds greater than 1kb, respectively, correcting several errors in the underlying source data. This work provides a blueprint for the next generation of rapid microbial identification and full-genome assembly. PMID:22750883

Mixing Characteristics of Strongly-Forced Jet Flames in Crossflow

NASA Astrophysics Data System (ADS)

Marr, Kevin; Clemens, Noel; Ezekoye, Ofodike

2008-11-01

The effects of high frequency, large-amplitude forcing on the characteristics of a non-premixed jet flame in crossflow (JFICF) at mean Reynolds numbers of 3,200 and 4,850 are studied experimentally. Harmonic forcing of the jet fuel results in a drastic decrease in flame length and complete suppression of soot luminosity. Visualization by planar laser Mie scattering shows that forced JFICF, similar to forced free or coflow jet flames, are characterized by ejection of high-momentum, deeply penetrating vortical structures. These structures rapidly breakdown and promote intense turbulent mixing in the near region of the jet. The rapid mixing resembles a ``one-step'' process going from a fuel rich state far in the nozzle to a well-mixed, but significantly diluted, state just a few diameters from the jet exit plane. Exhaust gas emissions measurements indicate a decrease in NOx, but increases in CO and unburned hydrocarbons with increasing forcing amplitude. Acetone PLIF measurements are used to investigate the effect of partial-premixing on these emissions findings.

Facile synthesis of hollow Co3O4 microspheres and its use as a rapid responsive CL sensor of combustible gases.

PubMed

Teng, Fei; Yao, Wenqing; Zheng, Youfei; Ma, Yutao; Xu, Tongguang; Gao, Guizhi; Liang, Shuhui; Teng, Yang; Zhu, Yongfa

2008-09-15

The hollow Co(3)O(4) microspheres (HCMs) were prepared by the carbonaceous templates, which did not need the surface pretreatment. The chemiluminescence (CL) and catalytic properties for CO oxidation over these hollow samples were evaluated. The samples were characterized by scanning electron microscopy (SEM), energy disperse spectra (EDS), transmission electron microscopy (TEM), selected area electron diffraction (ED), X-ray diffraction (XRD), temperature-programmed desorption (TPD) and N(2) adsorption. The influences of filter' band length, flow rate of gas, test temperature, and particle structure on CL intensities were mainly investigated. It was found that compared with the solid Co(3)O(4) particles (SCPs), HCMs had a stronger CL intensity, which was ascribed to its hollow structure; and that CL properties of the catalysts were well correlated with their reaction activities. Moreover, HCMs were used to fabricate a highly sensitive gas detector, which is a rapid and effective method for the selection of catalysts or the detection of environmental deleterious gases.

Climate-driven regime shifts in Arctic marine benthos

PubMed Central

Kortsch, Susanne; Primicerio, Raul; Beuchel, Frank; Renaud, Paul E.; Rodrigues, João; Lønne, Ole Jørgen; Gulliksen, Bjørn

2012-01-01

Climate warming can trigger abrupt ecosystem changes in the Arctic. Despite the considerable interest in characterizing and understanding the ecological impact of rapid climate warming in the Arctic, few long time series exist that allow addressing these research goals. During a 30-y period (1980–2010) of gradually increasing seawater temperature and decreasing sea ice cover in Svalbard, we document rapid and extensive structural changes in the rocky-bottom communities of two Arctic fjords. The most striking component of the benthic reorganization was an abrupt fivefold increase in macroalgal cover in 1995 in Kongsfjord and an eightfold increase in 2000 in Smeerenburgfjord. Simultaneous changes in the abundance of benthic invertebrates suggest that the macroalgae played a key structuring role in these communities. The abrupt, substantial, and persistent nature of the changes observed is indicative of a climate-driven ecological regime shift. The ecological processes thought to drive the observed regime shifts are likely to promote the borealization of these Arctic marine communities in the coming years. PMID:22891319

Ab initio folding of proteins using all-atom discrete molecular dynamics

PubMed Central

Ding, Feng; Tsao, Douglas; Nie, Huifen; Dokholyan, Nikolay V.

2008-01-01

Summary Discrete molecular dynamics (DMD) is a rapid sampling method used in protein folding and aggregation studies. Until now, DMD was used to perform simulations of simplified protein models in conjunction with structure-based force fields. Here, we develop an all-atom protein model and a transferable force field featuring packing, solvation, and environment-dependent hydrogen bond interactions. Using the replica exchange method, we perform folding simulations of six small proteins (20–60 residues) with distinct native structures. In all cases, native or near-native states are reached in simulations. For three small proteins, multiple folding transitions are observed and the computationally-characterized thermodynamics are in quantitative agreement with experiments. The predictive power of all-atom DMD highlights the importance of environment-dependent hydrogen bond interactions in modeling protein folding. The developed approach can be used for accurate and rapid sampling of conformational spaces of proteins and protein-protein complexes, and applied to protein engineering and design of protein-protein interactions. PMID:18611374

Tertiary structural propensities reveal fundamental sequence/structure relationships.

PubMed

Zheng, Fan; Zhang, Jian; Grigoryan, Gevorg

2015-05-05

Extracting useful generalizations from the continually growing Protein Data Bank (PDB) is of central importance. We hypothesize that the PDB contains valuable quantitative information on the level of local tertiary structural motifs (TERMs). We show that by breaking a protein structure into its constituent TERMs, and querying the PDB to characterize the natural ensemble matching each, we can estimate the compatibility of the structure with a given amino acid sequence through a metric we term "structure score." Considering submissions from recent Critical Assessment of Structure Prediction (CASP) experiments, we found a strong correlation (R = 0.69) between structure score and model accuracy, with poorly predicted regions readily identifiable. This performance exceeds that of leading atomistic statistical energy functions. Furthermore, TERM-based analysis of two prototypical multi-state proteins rapidly produced structural insights fully consistent with prior extensive experimental studies. We thus find that TERM-based analysis should have considerable utility for protein structural biology. Copyright © 2015 Elsevier Ltd. All rights reserved.

Application’s Method of Quadratic Programming for Optimization of Portfolio Selection

NASA Astrophysics Data System (ADS)

Kawamoto, Shigeru; Takamoto, Masanori; Kobayashi, Yasuhiro

Investors or fund-managers face with optimization of portfolio selection, which means that determine the kind and the quantity of investment among several brands. We have developed a method to obtain optimal stock’s portfolio more rapidly from twice to three times than conventional method with efficient universal optimization. The method is characterized by quadratic matrix of utility function and constrained matrices divided into several sub-matrices by focusing on structure of these matrices.

Rheology of Self-Assembling Silk Fibroin Solutions

NASA Astrophysics Data System (ADS)

Zhou, Rui; Chen, Song-Bi; Yuan, Xue-Feng

2008-07-01

A robust procedure for preparation of aqueous silk fibroin solutions with a range of concentration up to 25 wt% from domestic Bombyx mori cocoon shells has been established. We have carried out molecular and rheometric characterizations of silk fibroin solutions, and constructed an equilibrium phase diagram. The sharp sol-gel transition can be exploited for rapid solidification of micro-morphological structure. We will discuss the correlations between fluid formulation, rheological properties and processibility of silk fibroin in the talk.

Supercritical fluid extraction and ultra performance liquid chromatography of respiratory quinones for microbial community analysis in environmental and biological samples.

PubMed

Hanif, Muhammad; Atsuta, Yoichi; Fujie, Koichi; Daimon, Hiroyuki

2012-03-05

Microbial community structure plays a significant role in environmental assessment and animal health management. The development of a superior analytical strategy for the characterization of microbial community structure is an ongoing challenge. In this study, we developed an effective supercritical fluid extraction (SFE) and ultra performance liquid chromatography (UPLC) method for the analysis of bacterial respiratory quinones (RQ) in environmental and biological samples. RQ profile analysis is one of the most widely used culture-independent tools for characterizing microbial community structure. A UPLC equipped with a photo diode array (PDA) detector was successfully applied to the simultaneous determination of ubiquinones (UQ) and menaquinones (MK) without tedious pretreatment. Supercritical carbon dioxide (scCO(2)) extraction with the solid-phase cartridge trap proved to be a more effective and rapid method for extracting respiratory quinones, compared to a conventional organic solvent extraction method. This methodology leads to a successful analytical procedure that involves a significant reduction in the complexity and sample preparation time. Application of the optimized methodology to characterize microbial communities based on the RQ profile was demonstrated for a variety of environmental samples (activated sludge, digested sludge, and compost) and biological samples (swine and Japanese quail feces).

Characterization of Nanocomposites by Thermal Analysis

PubMed Central

Corcione, Carola Esposito; Frigione, Mariaenrica

2012-01-01

In materials research, the development of polymer nanocomposites (PN) is rapidly emerging as a multidisciplinary research field with results that could broaden the applications of polymers to many different industries. PN are polymer matrices (thermoplastics, thermosets or elastomers) that have been reinforced with small quantities of nano-sized particles, preferably characterized by high aspect ratios, such as layered silicates and carbon nanotubes. Thermal analysis (TA) is a useful tool to investigate a wide variety of properties of polymers and it can be also applied to PN in order to gain further insight into their structure. This review illustrates the versatile applications of TA methods in the emerging field of polymer nanomaterial research, presenting some examples of applications of differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), dynamic mechanical thermal analysis (DMTA) and thermal mechanical analysis (TMA) for the characterization of nanocomposite materials.

Optical Spectroscopy of New Materials

NASA Technical Reports Server (NTRS)

White, Susan M.; Arnold, James O. (Technical Monitor)

1993-01-01

Composites are currently used for a rapidly expanding number of applications including aircraft structures, rocket nozzles, thermal protection of spacecraft, high performance ablative surfaces, sports equipment including skis, tennis rackets and bicycles, lightweight automobile components, cutting tools, and optical-grade mirrors. Composites are formed from two or more insoluble materials to produce a material with superior properties to either component. Composites range from dispersion-hardened alloys to advanced fiber-reinforced composites. UV/VIS and FTIR spectroscopy currently is used to evaluate the bonding between the matrix and the fibers, monitor the curing process of a polymer, measure surface contamination, characterize the interphase material, monitor anion transport in polymer phases, characterize the void formation (voids must be minimized because, like cracks in a bulk material, they lead to failure), characterize the surface of the fiber component, and measure the overall optical properties for energy balances.

Fourier Transform Mass Spectrometry and Nuclear Magnetic Resonance Analysis for the Rapid and Accurate Characterization of Hexacosanoylceramide.

PubMed

Ross, Charles W; Simonsick, William J; Bogusky, Michael J; Celikay, Recep W; Guare, James P; Newton, Randall C

2016-06-28

Ceramides are a central unit of all sphingolipids which have been identified as sites of biological recognition on cellular membranes mediating cell growth and differentiation. Several glycosphingolipids have been isolated, displaying immunomodulatory and anti-tumor activities. These molecules have generated considerable interest as potential vaccine adjuvants in humans. Accurate analyses of these and related sphingosine analogues are important for the characterization of structure, biological function, and metabolism. We report the complementary use of direct laser desorption ionization (DLDI), sheath flow electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) and high-field nuclear magnetic resonance (NMR) analysis for the rapid, accurate identification of hexacosanoylceramide and starting materials. DLDI does not require stringent sample preparation and yields representative ions. Sheath-flow ESI yields ions of the product and byproducts and was significantly better than monospray ESI due to improved compound solubility. Negative ion sheath flow ESI provided data of starting materials and products all in one acquisition as hexacosanoic acid does not ionize efficiently when ceramides are present. NMR provided characterization of these lipid molecules complementing the results obtained from MS analyses. NMR data was able to differentiate straight chain versus branched chain alkyl groups not easily obtained from mass spectrometry.

A strategy to improve the identification reliability of the chemical constituents by high-resolution mass spectrometry-based isomer structure prediction combined with a quantitative structure retention relationship analysis: Phthalide compounds in Chuanxiong as a test case.

PubMed

Zhang, Qingqing; Huo, Mengqi; Zhang, Yanling; Qiao, Yanjiang; Gao, Xiaoyan

2018-06-01

High-resolution mass spectrometry (HRMS) provides a powerful tool for the rapid analysis and identification of compounds in herbs. However, the diversity and large differences in the content of the chemical constituents in herbal medicines, especially isomerisms, are a great challenge for mass spectrometry-based structural identification. In the current study, a new strategy for the structural characterization of potential new phthalide compounds was proposed by isomer structure predictions combined with a quantitative structure-retention relationship (QSRR) analysis using phthalide compounds in Chuanxiong as an example. This strategy consists of three steps. First, the structures of phthalide compounds were reasonably predicted on the basis of the structure features and MS/MS fragmentation patterns: (1) the collected raw HRMS data were preliminarily screened by an in-house database; (2) the MS/MS fragmentation patterns of the analogous compounds were summarized; (3) the reported phthalide compounds were identified, and the structures of the isomers were reasonably predicted. Second, the QSRR model was established and verified using representative phthalide compound standards. Finally, the retention times of the predicted isomers were calculated by the QSRR model, and the structures of these peaks were rationally characterized by matching retention times of the detected chromatographic peaks and the predicted isomers. A multiple linear regression QSRR model in which 6 physicochemical variables were screened was built using 23 phthalide standards. The retention times of the phthalide isomers in Chuanxiong were well predicted by the QSRR model combined with reasonable structure predictions (R 2 =0.955). A total of 81 peaks were detected from Chuanxiong and assigned to reasonable structures, and 26 potential new phthalide compounds were structurally characterized. This strategy can improve the identification efficiency and reliability of homologues in complex materials. Copyright © 2018 Elsevier B.V. All rights reserved.

Manufacturing and advanced characterization of sub-25nm diameter CD-AFM probes with sub-10nm tip edges radius

NASA Astrophysics Data System (ADS)

Foucher, Johann; Filippov, Pavel; Penzkofer, Christian; Irmer, Bernd; Schmidt, Sebastian W.

2013-04-01

Atomic force microscopy (AFM) is increasingly used in the semiconductor industry as a versatile monitoring tool for highly critical lithography and etching process steps. Applications range from the inspection of the surface roughness of new materials, over accurate depth measurements to the determination of critical dimension structures. The aim to address the rapidly growing demands on measurement uncertainty and throughput more and more shifts the focus of attention to the AFM tip, which represents the crucial link between AFM tool and the sample to be monitored. Consequently, in order to reach the AFM tool's full potential, the performance of the AFM tip has to be considered as a determining parameter. Currently available AFM tips made from silicon are generally limited by their diameter, radius, and sharpness, considerably restricting the AFM measurement capabilities on sub-30nm spaces. In addition to that, there's lack of adequate characterization structures to accurately characterize sub-25nm tip diameters. Here, we present and discuss a recently introduced AFM tip design (T-shape like design) with precise tip diameters down to 15nm and tip radii down to 5nm fabricated from amorphous, high density diamond-like carbon (HDC/DLC) using electron beam induced processing (EBIP). In addition to that advanced design, we propose a new characterizer structure, which allows for accurate characterization and design control of sub-25nm tip diameters and sub-10nm tip edges radii. We demonstrate the potential advantages of combining a small tip shape design, i.e. tip diameter and tip edge radius, and an advanced tip characterizer for the semiconductor industry by the measurement of advanced lithography patterns.

An integrated strategy for the systematic characterization and discovery of new indole alkaloids from Uncaria rhynchophylla by UHPLC/DAD/LTQ-Orbitrap-MS.

PubMed

Pan, Huiqin; Yang, Wenzhi; Zhang, Yibei; Yang, Min; Feng, Ruihong; Wu, Wanying; Guo, Dean

2015-08-01

The exploration of new chemical entities from herbal medicines may provide candidates for the in silico screening of drug leads. However, this significant work is hindered by the presence of multiple classes of plant metabolites and many re-discovered structures. This study presents an integrated strategy that uses ultrahigh-performance liquid chromatography/linear ion-trap quadrupole/Orbitrap mass spectrometry (UHPLC/LTQ-Orbitrap-MS) coupled with in-house library data for the systematic characterization and discovery of new potentially bioactive molecules. Exploration of the indole alkaloids from Uncaria rhynchophylla (UR) is presented as a model study. Initially, the primary characterization of alkaloids was achieved using mass defect filtering and neutral loss filtering. Subsequently, phytochemical isolation obtained 14 alkaloid compounds as reference standards, including a new one identified as 16,17-dihydro-O-demethylhirsuteine by NMR analyses. The direct-infusion fragmentation behaviors of these isolated alkaloids were studied to provide diagnostic structural information facilitating the rapid differentiation and characterization of four different alkaloid subtypes. Ultimately, after combining the experimental results with a survey of an in-house library containing 129 alkaloids isolated from the Uncaria genus, a total of 92 alkaloids (60 free alkaloids and 32 alkaloid O-glycosides) were identified or tentatively characterized, 56 of which are potential new alkaloids for the Uncaria genus. Hydroxylation on ring A, broad variations in the C-15 side chain, new N-oxides, and numerous O-glycosides, represent the novel features of the newly discovered indole alkaloid structures. These results greatly expand our knowledge of UR chemistry and are useful for the computational screening of potentially bioactive molecules from indole alkaloids. Graphical Abstract A four-step integrated strategy for the systematic characterization and efficient discovery of new indole alkaloids from Uncaria rhynchophylla.

Modeling of intense pulsed ion beam heated masked targets for extreme materials characterization

DOE PAGES

Barnard, John J.; Schenkel, Thomas

2017-11-15

Intense, pulsed ion beams locally heat materials and deliver dense electronic excitations that can induce material modifications and phase transitions. Material properties can potentially be stabilized by rapid quenching. Pulsed ion beams with pulse lengths of order ns have recently become available for materials processing. Here, we optimize mask geometries for local modification of materials by intense ion pulses. The goal is to rapidly excite targets volumetrically to the point where a phase transition or local lattice reconstruction is induced followed by rapid cooling that stabilizes desired material's properties fast enough before the target is altered or damaged by, e.g.,more » hydrodynamic expansion. By using a mask, the longitudinal dimension can be large compared to the transverse dimension, allowing the possibility of rapid transverse cooling. We performed HYDRA simulations that calculate peak temperatures for a series of excitation conditions and cooling rates of silicon targets with micro-structured masks and compare these to a simple analytical model. In conclusion, the model gives scaling laws that can guide the design of targets over a wide range of pulsed ion beam parameters.« less

Modeling of intense pulsed ion beam heated masked targets for extreme materials characterization

NASA Astrophysics Data System (ADS)

Barnard, John J.; Schenkel, Thomas

2017-11-01

Intense, pulsed ion beams locally heat materials and deliver dense electronic excitations that can induce material modifications and phase transitions. Material properties can potentially be stabilized by rapid quenching. Pulsed ion beams with pulse lengths of order ns have recently become available for materials processing. Here, we optimize mask geometries for local modification of materials by intense ion pulses. The goal is to rapidly excite targets volumetrically to the point where a phase transition or local lattice reconstruction is induced followed by rapid cooling that stabilizes desired material's properties fast enough before the target is altered or damaged by, e.g., hydrodynamic expansion. By using a mask, the longitudinal dimension can be large compared to the transverse dimension, allowing the possibility of rapid transverse cooling. We performed HYDRA simulations that calculate peak temperatures for a series of excitation conditions and cooling rates of silicon targets with micro-structured masks and compare these to a simple analytical model. The model gives scaling laws that can guide the design of targets over a wide range of pulsed ion beam parameters.

Mapping the Small Molecule Interactome by Mass Spectrometry.

PubMed

Flaxman, Hope A; Woo, Christina M

2018-01-16

Mapping small molecule interactions throughout the proteome provides the critical structural basis for functional analysis of their impact on biochemistry. However, translation of mass spectrometry-based proteomics methods to directly profile the interaction between a small molecule and the whole proteome is challenging because of the substoichiometric nature of many interactions, the diversity of covalent and noncovalent interactions involved, and the subsequent computational complexity associated with their spectral assignment. Recent advances in chemical proteomics have begun fill this gap to provide a structural basis for the breadth of small molecule-protein interactions in the whole proteome. Innovations enabling direct characterization of the small molecule interactome include faster, more sensitive instrumentation coupled to chemical conjugation, enrichment, and labeling methods that facilitate detection and assignment. These methods have started to measure molecular interaction hotspots due to inherent differences in local amino acid reactivity and binding affinity throughout the proteome. Measurement of the small molecule interactome is producing structural insights and methods for probing and engineering protein biochemistry. Direct structural characterization of the small molecule interactome is a rapidly emerging area pushing new frontiers in biochemistry at the interface of small molecules and the proteome.

Heterogeneous activation in 2D colloidal glass-forming liquids classified by machine learning

NASA Astrophysics Data System (ADS)

Ma, Xiaoguang; Davidson, Zoey; Still, Tim; Ivancic, Robert; Schoenholz, Sam S.; Sussman, Daniel M.; Liu, A. J.; Yodh, A. G.

The trajectories of particles in colloidal glass-forming liquids are often characterized by long periods of ``in-cage'' fluctuations and rapid ``cage-breaking'' rearrangements. We study the rate of such rearrangements and its connection with local cage structures in a 2D binary mixture of poly(N-isopropyl acrylamide) spheres. We use the hopping function, Phop (t) , to identify rearrangements within particle trajectories. Then we obtain distributions of the residence time tR between consecutive rearrangements. The mean residence time tR (S) is found to correlate with the local configurations for the rearranging particles, characterized by 70 radial structural features and softness S, which ranks the structural similarities with respect to rearranging particles. Furthermore, tR (S) for particles with similar softness decays monotonically with increasing softness, indicating correlation between rearrangement rates and softness S. Finally we find that the conditional and full probability distribution functions, P (tR | S) and P (tR) , are well explained by a thermal activation model. We acknowledge financial supports from NSF-MRSEC DMR11-20901, NSF DMR16-07378, and NASA NNX08AO0G.

Market returns? Gender and theories of change in employment relations.

PubMed

Irwin, S; Bottero, W

2000-06-01

This paper explores recent arguments about the marketization of female labour, in the context of a wider analysis of the role of concepts like 'the market' and 'individualization' in sociological accounts of change in employment relations. It will be argued that within sociology there has been a tendency for rapid, large-scale changes in employment relations to be characterized as the breakdown of social influences or structures and as the emergence of atomized, individuated market forces. In the most recent models, change in the nature of gendered positions within employment are presented in terms of a decline of social structuring and social constraint. These emergent accounts hold similarities to classical economics, and to Marx's and Weber's accounts of employment, which also characterized new forms of employment relations in terms of the emptying of their social content and their replacement by market forms. We offer an alternative, moral economy, perspective which foregrounds the continued significance of social relations in the structuring of employment and employment change. We develop the argument through an analysis of gendered patterns of employment and change in family form.

Fe/Si(001) Ferromagnetic Layers: Reactivity, Local Atomic Structure and Magnetism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lungu, G. A.; Costescu, R. M.; Husanu, M. A.

2011-10-03

Ultrathin ferromagnetic Fe layers on Si(001) have recently been synthesized using the molecular beam epitaxy (MBE) technique, and their structural and magnetic properties, as well as their interface reactivity have been investigated. The study was undertaken as function of the amount of Fe deposited and of substrate temperature. The interface reactivity was characterized by Auger electron spectroscopy (AES). The surface structure was characterized by low-energy electron diffraction (LEED). The magnetism was investigated by magneto-optical Kerr effect (MOKE). A higher deposition temperature stabilizes a better surface ordering, but it also enhances Fe and Si interdiffusion and it therefore decreases the magnetism.more » Despite the rapid disappearance of the long range order with Fe deposition at room temperature, the material exhibits a significant uniaxial in-plane magnetic anisotropy. For the Fe deposition performed at high temperature (500 deg. C), a weak ferromagnetism is still observed, with saturation magnetization of about 10% of the value obtained previously. MOKE studies allowed inferring the main properties of the distinct formed layers.« less

Preparation and physicochemical characterization of 5 niclosamide solvates and 1 hemisolvate.

PubMed

van Tonder, Elsa C; Mahlatji, Mabatane D; Malan, Sarel F; Liebenberg, Wilna; Caira, Mino R; Song, Mingna; de Villiers, Melgardt M

2004-02-23

The purpose of the study was to characterize the physicochemical, structural, and spectral properties of the 1:1 niclosamide and methanol, diethyl ether, dimethyl sulfoxide, N,N' dimethylformamide, and tetrahydrofuran solvates and the 2:1 niclosamide and tetraethylene glycol hemisolvate prepared by recrystallization from these organic solvents. Structural, spectral, and thermal analysis results confirmed the presence of the solvents and differences in the structural properties of these solvates. In addition, differences in the activation energy of desolvation, batch solution calorimetry, and the aqueous solubility at 25 degrees C, 24 hours, showed the stability of the solvates to be in the order: anhydrate > diethyl ether solvate > tetraethylene glycol hemisolvate > methanol solvate > dimethyl sulfoxide solvate > N,N' dimethylformamide solvate. The intrinsic and powder dissolution rates of the solvates were in the order: anhydrate > diethyl ether solvate > tetraethylene glycol hemisolvate > N,N' dimethylformamide solvate > methanol solvate > dimethyl sulfoxide solvate. Although these nonaqueous solvates had higher solubility and dissolution rates than the monohydrous forms, they were unstable in aqueous media and rapidly transformed to one of the monohydrous forms.

Comparative analysis and validation of the malachite green assay for the high throughput biochemical characterization of terpene synthases

PubMed Central

Vardakou, Maria; Salmon, Melissa; Faraldos, Juan A.; O’Maille, Paul E.

2014-01-01

Terpenes are the largest group of natural products with important and diverse biological roles, while of tremendous economic value as fragrances, flavours and pharmaceutical agents. Class-I terpene synthases (TPSs), the dominant type of TPS enzymes, catalyze the conversion of prenyl diphosphates to often structurally diverse bioactive terpene hydrocarbons, and inorganic pyrophosphate (PPi). To measure their kinetic properties, current bio-analytical methods typically rely on the direct detection of hydrocarbon products by radioactivity measurements or gas chromatography–mass spectrometry (GC–MS). In this study we employed an established, rapid colorimetric assay, the pyrophosphate/malachite green assay (MG), as an alternative means for the biochemical characterization of class I TPSs activity.•We describe the adaptation of the MG assay for turnover and catalytic efficiency measurements of TPSs.•We validate the method by direct comparison with established assays. The agreement of kcat/KM among methods makes this adaptation optimal for rapid evaluation of TPSs.•We demonstrate the application of the MG assay for the high-throughput screening of TPS gene libraries. PMID:26150952

Comparative analysis and validation of the malachite green assay for the high throughput biochemical characterization of terpene synthases.

PubMed

Vardakou, Maria; Salmon, Melissa; Faraldos, Juan A; O'Maille, Paul E

2014-01-01

Terpenes are the largest group of natural products with important and diverse biological roles, while of tremendous economic value as fragrances, flavours and pharmaceutical agents. Class-I terpene synthases (TPSs), the dominant type of TPS enzymes, catalyze the conversion of prenyl diphosphates to often structurally diverse bioactive terpene hydrocarbons, and inorganic pyrophosphate (PPi). To measure their kinetic properties, current bio-analytical methods typically rely on the direct detection of hydrocarbon products by radioactivity measurements or gas chromatography-mass spectrometry (GC-MS). In this study we employed an established, rapid colorimetric assay, the pyrophosphate/malachite green assay (MG), as an alternative means for the biochemical characterization of class I TPSs activity.•We describe the adaptation of the MG assay for turnover and catalytic efficiency measurements of TPSs.•We validate the method by direct comparison with established assays. The agreement of k cat/K M among methods makes this adaptation optimal for rapid evaluation of TPSs.•We demonstrate the application of the MG assay for the high-throughput screening of TPS gene libraries.

Equatorial Density Irregularity Structures at Intermediate Scales and Their Temporal Evolution

NASA Technical Reports Server (NTRS)

Kil, Hyosub; Heelis, R. A.

1998-01-01

We examine high resolution measurements of ion density in the equatorial ionosphere from the AE-E satellite during the years 1977-1981. Structure over spatial scales from 18 km to 200 m is characterized by the spectrum of irregularities at larger and smaller scales and at altitudes above 350 km and below 300 km. In the low-altitude region, only small amplitude large-scale (lambda greater than 5 km) density modulations are often observed, and thus the power spectrum of these density structures exhibits a steep spectral slope at kilometer scales. In the high-altitude region, sinusoidal density fluctuations, characterized by enhanced power near 1-km scale, are frequently observed during 2000-0200 LT. However, such fluctuations are confined to regions at the edges of larger bubble structures where the average background density is high. Small amplitude irregularity structures, observed at early local time hours, grow rapidly to high-intensity structures in about 90 min. Fully developed structures, which are observed at late local time hours, decay very slowly producing only-small differences in spectral characteristics even 4 hours later. The local time evolution of irregularity structure is investigated by using average statistics for low-(1% less than sigma less than 5%) and high-intensity (sigma greater than 10%) structures. At lower altitudes, little chance in the spectral slope is seen as a function of local time, while at higher attitudes the growth and maintenance of structures near 1 km scales dramatically affects the spectral slope.

Rapid prototyping of flexible intrafascicular electrode arrays by picosecond laser structuring.

PubMed

Mueller, Matthias; de la Oliva, Natalia; Del Valle, Jaume; Delgado-Martínez, Ignacio; Navarro, Xavier; Stieglitz, Thomas

2017-12-01

Interfacing the peripheral nervous system can be performed with a large variety of electrode arrays. However, stimulating and recording a nerve while having a reasonable amount of channels limits the number of available systems. Translational research towards human clinical trial requires device safety and biocompatibility but would benefit from design flexibility in the development process to individualize probes. We selected established medical grade implant materials like precious metals and Parylene C to develop a rapid prototyping process for novel intrafascicular electrode arrays using a picosecond laser structuring. A design for a rodent animal model was developed in conjunction with an intrafascicular implantation strategy. Electrode characterization and optimization was performed first in saline solution in vitro before performance and biocompatibility were validated in sciatic nerves of rats in chronic implantation. The novel fabrication process proved to be suitable for prototyping and building intrafascicular electrode arrays. Electrochemical properties of the electrode sites were enhanced and tested for long-term stability. Chronic implantation in the sciatic nerve of rats showed good biocompatibility, selectivity and stable stimulation thresholds. Established medical grade materials can be used for intrafascicular nerve electrode arrays when laser structuring defines structure size in the micro-scale. Design flexibility reduces re-design cycle time and material certificates are beneficial support for safety studies on the way to clinical trials.

Dimensional metrology of lab-on-a-chip internal structures: a comparison of optical coherence tomography with confocal fluorescence microscopy.

PubMed

Reyes, D R; Halter, M; Hwang, J

2015-07-01

The characterization of internal structures in a polymeric microfluidic device, especially of a final product, will require a different set of optical metrology tools than those traditionally used for microelectronic devices. We demonstrate that optical coherence tomography (OCT) imaging is a promising technique to characterize the internal structures of poly(methyl methacrylate) devices where the subsurface structures often cannot be imaged by conventional wide field optical microscopy. The structural details of channels in the devices were imaged with OCT and analyzed with an in-house written ImageJ macro in an effort to identify the structural details of the channel. The dimensional values obtained with OCT were compared with laser-scanning confocal microscopy images of channels filled with a fluorophore solution. Attempts were also made using confocal reflectance and interferometry microscopy to measure the channel dimensions, but artefacts present in the images precluded quantitative analysis. OCT provided the most accurate estimates for the channel height based on an analysis of optical micrographs obtained after destructively slicing the channel with a microtome. OCT may be a promising technique for the future of three-dimensional metrology of critical internal structures in lab-on-a-chip devices because scans can be performed rapidly and noninvasively prior to their use. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

Rapid thermal process by RF heating of nano-graphene layer/silicon substrate structure: Heat explosion theory approach

NASA Astrophysics Data System (ADS)

Sinder, M.; Pelleg, J.; Meerovich, V.; Sokolovsky, V.

2018-03-01

RF heating kinetics of a nano-graphene layer/silicon substrate structure is analyzed theoretically as a function of the thickness and sheet resistance of the graphene layer, the dimensions and thermal parameters of the structure, as well as of cooling conditions and of the amplitude and frequency of the applied RF magnetic field. It is shown that two regimes of the heating can be realized. The first one is characterized by heating of the structure up to a finite temperature determined by equilibrium between the dissipated loss power caused by induced eddy-currents and the heat transfer to environment. The second regime corresponds to a fast unlimited temperature increase (heat explosion). The criterions of realization of these regimes are presented in the analytical form. Using the criterions and literature data, it is shown the possibility of the heat explosion regime for a graphene layer/silicon substrate structure at RF heating.

Helix-length compensation studies reveal the adaptability of the VS ribozyme architecture.

PubMed

Lacroix-Labonté, Julie; Girard, Nicolas; Lemieux, Sébastien; Legault, Pascale

2012-03-01

Compensatory mutations in RNA are generally regarded as those that maintain base pairing, and their identification forms the basis of phylogenetic predictions of RNA secondary structure. However, other types of compensatory mutations can provide higher-order structural and evolutionary information. Here, we present a helix-length compensation study for investigating structure-function relationships in RNA. The approach is demonstrated for stem-loop I and stem-loop V of the Neurospora VS ribozyme, which form a kissing-loop interaction important for substrate recognition. To rapidly characterize the substrate specificity (k(cat)/K(M)) of several substrate/ribozyme pairs, a procedure was established for simultaneous kinetic characterization of multiple substrates. Several active substrate/ribozyme pairs were identified, indicating the presence of limited substrate promiscuity for stem Ib variants and helix-length compensation between stems Ib and V. 3D models of the I/V interaction were generated that are compatible with the kinetic data. These models further illustrate the adaptability of the VS ribozyme architecture for substrate cleavage and provide global structural information on the I/V kissing-loop interaction. By exploring higher-order compensatory mutations in RNA our approach brings a deeper understanding of the adaptability of RNA structure, while opening new avenues for RNA research.

A study of reduced chromium content in a nickel-base superalloy via element substitution and rapid solidification processing. Ph.D. ThesisFinal Report

NASA Technical Reports Server (NTRS)

Powers, William O.

1987-01-01

A study of reduced chromium content in a nickel base superalloy via element substitution and rapid solidification processing was performed. The two elements used as partial substitutes for chromium were Si and Zr. The microstructure of conventionally solidified materials was characterized using microscopy techniques. These alloys were rapidly solidified using the chill block melt spinning technique and the rapidly solidified microstructures were characterized using electron microscopy. The spinning technique and the rapidly solidified microstructures was assessed following heat treatments at 1033 and 1272 K. Rapidly solidified material of three alloys was reduced to particulate form and consolidated using hot isostatic pressing (HIP). The consolidated materials were also characterized using microscopy techniques. In order to evaluate the relative strengths of the consolidated alloys, compression tests were performed at room temperature and 1033 K on samples of as-HIPed and HIPed plus solution treated material. Yield strength, porosity, and oxidation resistance characteristics are given and compared.

Microlensing observations rapid search for exoplanets: MORSE code for GPUs

NASA Astrophysics Data System (ADS)

McDougall, Alistair; Albrow, Michael D.

2016-02-01

The rapid analysis of ongoing gravitational microlensing events has been integral to the successful detection and characterization of cool planets orbiting low-mass stars in the Galaxy. In this paper, we present an implementation of search and fit techniques on graphical processing unit (GPU) hardware. The method allows for the rapid identification of candidate planetary microlensing events and their subsequent follow-up for detailed characterization.

Reactivity of Ala-Gly dipeptide with β-turn secondary structure

NASA Astrophysics Data System (ADS)

Yu, Craig P.; Gerlei, Klára Z.; Rágyanszki, Anita; Jensen, Svend J. Knak; Viskolcz, Béla; Csizmadia, Imre G.

2018-01-01

The conformational space of β-turns of Ala-Gly dipeptide is analyzed theoretically using quantum mechanical methods. A number of potential minima are obtained and characterized. The potential energy surface suggests that β-turn conformers are susceptible to rapid radical formation, which leads to potential L and D epimerization. The calculated thermodynamics show that the radical mediated epimerization is possible and that the estimated barrier height for hydrogen abstraction on the Cα is the lowest for the Gly residue.

Design and Fabrication of a Radio Frequency GRIN Lens Using 3D Printing Technology

DTIC Science & Technology

2013-04-01

simulation of a homogenized 3D lens ..................... 6 Figure 4: GRIN lens fabricated using 3D printer ...properties of the dielectric used by the 3D printer are ε=2.86 in the frequency regime of interest. We begin with a structure where the dimensions are...CHARACTERIZATION OF THE LENS We used a 3D rapid prototyping printer to fabricate the GRIN lens shown in Figure 4. 3D printers can be used to print a diverse

Finite-element analysis of dynamic fracture

NASA Technical Reports Server (NTRS)

Aberson, J. A.; Anderson, J. M.; King, W. W.

1976-01-01

Applications of the finite element method to the two dimensional elastodynamics of cracked structures are presented. Stress intensity factors are computed for two problems involving stationary cracks. The first serves as a vehicle for discussing lumped-mass and consistent-mass characterizations of inertia. In the second problem, the behavior of a photoelastic dynamic tear test specimen is determined for the time prior to crack propagation. Some results of a finite element simulation of rapid crack propagation in an infinite body are discussed.

A high throughput spectral image microscopy system

NASA Astrophysics Data System (ADS)

Gesley, M.; Puri, R.

2018-01-01

A high throughput spectral image microscopy system is configured for rapid detection of rare cells in large populations. To overcome flow cytometry rates and use of fluorophore tags, a system architecture integrates sample mechanical handling, signal processors, and optics in a non-confocal version of light absorption and scattering spectroscopic microscopy. Spectral images with native contrast do not require the use of exogeneous stain to render cells with submicron resolution. Structure may be characterized without restriction to cell clusters of differentiation.

Resonant Mode-hopping Micromixing

PubMed Central

Jang, Ling-Sheng; Chao, Shih-Hui; Holl, Mark R.; Meldrum, Deirdre R.

2009-01-01

A common micromixer design strategy is to generate interleaved flow topologies to enhance diffusion. However, problems with these designs include complicated structures and dead volumes within the flow fields. We present an active micromixer using a resonating piezoceramic/silicon composite diaphragm to generate acoustic streaming flow topologies. Circulation patterns are observed experimentally and correlate to the resonant mode shapes of the diaphragm. The dead volumes in the flow field are eliminated by rapidly switching from one discrete resonant mode to another (i.e., resonant mode-hop). Mixer performance is characterized by mixing buffer with a fluorescence tracer containing fluorescein. Movies of the mixing process are analyzed by converting fluorescent images to two-dimensional fluorescein concentration distributions. The results demonstrate that mode-hopping operation rapidly homogenized chamber contents, circumventing diffusion-isolated zones. PMID:19551159

Long lifetime fast spectrum reactor for lunar surface power system

NASA Astrophysics Data System (ADS)

Kambe, Mitsuru

1993-01-01

In the framework of innovative reactor research activities, a conceptual design study of fast spectrum reactor and primary system for 800 kWe lunar surface power system to be combined with potassium Rankine cycle power conversion has been conducted to meet the power requirements of the lunar base activities in the next century. The reactor subsystem is characterized by RAPID (Refueling by All Pins Integrated Design) concept to enhance inherent safety and to enable quick and simplifed refueling in every 10 years. RAPID concept affords power plant design lifetime of up to 30 years. Integrity of the reactor structure and replacement of failed primary circuits are also discussed. Substantial reduction in per-kWh cost on considering launch, emplacement, and final disposition can be expected by a long system lifetime.

Determining the atmospheric structure and dynamics of the FK Comae Star HD32918

NASA Technical Reports Server (NTRS)

Robinson, R. D.

1995-01-01

The results of UV observations taken with the International Ultraviolet Explorer (IUE) satellite and microwave observations obtained with the Australia Telescope during an observing campaign of the rapidly rotating K0 dwarf star HD 197890, nicknamed 'Speedy Mic' are presented. This star was recently recognized as a powerful, transient EUV source by the ROSAT WFC, and subsequent investigation showed it to be a ZAMS or possibly a PMS dwarf which may be a member of the Local Association. Our observations show it to have strong, variable UV emission lines near the 'saturation' levels. The radio observations show a level of 'quiescent' emission consistent with other rapidly rotating stars, but there is no evidence for the large flux variations that normally characterize the time history of such objects.

The performance studies of DKDP crystals grown by a rapid horizontal growth method

NASA Astrophysics Data System (ADS)

Xie, Xiaoyi; Qi, Hongji; Wang, Bin; Wang, Hu; Chen, Duanyang; Shao, Jianda

2018-04-01

A deuterated potassium dihydrogen phosphate (DKDP) crystal with about 70% deuterium level was grown by a rapid horizontal growth method with independent design equipment, which includes a continuous filtration system. The cooling program during crystal growth was designed according to a self-developed software to catch the size of growing crystal in real time. The crystal structure, optical performance and laser induced damage threshold (LIDT) of this DKDP crystal were investigated in this paper. The deuterium concentration of the crystal was confirmed by the neutron diffraction technique, which was effective and available in determining a complete range of deuteration level. The dielectric property was measured to evaluate the perfection of the lattice. The transmittance and LIDT were carried out further to evaluate the optical and functional properties of this DKDP crystal grown in the rapid horizontal growth technique. All of the detailed characterization for DKDP figured out that the 70% deuterated KDP crystal grown in this way had relatively good qualities.

A Fluorescent Tile DNA Diagnocode System for In Situ Rapid and Selective Diagnosis of Cytosolic RNA Cancer Markers

PubMed Central

Park, Kyung Soo; Shin, Seung Won; Jang, Min Su; Shin, Woojung; Yang, Kisuk; Min, Junhong; Cho, Seung-Woo; Oh, Byung-Keun; Bae, Jong Wook; Jung, Sunghwan; Choi, Jeong-Woo; Um, Soong Ho

2015-01-01

Accurate cancer diagnosis often requires extraction and purification of genetic materials from cells, and sophisticated instrumentations that follow. Otherwise in order to directly treat the diagnostic materials to cells, multiple steps to optimize dose concentration and treatment time are necessary due to diversity in cellular behaviors. These processes may offer high precision but hinder fast analysis of cancer, especially in clinical situations that need rapid detection and characterization of cancer. Here we present a novel fluorescent tile DNA nanostructure delivered to cancer cytosol by employing nanoparticle technology. Its structural anisotropicity offers easy manipulation for multifunctionalities, enabling the novel DNA nanostructure to detect intracellular cancer RNA markers with high specificity within 30 minutes post treatment, while the nanoparticle property bypasses the requirement of treatment optimization, effectively reducing the complexity of applying the system for cancer diagnosis. Altogether, the system offers a precise and rapid detection of cancer, suggesting the future use in the clinical fields. PMID:26678430

Enhancing Bottom-up and Top-down Proteomic Measurements with Ion Mobility Separations

DOE PAGES

Baker, Erin Shammel; Burnum-Johnson, Kristin E.; Ibrahim, Yehia M.; ...

2015-07-03

Proteomic measurements with greater throughput, sensitivity and additional structural information enhance the in-depth characterization of complex mixtures and targeted studies with additional information and higher confidence. While liquid chromatography separation coupled with mass spectrometry (LC-MS) measurements have provided information on thousands of proteins in different sample types, the additional of another rapid separation stage providing structural information has many benefits for analyses. Technical advances in ion funnels and multiplexing have enabled ion mobility separations to be easily and effectively coupled with LC-MS proteomics to enhance the information content of measurements. Finally, herein, we report on applications illustrating increased sensitivity, throughput,more » and structural information by utilizing IMS-MS and LC-IMS-MS measurements for both bottom-up and top-down proteomics measurements.« less

Dynamic Nuclear Polarization NMR Spectroscopy of Polymeric Carbon Nitride Photocatalysts: Insights into Structural Defects and Reactivity.

PubMed

Li, Xiaobo; Sergeyev, Ivan V; Aussenac, Fabien; Masters, Anthony F; Maschmeyer, Thomas; Hook, James M

2018-06-04

Metal-free polymeric carbon nitrides (PCNs) are promising photocatalysts for solar hydrogen production, but their structure-photoactivity relationship remains elusive. Two PCNs were characterized by dynamic-nuclear-polarization-enhanced solid-state NMR spectroscopy, which circumvented the need for specific labeling with either 13 C- or 15 N-enriched precursors. Rapid 1D and 2D data acquisition was possible, providing insights into the structural contrasts between the PCNs. Compared to PCN_B with lower performance, PCN_P is a more porous and more active photocatalyst that is richer in terminal N-H bonds not associated with interpolymer chains. It is proposed that terminal N-H groups act as efficient carrier traps and reaction sites. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Sol-gel synthesized ZnO for optoelectronics applications: a characterization review

NASA Astrophysics Data System (ADS)

Harun, Kausar; Hussain, Fayaz; Purwanto, Agus; Sahraoui, Bouchta; Zawadzka, Anna; Azmin Mohamad, Ahmad

2017-12-01

The rapid growth in green technology has resulted in a marked increase in the incorporation of ZnO in energy and optoelectronic devices. Research involving ZnO is being given renewed attention in the quest to fully exploit its promising properties. The purity and state of defects in the ZnO system are optimized through several modifications to the synthesis conditions and the starting materials. These works have been verified through a series of characterizations. This review covers the essential characterization outcomes of pure ZnO nanoparticles. Emphasis is placed on recent techniques, examples and some issues concerning sol-gel synthesized ZnO nanoparticles. Thermal, phase, structural and morphological observations are combined to ascertain the level of purity of ZnO. The subsequent elemental and optical characterizations are also discussed. This review would be the collective information and suggestions at one place for investigators to focus on the best development of ZnO-based optical and energy devices.

Hyaluronan and Its Binding Proteins during Cervical Ripening and Parturition: Dynamic Changes in Size, Distribution and Temporal Sequence

PubMed Central

Ruscheinsky, Monika; De la Motte, Carol; Mahendroo, Mala

2008-01-01

The uterine cervix undergoes changes during pregnancy and labor that transform it from a closed, rigid, collagen dense structure to one that is distensible, has a disorganized collagen matrix, and dilates sufficiently to allow birth. To protect the reproductive tract from exposure to the external environment, the cervix must be rapidly altered to a closed, undistensible structure after birth. Preparturition remodeling is characterized by increased synthesis of hyaluronan, decreased expression of collagen assembly genes and increased distribution of inflammatory cells into the cervical matrix. Postpartum remodeling is characterized by decreased hyaluronan (HA) content, increased expression of genes involved in assembly of mature collagen and inflammation. The focus of this study is to advance our understanding of functions HA plays in this dynamic process through characterization of HA size, structure and binding proteins in the mouse cervix. Changes in size and structure of HA before and after birth were observed as well as cell specific expression of HA binding proteins. CD44 expression is localized to the pericellular matrix surrounding the basal epithelia and on immune cells while inter α trypsin inhibitor (IαI) and versican are localized to the stromal matrix. Co-localization of HA and IαI is most pronounced after birth. Upregulation of the versican degrading protease, ADAMTS1 occurs in the cervix prior to birth. These studies suggest that HA has multiple, cell specific functions in the cervix that may include modulation of tissue structure and integrity, epithelial cell migration and differentiation, and inflammatory responses. PMID:18353623

Enzyme catalysis captured using multiple structures from one crystal at varying temperatures.

PubMed

Horrell, Sam; Kekilli, Demet; Sen, Kakali; Owen, Robin L; Dworkowski, Florian S N; Antonyuk, Svetlana V; Keal, Thomas W; Yong, Chin W; Eady, Robert R; Hasnain, S Samar; Strange, Richard W; Hough, Michael A

2018-05-01

High-resolution crystal structures of enzymes in relevant redox states have transformed our understanding of enzyme catalysis. Recent developments have demonstrated that X-rays can be used, via the generation of solvated electrons, to drive reactions in crystals at cryogenic temperatures (100 K) to generate 'structural movies' of enzyme reactions. However, a serious limitation at these temperatures is that protein conformational motion can be significantly supressed. Here, the recently developed MSOX (multiple serial structures from one crystal) approach has been applied to nitrite-bound copper nitrite reductase at room temperature and at 190 K, close to the glass transition. During both series of multiple structures, nitrite was initially observed in a 'top-hat' geometry, which was rapidly transformed to a 'side-on' configuration before conversion to side-on NO, followed by dissociation of NO and substitution by water to reform the resting state. Density functional theory calculations indicate that the top-hat orientation corresponds to the oxidized type 2 copper site, while the side-on orientation is consistent with the reduced state. It is demonstrated that substrate-to-product conversion within the crystal occurs at a lower radiation dose at 190 K, allowing more of the enzyme catalytic cycle to be captured at high resolution than in the previous 100 K experiment. At room temperature the reaction was very rapid, but it remained possible to generate and characterize several structural states. These experiments open up the possibility of obtaining MSOX structural movies at multiple temperatures (MSOX-VT), providing an unparallelled level of structural information during catalysis for redox enzymes.

The rat whole embryo culture assay using the Dysmorphology Score system.

PubMed

Zhang, Cindy; Panzica-Kelly, Julie; Augustine-Rauch, Karen

2013-01-01

The rat whole embryo culture (WEC) system has been used extensively for characterizing teratogenic properties of test chemicals. In this chapter, we describe the methodology for culturing rat embryos as well as a new morphological score system, the Dysmorphology Score (DMS) system for assessing morphology of mid gestation (gestational day 11) rat embryos. In contrast to the developmental stage focused scoring associated with the Brown and Fabro score system, this new score system assesses the respective degree of severity of dysmorphology, which delineates normal from abnormal morphology of specific embryonic structures and organ systems. This score system generates an approach that allows rapid identification and quantification of adverse developmental findings, making it conducive for characterization of compounds for teratogenic properties and screening activities.

ANDERS: future of concrete bridge deck evaluation and rehabilitation

NASA Astrophysics Data System (ADS)

Gucunski, Nenad; Moon, Franklin

2011-04-01

The Automated Nondestructive Evaluation and Rehabilitation System (ANDERS) aims to provide a uniquely comprehensive tool that will transform the manner in which bridge decks are assessed and rehabilitated. It is going to be achieved through: 1) much higher evaluation detail and comprehensiveness of detection at an early stage deterioration, 2) comprehensive condition and structural assessment at all stages of deterioration, and 3) integrated assessment and rehabilitation that will be minimally invasive, rapid and cost effective. ANDERS is composed of four systems. that merge novel imaging and NDE techniques, together with novel intervention approaches to arrest the deterioration processes. These technologies are incorporated within a series of human-operated and robotic vehicles. To perform assessments, ANDERS will be equipped with two complimentary nondestructive approaches. The first, Multi-Modal Nondestructive Evaluation (MM-NDE) System aims to identify and characterize localized deterioration with a high degree of resolution. The second, Global Structural Assessment (GSA) System aims to capture global structural characteristics and identify any appreciable effects of deterioration on a bridge structure. Output from these two approaches will be merged through a novel Automated Structural Identification (Auto St-Id) approach that will construct, calibrate, and utilize simulation models to assess overall structural vulnerability and capacity. These three systems comprise the assessment suite of ANDERS and will directly inform the Nondestructive Rehabilitation (NDR) System. The NDR System leverages robotics for the precision and rapid delivery of novel materials capable of halting the early-stage deterioration identified.

Automatic analysis of microscopic images of red blood cell aggregates

NASA Astrophysics Data System (ADS)

Menichini, Pablo A.; Larese, Mónica G.; Riquelme, Bibiana D.

2015-06-01

Red blood cell aggregation is one of the most important factors in blood viscosity at stasis or at very low rates of flow. The basic structure of aggregates is a linear array of cell commonly termed as rouleaux. Enhanced or abnormal aggregation is seen in clinical conditions, such as diabetes and hypertension, producing alterations in the microcirculation, some of which can be analyzed through the characterization of aggregated cells. Frequently, image processing and analysis for the characterization of RBC aggregation were done manually or semi-automatically using interactive tools. We propose a system that processes images of RBC aggregation and automatically obtains the characterization and quantification of the different types of RBC aggregates. Present technique could be interesting to perform the adaptation as a routine used in hemorheological and Clinical Biochemistry Laboratories because this automatic method is rapid, efficient and economical, and at the same time independent of the user performing the analysis (repeatability of the analysis).

Surface texture measurement for dental wear applications

NASA Astrophysics Data System (ADS)

Austin, R. S.; Mullen, F.; Bartlett, D. W.

2015-06-01

The application of surface topography measurement and characterization within dental materials science is highly active and rapidly developing, in line with many modern industries. Surface measurement and structuring is used extensively within oral and dental science to optimize the optical, tribological and biological performance of natural and biomimetic dental materials. Although there has historically been little standardization in the use and reporting of surface metrology instrumentation and software, the dental industry is beginning to adopt modern areal measurement and characterization techniques, especially as the dental industry is increasingly adopting digital impressioning techniques in order to leverage CAD/CAM technologies for the design and construction of dental restorations. As dental treatment becomes increasingly digitized and reliant on advanced technologies such as dental implants, wider adoption of standardized surface topography and characterization techniques will become evermore essential. The dental research community welcomes the advances that are being made in surface topography measurement science towards realizing this ultimate goal.

Structural and functional characterization of an arylamine N-acetyltransferase from the pathogen Mycobacterium abscessus: differences from other mycobacterial isoforms and implications for selective inhibition.

PubMed

Cocaign, Angélique; Kubiak, Xavier; Xu, Ximing; Garnier, Guillaume; Li de la Sierra-Gallay, Inès; Chi-Bui, Linh; Dairou, Julien; Busi, Florent; Abuhammad, Areej; Haouz, Ahmed; Dupret, Jean Marie; Herrmann, Jean Louis; Rodrigues-Lima, Fernando

2014-11-01

Mycobacterium abscessus is the most pathogenic rapid-growing mycobacterium and is one of the most resistant organisms to chemotherapeutic agents. However, structural and functional studies of M. abscessus proteins that could modify/inactivate antibiotics remain nonexistent. Here, the structural and functional characterization of an arylamine N-acetyltransferase (NAT) from M. abscessus [(MYCAB)NAT1] are reported. This novel prokaryotic NAT displays significant N-acetyltransferase activity towards aromatic substrates, including antibiotics such as isoniazid and p-aminosalicylate. The enzyme is endogenously expressed and functional in both the rough and smooth M. abscessus morphotypes. The crystal structure of (MYCAB)NAT1 at 1.8 Å resolution reveals that it is more closely related to Nocardia farcinica NAT than to mycobacterial isoforms. In particular, structural and physicochemical differences from other mycobacterial NATs were found in the active site. Peculiarities of (MYCAB)NAT1 were further supported by kinetic and docking studies showing that the enzyme was poorly inhibited by the piperidinol inhibitor of mycobacterial NATs. This study describes the first structure of an antibiotic-modifying enzyme from M. abscessus and provides bases to better understand the substrate/inhibitor-binding specificities among mycobacterial NATs and to identify/optimize specific inhibitors. These data should also contribute to the understanding of the mechanisms that are responsible for the pathogenicity and extensive chemotherapeutic resistance of M. abscessus.

Recent advances in studies on milk oligosaccharides of cows and other domestic farm animals.

PubMed

Urashima, Tadasu; Taufik, Epi; Fukuda, Kenji; Asakuma, Sadaki

2013-01-01

Human mature milk and colostrum contain 12-13 g/L and 22-24 g/L of milk oligosaccharides respectively, and the structures of least 115 human milk oligosaccharides (HMOs) have been characterized to date. By way of comparison, bovine colostrum collected immediately post partum contains only around 1 g/L of oligosaccharides, and this concentration rapidly decreases after 48 h. It was recently recognized that HMOs have several biological functions, and this study area has become very active, as illustrated by a recent symposium, but it appears that advances in studies on the milk oligosaccharides of domestic farm animals, including cows, have been rather slow compared with those on HMOs. Nevertheless, studies on bovine milk oligosaccharides (BMOs) have progressed recently, especially in regard to structural characterization, with the development of methods termed glycomics. This review is concerned with recent progress in studies on the milk oligosaccharides of domestic farm animals, especially of BMOs and bovine glycoproteins, and it discusses the possibility of industrial utilization in the near future.

Versatility of Evaporation-Induced Self-Assembly (EISA) Method for Preparation of Mesoporous TiO2 for Energy and Environmental Applications

PubMed Central

Mahoney, Luther; Koodali, Ranjit T.

2014-01-01

Evaporation-Induced Self-Assembly (EISA) method for the preparation of mesoporous titanium dioxide materials is reviewed. The versatility of EISA method for the rapid and facile synthesis of TiO2 thin films and powders is highlighted. Non-ionic surfactants such as Pluronic P123, F127 and cationic surfactants such as cetyltrimethylammonium bromide have been extensively employed for the preparation of mesoporous TiO2. In particular, EISA method allows for fabrication of highly uniform, robust, crack-free films with controllable thickness. Eleven characterization techniques for elucidating the structure of the EISA prepared mesoporous TiO2 are discussed in this paper. These many characterization methods provide a holistic picture of the structure of mesoporous TiO2. Mesoporous titanium dioxide materials have been employed in several applications that include Dye Sensitized Solar Cells (DSSCs), photocatalytic degradation of organics and splitting of water, and batteries. PMID:28788590

Realization of a topological phase transition in a gyroscopic lattice

NASA Astrophysics Data System (ADS)

Mitchell, Noah P.; Nash, Lisa M.; Irvine, William T. M.

2018-03-01

Topological metamaterials exhibit unusual behaviors at their boundaries, such as unidirectional chiral waves, that are protected by a topological feature of their band structures. The ability to tune such a material through a topological phase transition in real time could enable the use of protected waves for information storage and readout. Here we dynamically tune through a topological phase transition by breaking inversion symmetry in a metamaterial composed of interacting gyroscopes. Through the transition, we track the divergence of the edge modes' localization length and the change in Chern number characterizing the topology of the material's band structure. This Rapid Communication provides a new axis with which to tune the response of mechanical topological metamaterials.

Pathway to oxide photovoltaics via band-structure engineering of SnO

DOE PAGES

Peng, Haowei; Bikowski, Andre; Zakutayev, Andriy; ...

2016-10-04

All-oxide photovoltaics could open rapidly scalable manufacturing routes, if only oxide materials with suitable electronic and optical properties were developed. SnO has exceptional doping and transport properties among oxides, but suffers from a strongly indirect band gap. Here, we address this shortcoming by band-structure engineering through isovalent but heterostructural alloying with divalent cations (Mg, Ca, Sr, and Zn). Furthermore, using first-principles calculations, we show that suitable band gaps and optical properties close to that of direct semiconductors are achievable, while the comparatively small effective masses are preserved in the alloys. Initial thin film synthesis and characterization support the feasibility ofmore » the approach.« less

Crystallization dynamics on curved surfaces

NASA Astrophysics Data System (ADS)

García, Nicolás A.; Register, Richard A.; Vega, Daniel A.; Gómez, Leopoldo R.

2013-07-01

We study the evolution from a liquid to a crystal phase in two-dimensional curved space. At early times, while crystal seeds grow preferentially in regions of low curvature, the lattice frustration produced in regions with high curvature is rapidly relaxed through isolated defects. Further relaxation involves a mechanism of crystal growth and defect annihilation where regions with high curvature act as sinks for the diffusion of domain walls. The pinning of grain boundaries at regions of low curvature leads to the formation of a metastable structure of defects, characterized by asymptotically slow dynamics of ordering and activation energies dictated by the largest curvatures of the system. These glassylike ordering dynamics may completely inhibit the appearance of the ground-state structures.

Rapid Characterization of Magnetic Moment of Cells for Magnetic Separation

PubMed Central

Ooi, Chinchun; Earhart, Christopher M.; Wilson, Robert J.; Wang, Shan X.

2014-01-01

NCI-H1650 lung cancer cell lines labeled with magnetic nanoparticles via the Epithelial Cell Adhesion Molecule (EpCAM) antigen were previously shown to be captured at high efficiencies by a microfabricated magnetic sifter. If fine control and optimization of the magnetic separation process is to be achieved, it is vital to be able to characterize the labeled cells’ magnetic moment rapidly. We have thus adapted a rapid prototyping method to obtain the saturation magnetic moment of these cells. This method utilizes a cross-correlation algorithm to analyze the cells’ motion in a simple fluidic channel to obtain their magnetophoretic velocity, and is effective even when the magnetic moments of cells are small. This rapid characterization is proven useful in optimizing our microfabricated magnetic sifter procedures for magnetic cell capture. PMID:24771946

Form and function in hillslope hydrology: in situ imaging and characterization of flow-relevant structures

NASA Astrophysics Data System (ADS)

Jackisch, Conrad; Angermann, Lisa; Allroggen, Niklas; Sprenger, Matthias; Blume, Theresa; Tronicke, Jens; Zehe, Erwin

2017-07-01

The study deals with the identification and characterization of rapid subsurface flow structures through pedo- and geo-physical measurements and irrigation experiments at the point, plot and hillslope scale. Our investigation of flow-relevant structures and hydrological responses refers to the general interplay of form and function, respectively. To obtain a holistic picture of the subsurface, a large set of different laboratory, exploratory and experimental methods was used at the different scales. For exploration these methods included drilled soil core profiles, in situ measurements of infiltration capacity and saturated hydraulic conductivity, and laboratory analyses of soil water retention and saturated hydraulic conductivity. The irrigation experiments at the plot scale were monitored through a combination of dye tracer, salt tracer, soil moisture dynamics, and 3-D time-lapse ground penetrating radar (GPR) methods. At the hillslope scale the subsurface was explored by a 3-D GPR survey. A natural storm event and an irrigation experiment were monitored by a dense network of soil moisture observations and a cascade of 2-D time-lapse GPR trenches. We show that the shift between activated and non-activated state of the flow paths is needed to distinguish structures from overall heterogeneity. Pedo-physical analyses of point-scale samples are the basis for sub-scale structure inference. At the plot and hillslope scale 3-D and 2-D time-lapse GPR applications are successfully employed as non-invasive means to image subsurface response patterns and to identify flow-relevant paths. Tracer recovery and soil water responses from irrigation experiments deliver a consistent estimate of response velocities. The combined observation of form and function under active conditions provides the means to localize and characterize the structures (this study) and the hydrological processes (companion study Angermann et al., 2017, this issue).

Cloning and characterization of WRKY gene homologs in Chieh-qua (Benincasa hispida Cogn. var. Chieh-qua How) and their expression in response to fusaric acid treatment.

PubMed

Mao, Yizhou; Jiang, Biao; Peng, Qingwu; Liu, Wenrui; Lin, Yue; Xie, Dasen; He, Xiaoming; Li, Shaoshan

2017-05-01

The WRKY transcription factors play an important role in plant resistance for biotic and abiotic stresses. In the present study, we cloned 10 WRKY gene homologs (CqWRKY) in Chieh-qua (Benincasa hispida Cogn. var. Chieh-qua) using the rapid-amplification of cDNA ends (RACE) or homology-based cloning methods. We characterized the structure of these CqWRKY genes. Phylogenetic analysis of these sequences with cucumber homologs suggested possible structural conservation of these genes among cucurbit crops. We examined the expression levels of these genes in response to fusaric acid (FA) treatment between resistant and susceptible Chieh-qua lines with quantitative real-time PCR. All genes could be upregulated upon FA treatment, but four CqWRKY genes exhibited differential expression between resistant and susceptible lines before and after FA application. CqWRKY31 seemed to be a positive regulator while CqWRKY1, CqWRKY23 and CqWRKY53 were negative regulators of fusaric resistance. This is the first report of characterization of WRKY family genes in Chieh-qua. The results may also be useful in breeding Chieh-qua for Fusarium wilt resistance.

RapTOR: Automated Sequencing Library Preparation and Suppression for Rapid Pathogen Characterization (7th Annual SFAF Meeting, 2012)

ScienceCinema

Lane, Todd

2018-05-18

Todd Lane on "RapTOR: Automated sequencing library preparation and suppression for rapid pathogen characterization" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

A BIOINFORMATIC STRATEGY TO RAPIDLY CHARACTERIZE CDNA LIBRARIES

EPA Science Inventory

A Bioinformatic Strategy to Rapidly Characterize cDNA Libraries

G. Charles Ostermeier1, David J. Dix2 and Stephen A. Krawetz1.
1Departments of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, & Institute for Scientific Computing, Wayne State Univer...

RapTOR: Automated Sequencing Library Preparation and Suppression for Rapid Pathogen Characterization (7th Annual SFAF Meeting, 2012)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lane, Todd

2012-06-01

Todd Lane on "RapTOR: Automated sequencing library preparation and suppression for rapid pathogen characterization" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

[Rapid analysis on phenolic compounds in Rheum palmatum based on UPLC-Q-TOF/MSE combined with diagnostic ions filter].

PubMed

Wang, Qing; Lu, Zhi-Wei; Liu, Yue-Hong; Wang, Ming-Ling; Fu, Shuang; Zhang, Qing-Qing; Zhao, Hui-Zhen; Zhang, Zhi-Xin; Xie, Zi-Ye; Huang, Zheng-Hai; Yu, Hong-Hong; Zhou, Wen-Juan; Gao, Xiao-Yan

2017-05-01

Diagnostic ions filter method was used to rapidly detect and identify the phenolic compounds in Rheum palmatum based on ultra performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MSE). The representative authentic standards of phenolic compounds, including gallic acid, (+)-catechin, (－)-epicatechin, (－)-epicatechin-3-O-gallate and procyanidin B2, were subjected to analysis by UPLC-Q-TOF/MSE system with negative ion mode. Fragmentation patterns of each standard were summarized based on assigned fragment ions. The prominent product ions were selected as diagnostic ions. Subsequently, diagnostic ions filter was employed to rapidly recognize analogous skeletons. Combined with retention time, accurate mass, characteristic fragments and previous literature data, the structures of the filtered compounds were identified or tentatively characterized. A total 63 phenolic compounds (36 phenolic acid derivatives, 8 flavonoid derivatives and 19 tennis derivatives) in R. palmatum were identified, including 6 potential new compounds. The method of diagnostic ions filter could rapidly detect and identify phenolic compounds in R. palmatum This study provides a method for rapid detection of phenolic compounds in R. palmatum and is expected to complete the material basis of rhubarb. Copyright© by the Chinese Pharmaceutical Association.

Fast-scan Cyclic Voltammetry for the Characterization of Rapid Adenosine Release.

PubMed

Nguyen, Michael D; Venton, B Jill

2015-01-01

Adenosine is a signaling molecule and downstream product of ATP that acts as a neuromodulator. Adenosine regulates physiological processes, such as neurotransmission and blood flow, on a time scale of minutes to hours. Recent developments in electrochemical techniques, including fast-scan cyclic voltammetry (FSCV), have allowed direct detection of adenosine with sub-second temporal resolution. FSCV studies have revealed a novel mode of rapid signaling that lasts only a few seconds. This rapid release of adenosine can be evoked by electrical or mechanical stimulations or it can be observed spontaneously without stimulation. Adenosine signaling on this time scale is activity dependent; however, the mode of release is not fully understood. Rapid adenosine release modulates oxygen levels and evoked dopamine release, indicating that adenosine may have a rapid modulatory role. In this review, we outline how FSCV can be used to detect adenosine release, compare FSCV with other techniques used to measure adenosine, and present an overview of adenosine signaling that has been characterized using FSCV. These studies point to a rapid mode of adenosine modulation, whose mechanism and function will continue to be characterized in the future.

Structural evolution of maize stalk/char particles during pyrolysis.

PubMed

Fu, Peng; Hu, Song; Sun, Lushi; Xiang, Jun; Yang, Tao; Zhang, Anchao; Zhang, Junying

2009-10-01

The structural evolution characteristics of maize stalk/char particles during pyrolysis were investigated. The char was prepared by pyrolyzing at temperatures ranging from 200 to 900 degrees C. Maize stalk and chars were characterized by thermogravimetric analysis, ultimate analysis (TGA), Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), helium density measurement and N(2) adsorption/desorption method. The char yield decreased rapidly with increasing temperature until 400 degrees C. As temperature increased, the char became progressively more aromatic and carbonaceous. The hydroxyl, aliphatic C-H, carbonyl and olefinic C=C groups were lost at high temperatures. Below 500 degrees C, the removal of volatile matter made pore opening. High temperatures led to the occurrence of softening, melting, fusing and carbon structural ordering. The aromatization process started at approximately 350 degrees C and continued to higher temperatures. The shrinkage of carbon structure occurred above 500 degrees C, which was concurrent with the aromatization process.

High Contrast Imaging of Exoplanets and Exoplanetary Systems with JWST

NASA Astrophysics Data System (ADS)

Hinkley, Sasha; Skemer, Andrew; Biller, Beth; Baraffe, I.; Bonnefoy, M.; Bowler, B.; Carter, A.; Chen, C.; Choquet, E.; Currie, T.; Danielski, C.; Fortney, J.; Grady, C.; Greenbaum, A.; Hines, D.; Janson, M.; Kalas, P.; Kennedy, G.; Kraus, A.; Lagrange, A.; Liu, M.; Marley, M.; Marois, C.; Matthews, B.; Mawet, D.; Metchev, S.; Meyer, M.; Millar-Blanchaer, M.; Perrin, M.; Pueyo, L.; Quanz, S.; Rameau, J.; Rodigas, T.; Sallum, S.; Sargent, B.; Schlieder, J.; Schneider, G.; Stapelfeldt, K.; Tremblin, P.; Vigan, A.; Ygouf, M.

2017-11-01

JWST will transform our ability to characterize directly imaged planets and circumstellar debris disks, including the first spectroscopic characterization of directly imaged exoplanets at wavelengths beyond 5 microns, providing a powerful diagnostic of cloud particle properties, atmospheric structure, and composition. To lay the groundwork for these science goals, we propose a 39-hour ERS program to rapidly establish optimal strategies for JWST high contrast imaging. We will acquire: a) coronagraphic imaging of a newly discovered exoplanet companion, and a well-studied circumstellar debris disk with NIRCam & MIRI; b) spectroscopy of a wide separation planetary mass companion with NIRSPEC & MIRI; and c) deep aperture masking interferometry with NIRISS. Our primary goals are to: 1) generate representative datasets in modes to be commonly used by the exoplanet and disk imaging communities; 2) deliver science enabling products to empower a broad user base to develop successful future investigations; and 3) carry out breakthrough science by characterizing exoplanets for the first time over their full spectral range from 2-28 microns, and debris disk spectrophotometry out to 15 microns sampling the 3 micron water ice feature. Our team represents the majority of the community dedicated to exoplanet and disk imaging and has decades of experience with high contrast imaging algorithms and pipelines. We have developed a collaboration management plan and several organized working groups to ensure we can rapidly and effectively deliver high quality Science Enabling Products to the community.

Skeletal muscle is a biological example of a linear electroactive actuator

NASA Astrophysics Data System (ADS)

Lieber, Richard L.

1999-05-01

Skeletal muscle represents a classic biological example of a structure-function relationship. This paper reviews basic muscle anatomy and demonstrates how molecular motion on the order of nm distances is converted into the macroscopic movements that are possible with skeletal muscle. Muscle anatomy provides a structural basis for understanding the basic mechanical properties of skeletal muscle -- namely, the length-tension relationship and the force-velocity relationships. The length-tension relationship illustrates that muscle force generation is extremely length dependent due to the interdigitation of the contractile filaments. The force-velocity relationship is characterized by a rapid force drop in muscle with increasing shortening velocity and a rapid rise in force when muscles are forced to lengthen. Finally, muscle architecture -- the number and arrangement of muscle fibers -- has a profound effect on the magnitude of muscle force generated and the magnitude of muscle excursion. These concepts demonstrate the elegant manner in which muscle acts as a biologically regenerating linear motor. These concepts can be used in developing artificial muscles as well as in performing surgical reconstructive procedures with various donor muscles.

Novel immunoassay and rapid immunoaffinity chromatography method for the detection and selective extraction of naringin in Citrus aurantium.

PubMed

Qu, Huihua; Zhang, Yue; Qu, Baoping; Cheng, Jinjun; Liu, Shuchen; Feng, Shenglan; Wang, Qingguo; Zhao, Yan

2016-04-01

In this work, a novel monoclonal antibody specific for naringin was prepared and characterized. Subsequently, an indirect competitive enzyme-linked immunosorbent assay for naringin was developed, with an effective range from 4.8 to 156 ng/mL naringin. Next, an immunoaffinity column was obtained by coupling anti-naringin monoclonal antibodies to CNBr-activated Sepharose 4B and a rapid immunoaffinity chromatography assay for naringin was developed. The immunoaffinity column was used to separate naringin from Citrus aurantium. The results showed that 1 g of the dry Sepharose 4B can couple 10 mg of immunoglobulin G. And the immunoaffinity column can efficiently and specifically capture approximately 250 μg of naringin without cross reacting with its structurally similar compounds. Moreover, our results indicate that the application of immunoaffinity chromatography can simplify the pretreatment and the isolation process greatly compared to conventional methods, providing a potential method for extracting the target component from structurally similar compounds in natural products. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Highly conductive ribbons prepared by stick-slip assembly of organosoluble gold nanoparticles.

PubMed

Lawrence, Jimmy; Pham, Jonathan T; Lee, Dong Yun; Liu, Yujie; Crosby, Alfred J; Emrick, Todd

2014-02-25

Precisely positioning and assembling nanoparticles (NPs) into hierarchical nanostructures is opening opportunities in a wide variety of applications. Many techniques employed to produce hierarchical micrometer and nanoscale structures are limited by complex fabrication of templates and difficulties with scalability. Here we describe the fabrication and characterization of conductive nanoparticle ribbons prepared from surfactant-free organosoluble gold nanoparticles (Au NPs). We used a flow-coating technique in a controlled, stick-slip assembly to regulate the deposition of Au NPs into densely packed, multilayered structures. This affords centimeter-scale long, high-resolution Au NP ribbons with precise periodic spacing in a rapid manner, up to 2 orders-of-magnitude finer and faster than previously reported methods. These Au NP ribbons exhibit linear ohmic response, with conductivity that varies by changing the binding headgroup of the ligands. Controlling NP percolation during sintering (e.g., by adding polymer to retard rapid NP coalescence) enables the formation of highly conductive ribbons, similar to thermally sintered conductive adhesives. Hierarchical, conductive Au NP ribbons represent a promising platform to enable opportunities in sensing, optoelectronics, and electromechanical devices.

How Does Your Protein Fold? Elucidating the Apomyoglobin Folding Pathway

PubMed Central

Dyson, H. Jane; Wright, Peter E.

2017-01-01

Conspectus Although each type of protein fold and in some cases individual proteins within a fold classification can have very different mechanisms of folding, the underlying biophysical and biochemical principles that operate to cause a linear polypeptide chain to fold into a globular structure must be the same. In an aqueous solution, the protein takes up the thermodynamically most stable structure, but the pathway along which the polypeptide proceeds in order to reach that structure is a function of the amino acid sequence, which must be the final determining factor, not only in shaping the final folded structure, but in dictating the folding pathway. A number of groups have focused on a single protein or group of proteins, to determine in detail the factors that influence the rate and mechanism of folding in a defined system, with the hope that hypothesis-driven experiments can elucidate the underlying principles governing the folding process. Our research group has focused on the folding of the globin family of proteins, and in particular on the monomeric protein apomyoglobin. Apomyoglobin (apoMb) folds relatively slowly (~2 seconds) via an ensemble of obligatory intermediates that form rapidly after the initiation of folding. The folding pathway can be dissected using rapid-mixing techniques, which can probe processes in the millisecond time range. Stopped-flow measurements detected by circular dichroism (CD) or fluorescence spectroscopy give information on the rates of folding events. Quench-flow experiments utilize the differential rates of hydrogen-deuterium exchange of amide protons protected in parts of the structure that are folded early; protection of amides can be detected by mass spectrometry or proton nuclear magnetic resonance spectroscopy (NMR). In addition, apoMb forms an intermediate at equilibrium at pH ~ 4, which is sufficiently stable for it to be structurally characterized by solution methods such as CD, fluorescence and NMR spectroscopies, and the conformational ensembles formed in the presence of denaturing agents and low pH can be characterized as models for the unfolded states of the protein. Newer NMR techniques such as measurement of residual dipolar couplings in the various partly folded states, and relaxation dispersion measurements to probe invisible states present at low concentrations, have contributed to providing a detailed picture of the apomyoglobin folding pathway. The research summarized in this review was aimed at characterizing and comparing the equilibrium and kinetic intermediates both structurally and dynamically, as well as delineating the complete folding pathway at a residue-specific level, in order to answer the question “What is it about the amino acid sequence that causes each molecule in the unfolded protein ensemble to start folding, and, once started, to proceed towards the formation of the correctly folded three-dimensional structure?” PMID:28032989

Exploiting the Complementarity between Dereplication and Computer-Assisted Structure Elucidation for the Chemical Profiling of Natural Cosmetic Ingredients: Tephrosia purpurea as a Case Study.

PubMed

Hubert, Jane; Chollet, Sébastien; Purson, Sylvain; Reynaud, Romain; Harakat, Dominique; Martinez, Agathe; Nuzillard, Jean-Marc; Renault, Jean-Hugues

2015-07-24

The aqueous-ethanolic extract of Tephrosia purpurea seeds is currently exploited in the cosmetic industry as a natural ingredient of skin lotions. The aim of this study was to chemically characterize this ingredient by combining centrifugal partition extraction (CPE) as a fractionation tool with two complementary identification approaches involving dereplication and computer-assisted structure elucidation. Following two rapid fractionations of the crude extract (2 g), seven major compounds namely, caffeic acid, quercetin-3-O-rutinoside, ethyl galactoside, ciceritol, stachyose, saccharose, and citric acid, were unambiguously identified within the CPE-generated simplified mixtures by a recently developed (13)C NMR-based dereplication method. The structures of four additional compounds, patuletin-3-O-rutinoside, kaempferol-3-O-rutinoside, guaiacylglycerol 8-vanillic acid ether, and 2-methyl-2-glucopyranosyloxypropanoic acid, were automatically elucidated by using the Logic for Structure Determination program based on the interpretation of 2D NMR (HSQC, HMBC, and COSY) connectivity data. As more than 80% of the crude extract mass was characterized without need for tedious and labor-intensive multistep purification procedures, the identification tools involved in this work constitute a promising strategy for an efficient and time-saving chemical profiling of natural extracts.

Competitive annealing of multiple DNA origami: formation of chimeric origami

NASA Astrophysics Data System (ADS)

Majikes, Jacob M.; Nash, Jessica A.; LaBean, Thomas H.

2016-11-01

Scaffolded DNA origami are a robust tool for building discrete nanoscale objects at high yield. This strategy ensures, in the design process, that the desired nanostructure is the minimum free energy state for the designed set of DNA sequences. Despite aiming for the minimum free energy structure, the folding process which leads to that conformation is difficult to characterize, although it has been the subject of much research. In order to shed light on the molecular folding pathways, this study intentionally frustrates the folding process of these systems by simultaneously annealing the staple pools for multiple target or parent origami structures, forcing competition. A surprising result of these competitive, simultaneous anneals is the formation of chimeric DNA origami which inherit structural regions from both parent origami. By comparing the regions inherited from the parent origami, relative stability of substructures were compared. This allowed examination of the folding process with typical characterization techniques and materials. Anneal curves were then used as a means to rapidly generate a phase diagram of anticipated behavior as a function of staple excess and parent staple ratio. This initial study shows that competitive anneals provide an exciting way to create diverse new nanostructures and may be used to examine the relative stability of various structural motifs.

Tropical vegetation evidence for rapid sea level changes associated with Heinrich Events

NASA Astrophysics Data System (ADS)

González, Catalina; Dupont, Lydie M.

2010-03-01

A Cariaco Basin pollen record shows the development of tropical salt marshes during marine isotope stage 3. Rapid and abrupt expansions of salt marsh vegetation in tropical South America are associated with north Atlantic Heinrich Events stadials (HE-stadials). Intervals of salt marsh expansion have an internal structure, which consists of a recurrent alternation of species that starts with pollen increments of Chenopodiaceae, that are followed by increments of grasses, and subsequently by increments of Cyperaceae. This pattern suggests a successional process that is determined by the close relationship between sea-level and plant community dynamics. The salt tolerant Chenopodiaceae, indicate hypersaline intertidal environments, which were most likely promoted by extremely dry atmospheric conditions. Rapid sea-level rise characterizes the onset of HE-stadials, causing the continued recruitment of pioneer species, which are the only ones tolerating rapid rates of disturbance. Once sea-level rise decelerates, marsh plants are able to trap and stabilize sediments, favouring the establishment of more competitive species. These results add to the scarce knowledge on the dynamics of tropical salt marsh ecosystems, and provide independent paleoclimatic evidence on sea-level changes following Antarctic climate variability.

Rapid, synchronous, and stable induction of type 1 piliation in Escherichia coli by using a chromosomal lacUV5 promoter.

PubMed Central

Woodall, L D; Russell, P W; Harris, S L; Orndorff, P E

1993-01-01

Type 1 pili are filamentous proteinaceous appendages produced by certain members of the family Enterobacteriaceae. In Escherichia coli, the adhesive properties of these pili are due to the binding of at least one minor pilus component to mannose, a sugar common to cell surface molecules of many eukaryotic cells. The study of pilus assembly may be benefited by a rapid way of inducing pilus synthesis de novo. We describe herein the construction and characterization of a strain in which piliation can be rapidly induced by the addition of lactose or its analog isopropyl-beta-D-thiogalactopyranoside. This was accomplished by placing the chromosomal fimA gene (encoding the major structural subunit of pili) under lacUV5 promoter control. Further experiments suggested that transcription of genes downstream of fimA, whose products are required for normal pilus assembly and function, may also be controlled by the lacUV5 promoter. The construction described herein may have a variety of applications apart from aiding the study of pilus assembly since its adhesive properties can be rapidly and easily turned on and off. Images PMID:8097517

Effect of rapid oxidation on optical and electrical properties of silicon nanowires obtained by chemical etching

NASA Astrophysics Data System (ADS)

Karyaoui, M.; Bardaoui, A.; Ben Rabha, M.; Harmand, J. C.; Amlouk, M.

2012-05-01

In the present work, we report the investigation of passivated silicon nanowires (SiNWs) having an average radius of 3.7 μm, obtained by chemical etching of p-type silicon (p-Si). The surface passivation of the SiNWs was performed through a rapid oxidation conducted under a controlled atmosphere at different temperatures and durations. The morphology of the SiNWs was examined using a scanning electron microscope (SEM) that revealed a wave-like structure of dense and vertically aligned one-dimensional silicon nanostructures. On the other hand, optical and electrical characterizations of the SiNWs were studied using a UV-Vis-NIR spectrometer, the Fourier transform infrared spectroscopy (FTIR) and I-V measurements. The reflectance of SiNWs has been dropped to approximately 2% in comparison to that of bare p-Si. This low reflectance slightly increased after carrying out the rapid thermal annealing. The observed behavior was attributed to the formation of a SiO2 layer, as confirmed by FTIR measurements. Finally, the electrical measurements have shown that the rapid oxidation, at certain conditions, contributes to the improvement of the electrical responses of the SiNWs, which can be of great interest for photovoltaic applications.

Light sheet theta microscopy for rapid high-resolution imaging of large biological samples.

PubMed

Migliori, Bianca; Datta, Malika S; Dupre, Christophe; Apak, Mehmet C; Asano, Shoh; Gao, Ruixuan; Boyden, Edward S; Hermanson, Ola; Yuste, Rafael; Tomer, Raju

2018-05-29

Advances in tissue clearing and molecular labeling methods are enabling unprecedented optical access to large intact biological systems. These developments fuel the need for high-speed microscopy approaches to image large samples quantitatively and at high resolution. While light sheet microscopy (LSM), with its high planar imaging speed and low photo-bleaching, can be effective, scaling up to larger imaging volumes has been hindered by the use of orthogonal light sheet illumination. To address this fundamental limitation, we have developed light sheet theta microscopy (LSTM), which uniformly illuminates samples from the same side as the detection objective, thereby eliminating limits on lateral dimensions without sacrificing the imaging resolution, depth, and speed. We present a detailed characterization of LSTM, and demonstrate its complementary advantages over LSM for rapid high-resolution quantitative imaging of large intact samples with high uniform quality. The reported LSTM approach is a significant step for the rapid high-resolution quantitative mapping of the structure and function of very large biological systems, such as a clarified thick coronal slab of human brain and uniformly expanded tissues, and also for rapid volumetric calcium imaging of highly motile animals, such as Hydra, undergoing non-isomorphic body shape changes.

Low-energy transmission electron diffraction and imaging of large-area graphene

PubMed Central

Zhao, Wei; Xia, Bingyu; Lin, Li; Xiao, Xiaoyang; Liu, Peng; Lin, Xiaoyang; Peng, Hailin; Zhu, Yuanmin; Yu, Rong; Lei, Peng; Wang, Jiangtao; Zhang, Lina; Xu, Yong; Zhao, Mingwen; Peng, Lianmao; Li, Qunqing; Duan, Wenhui; Liu, Zhongfan; Fan, Shoushan; Jiang, Kaili

2017-01-01

Two-dimensional (2D) materials have attracted interest because of their excellent properties and potential applications. A key step in realizing industrial applications is to synthesize wafer-scale single-crystal samples. Until now, single-crystal samples, such as graphene domains up to the centimeter scale, have been synthesized. However, a new challenge is to efficiently characterize large-area samples. Currently, the crystalline characterization of these samples still relies on selected-area electron diffraction (SAED) or low-energy electron diffraction (LEED), which is more suitable for characterizing very small local regions. This paper presents a highly efficient characterization technique that adopts a low-energy electrostatically focused electron gun and a super-aligned carbon nanotube (SACNT) film sample support. It allows rapid crystalline characterization of large-area graphene through a single photograph of a transmission-diffracted image at a large beam size. Additionally, the low-energy electron beam enables the observation of a unique diffraction pattern of adsorbates on the suspended graphene at room temperature. This work presents a simple and convenient method for characterizing the macroscopic structures of 2D materials, and the instrument we constructed allows the study of the weak interaction with 2D materials. PMID:28879233

Low-energy transmission electron diffraction and imaging of large-area graphene.

PubMed

Zhao, Wei; Xia, Bingyu; Lin, Li; Xiao, Xiaoyang; Liu, Peng; Lin, Xiaoyang; Peng, Hailin; Zhu, Yuanmin; Yu, Rong; Lei, Peng; Wang, Jiangtao; Zhang, Lina; Xu, Yong; Zhao, Mingwen; Peng, Lianmao; Li, Qunqing; Duan, Wenhui; Liu, Zhongfan; Fan, Shoushan; Jiang, Kaili

2017-09-01

Two-dimensional (2D) materials have attracted interest because of their excellent properties and potential applications. A key step in realizing industrial applications is to synthesize wafer-scale single-crystal samples. Until now, single-crystal samples, such as graphene domains up to the centimeter scale, have been synthesized. However, a new challenge is to efficiently characterize large-area samples. Currently, the crystalline characterization of these samples still relies on selected-area electron diffraction (SAED) or low-energy electron diffraction (LEED), which is more suitable for characterizing very small local regions. This paper presents a highly efficient characterization technique that adopts a low-energy electrostatically focused electron gun and a super-aligned carbon nanotube (SACNT) film sample support. It allows rapid crystalline characterization of large-area graphene through a single photograph of a transmission-diffracted image at a large beam size. Additionally, the low-energy electron beam enables the observation of a unique diffraction pattern of adsorbates on the suspended graphene at room temperature. This work presents a simple and convenient method for characterizing the macroscopic structures of 2D materials, and the instrument we constructed allows the study of the weak interaction with 2D materials.

State-of-the-art study of resource characterization and planning for underground coal mining. Final technical report as of June 30, 1980

DOE Office of Scientific and Technical Information (OSTI.GOV)

Walton, D.; Ingham, W.; Kauffman, P.

With the rapid developments taking place in coal mining technology and due to high investment costs, optimization of the structure of underground coal mines is crucial to the success of the mining project. The structure of a mine, once it is developed, cannot be readily changed and has a decisive influence on the productivity, safety, economics, and production capacity of the mine. The Department of Energy desires to ensure that the resource characterization and planning activity for underground coal mining will focus on those areas that offer the most promise of being advanced. Thus, this project was undertaken by Managementmore » Engineers Incorporated to determine the status in all aspects of the resource characterization and planning activities for underground coal mining as presently performed in the industry. The study team conducted a comprehensive computerized literature search and reviewed the results. From this a selection of the particularly relevant sources were annotated and a reference list was prepared, catalogued by resource characterization and mine planning activity. From this data, and discussions with industry representatives, academia, and research groups, private and federal, an assessment and evaluation was made of the state-of-the-art of each element in the resource characterization and mine planning process. The results of this analysis lead to the identifcation of areas requiring research and, specifically, those areas where DOE research efforts may be focused.« less

Automated tandem mass spectrometry by orthogonal acceleration TOF data acquisition and simultaneous magnet scanning for the characterization of petroleum mixtures.

PubMed

Roussis, S G

2001-08-01

The automated acquisition of the product ion spectra of all precursor ions in a selected mass range by using a magnetic sector/orthogonal acceleration time-of-flight (oa-TOF) tandem mass spectrometer for the characterization of complex petroleum mixtures is reported. Product ion spectra are obtained by rapid oa-TOF data acquisition and simultaneous scanning of the magnet. An analog signal generator is used for the scanning of the magnet. Slow magnet scanning rates permit the accurate profiling of precursor ion peaks and the acquisition of product ion spectra for all isobaric ion species. The ability of the instrument to perform both high- and low-energy collisional activation experiments provides access to a large number of dissociation pathways useful for the characterization of precursor ions. Examples are given that illustrate the capability of the method for the characterization of representative petroleum mixtures. The structural information obtained by the automated MS/MS experiment is used in combination with high-resolution accurate mass measurement results to characterize unknown components in a polar extract of a refinery product. The exhaustive mapping of all precursor ions in representative naphtha and middle-distillate fractions is presented. Sets of isobaric ion species are separated and their structures are identified by interpretation from first principles or by comparison with standard 70-eV EI libraries of spectra. The utility of the method increases with the complexity of the samples.

Rapid prototyping of flexible intrafascicular electrode arrays by picosecond laser structuring

NASA Astrophysics Data System (ADS)

Mueller, Matthias; de la Oliva, Natalia; del Valle, Jaume; Delgado-Martínez, Ignacio; Navarro, Xavier; Stieglitz, Thomas

2017-12-01

Objective. Interfacing the peripheral nervous system can be performed with a large variety of electrode arrays. However, stimulating and recording a nerve while having a reasonable amount of channels limits the number of available systems. Translational research towards human clinical trial requires device safety and biocompatibility but would benefit from design flexibility in the development process to individualize probes. Approach. We selected established medical grade implant materials like precious metals and Parylene C to develop a rapid prototyping process for novel intrafascicular electrode arrays using a picosecond laser structuring. A design for a rodent animal model was developed in conjunction with an intrafascicular implantation strategy. Electrode characterization and optimization was performed first in saline solution in vitro before performance and biocompatibility were validated in sciatic nerves of rats in chronic implantation. Main results. The novel fabrication process proved to be suitable for prototyping and building intrafascicular electrode arrays. Electrochemical properties of the electrode sites were enhanced and tested for long-term stability. Chronic implantation in the sciatic nerve of rats showed good biocompatibility, selectivity and stable stimulation thresholds. Significance. Established medical grade materials can be used for intrafascicular nerve electrode arrays when laser structuring defines structure size in the micro-scale. Design flexibility reduces re-design cycle time and material certificates are beneficial support for safety studies on the way to clinical trials.

Characterizing polymorphic inversions in human genomes by single-cell sequencing

PubMed Central

Sanders, Ashley D.; Hills, Mark; Porubský, David; Guryev, Victor; Falconer, Ester; Lansdorp, Peter M.

2016-01-01

Identifying genomic features that differ between individuals and cells can help uncover the functional variants that drive phenotypes and disease susceptibilities. For this, single-cell studies are paramount, as it becomes increasingly clear that the contribution of rare but functional cellular subpopulations is important for disease prognosis, management, and progression. Until now, studying these associations has been challenged by our inability to map structural rearrangements accurately and comprehensively. To overcome this, we coupled single-cell sequencing of DNA template strands (Strand-seq) with custom analysis software to rapidly discover, map, and genotype genomic rearrangements at high resolution. This allowed us to explore the distribution and frequency of inversions in a heterogeneous cell population, identify several polymorphic domains in complex regions of the genome, and locate rare alleles in the reference assembly. We then mapped the entire genomic complement of inversions within two unrelated individuals to characterize their distinct inversion profiles and built a nonredundant global reference of structural rearrangements in the human genome. The work described here provides a powerful new framework to study structural variation and genomic heterogeneity in single-cell samples, whether from individuals for population studies or tissue types for biomarker discovery. PMID:27472961

Characterization of the macrocyclase involved in the biosynthesis of RiPP cyclic peptides in plants.

PubMed

Chekan, Jonathan R; Estrada, Paola; Covello, Patrick S; Nair, Satish K

2017-06-20

Enzymes that can catalyze the macrocyclization of linear peptide substrates have long been sought for the production of libraries of structurally diverse scaffolds via combinatorial gene assembly as well as to afford rapid in vivo screening methods. Orbitides are plant ribosomally synthesized and posttranslationally modified peptides (RiPPs) of various sizes and topologies, several of which are shown to be biologically active. The diversity in size and sequence of orbitides suggests that the corresponding macrocyclases may be ideal catalysts for production of cyclic peptides. Here we present the biochemical characterization and crystal structures of the plant enzyme PCY1 involved in orbitide macrocyclization. These studies demonstrate how the PCY1 S9A protease fold has been adapted for transamidation, rather than hydrolysis, of acyl-enzyme intermediates to yield cyclic products. Notably, PCY1 uses an unusual strategy in which the cleaved C-terminal follower peptide from the substrate stabilizes the enzyme in a productive conformation to facilitate macrocyclization of the N-terminal fragment. The broad substrate tolerance of PCY1 can be exploited as a biotechnological tool to generate structurally diverse arrays of macrocycles, including those with nonproteinogenic elements.

Rapid Characterization of Molecular Chemistry, Nutrient Make-Up and Microlocation of Internal Seed Tissue

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu,P.; Block, H.; Niu, Z.

2007-01-01

Wheat differs from corn in biodegradation kinetics and fermentation characteristics. Wheat exhibits a relatively high rate (23% h{sup 01}) and extent (78% DM) of biodegradation, which can lead to metabolic problems such as acidosis and bloat in ruminants. The objective of this study was to rapidly characterize the molecular chemistry of the internal structure of wheat (cv. AC Barrie) and reveal both its structural chemical make-up and nutrient component matrix by analyzing the intensity and spatial distribution of molecular functional groups within the intact seed using advanced synchrotron-powered Fourier transform infrared (FTIR) microspectroscopy. The experiment was performed at the U2Bmore » station of the National Synchrotron Light Source at Brookhaven National Laboratory, New York, USA. The wheat tissue was imaged systematically from the pericarp, seed coat, aleurone layer and endosperm under the peaks at {approx}1732 (carbonyl C{double_bond}O ester), 1515 (aromatic compound of lignin), 1650 (amide I), 1025 (non-structural CHO), 1550 (amide II), 1246 (cellulosic material), 1160, 1150, 1080, 930, 860 (all CHO), 3350 (OH and NH stretching), 2928 (CH{sub 2} stretching band) and 2885 cm{sup -1} (CH{sub 3} stretching band). Hierarchical cluster analysis and principal component analysis were applied to analyze the molecular FTIR spectra obtained from the different inherent structures within the intact wheat tissues. The results showed that, with synchrotron-powered FTIR microspectroscopy, images of the molecular chemistry of wheat could be generated at an ultra-spatial resolution. The features of aromatic lignin, structural and non-structural carbohydrates, as well as nutrient make-up and interactions in the seeds, could be revealed. Both principal component analysis and hierarchical cluster analysis methods are conclusive in showing that they can discriminate and classify the different inherent structures within the seed tissue. The wheat exhibited distinguishable differences in the structural and nutrient make-up among the pericarp, seed coat, aleurone layer and endosperm. Such information on the molecular chemistry can be used for grain-breeding programs for selecting a superior variety of wheat targeted for food and feed purposes and for predicting wheat quality and nutritive value in humans and animals. Thus advanced synchrotron-powered FTIR technology can provide a greater understanding of the plant-animal interface.« less

Spectroscopic and Kinetic Properties of the Molybdenum-containing, NAD+-dependent Formate Dehydrogenase from Ralstonia eutropha*

PubMed Central

Niks, Dimitri; Duvvuru, Jayant; Escalona, Miguel; Hille, Russ

2016-01-01

We have examined the rapid reaction kinetics and spectroscopic properties of the molybdenum-containing, NAD+-dependent FdsABG formate dehydrogenase from Ralstonia eutropha. We confirm previous steady-state studies of the enzyme and extend its characterization to a rapid kinetic study of the reductive half-reaction (the reaction of formate with oxidized enzyme). We have also characterized the electron paramagnetic resonance signal of the molybdenum center in its MoV state and demonstrated the direct transfer of the substrate Cα hydrogen to the molybdenum center in the course of the reaction. Varying temperature, microwave power, and level of enzyme reduction, we are able to clearly identify the electron paramagnetic resonance signals for four of the iron/sulfur clusters of the enzyme and find suggestive evidence for two others; we observe a magnetic interaction between the molybdenum center and one of the iron/sulfur centers, permitting assignment of this signal to a specific iron/sulfur cluster in the enzyme. In light of recent advances in our understanding of the structure of the molybdenum center, we propose a reaction mechanism involving direct hydride transfer from formate to a molybdenum-sulfur group of the molybdenum center. PMID:26553877

Research progress of Ge on insulator grown by rapid melting growth

NASA Astrophysics Data System (ADS)

Liu, Zhi; Wen, Juanjuan; Li, Chuanbo; Xue, Chunlai; Cheng, Buwen

2018-06-01

Ge is an attractive material for Si-based microelectronics and photonics due to its high carries mobility, pseudo direct bandgap structure, and the compatibility with complementary metal oxide semiconductor (CMOS) processes. Based on Ge, Ge on insulator (GOI) not only has these advantages, but also provides strong electronic and optical confinement. Recently, a novel technique to fabricate GOI by rapid melting growth (RMG) has been described. Here, we introduce the RMG technique and review recent efforts and progress in RMG. Firstly, we will introduce process steps of RMG. We will then review the researches which focus on characterizations of the GOI including growth dimension, growth mechanism, growth orientation, concentration distribution, and strain status. Finally, GOI based applications including high performance metal–oxide–semiconductor field effect transistors (MOSFETs) and photodetectors will be discussed. These results show that RMG is a promising technique for growth of high quality GOIs with different characterizations. The GOI grown by RMG is a potential material for the next-generation of integrated circuits and optoelectronic circuits. Project supported in part by the National Key Research and Development Program of China (No. 2017YFA0206404) and the National Natural Science Foundation of China (Nos. 61435013, 61534005, 61534004, 61604146).

Analysis of fluorescently labeled glycosphingolipid-derived oligosaccharides following ceramide glycanase digestion and anthranilic acid labeling.

PubMed

Neville, David C A; Coquard, Virginie; Priestman, David A; te Vruchte, Danielle J M; Sillence, Daniel J; Dwek, Raymond A; Platt, Frances M; Butters, Terry D

2004-08-15

Interest in cellular glycosphingolipid (GSL) function has necessitated the development of a rapid and sensitive method to both analyze and characterize the full complement of structures present in various cells and tissues. An optimized method to characterize oligosaccharides released from glycosphingolipids following ceramide glycanase digestion has been developed. The procedure uses the fluorescent compound anthranilic acid (2-aminobenzoic acid; 2-AA) to label oligosaccharides prior to analysis using normal-phase high-performance liquid chromatography. The labeling procedure is rapid, selective, and easy to perform and is based on the published method of Anumula and Dhume [Glycobiology 8 (1998) 685], originally used to analyze N-linked oligosaccharides. It is less time consuming than a previously published 2-aminobenzamide labeling method [Anal. Biochem. 298 (2001) 207] for analyzing GSL-derived oligosaccharides, as the fluorescent labeling is performed on the enzyme reaction mixture. The purification of 2-AA-labeled products has been improved to ensure recovery of oligosaccharides containing one to four monosaccharide units, which was not previously possible using the Anumula and Dhume post-derivatization purification procedure. This new approach may also be used to analyze both N- and O-linked oligosaccharides.

Pseudogap and electronic structure of electron-doped Sr2IrO4

NASA Astrophysics Data System (ADS)

Moutenet, Alice; Georges, Antoine; Ferrero, Michel

2018-04-01

We present a theoretical investigation of the effects of correlations on the electronic structure of the Mott insulator Sr2IrO4 upon electron doping. A rapid collapse of the Mott gap upon doping is found, and the electronic structure displays a strong momentum-space differentiation at low doping level: The Fermi surface consists of pockets centered around (π /2 ,π /2 ) , while a pseudogap opens near (π ,0 ) . Its physical origin is shown to be related to short-range spin correlations. The pseudogap closes upon increasing doping, but a differentiated regime characterized by a modulation of the spectral intensity along the Fermi surface persists to higher doping levels. These results, obtained within the cellular dynamical mean-field-theory framework, are discussed in comparison to recent photoemission experiments and an overall good agreement is found.

Modification of Silk Fibroin Using Diazonium Coupling Chemistry and the Effects on hMSC Proliferation and Differentiation

PubMed Central

Murphy, Amanda R.; John, Peter St.; Kaplan, David L.

2009-01-01

A simple chemical modification method using diazonium coupling chemistry was developed to tailor the structure and hydrophilicity of silk fibroin protein. The extent of modification using several aniline derivatives was characterized using UV/vis and 1H NMR spectroscopy, and the resulting protein structure was analyzed with ATR-FTIR spectroscopy. Introduction of hydrophobic functional groups facilitated rapid conversion of the protein from a random coil to a β-sheet structure, while addition of hydrophilic groups inhibited this process. hMSCs were grown on these modified silks to assess the biocompatibility of these materials. The hydrophilicity of the silk derivatives was found to affect the growth rate and morphology, but hMSCs were able to attach, proliferate and differentiate into an osteogenic lineage on all of the silk derivatives. PMID:18417206

3D metal-organic framework as highly efficient biosensing platform for ultrasensitive and rapid detection of bisphenol A.

PubMed

Wang, Xue; Lu, Xianbo; Wu, Lidong; Chen, Jiping

2015-03-15

As is well known, bisphenol A (BPA), usually exists in daily plastic products, is one of the most important endocrine disrupting chemicals. In this work, copper-centered metal-organic framework (Cu-MOF) was synthesized, which was characterized by SEM, TEM, XRD, FTIR and electrochemical method. The resultant Cu-MOF was explored as a robust electrochemical biosensing platform by choosing tyrosinase (Tyr) as a model enzyme for ultrasensitive and rapid detection of BPA. The Cu-MOF provided a 3D structure with a large specific surface area, which was beneficial for enzyme and BPA absorption, and thus improved the sensitivity of the biosensor. Furthermore, Cu-MOF as a novel sorbent could increase the available BPA concentration to react with tyrosinase through π-π stacking interactions between BPA and Cu-MOF. The Tyr biosensor exhibited a high sensitivity of 0.2242A M(-1) for BPA, a wide linear range from 5.0×10(-8) to 3.0×10-6moll(-1), and a low detection limit of 13nmoll(-1). The response time for detection of BPA is less than 11s. The proposed method was successfully applied to rapid and selective detection of BPA in plastic products with satisfactory results. The recoveries are in the range of 94.0-101.6% for practical applications. With those remarkable advantages, MOFs-based 3D structures show great prospect as robust biosensing platform for ultrasensitive and rapid detection of BPA. Crown Copyright © 2014. Published by Elsevier B.V. All rights reserved.

Fabrication and characterization of dichroic fine crystals by the reprecipitation method

NASA Astrophysics Data System (ADS)

Iino, Tatsuya; Mori, Shunsuke; Shito, Keiji; Kimura, Ayaka; Morishita, Yoshii; Chiba, Takayuki; Katagiri, Hiroshi; Okada, Shuji; Masuhara, Akito

2018-06-01

Suspended particle devices can rapidly switch from a dark blue state to a clear state by applying AC voltage, but their maximum transmittance has to be improved. In this work, we have targeted dichroic dyes and applied the reprecipitation method to KPD-503, a trisazo dye showing little dichroism in bulk crystals despite the dye molecules having large dichroism. As a result, microcrystals showing large dichroism were obtained. These microcrystals were considered to have a kinetically stable structure and oriented by voltage in a dispersing medium.

In Situ Investigation of a Self-Accelerated Cocrystal Formation by Grinding Pyrazinamide with Oxalic Acid.

PubMed

Kulla, Hannes; Greiser, Sebastian; Benemann, Sigrid; Rademann, Klaus; Emmerling, Franziska

2016-07-14

A new cocrystal of pyrazinamide with oxalic acid was prepared mechanochemically and characterized by PXRD, Raman spectroscopy, solid-state NMR spectroscopy, DTA-TG, and SEM. Based on powder X-ray diffraction data the structure was solved. The formation pathway of the reaction was studied in situ using combined synchrotron PXRD and Raman spectroscopy. Using oxalic acid dihydrate the initially neat grinding turned into a rapid self-accelerated liquid-assisted grinding process by the release of crystallization water. Under these conditions, the cocrystal was formed directly within two minutes.

Novel Ballistic Processing of Sn-0.7Cu Thick Films

NASA Astrophysics Data System (ADS)

Cavero, D.; Stewart, K.; Morsi, K.

2017-01-01

The present paper discusses a novel process (Ballistic Processing) for the ultra-rapid processing of textured and un-textured thick and potentially thin films. The effect of processing velocity (14.6 to 36.1 m/s) on the developed external structure and internal microstructure of Sn-0.7Cu thick film is discussed. Film thicknesses ranging from 6.08 to 12.79 μm were produced and characterized by two-dimensional hypoeutectic microstructures. Both film thickness and dendrite arm spacing decreased with an increase in processing velocity.

Surveillance theory applied to virus detection: a case for targeted discovery

USGS Publications Warehouse

Bogich, Tiffany L.; Anthony, Simon J.; Nichols, James D.

2013-01-01

Virus detection and mathematical modeling have gone through rapid developments in the past decade. Both offer new insights into the epidemiology of infectious disease and characterization of future risk; however, modeling has not yet been applied to designing the best surveillance strategies for viral and pathogen discovery. We review recent developments and propose methods to integrate viral and pathogen discovery and mathematical modeling through optimal surveillance theory, arguing for a more targeted approach to novel virus detection guided by the principles of adaptive management and structured decision-making.

Smooth and rapid microwave synthesis of MIL-53(Fe) including superparamagnetic γ-Fe2O3 nanoparticles

NASA Astrophysics Data System (ADS)

Wengert, Simon; Albrecht, Joachim; Ruoss, Stephen; Stahl, Claudia; Schütz, Gisela; Schäfer, Ronald

2017-12-01

MIL-53(Fe) linked to superparamagnetic γ-Fe2O3 nanoparticles was created using time-efficient microwave synthesis. Intermediates as well as the final product have been characterized by Dynamic Light Scattering (DLS), Infrared Spectroscopy (FTIR) and Thermal Gravimetric Analysis (TGA). It is found that this route allows the production of Fe nanoparticles with typical sizes of about 80 nm that are embedded inside the metal-organic structures. Detailed magnetization measurements using SQUID magnetometry revealed a nearly reversible magnetization loop indicating essentially superparamagnetic behavior.

Effect of rapid thermal annealing on nanocrystalline TiO2 thin films synthesized by swift heavy ion irradiation

NASA Astrophysics Data System (ADS)

Thakurdesai, Madhavi; Kanjilal, D.; Bhattacharyya, Varsha

2012-08-01

Irradiation by swift heavy ions (SHI) is unique tool to synthesize nanocrystalline thin films. We have reported transformation of 100 nm thick amorphous films into nanocrystalline film due to irradiation by 100 MeV Ag ion beam. Oblate shaped nanoparticles having anatase phase of TiO2 were formed on the surface of the irradiated films. In the present investigation, these films are annealed at 350 °C for 2 min in oxygen atmosphere by Rapid Thermal Annealing (RTA) method. During RTA processing, the temperature rises abruptly and this thermal instability is expected to alter surface morphology, structural and optical properties of nanocrystalline TiO2 thin films. Thus in the present work, effect of RTA on SHI induced nanocrystalline thin films of TiO2 is studied. The effect of RTA processing on the shape and size of TiO2 nanoparticles is studied by Atomic Force Microscopy (AFM) and Scanning Electron Microscopy (SEM). Glancing Angle X-ray Diffraction (GAXRD) studies are carried to investigate structural changes induced by RTA processing. Optical characterization is carried out by UV-vis spectroscopy and photoluminescence (PL) spectroscopy. The changes observed in structural and optical properties of nanocrystalline TiO2 thin films after RTA processing are attributed to the annihilation of SHI induced defects.

The Developmental Toxicity of Complex Silica-Embedded Nickel Nanoparticles Is Determined by Their Physicochemical Properties

PubMed Central

Mahoney, Sharlee; Najera, Michelle; Bai, Qing; Burton, Edward A.; Veser, Götz

2016-01-01

Complex engineered nanomaterials (CENs) are a rapidly developing class of structurally and compositionally complex materials that are expected to dominate the next generation of functional nanomaterials. The development of methods enabling rapid assessment of the toxicity risk associated with this type of nanomaterial is therefore critically important. We evaluated the toxicity of three differently structured nickel-silica nanomaterials as prototypical CENs: simple, surface-deposited Ni-SiO2 and hollow and non-hollow core-shell Ni@SiO2 materials (i.e., ~1–2 nm Ni nanoparticles embedded into porous silica shells with and without a central cavity, respectively). Zebrafish embryos were exposed to these CENs, and morphological (survival and malformations) and physiological (larval motility) endpoints were coupled with thorough characterization of physiochemical characteristics (including agglomeration, settling and nickel ion dissolution) to determine how toxicity differed between these CENs and equivalent quantities of Ni2+ salt (based on total Ni). Exposure to Ni2+ ions strongly compromised zebrafish larva viability, and surviving larvae showed severe malformations. In contrast, exposure to the equivalent amount of Ni CEN did not result in these abnormalities. Interestingly, exposure to Ni-SiO2 and hollow Ni@SiO2 provoked abnormalities of zebrafish larval motor function, indicating developmental toxicity, while non-hollow Ni@SiO2 showed no toxicity. Correlating these observations with physicochemical characterization of the CENs suggests that the toxicity of the Ni-SiO2 and hollow Ni@SiO2 material may result partly from an increased effective exposure at the bottom of the well due to rapid settling. Overall, our data suggest that embedding nickel NPs in a porous silica matrix may be a straightforward way to mitigate their toxicity without compromising their functional properties. At the same time, our results also indicate that it is critical to consider modification of the effective exposure when comparing different nanomaterial configurations, because effective exposure might influence NP toxicity more than specific “nano-chemistry” effects. PMID:27031643

A multi-method approach toward de novo glycan characterization: a Man-5 case study.

PubMed

Prien, Justin M; Prater, Bradley D; Cockrill, Steven L

2010-05-01

Regulatory agencies' expectations for biotherapeutic approval are becoming more stringent with regard to product characterization, where minor species as low as 0.1% of a given profile are typically identified. The mission of this manuscript is to demonstrate a multi-method approach toward de novo glycan characterization and quantitation, including minor species at or approaching the 0.1% benchmark. Recently, unexpected isomers of the Man(5)GlcNAc(2) (M(5)) were reported (Prien JM, Ashline DJ, Lapadula AJ, Zhang H, Reinhold VN. 2009. The high mannose glycans from bovine ribonuclease B isomer characterization by ion trap mass spectrometry (MS). J Am Soc Mass Spectrom. 20:539-556). In the current study, quantitative analysis of these isomers found in commercial M(5) standard demonstrated that they are in low abundance (<1% of the total) and therefore an exemplary "litmus test" for minor species characterization. A simple workflow devised around three core well-established analytical procedures: (1) fluorescence derivatization; (2) online rapid resolution reversed-phase separation coupled with negative-mode sequential mass spectrometry (RRRP-(-)-MS(n)); and (3) permethylation derivatization with nanospray sequential mass spectrometry (NSI-MS(n)) provides comprehensive glycan structural determination. All methods have limitations; however, a multi-method workflow is an at-line stopgap/solution which mitigates each method's individual shortcoming(s) providing greater opportunity for more comprehensive characterization. This manuscript is the first to demonstrate quantitative chromatographic separation of the M(5) isomers and the use of a commercially available stable isotope variant of 2-aminobenzoic acid to detect and chromatographically resolve multiple M(5) isomers in bovine ribonuclease B. With this multi-method approach, we have the capabilities to comprehensively characterize a biotherapeutic's glycan array in a de novo manner, including structural isomers at >/=0.1% of the total chromatographic peak area.

Covalent Organic Frameworks as a Platform for Multidimensional Polymerization.

PubMed

Bisbey, Ryan P; Dichtel, William R

2017-06-28

The simultaneous polymerization and crystallization of monomers featuring directional bonding designs provides covalent organic frameworks (COFs), which are periodic polymer networks with robust covalent bonds arranged in two- or three-dimensional topologies. The range of properties characterized in COFs has rapidly expanded to include those of interest for heterogeneous catalysis, energy storage and photovoltaic devices, and proton-conducting membranes. Yet many of these applications will require materials quality, morphological control, and synthetic efficiency exceeding the capabilities of contemporary synthetic methods. This level of control will emerge from an improved fundamental understanding of COF nucleation and growth processes. More powerful characterization of structure and defects, improved syntheses guided by mechanistic understanding, and accessing diverse isolated forms, ranging from single crystals to thin films to colloidal suspensions, remain important frontier problems.

Covalent Organic Frameworks as a Platform for Multidimensional Polymerization

PubMed Central

2017-01-01

The simultaneous polymerization and crystallization of monomers featuring directional bonding designs provides covalent organic frameworks (COFs), which are periodic polymer networks with robust covalent bonds arranged in two- or three-dimensional topologies. The range of properties characterized in COFs has rapidly expanded to include those of interest for heterogeneous catalysis, energy storage and photovoltaic devices, and proton-conducting membranes. Yet many of these applications will require materials quality, morphological control, and synthetic efficiency exceeding the capabilities of contemporary synthetic methods. This level of control will emerge from an improved fundamental understanding of COF nucleation and growth processes. More powerful characterization of structure and defects, improved syntheses guided by mechanistic understanding, and accessing diverse isolated forms, ranging from single crystals to thin films to colloidal suspensions, remain important frontier problems. PMID:28691064

Characterization of the conformational equilibrium between the two major substates of RNase A using NMR chemical shifts.

PubMed

Camilloni, Carlo; Robustelli, Paul; De Simone, Alfonso; Cavalli, Andrea; Vendruscolo, Michele

2012-03-07

Following the recognition that NMR chemical shifts can be used for protein structure determination, rapid advances have recently been made in methods for extending this strategy for proteins and protein complexes of increasing size and complexity. A remaining major challenge is to develop approaches to exploit the information contained in the chemical shifts about conformational fluctuations in native states of proteins. In this work we show that it is possible to determine an ensemble of conformations representing the free energy surface of RNase A using chemical shifts as replica-averaged restraints in molecular dynamics simulations. Analysis of this surface indicates that chemical shifts can be used to characterize the conformational equilibrium between the two major substates of this protein. © 2012 American Chemical Society

Rapid and sensitive detection of foodborne pathogenic bacteria (Staphylococcus aureus) using an electrochemical DNA genomic biosensor and its application in fresh beef.

PubMed

Abdalhai, Mandour H; Fernandes, António Maximiano; Bashari, Mohand; Ji, Jian; He, Qian; Sun, Xiulan

2014-12-31

Rapid early detection of food contamination is the main key in food safety and quality control. Biosensors are emerging as a vibrant area of research, and the use of DNA biosensor recognition detectors is relatively new. In this study a genomic DNA biosensor system with a fixing and capture probe was modified by a sulfhydryl and amino group, respectively, as complementary with target DNA. After immobilization and hybridization, the following sandwich structure fixing DNA-target DNA-capture DNA-PbS NPs was formed to detect pathogenic bacteria (Staphylococuus aureus EF529607.1) by using GCE modified with (multiwalled carbon nanotubes-chitosan-bismuth) to increase the sensitivity of the electrode. The modification procedure was characterized by cyclic voltammetry and electrochemical impedance spectroscopy. The sandwich structure was dissolved in 1 M nitric acid to become accessible to the electrode, and the PbS NPs was measured in solution by differential pulse voltammetry (DPV). The results showed that the detection limit of the DNA sensor was 3.17 × 10(-14) M S. aureus using PbS NPs, whereas the result for beef samples was 1.23 ng/mL. Thus, according to the experimental results presented, the DNA biosensor exhibited high sensitivity and rapid response, and it will be useful for the food matrix.

A new UV-curing elastomeric substrate for rapid prototyping of microfluidic devices

NASA Astrophysics Data System (ADS)

Alvankarian, Jafar; Yeop Majlis, Burhanuddin

2012-03-01

Rapid prototyping in the design cycle of new microfluidic devices is very important for shortening time-to-market. Researchers are facing the challenge to explore new and suitable substrates with simple and efficient microfabrication techniques. In this paper, we introduce and characterize a UV-curing elastomeric polyurethane methacrylate (PUMA) for rapid prototyping of microfluidic devices. The swelling and solubility of PUMA in different chemicals is determined. Time-dependent measurements of water contact angle show that the native PUMA is hydrophilic without surface treatment. The current monitoring method is used for measurement of the electroosmotic flow mobility in the microchannels made from PUMA. The optical, physical, thermal and mechanical properties of PUMA are evaluated. The UV-lithography and molding process is used for making micropillars and deep channel microfluidic structures integrated to the supporting base layer. Spin coating is characterized for producing different layer thicknesses of PUMA resin. A device is fabricated and tested for examining the strength of different bonding techniques such as conformal, corona treating and semi-curing of two PUMA layers in microfluidic application and the results show that the bonding strengths are comparable to that of PDMS. We also report fabrication and testing of a three-layer multi inlet/outlet microfluidic device including a very effective fluidic interconnect for application demonstration of PUMA as a promising new substrate. A simple micro-device is developed and employed for observing the pressure deflection of membrane made from PUMA as a very effective elastomeric valve in microfluidic devices.

Improved ultra-performance liquid chromatography with electrospray ionization quadrupole-time-of-flight high-definition mass spectrometry method for the rapid analysis of the chemical constituents of a typical medical formula: Liuwei Dihuang Wan.

PubMed

Wang, Ping; Lv, Hai tao; Zhang, Ai hua; Sun, Hui; Yan, Guang li; Han, Ying; Wu, Xiu hong; Wang, Xi jun

2013-11-01

Liuwei Dihuang Wan (LDW), a classic Chinese medicinal formula, has been used to improve or restore declined functions related to aging and geriatric diseases, such as impaired mobility, vision, hearing, cognition, and memory. It has attracted increasing attention as one of the most popular and valuable herbal medicines. However, the systematic analysis of the chemical constituents of LDW is difficult and thus has not been well established. In this paper, a rapid, sensitive, and reliable ultra-performance LC with ESI quadrupole TOF high-definition MS method with automated MetaboLynx analysis in positive and negative ion mode was established to characterize the chemical constituents of LDW. The analysis was performed on a Waters UPLC™ HSS T3 using a gradient elution system. MS/MS fragmentation behavior was proposed for aiding the structural identification of the components. Under the optimized conditions, a total of 50 peaks were tentatively characterized by comparing the retention time and MS data. It is concluded that a rapid and robust platform based on ultra-performance LC with ESI quadrupole TOF high-definition MS has been successfully developed for globally identifying multiple constituents of traditional Chinese medicine prescriptions. This is the first report on the systematic analysis of the chemical constituents of LDW. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Kinetic, Thermodynamic, and Structural Characterizations of the Association between Nrf2-DLGex Degron and Keap1

PubMed Central

Fukutomi, Toshiaki; Takagi, Kenji; Mizushima, Tsunehiro; Ohuchi, Noriaki

2014-01-01

Transcription factor Nrf2 (NF-E2-related factor 2) coordinately regulates cytoprotective gene expression, but under unstressed conditions, Nrf2 is degraded rapidly through Keap1 (Kelch-like ECH-associated protein 1)-mediated ubiquitination. Nrf2 harbors two Keap1-binding motifs, DLG and ETGE. Interactions between these two motifs and Keap1 constitute a key regulatory nexus for cellular Nrf2 activity through the formation of a two-site binding hinge-and-latch mechanism. In this study, we determined the minimum Keap1-binding sequence of the DLG motif, the low-affinity latch site, and defined a new DLGex motif that covers a sequence much longer than that previously defined. We have successfully clarified the crystal structure of the Keap1-DC-DLGex complex at 1.6 Å. DLGex possesses a complicated helix structure, which interprets well the human-cancer-derived loss-of-function mutations in DLGex. In thermodynamic analyses, Keap1-DLGex binding is characterized as enthalpy and entropy driven, while Keap1-ETGE binding is characterized as purely enthalpy driven. In kinetic analyses, Keap1-DLGex binding follows a fast-association and fast-dissociation model, while Keap1-ETGE binding contains a slow-reaction step that leads to a stable conformation. These results demonstrate that the mode of DLGex binding to Keap1 is distinct from that of ETGE structurally, thermodynamically, and kinetically and support our contention that the DLGex motif serves as a converter transmitting environmental stress to Nrf2 induction as the latch site. PMID:24366543

Nonmonotonic spatial structure of interneuronal correlations in prefrontal microcircuits

PubMed Central

Safavi, Shervin; Dwarakanath, Abhilash; Kapoor, Vishal; Werner, Joachim; Hatsopoulos, Nicholas G.; Logothetis, Nikos K.; Panagiotaropoulos, Theofanis I.

2018-01-01

Correlated fluctuations of single neuron discharges, on a mesoscopic scale, decrease as a function of lateral distance in early sensory cortices, reflecting a rapid spatial decay of lateral connection probability and excitation. However, spatial periodicities in horizontal connectivity and associational input as well as an enhanced probability of lateral excitatory connections in the association cortex could theoretically result in nonmonotonic correlation structures. Here, we show such a spatially nonmonotonic correlation structure, characterized by significantly positive long-range correlations, in the inferior convexity of the macaque prefrontal cortex. This functional connectivity kernel was more pronounced during wakefulness than anesthesia and could be largely attributed to the spatial pattern of correlated variability between functionally similar neurons during structured visual stimulation. These results suggest that the spatial decay of lateral functional connectivity is not a common organizational principle of neocortical microcircuits. A nonmonotonic correlation structure could reflect a critical topological feature of prefrontal microcircuits, facilitating their role in integrative processes. PMID:29588415

High-throughput determination of structural phase diagram and constituent phases using GRENDEL

NASA Astrophysics Data System (ADS)

Kusne, A. G.; Keller, D.; Anderson, A.; Zaban, A.; Takeuchi, I.

2015-11-01

Advances in high-throughput materials fabrication and characterization techniques have resulted in faster rates of data collection and rapidly growing volumes of experimental data. To convert this mass of information into actionable knowledge of material process-structure-property relationships requires high-throughput data analysis techniques. This work explores the use of the Graph-based endmember extraction and labeling (GRENDEL) algorithm as a high-throughput method for analyzing structural data from combinatorial libraries, specifically, to determine phase diagrams and constituent phases from both x-ray diffraction and Raman spectral data. The GRENDEL algorithm utilizes a set of physical constraints to optimize results and provides a framework by which additional physics-based constraints can be easily incorporated. GRENDEL also permits the integration of database data as shown by the use of critically evaluated data from the Inorganic Crystal Structure Database in the x-ray diffraction data analysis. Also the Sunburst radial tree map is demonstrated as a tool to visualize material structure-property relationships found through graph based analysis.

Magnetic fields and flows between 1 AU and 0.3 AU during the primary mission of HELIOS 1

NASA Technical Reports Server (NTRS)

Burlaga, L. F.; Ness, N. F.; Mariani, F.; Bavassano, B.; Villante, U.; Rosenbauer, H.; Schwenn, R.; Harvey, J.

1978-01-01

The recurrent flow and field patterns observed by HELIOS 1, and the relation between these patterns and coronal holes are discussed. Four types of recurrent patterns were observed: a large recurrent stream, a recurrent slow (quiet) flow, a rapidly evolving flow, and a recurrent compound stream. There recurrent streams were not stationary, for although the sources recurred at approximately the same longitudes on successive rotations, the shapes and latitudinal patterns changed from one rotation to the next. A type of magnetic field and plasma structure characterized by a low ion temperature and a high magnetic field intensity is described as well as the structures of stream boundaries between the sun at approximately 0.3 AU.

Rapid synthesis of flower shaped Cu{sub 2}ZnSnS{sub 4} nanoparticles by microwave irradiation for solar cell application

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ansari, Mohd Zubair, E-mail: mhd.zubair1@gmail.com; Khare, Neeraj

Single phase Cu{sub 2}ZnSnS{sub 4} (CZTS) nanoparticles have been synthesized by the microwave-assisted solution method in a one step process. Structural, morphological and optical characterizations of the CZTS nanoparticles have been carried out. X-ray diffraction confirms the single phase formation of CZTS nanoparticles with kesterite structure. SEM confirms the homogenous distribution of CZTS nanoparticles flower like assemblies. High resolution TEM image confirms the good crystallinity of the CZTS nanoparticles with the average grain size ~20 nm. The CZTS nanoparticles have strong optical absorption in the visible region with direct band gap as ~1.6 eV which is optimal for photovoltaic application.

Fast-scan Cyclic Voltammetry for the Characterization of Rapid Adenosine Release

PubMed Central

Nguyen, Michael D.; Venton, B. Jill

2014-01-01

Adenosine is a signaling molecule and downstream product of ATP that acts as a neuromodulator. Adenosine regulates physiological processes, such as neurotransmission and blood flow, on a time scale of minutes to hours. Recent developments in electrochemical techniques, including fast-scan cyclic voltammetry (FSCV), have allowed direct detection of adenosine with sub-second temporal resolution. FSCV studies have revealed a novel mode of rapid signaling that lasts only a few seconds. This rapid release of adenosine can be evoked by electrical or mechanical stimulations or it can be observed spontaneously without stimulation. Adenosine signaling on this time scale is activity dependent; however, the mode of release is not fully understood. Rapid adenosine release modulates oxygen levels and evoked dopamine release, indicating that adenosine may have a rapid modulatory role. In this review, we outline how FSCV can be used to detect adenosine release, compare FSCV with other techniques used to measure adenosine, and present an overview of adenosine signaling that has been characterized using FSCV. These studies point to a rapid mode of adenosine modulation, whose mechanism and function will continue to be characterized in the future. PMID:26900429

Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology

PubMed Central

Chappell, James; Jensen, Kirsten; Freemont, Paul S.

2013-01-01

A bottleneck in our capacity to rationally and predictably engineer biological systems is the limited number of well-characterized genetic elements from which to build. Current characterization methods are tied to measurements in living systems, the transformation and culturing of which are inherently time-consuming. To address this, we have validated a completely in vitro approach for the characterization of DNA regulatory elements using Escherichia coli extract cell-free systems. Importantly, we demonstrate that characterization in cell-free systems correlates and is reflective of performance in vivo for the most frequently used DNA regulatory elements. Moreover, we devise a rapid and completely in vitro method to generate DNA templates for cell-free systems, bypassing the need for DNA template generation and amplification from living cells. This in vitro approach is significantly quicker than current characterization methods and is amenable to high-throughput techniques, providing a valuable tool for rapidly prototyping libraries of DNA regulatory elements for synthetic biology. PMID:23371936

Selective Laser Melting: a regular unit cell approach for the manufacture of porous, titanium, bone in-growth constructs, suitable for orthopedic applications.

PubMed

Mullen, Lewis; Stamp, Robin C; Brooks, Wesley K; Jones, Eric; Sutcliffe, Christopher J

2009-05-01

In this study, a novel porous titanium structure for the purpose of bone in-growth has been designed, manufactured and evaluated. The structure was produced by Selective Laser Melting (SLM); a rapid manufacturing process capable of producing highly intricate, functionally graded parts. The technique described utilizes an approach based on a defined regular unit cell to design and produce structures with a large range of both physical and mechanical properties. These properties can be tailored to suit specific requirements; in particular, functionally graded structures with bone in-growth surfaces exhibiting properties comparable to those of human bone have been manufactured. The structures were manufactured and characterized by unit cell size, strand diameter, porosity, and compression strength. They exhibited a porosity (10-95%) dependant compression strength (0.5-350 Mpa) comparable to the typical naturally occurring range. It is also demonstrated that optimized structures have been produced that possesses ideal qualities for bone in-growth applications and that these structures can be applied in the production of orthopedic devices. (c) 2008 Wiley Periodicals, Inc.

Rapid Prototyping of Continuous Fiber Reinforced Ceramic Matrix Composites

NASA Technical Reports Server (NTRS)

Vaidyanathan, R.; Green, C.; Phillips, T.; Cipriani, R.; Yarlagadda, S.; Gillespie, J.; Effinger, M.; Cooper, K. C.; Gordon, Gail (Technical Monitor)

2002-01-01

For ceramics to be used as structural components in high temperature applications, their fracture toughness is improved by embedding continuous ceramic fibers. Ceramic matrix composite (CMC) materials allow increasing the overall operating temperature, raising the temperature safety margins, avoiding the need for cooling, and improving the damping capacity, while reducing the weight at the same time. They also need to be reliable and available in large quantities as well. In this paper, an innovative rapid prototyping technique to fabricate continuous fiber reinforced ceramic matrix composites is described. The process is simple, robust and will be widely applicable to a number of high temperature material systems. This technique was originally developed at the University of Delaware Center for Composite Materials (UD-CCM) for rapid fabrication of polymer matrix composites by a technique called automated tow placement or ATP. The results of mechanical properties and microstructural characterization are presented, together with examples of complex shapes and parts. It is believed that the process will be able to create complex shaped parts at an order of magnitude lower cost than current CVI and PIP processes.

Laser rapid forming technology of high-performance dense metal components with complex structure

NASA Astrophysics Data System (ADS)

Huang, Weidong; Chen, Jing; Li, Yanming; Lin, Xin

2005-01-01

Laser rapid forming (LRF) is a new and advanced manufacturing technology that has been developed on the basis of combining high power laser cladding technology with rapid prototyping (RP) to realize net shape forming of high performance dense metal components without dies. Recently we have developed a set of LRF equipment. LRF experiments were carried out on the equipment to investigate the influences of processing parameters on forming characterizations systematically with the cladding powder materials as titanium alloys, superalloys, stainless steel, and copper alloys. The microstructure of laser formed components is made up of columnar grains or columnar dendrites which grow epitaxially from the substrate since the solid components were prepared layer by layer additionally. The result of mechanical testing proved that the mechanical properties of laser formed samples are similar to or even over that of forging and much better than that of casting. It is shown in this paper that LRF technology is providing a new solution for some difficult processing problems in the high tech field of aviation, spaceflight and automobile industries.

Rapid Identification of Sequences for Orphan Enzymes to Power Accurate Protein Annotation

PubMed Central

Ojha, Sunil; Watson, Douglas S.; Bomar, Martha G.; Galande, Amit K.; Shearer, Alexander G.

2013-01-01

The power of genome sequencing depends on the ability to understand what those genes and their proteins products actually do. The automated methods used to assign functions to putative proteins in newly sequenced organisms are limited by the size of our library of proteins with both known function and sequence. Unfortunately this library grows slowly, lagging well behind the rapid increase in novel protein sequences produced by modern genome sequencing methods. One potential source for rapidly expanding this functional library is the “back catalog” of enzymology – “orphan enzymes,” those enzymes that have been characterized and yet lack any associated sequence. There are hundreds of orphan enzymes in the Enzyme Commission (EC) database alone. In this study, we demonstrate how this orphan enzyme “back catalog” is a fertile source for rapidly advancing the state of protein annotation. Starting from three orphan enzyme samples, we applied mass-spectrometry based analysis and computational methods (including sequence similarity networks, sequence and structural alignments, and operon context analysis) to rapidly identify the specific sequence for each orphan while avoiding the most time- and labor-intensive aspects of typical sequence identifications. We then used these three new sequences to more accurately predict the catalytic function of 385 previously uncharacterized or misannotated proteins. We expect that this kind of rapid sequence identification could be efficiently applied on a larger scale to make enzymology’s “back catalog” another powerful tool to drive accurate genome annotation. PMID:24386392

Rapid identification of sequences for orphan enzymes to power accurate protein annotation.

PubMed

Ramkissoon, Kevin R; Miller, Jennifer K; Ojha, Sunil; Watson, Douglas S; Bomar, Martha G; Galande, Amit K; Shearer, Alexander G

2013-01-01

The power of genome sequencing depends on the ability to understand what those genes and their proteins products actually do. The automated methods used to assign functions to putative proteins in newly sequenced organisms are limited by the size of our library of proteins with both known function and sequence. Unfortunately this library grows slowly, lagging well behind the rapid increase in novel protein sequences produced by modern genome sequencing methods. One potential source for rapidly expanding this functional library is the "back catalog" of enzymology--"orphan enzymes," those enzymes that have been characterized and yet lack any associated sequence. There are hundreds of orphan enzymes in the Enzyme Commission (EC) database alone. In this study, we demonstrate how this orphan enzyme "back catalog" is a fertile source for rapidly advancing the state of protein annotation. Starting from three orphan enzyme samples, we applied mass-spectrometry based analysis and computational methods (including sequence similarity networks, sequence and structural alignments, and operon context analysis) to rapidly identify the specific sequence for each orphan while avoiding the most time- and labor-intensive aspects of typical sequence identifications. We then used these three new sequences to more accurately predict the catalytic function of 385 previously uncharacterized or misannotated proteins. We expect that this kind of rapid sequence identification could be efficiently applied on a larger scale to make enzymology's "back catalog" another powerful tool to drive accurate genome annotation.

Cognitive-Behavioral Therapy for Rapid Cycling Bipolar Disorder

ERIC Educational Resources Information Center

Reilly-Harrington, Noreen A.; Knauz, Robert O.

2005-01-01

This article describes the application of cognitive-behavioral therapy (CBT) to the treatment of rapid cycling bipolar disorder. Between 10% and 24% of bipolar patients experience a rapid cycling course, with 4 or more mood episodes occurring per year. Characterized by nonresponse to standard mood-stabilizing medications, rapid cyclers are…

Impacts of SST Patterns on Rapid Intensification of Typhoon Megi (2010)

NASA Astrophysics Data System (ADS)

Kanada, Sachie; Tsujino, Satoki; Aiki, Hidenori; Yoshioka, Mayumi K.; Miyazawa, Yasumasa; Tsuboki, Kazuhisa; Takayabu, Izuru

2017-12-01

Typhoon Megi (2010), a very intense tropical cyclone with a minimum central pressure of 885 hPa, was characterized by especially rapid intensification. We investigated this intensification process by a simulation experiment using a high-resolution (0.02° × 0.02°) three-dimensional atmosphere-ocean coupled regional model. We also performed a sensitivity experiment with a time-fixed sea surface temperature (SST). The coupled model successfully simulated the minimum central pressure of Typhoon Megi, whereas the fixed SST experiment simulated an excessively low minimum central pressure of 839 hPa. The simulation results also showed a close relationship between the radial SST profiles and the rapid intensification process. Because the warm sea increased near-surface water vapor and hence the convective available potential energy, the high SST in the eye region facilitated tall and intense updrafts inside the radius of maximum wind speed and led to the start of rapid intensification. In contrast, high SST outside this radius induced local secondary updrafts that inhibited rapid intensification even if the mean SST in the core region exceeded 29.0°C. These secondary updrafts moved inward and eventually merged with the primary eyewall updrafts. Then the storm intensified rapidly when the high SST appeared in the eye region. Thus, the changes in the local SST pattern around the storm center strongly affected the rapid intensification process by modulating the radial structure of core convection. Our results also show that the use of a high-resolution three-dimensional atmosphere-ocean coupled model offers promise for improving intensity forecasts of tropical cyclones.

Discovery and characterization of natural products that act as pheromones in fish.

PubMed

Li, Ke; Buchinger, Tyler J; Li, Weiming

2018-06-20

Covering: up to 2018 Fish use a diverse collection of molecules to communicate with conspecifics. Since Karlson and Lüscher termed these molecules 'pheromones', chemists and biologists have joined efforts to characterize their structures and functions. In particular, the understanding of insect pheromones developed at a rapid pace, set, in part, by the use of bioassay-guided fractionation and natural product chemistry. Research on vertebrate pheromones, however, has progressed more slowly. Initially, biologists characterized fish pheromones by screening commercially available compounds suspected to act as pheromones based upon their physiological function. Such biology-driven screening has proven a productive approach to studying pheromones in fish. However, the many functions of fish pheromones and diverse metabolites that fish release make predicting pheromone identity difficult and necessitate approaches led by chemistry. Indeed, the few cases in which pheromone identification was led by natural product chemistry indicated novel or otherwise unpredicted compounds act as pheromones. Here, we provide a brief review of the approaches to identifying pheromones, placing particular emphasis on the promise of using natural product chemistry together with assays of biological activity. Several case studies illustrate bioassay-guided fractionation as an approach to pheromone identification in fish and the unexpected diversity of pheromone structures discovered by natural product chemistry. With recent advances in natural product chemistry, bioassay-guided fractionation is likely to unveil an even broader collection of pheromone structures and enable research that spans across disciplines.

Treatability and characterization of Natural Organic Matter (NOM) in South African waters using newly developed methods

NASA Astrophysics Data System (ADS)

Nkambule, T. I.; Krause, R. W. M.; Haarhoff, J.; Mamba, B. B.

Managing the removal of Natural Organic Matter (NOM) or problematic components from water has become increasingly important. NOM is a heterogeneous mixture of organic compounds of human origin and derived from plant and microbial residues. The inadequate removal of NOM has a bearing on the capacity of the other treatment processes to remove organic micro-pollutants or inorganic species that may be present in the water. In addition the action of certain disinfection processes has been shown to lead to the formation of harmful disinfection by-products (DBPs). Owing to the complexity, in composition and structure, of NOM, the techniques currently employed for its characterization have a number of limitations, both in terms of quantification and removal of the NOM within short periods of time. The dissolved organic carbon (DOC), biodegradable dissolved organic carbon (BDOC) and Fluorescence Emission Excitation Matrices (FEEM) were used to characterize NOM from various water samples collected around South Africa. Characterization results gave an indication of the character of NOM present in all the water samples. FEEM and UV-Vis results indicated that most of the water samples were aromatic in nature, since they had high hydrophobic and humic acid-like materials content. Generally, the characterization data indicated a varying composition of NOM amongst the various sampling points. The polarity rapid assessment method (PRAM) was then employed as a rapid NOM characterization tool. The characterization under PRAM is based on preferential adsorption of dissolved organic matter (DOM) fractions onto solid phase extraction (SPE) sorbents. The PRAM also allows the separation of DOM into fractions by polarity, hence reducing the molecular heterogeneity of NOM and thus aiding the removal of specific NOM fractions from water. The PRAM provided a quick characterization of the NOM character. However, DOC quantification by the PRAM analysis was hindered by excessive carbon leaching from the SPE cartridges. The BDOC method of analysis is based on the bacteria fixed on the biologically active sand and gives a ratio of the biodegradable NOM versus the non-biodegradable NOM. For the BDOC analysis, the percentage DOC removal for the samples ranged from 12% to 61%.

One-pot synthesis of monodisperse CoFe2O4@Ag core-shell nanoparticles and their characterization.

PubMed

Hara, Shuta; Aisu, Jumpei; Kato, Masahiro; Aono, Takashige; Sugawa, Kosuke; Takase, Kouichi; Otsuki, Joe; Shimizu, Shigeru; Ikake, Hiroki

2018-06-08

In recent years, monodispersed magnetic nanoparticles with a core/shell structure are expected for their wide applications including magnetic fluid, recoverable catalysts, and biological analysis. However, their synthesis method needs numerous processes such as solvent substitution, exchange of protective agents, and centrifugation. A simple and rapid method for the synthesis of monodispersed core-shell nanoparticles makes it possible to accelerate their further applications. This paper describes a simple and rapid one-pot synthesis of core (CoFe 2 O 4 )-shell (Ag) nanoparticles with high monodispersity. The synthesized nanoparticles showed plasmonic light absorption owing to the Ag shell. Moreover, the magnetic property of the nanoparticles had a soft magnetic behavior at room temperature and a hard magnetic behavior at 5 K. In addition, the nanoparticles showed high monodispersity with a low polydispersity index (PDI) value of 0.083 in hexane.

Rapid synthesis of dendritic Pt/Pb nanoparticles and their electrocatalytic performance toward ethanol oxidation

NASA Astrophysics Data System (ADS)

Zhang, Ke; Xu, Hui; Yan, Bo; Wang, Jin; Gu, Zhulan; Du, Yukou

2017-12-01

This article reports a rapid synthetic method for the preparation of dendritic platinum-lead bimetallic catalysts by using an oil bath for 5 min in the presence of hexadecyltrimethylammonium chloride (CTAC) and ascorbic acid (AA). CTAC acts as a shape-direction agent, and AA acts as a reducing agent during the reaction process. A series of physical techniques are used to characterize the morphology, structure and electronic properties of the dendritic Pt/Pb nanoparticles, indicating the Pt/Pb dendrites are porous, highly alloying, and self-supported nanostructures. Various electrochemical techniques were also investigated the catalytic performance of the Pt/Pb catalysts toward the ethanol electrooxidation reaction. Cyclic voltammetry and chronoamperometry indicated that the synthesized dendritic Pt/Pb nanoparticles possessed much higher electrocatalytic performance than bulk Pt catalyst. This study may inspire the engineering of dendritic bimetallic catalysts, which are expected to have great potential applications in fuel cells.

Multiscale Analysis of Rapidly Rotating Dynamo Simulations

NASA Astrophysics Data System (ADS)

Orvedahl, R.; Calkins, M. A.; Featherstone, N. A.

2017-12-01

The magnetic field of the planets and stars are generated by dynamo action in their electrically conducting fluid interiors. Numerical models of this process solve the fundamental equations of magnetohydrodynamics driven by convection in a rotating spherical shell. Rotation plays an important role in modifying the resulting convective flows and the self-generated magnetic field. We present results of simulating rapidly rotating systems that are unstable to dynamo action. We use the pseudo-spectral code Rayleigh to generate a suite of direct numerical simulations. Each simulation uses the Boussinesq approximation and is characterized by an Ekman number (Ek=ν /Ω L2) of 10-5. We vary the degree of convective forcing to obtain a range of convective Rossby numbers. The resulting flows and magnetic structures are analyzed using a Reynolds decomposition. We determine the relative importance of each term in the scale-separated governing equations and estimate the relevant spatial scales responsible for generating the mean magnetic field.

One-pot synthesis of monodisperse CoFe2O4@Ag core-shell nanoparticles and their characterization

NASA Astrophysics Data System (ADS)

Hara, Shuta; Aisu, Jumpei; Kato, Masahiro; Aono, Takashige; Sugawa, Kosuke; Takase, Kouichi; Otsuki, Joe; Shimizu, Shigeru; Ikake, Hiroki

2018-06-01

In recent years, monodispersed magnetic nanoparticles with a core/shell structure are expected for their wide applications including magnetic fluid, recoverable catalysts, and biological analysis. However, their synthesis method needs numerous processes such as solvent substitution, exchange of protective agents, and centrifugation. A simple and rapid method for the synthesis of monodispersed core-shell nanoparticles makes it possible to accelerate their further applications. This paper describes a simple and rapid one-pot synthesis of core (CoFe2O4)-shell (Ag) nanoparticles with high monodispersity. The synthesized nanoparticles showed plasmonic light absorption owing to the Ag shell. Moreover, the magnetic property of the nanoparticles had a soft magnetic behavior at room temperature and a hard magnetic behavior at 5 K. In addition, the nanoparticles showed high monodispersity with a low polydispersity index (PDI) value of 0.083 in hexane.

Fabrication of magnetic macroporous chitosan-g-poly (acrylic acid) hydrogel for removal of Cd2+ and Pb2.

PubMed

Zhu, Yongfeng; Zheng, Yian; Wang, Feng; Wang, Aiqin

2016-12-01

A novel macroporous magnetic macroporous chitosan-g-poly (acrylic acid) hydrogel adsorbent was fabricated from the Pickering high internal emulsions template stabilized by modified Fe 3 O 4 nanoparticles. The structure and composition of modified Fe 3 O 4 and macroporous magnetic hydrogel were characterized by TEM, XRD, TG and SEM techniques. The characterization results suggest that the Fe 3 O 4 nanoparticles have been modified successfully with organosilane of 3-aminopropyltrimethoxysilane (APTES), and the porous structure of the macroporous hydrogel can be tuned with the amount of stabilized particles, volume fraction of dispersed phase and the amount of the cosurfactant. Adsorption experiments indicate that the adsorption equilibrium was rapidly reached within 20min and the maximal adsorption capacities were determined to be 308.84mg/g for Cd 2+ and 695.22mg/g for Pb 2+ . After five adsorption-desorption cycles, the adsorbent can retain its high adsorption capacity. The introduction of Fe 3 O 4 is beneficial to the recycle of adsorbent after usage. Copyright © 2016 Elsevier B.V. All rights reserved.

In situ characterization of silver nanoparticle synthesis in maltodextrin supramolecular structures

DOE PAGES

Bell, Nelson S.; Dunphy, Darren R.; Lambert, Timothy N.; ...

2015-06-26

In this study, the use of maltodextrin supramolecular structures (MD SMS) as a reducing agent and colloidal stabilizing agent for the synthesis of Ag nanoparticles (Ag NPs) identified three key points. First, the maltodextrin (MD) solutions are effective in the formation of well-dispersed Ag NPs utilizing alkaline solution conditions, with the resulting Ag NPs ranging in size from 5 to 50 nm diameter. Second, in situ characterization by Raman spectroscopy and small angle X-ray scattering (SAXS) are consistent with initial nucleation of Ag NPs within the MD SMS up to a critical size of ca. 1 nm, followed by amore » transition to more rapid growth by aggregation and fusion between MD SMS, similar to micelle aggregation reactions. Third, the stabilization of larger Ag NPs by adsorbed MD SMS is similar to hemi-micelle stabilization, and monomodal size distributions are proposed to relate to integer surface coverage of the Ag NPs. Conditions were identified for preparing Ag NPs with monomodal distributions centered at 30–35 nm Ag NPs.« less

Expedient preparative isolation and tandem mass spectrometric characterization of C-seco triterpenoids from Neem oil.

PubMed

Haldar, Saikat; Mulani, Fayaj A; Aarthy, Thiagarayaselvam; Dandekar, Devdutta S; Thulasiram, Hirekodathakallu V

2014-10-31

C-seco triterpenoids are widely bioactive class of natural products with high structural complexity and diversity. The preparative isolation of these molecules with high purity is greatly desirable, although restricted due to the complexity of natural extracts. In this article we have demonstrated a Medium Pressure Liquid Chromatography (MPLC) based protocol for the isolation of eight major C-seco triterpenoids of salannin skeleton from Neem (Azadirachta indica) oil. Successive application of normal phase pre-packed silica-gel columns for the fractionation followed by reverse phase in automated MPLC system expedited the process and furnished highly pure metabolites. Furthermore, eight isolated triterpenoids along with five semi-synthesized derivatives were characterized using ultra performance liquid chromatography-electrospray ionization-quadrupole/orbitrap-MS/MS spectrometry as a rapid and sensitive identification technique. The structure-fragment relationships were established on the basis of plausible mechanistic pathway for the generation of daughter ions. The MS/MS spectral information of the triterpenoids was further utilized for the identification of studied molecules in the complex extract of stem and bark tissues from Neem. Copyright © 2014 Elsevier B.V. All rights reserved.

Structural and electrical characterization of epitaxial Ge thin films on Si(001) formed by sputtering

NASA Astrophysics Data System (ADS)

Otsuka, Shintaro; Mori, Takahiro; Morita, Yukinori; Uchida, Noriyuki; Liu, Yongxun; O'uchi, Shin-ichi; Fuketa, Hiroshi; Migita, Shinji; Masahara, Meishoku; Matsukawa, Takashi

2017-04-01

We structurally and electrically characterize sub-10-nm-thick heteroepitaxial Ge films on Si(001), formed by heated sputtering and subsequent rapid thermal annealing (RTA). After RTA treatment at 720 °C, we find the heteroepitaxial Ge films to have smooth surfaces with a roughness root mean square value of 0.54 nm. Raman measurement reveals that the 720 °C RTA improves the crystallinity of Ge films while maintaining abrupt Ge/Si interfaces. Cross-sectional transmission electron microscopy confirms that the 720 °C RTA step effectively reduces stacking faults and dislocations in the Ge films. The Richardson plot of the TaN/Ge/n-Si diode indicates a Schottky barrier height (SBH) of 0.33 V, which is close to the height of 0.37 V measured from the capacitance-voltage measurement. These values are reasonable compared with the reported SBH of the TaN/bulk Ge Schottky barrier diode, indicating that the method involving heated sputtering and subsequent RTA provides adequate thin Ge films for Ge/Si heterostructures.

High-resolution mapping, characterization, and optimization of autonomously replicating sequences in yeast

PubMed Central

Liachko, Ivan; Youngblood, Rachel A.; Keich, Uri; Dunham, Maitreya J.

2013-01-01

DNA replication origins are necessary for the duplication of genomes. In addition, plasmid-based expression systems require DNA replication origins to maintain plasmids efficiently. The yeast autonomously replicating sequence (ARS) assay has been a valuable tool in dissecting replication origin structure and function. However, the dearth of information on origins in diverse yeasts limits the availability of efficient replication origin modules to only a handful of species and restricts our understanding of origin function and evolution. To enable rapid study of origins, we have developed a sequencing-based suite of methods for comprehensively mapping and characterizing ARSs within a yeast genome. Our approach finely maps genomic inserts capable of supporting plasmid replication and uses massively parallel deep mutational scanning to define molecular determinants of ARS function with single-nucleotide resolution. In addition to providing unprecedented detail into origin structure, our data have allowed us to design short, synthetic DNA sequences that retain maximal ARS function. These methods can be readily applied to understand and modulate ARS function in diverse systems. PMID:23241746

Development of a method for urine bikunin/urinary trypsin inhibitor (UTI) quantitation and structural characterization: Application to type 1 and type 2 diabetes.

PubMed

Lepedda, Antonio Junior; Nieddu, Gabriele; Rocchiccioli, Silvia; Fresu, Pietro; De Muro, Pierina; Formato, Marilena

2013-12-01

Bikunin is a plasma proteinase inhibitor often associated with inflammatory conditions. It has a half-life of few minutes and it is rapidly excreted into urine as urinary trypsin inhibitor (UTI). UTI levels are usually low in healthy individuals but they can increase up to tenfold in both acute and chronic inflammatory diseases. This article describes a sensitive method for both direct UTI quantitation and structural characterization. UTI purification was performed by anion exchange micro-chromatography followed by SDS-PAGE. A calibration curve for protein quantitation was set up by using a purified UTI fraction. UTI identification and structural characterization was performed by Nano-LC-MS/MS analysis. The method was applied on urine samples from 9 patients with type 1 diabetes, 11 patients with type 2 diabetes, and 28 healthy controls, matched for age and sex with patients, evidencing higher UTI levels in both groups of patients with respect to controls (p < 0.001 and p = 0.001, respectively). Spearman's correlation tests highlighted no association between UTI levels and age in each group tested. Owing to the elevated sensitivity and specificity, the described method allows UTI quantitation from very low quantities of specimen. Furthermore, as UTI concentration is normalized for creatinine level, the analysis could be also performed on randomly collected urine samples. Finally, MS/MS analysis prospects the possibility of characterizing PTM sites potentially able to affect UTI localization, function, and pathophysiological activity. Preliminary results suggest that UTI levels could represent a useful marker of chronic inflammatory condition in type 1 and 2 diabetes. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Resistant Starch Regulates Gut Microbiota: Structure, Biochemistry and Cell Signalling.

PubMed

Yang, Xiaoping; Darko, Kwame Oteng; Huang, Yanjun; He, Caimei; Yang, Huansheng; He, Shanping; Li, Jianzhong; Li, Jian; Hocher, Berthold; Yin, Yulong

2017-01-01

Starch is one of the most popular nutritional sources for both human and animals. Due to the variation of its nutritional traits and biochemical specificities, starch has been classified into rapidly digestible, slowly digestible and resistant starch. Resistant starch has its own unique chemical structure, and various forms of resistant starch are commercially available. It has been found being a multiple-functional regulator for treating metabolic dysfunction. Different functions of resistant starch such as modulation of the gut microbiota, gut peptides, circulating growth factors, circulating inflammatory mediators have been characterized by animal studies and clinical trials. In this mini-review, recent remarkable progress in resistant starch on gut microbiota, particularly the effect of structure, biochemistry and cell signaling on nutrition has been summarized, with highlights on its regulatory effect on gut microbiota. © 2017 The Author(s). Published by S. Karger AG, Basel.

X-Ray photoelectron diffraction and photoelectron holography as methods for investigating the local atomic structure of the surface of solids

NASA Astrophysics Data System (ADS)

Kuznetsov, M. V.; Ogorodnikov, I. I.; Vorokh, A. S.

2014-01-01

The state-of-the-art theory and experimental applications of X-ray photoelectron diffraction (XPD) and photoelectron holography (PH) are discussed. These methods are rapidly progressing and serve to examine the surface atomic structure of solids, including nanostructures formed on surfaces during adsorption of gases, epitaxial film growth, etc. The depth of analysis by these methods is several nanometres, which makes it possible to characterize the positions of atoms localized both on and beneath the surface. A remarkable feature of the XPD and PH methods is their sensitivity to the type of examined atoms and, in the case of high energy resolution, to the particular chemical form of the element under study. The data on experimental applications of XPD and PH to studies of various surface structures are analyzed and generalized. The bibliography includes 121 references.

Importance of interlayer H bonding structure to the stability of layered minerals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Conroy, Michele; Soltis, Jennifer A.; Wittman, Rick S.

2017-10-16

The exact atomic structures of layered minerals have been difficult to characterize because the layers often possess out-of-plane hydrogen atoms that cannot be detected by many analytical techniques. However, the ordering of these bonds are thought to play a fundamental role in the structural stability and solubility of layered minerals. We report a new strategy of using the intense radiation field of a focused electron beam to probe the effect of differences in hydrogen bonding networks on mineral solubility while simultaneously imaging the dissolution behavior in real time via liquid cell electron microscopy. We show the loss in hydrogens frommore » interlayers of boehmite (γ-AlOOH) resulted in 2D nanosheets exfoliating from the bulk that subsequently and rapidly dissolved. However gibbsite (γ-Al(OH)3), with its higher concentration of OH terminating groups, was more accommodating to the deprotonation and stable under the beam.« less

Plant centromere organization: a dynamic structure with conserved functions.

PubMed

Ma, Jianxin; Wing, Rod A; Bennetzen, Jeffrey L; Jackson, Scott A

2007-03-01

Although the structural features of centromeres from most multicellular eukaryotes remain to be characterized, recent analyses of the complete sequences of two centromeric regions of rice, together with data from Arabidopsis thaliana and maize, have illuminated the considerable size variation and sequence divergence of plant centromeres. Despite the severe suppression of meiotic chromosomal exchange in centromeric and pericentromeric regions of rice, the centromere core shows high rates of unequal homologous recombination in the absence of chromosomal exchange, resulting in frequent and extensive DNA rearrangement. Not only is the sequence of centromeric tandem and non-tandem repeats highly variable but also the copy number, spacing, order and orientation, providing ample natural variation as the basis for selection of superior centromere performance. This review article focuses on the structural and evolutionary dynamics of plant centromere organization and the potential molecular mechanisms responsible for the rapid changes of centromeric components.

Methods for isolation of marine-derived endophytic fungi and their bioactive secondary products.

PubMed

Kjer, Julia; Debbab, Abdessamad; Aly, Amal H; Proksch, Peter

2010-03-01

Marine-derived fungi have been shown in recent years to produce a plethora of new bioactive secondary metabolites, some of them featuring new carbon frameworks hitherto unprecedented in nature. These compounds are of interest as new lead structures for medicine as well as for plant protection. The aim of this protocol is to give a detailed description of methods useful for the isolation and cultivation of fungi associated with various marine organisms (sponges, algae and mangrove plants) for the extraction, characterization and structure elucidation of biologically active secondary metabolites produced by these marine-derived endophytic fungi, and for the preliminary evaluation of their pharmacological properties based on rapid 'in house' screening systems. Some results exemplifying the positive outcomes of the protocol are given at the end. From sampling in marine environment to completion of the structure elucidation and bioactivity screening, a period of at least 3 months has to be scheduled.

New porous water ice metastable at atmospheric pressure obtained by emptying a hydrogen-filled ice

PubMed Central

del Rosso, Leonardo; Celli, Milva; Ulivi, Lorenzo

2016-01-01

The properties of some forms of water ice reserve still intriguing surprises. Besides the several stable or metastable phases of pure ice, solid mixtures of water with gases are precursors of other ices, as in some cases they may be emptied, leaving a metastable hydrogen-bound water structure. We present here the first characterization of a new form of ice, obtained from the crystalline solid compound of water and molecular hydrogen called C0-structure filled ice. By means of Raman spectroscopy, we measure the hydrogen release at different temperatures and succeed in rapidly removing all the hydrogen molecules, obtaining a new form of ice (ice XVII). Its structure is determined by means of neutron diffraction measurements. Of paramount interest is that the emptied crystal can adsorb again hydrogen and release it repeatedly, showing a temperature-dependent hysteresis. PMID:27819265

Enabling Rapid Integration of Combined Arms Teams into a Brigade Combat Team Organizational Structure

DTIC Science & Technology

2017-06-01

organizational structure , fixed vs. mobile forward operating base (FOB) synchronization, prior preparation, and unit capabilities. 5. Ideas to Improve...Technical Report 1356 Enabling Rapid Integration of Combined Arms Teams into a Brigade Combat Team Organizational Structure ...2012 - May 2014 4. TITLE AND SUBTITLE Enabling Rapid Integration of Combined Arms Teams into a Brigade Combat Team Organizational Structure

Rapid characterization of the chemical constituents of Cortex Fraxini by homogenate extraction followed by UHPLC coupled with Fourier transform ion cyclotron resonance mass spectrometry and GC-MS.

PubMed

Wang, Yinan; Han, Fei; Song, Aihua; Wang, Miao; Zhao, Min; Zhao, Chunjie

2016-11-01

Cortex Fraxini is an important traditional Chinese medicine. In this work, a rapid and reliable homogenate extraction method was applied for the fast extraction for Cortex Fraxini, and the method was optimized by response surface methodology. Ultra high performance liquid chromatography combined with Fourier transform ion cyclotron resonance mass spectrometry and gas chromatography with mass spectrometry were established for the separation and characterization of the constituents of Cortex Fraxini. Liquid chromatography separation was conducted on a C 18 column (150 mm × 2.1 mm, 1.8 μm), and gas chromatography separation was performed on a capillary with a 5% phenyl-methylpolysiloxane stationary phase (30 m × 0.25 mm × 0.25 mm) by injection of silylated samples. According to the results, 33 chemical compounds were characterized by liquid chromatography with mass spectrometry, and 11 chemical compounds were characterized by gas chromatography with mass spectrometry, and coumarins were the major components characterized by both gas chromatography with mass spectrometry and liquid chromatography with mass spectrometry. The proposed homogenate extraction was an efficient and rapid method, and coumarins, phenylethanoid glycosides, iridoid glycosides, phenylpropanoids, and lignans were the main constituents of Cortex Fraxini. This work laid the foundation for further study of Cortex Fraxini and will be helpful for the rapid extraction and characterization of ingredients in other traditional Chinese medicines. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Tools for Designing and Analyzing Structures

NASA Technical Reports Server (NTRS)

Luz, Paul L.

2005-01-01

Structural Design and Analysis Toolset is a collection of approximately 26 Microsoft Excel spreadsheet programs, each of which performs calculations within a different subdiscipline of structural design and analysis. These programs present input and output data in user-friendly, menu-driven formats. Although these programs cannot solve complex cases like those treated by larger finite element codes, these programs do yield quick solutions to numerous common problems more rapidly than the finite element codes, thereby making it possible to quickly perform multiple preliminary analyses - e.g., to establish approximate limits prior to detailed analyses by the larger finite element codes. These programs perform different types of calculations, as follows: 1. determination of geometric properties for a variety of standard structural components; 2. analysis of static, vibrational, and thermal- gradient loads and deflections in certain structures (mostly beams and, in the case of thermal-gradients, mirrors); 3. kinetic energies of fans; 4. detailed analysis of stress and buckling in beams, plates, columns, and a variety of shell structures; and 5. temperature dependent properties of materials, including figures of merit that characterize strength, stiffness, and deformation response to thermal gradients

A global fingerprint of macro-scale changes in urban structure from 1999 to 2009

NASA Astrophysics Data System (ADS)

Frolking, Steve; Milliman, Tom; Seto, Karen C.; Friedl, Mark A.

2013-06-01

Urban population now exceeds rural population globally, and 60-80% of global energy consumption by households, businesses, transportation, and industry occurs in urban areas. There is growing evidence that built-up infrastructure contributes to carbon emissions inertia, and that investments in infrastructure today have delayed climate cost in the future. Although the United Nations statistics include data on urban population by country and select urban agglomerations, there are no empirical data on built-up infrastructure for a large sample of cities. Here we present the first study to examine changes in the structure of the world’s largest cities from 1999 to 2009. Combining data from two space-borne sensors—backscatter power (PR) from NASA’s SeaWinds microwave scatterometer, and nighttime lights (NL) from NOAA’s defense meteorological satellite program/operational linescan system (DMSP/OLS)—we report large increases in built-up infrastructure stock worldwide and show that cities are expanding both outward and upward. Our results reveal previously undocumented recent and rapid changes in urban areas worldwide that reflect pronounced shifts in the form and structure of cities. Increases in built-up infrastructure are highest in East Asian cities, with Chinese cities rapidly expanding their material infrastructure stock in both height and extent. In contrast, Indian cities are primarily building out and not increasing in verticality. This new dataset will help characterize the structure and form of cities, and ultimately improve our understanding of how cities affect regional-to-global energy use and greenhouse gas emissions.

Generation and characterization of a distonic biradical anion formed from an enediynone prodrug in the gas phase.

PubMed

Yang, Linan; Bekele, Tefsit; Lipton, Mark A; Kenttämaa, Hilkka I

2013-04-01

A negatively charged biradical intermediate was successfully generated in the gas phase via cyclization of the deprotonated bicyclo[8.3.0]trideca-12-ene-2,7-diyn-1-one precursor. The inherent negative charge of this biradical allows its characterization via collision-activated dissociation and reactions with a variety of neutral substrates in an FT-ICR mass spectrometer. Although the biradical is unreactive toward reagents that usually react rapidly with positively charged biradicals, such as dimethyl disulfide, it reacts with the halogen-containing substrates carbon tetrachloride, carbon tetrabromide, and bromotrichloromethane via bromine or chlorine atom abstraction, which supports its biradical structure. The results presented in this study indicate that cyclizations commonly used in solution to form biradical intermediates from enediyne compounds may also occur in the gas phase.

Generation and Characterization of a Distonic Biradical Anion Formed from an Enediynone Prodrug in the Gas Phase

PubMed Central

Yang, Linan; Bekele, Tefsit; Lipton, Mark A.

2013-01-01

A negatively charged biradical intermediate was successfully generated in the gas phase via cyclization of the deprotonated bicyclo[8.3.0]trideca-12-ene-2,7-diyn-1-one precursor. The inherent negative charge of this biradical allows its characterization via collision-activated dissociation and reactions with a variety of neutral substrates in an FT-ICR mass spectrometer. Although the biradical is unreactive toward reagents that usually react rapidly with positively charged biradicals, such as dimethyl disulfide, it reacts with the halogen-containing substrates carbon tetrachloride, carbon tetrabromide and bromotrichloromethane via bromine or chlorine atom abstraction, which supports its biradical structure. The results presented in this study indicate that cyclizations commonly used in solution to form biradical intermediates from enediyne compounds may also occur in the gas phase. PMID:23512422

Quantitative Ultrasound for Nondestructive Characterization of Engineered Tissues and Biomaterials

PubMed Central

Dalecki, Diane; Mercado, Karla P.; Hocking, Denise C.

2015-01-01

Non-invasive, non-destructive technologies for imaging and quantitatively monitoring the development of artificial tissues are critical for the advancement of tissue engineering. Current standard techniques for evaluating engineered tissues, including histology, biochemical assays and mechanical testing, are destructive approaches. Ultrasound is emerging as a valuable tool for imaging and quantitatively monitoring the properties of engineered tissues and biomaterials longitudinally during fabrication and post-implantation. Ultrasound techniques are rapid, non-invasive, non-destructive and can be easily integrated into sterile environments necessary for tissue engineering. Furthermore, high-frequency quantitative ultrasound techniques can enable volumetric characterization of the structural, biological, and mechanical properties of engineered tissues during fabrication and post-implantation. This review provides an overview of ultrasound imaging, quantitative ultrasound techniques, and elastography, with representative examples of applications of these ultrasound-based techniques to the field of tissue engineering. PMID:26581347

Characterization of constituents in Stellera chamaejasme L. by rapid-resolution liquid chromatography-diode array detection and electrospray ionization time-of-flight mass spectrometry.

PubMed

Zhao, Liang; Lou, Zi-Yang; Zhu, Zhen-Yu; Zhang, Guo-Qing; Chai, Yi-Feng

2008-01-01

A reliable and rapid method based on rapid-resolution liquid chromatography-diode array detection (RRLC-DAD) and electrospray ionization time-of-flight mass spectrometry (ESI-TOF/MS) has been developed for the isolation and characterization of multiple constituents in the root of Stellera chamaejasme L., which was extracted by sonication with methanol in an optimized procedure. Separation of the multiple constituents was achieved on an Agilent Zorbax XDB-C18 (50x3.0 mm i.d.; 1.8 microm) column using a gradient elution at a flow rate of 0.4 mL/min. The detection wavelength was 210 nm. Mass spectra were acquired in both positive and negative modes. A formula database of the known chemical constituents in the root of Stellera chamaejasme L. was established by an Agilent software. Twenty-two obvious peaks appeared in the total ion chromatogram and nine of them were characterized by TOF/MS. The RRLC-DAD and ESI-TOF/MS method with ultrasonic extraction would be useful for rapid and effective characterization of chemical constituents in the root of Stellera chamaejasme L. Copyright (c) 2007 John Wiley & Sons, Ltd.

Rapid Characterization of Microalgae and Microalgae Mixtures Using Matrix-Assisted Laser Desorption Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS)

PubMed Central

Barbano, Duane; Diaz, Regina; Zhang, Lin; Sandrin, Todd; Gerken, Henri; Dempster, Thomas

2015-01-01

Current molecular methods to characterize microalgae are time-intensive and expensive. Matrix Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) may represent a rapid and economical alternative approach. The objectives of this study were to determine whether MALDI-TOF MS can be used to: 1) differentiate microalgae at the species and strain levels and 2) characterize simple microalgal mixtures. A common protein extraction sample preparation method was used to facilitate rapid mass spectrometry-based analysis of 31 microalgae. Each yielded spectra containing between 6 and 56 peaks in the m/z 2,000 to 20,000 range. The taxonomic resolution of this approach appeared higher than that of 18S rDNA sequence analysis. For example, two strains of Scenedesmus acutus differed only by two 18S rDNA nucleotides, but yielded distinct MALDI-TOF mass spectra. Mixtures of two and three microalgae yielded relatively complex spectra that contained peaks associated with members of each mixture. Interestingly, though, mixture-specific peaks were observed at m/z 11,048 and 11,230. Our results suggest that MALDI-TOF MS affords rapid characterization of individual microalgae and simple microalgal mixtures. PMID:26271045

Ultrafast visualization of the structural evolution of dense hydrogen towards warm dense matter

NASA Astrophysics Data System (ADS)

Fletcher, Luke

2016-10-01

Hot dense hydrogen far from equilibrium is ubiquitous in nature occurring during some of the most violent and least understood events in our universe such as during star formation, supernova explosions, and the creation of cosmic rays. It is also a state of matter important for applications in inertial confinement fusion research and in laser particle acceleration. Rapid progress occurred in recent years characterizing the high-pressure structural properties of dense hydrogen under static or dynamic compression. Here, we show that spectrally and angularly resolved x-ray scattering measure the thermodynamic properties of dense hydrogen and resolve the ultrafast evolution and relaxation towards thermodynamic equilibrium. These studies apply ultra-bright x-ray pulses from the Linac Coherent Light (LCLS) source. The interaction of rapidly heated cryogenic hydrogen with a high-peak power optical laser is visualized with intense LCLS x-ray pulses in a high-repetition rate pump-probe setting. We demonstrate that electron-ion coupling is affected by the small number of particles in the Debye screening cloud resulting in much slower ion temperature equilibration than predicted by standard theory. This work was supported by the DOE Office of Science, Fusion Energy Science under FWP 100182.

Facile Preparation of Light Emitting Organic Metal Halide Crystals with Near-Unity Quantum Efficiency

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, Chenkun; Worku, Michael; Neu, Jennifer

Here, we report the synthesis and characterization of (Ph 4P) 2SbCl 5, a novel ionically bonded organic metal halide hybrid with a zero-dimensional (0D) structure at the molecular level. By cocrystallization of tetraphenylphosphonium (Ph 4P +) and antimony (Sb 3+) chloride salts, (Ph 4P) 2SbCl 5 bulk single crystals can be prepared in high yield, which exhibit a highly efficient broadband red emission peaked at 648 nm with a photoluminescence quantum efficiency (PLQE) of around 87%. Density functional theory (DFT) calculations reveal the origin of emission as phosphorescence from the excitons localized at SbCl 5 2– with strong excited-state structuralmore » distortion. Interestingly, (Ph 4P) 2SbCl 5 bulk crystals with a PLQE of around 100% can be prepared via a rapid crystal growth process within minutes, followed by a spontaneous structural transformation. It was found that the rapid growth process yielded a yellow emitting kinetically favored metastable product containing solvent molecules, which turned into the red emitting thermodynamically stable product slowly at room temperature or quickly upon thermal treatment.« less

Application of a three-tier framework to assess ecological condition of Gulf of Mexico coastal wetlands.

PubMed

Nestlerode, Janet A; Hansen, Virginia D; Teague, Aarin; Harwell, Matthew C

2014-06-01

A multi-level coastal wetland assessment strategy was applied to wetlands in the northern Gulf of Mexico (GOM) to evaluate the feasibility of this approach for a broad national scale wetland condition assessment (US Environmental Protection Agency's National Wetlands Condition Assessment). Landscape-scale assessment indicators (tier 1) were developed and applied at the sub-watershed (12-digit hydrologic unit code (HUC)) level within the GOM coastal wetland sample frame with scores calculated using land-use maps and geographic information system. Rapid assessment protocols (tier 2), using a combination of data analysis and field work, evaluated metrics associated with landscape context, hydrology, physical structure, and biological structure. Intensive site monitoring (tier 3) included measures of soil chemistry and composition, water column and pore-water chemistry, and dominant macrophyte community composition and tissue chemistry. Relationships within and among assessment levels were evaluated using multivariate analyses with few significant correlations found. More detailed measures of hydrology, soils, and macrophyte species composition from sites across a known condition gradient, in conjunction with validation of standardized rapid assessment method, may be necessary to fully characterize coastal wetlands across the region.

Facile Preparation of Light Emitting Organic Metal Halide Crystals with Near-Unity Quantum Efficiency

DOE PAGES

Zhou, Chenkun; Worku, Michael; Neu, Jennifer; ...

2018-03-12

Here, we report the synthesis and characterization of (Ph 4P) 2SbCl 5, a novel ionically bonded organic metal halide hybrid with a zero-dimensional (0D) structure at the molecular level. By cocrystallization of tetraphenylphosphonium (Ph 4P +) and antimony (Sb 3+) chloride salts, (Ph 4P) 2SbCl 5 bulk single crystals can be prepared in high yield, which exhibit a highly efficient broadband red emission peaked at 648 nm with a photoluminescence quantum efficiency (PLQE) of around 87%. Density functional theory (DFT) calculations reveal the origin of emission as phosphorescence from the excitons localized at SbCl 5 2– with strong excited-state structuralmore » distortion. Interestingly, (Ph 4P) 2SbCl 5 bulk crystals with a PLQE of around 100% can be prepared via a rapid crystal growth process within minutes, followed by a spontaneous structural transformation. It was found that the rapid growth process yielded a yellow emitting kinetically favored metastable product containing solvent molecules, which turned into the red emitting thermodynamically stable product slowly at room temperature or quickly upon thermal treatment.« less

A fine structure genomic map of the region of 12q13 containing SAS and CDK4

DOE Office of Scientific and Technical Information (OSTI.GOV)

Linder, C.Y.; Elkahloun, A.G.; Su, Y.A.

1994-09-01

We have recently adapted a method, originally described by Rackwitz, to the rapid restriction mapping of multiple cosmid DNA samples. Linearization of the cosmids at the lambda cohesive site using lambda terminase is followed by partial digestion with selected restriction enzymes and hybridization to oligonucleotides specific for the right or left hand termini. Partial digestions are performed in a microtiter plate thus allowing up to 12 cosmid clones to be digested with one restriction enzyme. We have applied this rapid restriction mapping method to cosmids derived from a region of chromosome 12q13 that has recently been shown to be amplifiedmore » in a variety of cancers including malignant fibrous histiocytoma, fibrosarcoma, liposarcoma, osteosarcoma and brain tumors. A small segment of this amplification unit containing three genes, SAS (a membrane protein), CDK4 (a cyclin dependent kinase) and OS-9 (a recently described cDNA) has been analyzed with the system described above. This fine structure genomic map will be useful for completing the expression map of this region as well as characterizing its pattern of amplification in tumor specimens.« less

Solution-based analysis of multiple analytes by a sensor array: toward the development of an electronic tongue

NASA Astrophysics Data System (ADS)

Savoy, Steven M.; Lavigne, John J.; Yoo, J. S.; Wright, John; Rodriguez, Marc; Goodey, Adrian; McDoniel, Bridget; McDevitt, John T.; Anslyn, Eric V.; Shear, Jason B.; Ellington, Andrew D.; Neikirk, Dean P.

1998-12-01

A micromachined sensor array has been developed for the rapid characterization of multi-component mixtures in aqueous media. The sensor functions in a manner analogous to that of the mammalian tongue, using an array composed of individually immobilized polystyrene-polyethylene glycol composite microspheres selectively arranged in micromachined etch cavities localized o n silicon wafers. Sensing occurs via colorimetric or fluorometric changes to indicator molecules that are covalently bound to amine termination sites on the polymeric microspheres. The hybrid micromachined structure has been interfaced directly to a charged-coupled-device that is used for the simultaneous acquisition of the optical data from the individually addressable `taste bud' elements. With the miniature sensor array, acquisition of data streams composed of red, green, and blue color patterns distinctive for the analytes in the solution are rapidly acquired. The unique combination of carefully chosen reporter molecules with water permeable microspheres allows for the simultaneous detection and quantification of a variety of analytes. The fabrication of the sensor structures and the initial colorimetric and fluorescent responses for pH, Ca+2, Ce+3, and sugar are reported. Interface to microfluidic components should also be possible, producing a complete sampling/sensing system.

A new family of β-helix proteins with similarities to the polysaccharide lyases

DOE PAGES

Close, Devin W.; D'Angelo, Sara; Bradbury, Andrew R. M.

2014-09-27

Microorganisms that degrade biomass produce diverse assortments of carbohydrate-active enzymes and binding modules. Despite tremendous advances in the genomic sequencing of these organisms, many genes do not have an ascribed function owing to low sequence identity to genes that have been annotated. Consequently, biochemical and structural characterization of genes with unknown function is required to complement the rapidly growing pool of genomic sequencing data. A protein with previously unknown function (Cthe_2159) was recently isolated in a genome-wide screen using phage display to identify cellulose-binding protein domains from the biomass-degrading bacterium Clostridium thermocellum. Here, the crystal structure of Cthe_2159 is presentedmore » and it is shown that it is a unique right-handed parallel β-helix protein. Despite very low sequence identity to known β-helix or carbohydrate-active proteins, Cthe_2159 displays structural features that are very similar to those of polysaccharide lyase (PL) families 1, 3, 6 and 9. Cthe_2159 is conserved across bacteria and some archaea and is a member of the domain of unknown function family DUF4353. This suggests that Cthe_2159 is the first representative of a previously unknown family of cellulose and/or acid-sugar binding β-helix proteins that share structural similarities with PLs. More importantly, these results demonstrate how functional annotation by biochemical and structural analysis remains a critical tool in the characterization of new gene products.« less

A new family of β-helix proteins with similarities to the polysaccharide lyases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Close, Devin W.; D'Angelo, Sara; Bradbury, Andrew R. M.

Microorganisms that degrade biomass produce diverse assortments of carbohydrate-active enzymes and binding modules. Despite tremendous advances in the genomic sequencing of these organisms, many genes do not have an ascribed function owing to low sequence identity to genes that have been annotated. Consequently, biochemical and structural characterization of genes with unknown function is required to complement the rapidly growing pool of genomic sequencing data. A protein with previously unknown function (Cthe_2159) was recently isolated in a genome-wide screen using phage display to identify cellulose-binding protein domains from the biomass-degrading bacterium Clostridium thermocellum. Here, the crystal structure of Cthe_2159 is presentedmore » and it is shown that it is a unique right-handed parallel β-helix protein. Despite very low sequence identity to known β-helix or carbohydrate-active proteins, Cthe_2159 displays structural features that are very similar to those of polysaccharide lyase (PL) families 1, 3, 6 and 9. Cthe_2159 is conserved across bacteria and some archaea and is a member of the domain of unknown function family DUF4353. This suggests that Cthe_2159 is the first representative of a previously unknown family of cellulose and/or acid-sugar binding β-helix proteins that share structural similarities with PLs. More importantly, these results demonstrate how functional annotation by biochemical and structural analysis remains a critical tool in the characterization of new gene products.« less

Glycation of H1 Histone by 3-Deoxyglucosone: Effects on Protein Structure and Generation of Different Advanced Glycation End Products

PubMed Central

Ashraf, Jalaluddin Mohammad; Rabbani, Gulam; Ahmad, Saheem; Hasan, Qambar; Khan, Rizwan Hasan; Alam, Khursheed; Choi, Inho

2015-01-01

Advanced glycation end products (AGEs) culminate from the non-enzymatic reaction between a free carbonyl group of a reducing sugar and free amino group of proteins. 3-deoxyglucosone (3-DG) is one of the dicarbonyl species that rapidly forms several protein-AGE complexes that are believed to be involved in the pathogenesis of several diseases, particularly diabetic complications. In this study, the generation of AGEs (Nε-carboxymethyl lysine and pentosidine) by 3-DG in H1 histone protein was characterized by evaluating extent of side chain modification (lysine and arginine) and formation of Amadori products as well as carbonyl contents using several physicochemical techniques. Results strongly suggested that 3-DG is a potent glycating agent that forms various intermediates and AGEs during glycation reactions and affects the secondary structure of the H1 protein. Structural changes and AGE formation may influence the function of H1 histone and compromise chromatin structures in cases of secondary diabetic complications. PMID:26121680

Rapid acquisition of beta-sheet structure in the prion protein prior to multimer formation.

PubMed

Post, K; Pitschke, M; Schäfer, O; Wille, H; Appel, T R; Kirsch, D; Mehlhorn, I; Serban, H; Prusiner, S B; Riesner, D

1998-11-01

The N-terminally truncated form of the prion protein, PrP 27-30, and the corresponding recombinant protein, rPrP, were solubilized in 0.2% SDS, and the transitions induced by changing the conditions from 0.2% SDS to physiological conditions, i.e. removing SDS, were characterized with respect to solubility, resistance to proteolysis, secondary structure and multimerization. Circular dichroism, electron microscopy and fluorescence correlation spectroscopy were used to study the structural transitions of PrP. Within one minute the alpha-helical structure of PrP was transformed into one that was enriched in beta-sheets and consisted mainly of dimers. Larger oligomers were found after 20 minutes and larger multimers exhibiting resistance to proteolysis were found after several hours. It was concluded that the monomeric alpha-helical conformation was stable in SDS or when attached to the membrane; however, the state of lowest free energy in aqueous solution at neutral pH seems to be the multimeric, beta-sheet enriched conformation.

Buckligami: Actuation of soft structures through mechanical instabilities

NASA Astrophysics Data System (ADS)

Lazarus, Arnaud; Reis, Pedro

2013-03-01

We present a novel mechanism for actuating soft structures, that is triggered through buckling. Our elastomeric samples are rapid-prototyped using digital fabrication and comprise of a cylindrical shell patterned with an array of voids, each of which is covered by a thin membrane. Decreasing the internal pressure of the structure induces local buckling of the ligaments of the pattern, resulting in controllable folding of the global structure. Using rigid inclusions to plug the voids in specific geometric arrangements allows us to excite a variety of different fundamental motions of the cylindrical shell, including flexure and twist. We refer to this new mechanism of buckling-induced folding as ``buckligami.'' Given that geometry, elasticity and buckling are the underlying ingredients of this local folding mechanism, the global actuation is scalable, reversible and repeatable. Characterization and rationalization of our experiments provide crucial fundamental understanding to aid the design of new scale-independent actuators, with potential implications in the field of soft robotics.

The Dynamic Architectural and Epigenetic Nuclear Landscape: Developing the Genomic Almanac of Biology and Disease

PubMed Central

Tai, Phillip W. L.; Zaidi, Sayyed K.; Wu, Hai; Grandy, Rodrigo A.; Montecino, Martin M.; van Wijnen, André J.; Lian, Jane B.; Stein, Gary S.; Stein, Janet L.

2014-01-01

Compaction of the eukaryotic genome into the confined space of the cell nucleus must occur faithfully throughout each cell cycle to retain gene expression fidelity. For decades, experimental limitations to study the structural organization of the interphase nucleus restricted our understanding of its contributions towards gene regulation and disease. However, within the past few years, our capability to visualize chromosomes in vivo with sophisticated fluorescence microscopy, and to characterize chromosomal regulatory environments via massively-parallel sequencing methodologies have drastically changed how we currently understand epigenetic gene control within the context of three-dimensional nuclear structure. The rapid rate at which information on nuclear structure is unfolding brings challenges to compare and contrast recent observations with historic findings. In this review, we discuss experimental breakthroughs that have influenced how we understand and explore the dynamic structure and function of the nucleus, and how we can incorporate historical perspectives with insights acquired from the ever-evolving advances in molecular biology and pathology. PMID:24242872

Eco-evo-devo in the Study of Adaptive Divergence: Examples from Threespine Stickleback (Gasterosteus aculeatus).

PubMed

Jamniczky, Heather A; Barry, Tegan N; Rogers, Sean M

2015-07-01

The tight fit between form and function in organisms suggests the influence of adaptive evolution in biomechanics; however, the prevalence of adaptive traits, the mechanisms by which they arise and the corresponding responses to selection are subjects of extensive debate. We used three-dimensional microcomputed tomography and geometric morphometrics to characterize the structure of phenotypic covariance within the G. aculeatus trophic apparatus and its supporting structures in wild and controlled crosses of fish from two different localities. Our results reveal that while the structure of phenotypic covariance is conserved in marine and freshwater forms, it may be disrupted in the progeny of artificial crosses or during rapid adaptive divergence events. We discuss these results within the context of integrating covariance structure with quantitative genetics, toward establishing predictive links between genes, development, biomechanics, and the environment. © The Author 2015. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Structure of rapidity divergences in multi-parton scattering soft factors

NASA Astrophysics Data System (ADS)

Vladimirov, Alexey

2018-04-01

We discuss the structure of rapidity divergences that are presented in the soft factors of transverse momentum dependent (TMD) factorization theorems. To provide the discussion on the most general level we consider soft factors for multi-parton scattering. We show that the rapidity divergences are result of the gluon exchanges with the distant transverse plane, and are structurally equivalent to the ultraviolet divergences. It allows to formulate and to prove the renormalization theorem for rapidity divergences. The proof is made with the help the conformal transformation which maps rapidity divergences to ultraviolet divergences. The theorem is the systematic form of the factorization of rapidity divergences, which is required for the definition of TMD parton distributions. In particular, the definition of multi parton distributions is presented. The equivalence of ultraviolet and rapidity divergences leads to the exact relation between soft and rapidity anomalous dimensions. Using this relation we derive the rapidity anomalous dimension at the three-loop order.

Quantifying Standing Dead Tree Volume and Structural Loss with Voxelized Terrestrial Lidar Data

NASA Astrophysics Data System (ADS)

Popescu, S. C.; Putman, E.

2017-12-01

Standing dead trees (SDTs) are an important forest component and impact a variety of ecosystem processes, yet the carbon pool dynamics of SDTs are poorly constrained in terrestrial carbon cycling models. The ability to model wood decay and carbon cycling in relation to detectable changes in tree structure and volume over time would greatly improve such models. The overall objective of this study was to provide automated aboveground volume estimates of SDTs and automated procedures to detect, quantify, and characterize structural losses over time with terrestrial lidar data. The specific objectives of this study were: 1) develop an automated SDT volume estimation algorithm providing accurate volume estimates for trees scanned in dense forests; 2) develop an automated change detection methodology to accurately detect and quantify SDT structural loss between subsequent terrestrial lidar observations; and 3) characterize the structural loss rates of pine and oak SDTs in southeastern Texas. A voxel-based volume estimation algorithm, "TreeVolX", was developed and incorporates several methods designed to robustly process point clouds of varying quality levels. The algorithm operates on horizontal voxel slices by segmenting the slice into distinct branch or stem sections then applying an adaptive contour interpolation and interior filling process to create solid reconstructed tree models (RTMs). TreeVolX estimated large and small branch volume with an RMSE of 7.3% and 13.8%, respectively. A voxel-based change detection methodology was developed to accurately detect and quantify structural losses and incorporated several methods to mitigate the challenges presented by shifting tree and branch positions as SDT decay progresses. The volume and structural loss of 29 SDTs, composed of Pinus taeda and Quercus stellata, were successfully estimated using multitemporal terrestrial lidar observations over elapsed times ranging from 71 - 753 days. Pine and oak structural loss rates were characterized by estimating the amount of volumetric loss occurring in 20 equal-interval height bins of each SDT. Results showed that large pine snags exhibited more rapid structural loss in comparison to medium-sized oak snags in this study.

Targeting the untargeted in molecular phenomics with structurally-selective ion mobility-mass spectrometry.

PubMed

May, Jody Christopher; Gant-Branum, Randi Lee; McLean, John Allen

2016-06-01

Systems-wide molecular phenomics is rapidly expanding through technological advances in instrumentation and bioinformatics. Strategies such as structural mass spectrometry, which utilizes size and shape measurements with molecular weight, serve to characterize the sum of molecular expression in biological contexts, where broad-scale measurements are made that are interpreted through big data statistical techniques to reveal underlying patterns corresponding to phenotype. The data density, data dimensionality, data projection, and data interrogation are all critical aspects of these approaches to turn data into salient information. Untargeted molecular phenomics is already having a dramatic impact in discovery science from drug discovery to synthetic biology. It is evident that these emerging techniques will integrate closely in broad efforts aimed at precision medicine. Copyright © 2016 Elsevier Ltd. All rights reserved.

Molecular structure of P2X receptors.

PubMed

Egan, Terrance M; Cox, Jane A; Voigt, Mark M

2004-01-01

P2X receptors are ligand-gated ion channels that transduce many of the physiological effects of extracellular ATP. There has been a dramatic increase in awareness of these receptors over the past 5 or so years, in great part due to their molecular cloning and characterization. The availability of cDNA clones for the various subunits has led to rapid progress in identifying their tissue-specific expression, resulting in new ideas concerning the functional roles these receptors might play in physiological and pathophysiological processes. In addition, molecular approaches have yielded much information regarding the structure and function of the receptor proteins themselves. In this review we seek to review recent findings concerning the molecular determinants of receptor-channel function, with particular focus on ligand binding and gating, ion selectivity, and subunit assembly.

Rapid crystallization of externally produced ions in a Penning trap

NASA Astrophysics Data System (ADS)

Murböck, T.; Schmidt, S.; Birkl, G.; Nörtershäuser, W.; Thompson, R. C.; Vogel, M.

2016-10-01

We have studied the cooling dynamics, formation process, and geometric structure of mesoscopic crystals of externally produced magnesium ions in a Penning trap. We present a cooling model and measurements for a combination of buffer gas cooling and laser cooling which has been found to reduce the ion kinetic energy by eight orders of magnitude from several hundreds of eV to μ eV and below within seconds. With ion numbers of the order of 1 ×103 to 1 ×105 , such cooling leads to the formation of ion Coulomb crystals which display a characteristic shell structure in agreement with the theory of non-neutral plasmas. We show the production and characterization of two-species ion crystals as a means of sympathetic cooling of ions lacking a suitable laser-cooling transition.

Efficient and optimized identification of generalized Maxwell viscoelastic relaxation spectra

PubMed Central

Babaei, Behzad; Davarian, Ali; Pryse, Kenneth M.; Elson, Elliot L.; Genin, Guy M.

2017-01-01

Viscoelastic relaxation spectra are essential for predicting and interpreting the mechanical responses of materials and structures. For biological tissues, these spectra must usually be estimated from viscoelastic relaxation tests. Interpreting viscoelastic relaxation tests is challenging because the inverse problem is expensive computationally. We present here an efficient algorithm that enables rapid identification of viscoelastic relaxation spectra. The algorithm was tested against trial data to characterize its robustness and identify its limitations and strengths. The algorithm was then applied to identify the viscoelastic response of reconstituted collagen, revealing an extensive distribution of viscoelastic time constants. PMID:26523785

Synthesis and characterization of Pd(II)-methyl complexes with N-heterocyclic carbene-amine ligands.

PubMed

Warsink, Stefan; de Boer, Sandra Y; Jongens, Lianne M; Fu, Ching-Feng; Liu, Shiuh-Tzung; Chen, Jwu-Ting; Lutz, Martin; Spek, Anthony L; Elsevier, Cornelis J

2009-09-21

A number of palladium(ii) complexes with a heteroditopic NHC-amine ligand and their precursor silver(i) carbene complexes have been efficiently prepared and their structural features have been investigated. The heteroditopic coordination of this ligand class was unequivocally shown by NMR-spectroscopy and X-ray crystallographic analysis. The neutral and cationic cis-methyl-palladium(NHC) complexes are not prone to reductive elimination, which is normally a major degenerative pathway for this type of complex. In contrast, under carbon monoxide atmosphere rapid reductive elimination of the acyl-imidazolium salt was observed.

Raman Spectroscopy of Microbial Pigments

PubMed Central

Edwards, Howell G. M.; Oren, Aharon

2014-01-01

Raman spectroscopy is a rapid nondestructive technique providing spectroscopic and structural information on both organic and inorganic molecular compounds. Extensive applications for the method in the characterization of pigments have been found. Due to the high sensitivity of Raman spectroscopy for the detection of chlorophylls, carotenoids, scytonemin, and a range of other pigments found in the microbial world, it is an excellent technique to monitor the presence of such pigments, both in pure cultures and in environmental samples. Miniaturized portable handheld instruments are available; these instruments can be used to detect pigments in microbiological samples of different types and origins under field conditions. PMID:24682303

Overview of methods in RNA nanotechnology: synthesis, purification, and characterization of RNA nanoparticles.

PubMed

Haque, Farzin; Guo, Peixuan

2015-01-01

RNA nanotechnology encompasses the use of RNA as a construction material to build homogeneous nanostructures by bottom-up self-assembly with defined size, structure, and stoichiometry; this pioneering concept demonstrated in 1998 (Guo et al., Molecular Cell 2:149-155, 1998; featured in Cell) has emerged as a new field that also involves materials engineering and synthetic structural biology (Guo, Nature Nanotechnology 5:833-842, 2010). The field of RNA nanotechnology has skyrocketed over the last few years, as evidenced by the burst of publications in prominent journals on RNA nanostructures and their applications in nanomedicine and nanotechnology. Rapid advances in RNA chemistry, RNA biophysics, and RNA biology have created new opportunities for translating basic science into clinical practice. RNA nanotechnology holds considerable promise in this regard. Increased evidence also suggests that substantial part of the 98.5 % of human genome (Lander et al. Nature 409:860-921, 2001) that used to be called "junk DNA" actually codes for noncoding RNA. As we understand more on how RNA structures are related to function, we can fabricate synthetic RNA nanoparticles for the diagnosis and treatment of diseases. This chapter provides a brief overview of the field regarding the design, construction, purification, and characterization of RNA nanoparticles for diverse applications in nanotechnology and nanomedicince.

Preparation, Characterization and Properties of Alginate/Poly(γ-glutamic acid) Composite Microparticles

PubMed Central

Tong, Zongrui; Chen, Yu; Liu, Yang; Tong, Li; Chu, Jiamian; Xiao, Kecen; Zhou, Zhiyu; Dong, Wenbo; Chu, Xingwu

2017-01-01

Alginate (Alg) is a renewable polymer with excellent hemostatic properties and biocapability and is widely used for hemostatic wound dressing. However, the swelling properties of alginate-based wound dressings need to be promoted to meet the requirements of wider application. Poly(γ-glutamic acid) (PGA) is a natural polymer with high hydrophility. In the current study, novel Alg/PGA composite microparticles with double network structure were prepared by the emulsification/internal gelation method. It was found from the structure characterization that a double network structure was formed in the composite microparticles due to the ion chelation interaction between Ca2+ and the carboxylate groups of Alg and PGA and the electrostatic interaction between the secondary amine group of PGA and the carboxylate groups of Alg and PGA. The swelling behavior of the composite microparticles was significantly improved due to the high hydrophility of PGA. Influences of the preparing conditions on the swelling behavior of the composites were investigated. The porous microparticles could be formed while compositing of PGA. Thermal stability was studied by thermogravimetric analysis method. Moreover, in vitro cytocompatibility test of microparticles exhibited good biocompatibility with L929 cells. All results indicated that such Alg/PGA composite microparticles are a promising candidate in the field of wound dressing for hemostasis or rapid removal of exudates. PMID:28398222

Phosphate uptake studies of cross-linked chitosan bead materials.

PubMed

Mahaninia, Mohammad H; Wilson, Lee D

2017-01-01

A systematic experimental study is reported that provides a molecular based understanding of cross-linked chitosan beads and their adsorption properties in aqueous solution containing phosphate dianion (HPO 4 2- ) species. Synthetically modified chitosan using epichlorohydrin and glutaraldehyde cross-linkers result in surface modified beads with variable hydrophile-lipophile character and tunable HPO 4 2- uptake properties. The kinetic and thermodynamic adsorption properties of cross-linked chitosan beads with HPO 4 2- species were studied in aqueous solution. Complementary structure and physicochemical characterization of chitosan beads via potentiometry, Raman spectroscopy, DSC, and dye adsorption measurements was carried out to establish structure-property relationships. The maximum uptake (Q m ) of bead systems with HPO 4 2- at equilibrium was 52.1mgg -1 ; whereas, kinetic uptake results for chitosan bead/phosphate systems are relatively rapid (0.111-0.113min -1 ) with an intraparticle diffusion rate-limiting step. The adsorption process follows a multi-step pathway involving inner- and outer-sphere complexes with significant changes in hydration. Phosphate uptake strongly depends on the composition and type of cross-linker used for preparation of chitosan beads. The adsorption isotherms and structural characterization of bead systems illustrate the role of surface charge, hydrophile-lipophile balance, adsorption site accessibility, and hydration properties of the chitosan bead surface. Copyright © 2016 Elsevier Inc. All rights reserved.

Preparation, Characterization and Properties of Alginate/Poly(γ-glutamic acid) Composite Microparticles.

PubMed

Tong, Zongrui; Chen, Yu; Liu, Yang; Tong, Li; Chu, Jiamian; Xiao, Kecen; Zhou, Zhiyu; Dong, Wenbo; Chu, Xingwu

2017-04-11

Alginate (Alg) is a renewable polymer with excellent hemostatic properties and biocapability and is widely used for hemostatic wound dressing. However, the swelling properties of alginate-based wound dressings need to be promoted to meet the requirements of wider application. Poly( γ -glutamic acid) (PGA) is a natural polymer with high hydrophility. In the current study, novel Alg/PGA composite microparticles with double network structure were prepared by the emulsification/internal gelation method. It was found from the structure characterization that a double network structure was formed in the composite microparticles due to the ion chelation interaction between Ca 2+ and the carboxylate groups of Alg and PGA and the electrostatic interaction between the secondary amine group of PGA and the carboxylate groups of Alg and PGA. The swelling behavior of the composite microparticles was significantly improved due to the high hydrophility of PGA. Influences of the preparing conditions on the swelling behavior of the composites were investigated. The porous microparticles could be formed while compositing of PGA. Thermal stability was studied by thermogravimetric analysis method. Moreover, in vitro cytocompatibility test of microparticles exhibited good biocompatibility with L929 cells. All results indicated that such Alg/PGA composite microparticles are a promising candidate in the field of wound dressing for hemostasis or rapid removal of exudates.

Materials, structures, and devices for high-speed electronics

NASA Technical Reports Server (NTRS)

Woollam, John A.; Snyder, Paul G.

1992-01-01

Advances in materials, devices, and instrumentation made under this grant began with ex-situ null ellipsometric measurements of simple dielectric films on bulk substrates. Today highly automated and rapid spectroscopic ellipsometers are used for ex-situ characterization of very complex multilayer epitaxial structures. Even more impressive is the in-situ capability, not only for characterization but also for the actual control of the growth and etching of epitaxial layers. Spectroscopic ellipsometry has expanded from the research lab to become an integral part of the production of materials and structures for state of the art high speed devices. Along the way, it has contributed much to our understanding of the growth characteristics and material properties. The following areas of research are summarized: Si3N4 on GaAs, null ellipsometry; diamondlike carbon films; variable angle spectroscopic ellipsometry (VASE) development; GaAs-AlGaAs heterostructures; Ta-Cu diffusion barrier films on GaAs; GaAs-AlGaAs superlattices and multiple quantum wells; superconductivity; in situ elevated temperature measurements of III-V's; optical constants of thermodynamically stable InGaAs; doping dependence of optical constants of GaAs; in situ ellipsometric studies of III-V epitaxial growth; photothermal spectroscopy; microellipsometry; and Si passivation and Si/SiGe strained-layer superlattices.

Physicochemical characterization and structural evaluation of a specific 2:1 cocrystal of naproxen-nicotinamide.

PubMed

Ando, Shigeru; Kikuchi, Junko; Fujimura, Yuko; Ida, Yasuo; Higashi, Kenjirou; Moribe, Kunikazu; Yamamoto, Keiji

2012-09-01

Physicochemical characterization and structural evaluation of a 2:1 naproxen-nicotinamide cocrystal were performed. The 2:1 cocrystal showed rapid naproxen dissolution and less water vapor adsorption, indicating better pharmaceutical properties of naproxen. The unique 2:1 cocrystal formation was evaluated by solid-state nuclear magnetic resonance (NMR). The assignments of all H and (13) C peaks for naproxen and the cocrystal were performed using dipolar-insensitive nuclei enhanced by polarization transfer and (1) H-(13) C cross-polarization (CP)-heteronuclear correlation (HETCOR) NMR measurements. The (13) C chemical shift revealed that two naproxen molecules and one nicotinamide molecule existed in the asymmetric unit of the cocrystal. The (1) H chemical shifts indicated that the carboxylic group of the naproxen in the cocrystal was nonionized, and the CH-π interaction between naproxens was very strong. From the (1) H-(13) C CP-HETCOR NMR spectrum with contact time of 5 ms, two different synthons, carboxylic acid-amide and carboxylic acid-pyridine ring, were found between naproxen and nicotinamide. Single-crystal X-ray analysis, which supported the solid-state NMR results, clarified the geometry and intermolecular interactions in more detail. The structure is unique among pharmaceutical cocrystals because each carboxyl group of the two naproxens formed different intermolecular synthons. Copyright © 2012 Wiley Periodicals, Inc.

Characterization of the Saccharomyces Golgi complex through the cell cycle by immunoelectron microscopy.

PubMed Central

Preuss, D; Mulholland, J; Franzusoff, A; Segev, N; Botstein, D

1992-01-01

The membrane compartments responsible for Golgi functions in wild-type Saccharomyces cerevisiae were identified and characterized by immunoelectron microscopy. Using improved fixation methods, Golgi compartments were identified by labeling with antibodies specific for alpha 1-6 mannose linkages, the Sec7 protein, or the Ypt1 protein. The compartments labeled by each of these antibodies appear as disk-like structures that are apparently surrounded by small vesicles. Yeast Golgi typically are seen as single, isolated cisternae, generally not arranged into parallel stacks. The location of the Golgi structures was monitored by immunoelectron microscopy through the yeast cell cycle. Several Golgi compartments, apparently randomly distributed, were always observed in mother cells. During the initiation of new daughter cells, additional Golgi structures cluster just below the site of bud emergence. These Golgi enter daughter cells at an early stage, raising the possibility that much of the bud's growth might be due to secretory vesicles formed as well as consumed entirely within the daughter. During cytokinesis, the Golgi compartments are concentrated near the site of cell wall synthesis. Clustering of Golgi both at the site of bud formation and at the cell septum suggests that these organelles might be directed toward sites of rapid cell surface growth. Images PMID:1381247

Fibroblast Growth Factor Signaling Mediates Pulmonary Endothelial Glycocalyx Reconstitution

PubMed Central

Yang, Yimu; Haeger, Sarah M.; Suflita, Matthew A.; Zhang, Fuming; Dailey, Kyrie L.; Colbert, James F.; Ford, Joshay A.; Picon, Mario A.; Stearman, Robert S.; Lin, Lei; Liu, Xinyue; Han, Xiaorui; Linhardt, Robert J.

2017-01-01

The endothelial glycocalyx is a heparan sulfate (HS)–rich endovascular structure critical to endothelial function. Accordingly, endothelial glycocalyx degradation during sepsis contributes to tissue edema and organ injury. We determined the endogenous mechanisms governing pulmonary endothelial glycocalyx reconstitution, and if these reparative mechanisms are impaired during sepsis. We performed intravital microscopy of wild-type and transgenic mice to determine the rapidity of pulmonary endothelial glycocalyx reconstitution after nonseptic (heparinase-III mediated) or septic (cecal ligation and puncture mediated) endothelial glycocalyx degradation. We used mass spectrometry, surface plasmon resonance, and in vitro studies of human and mouse samples to determine the structure of HS fragments released during glycocalyx degradation and their impact on fibroblast growth factor receptor (FGFR) 1 signaling, a mediator of endothelial repair. Homeostatic pulmonary endothelial glycocalyx reconstitution occurred rapidly after nonseptic degradation and was associated with induction of the HS biosynthetic enzyme, exostosin (EXT)-1. In contrast, sepsis was characterized by loss of pulmonary EXT1 expression and delayed glycocalyx reconstitution. Rapid glycocalyx recovery after nonseptic degradation was dependent upon induction of FGFR1 expression and was augmented by FGF-promoting effects of circulating HS fragments released during glycocalyx degradation. Although sepsis-released HS fragments maintained this ability to activate FGFR1, sepsis was associated with the downstream absence of reparative pulmonary endothelial FGFR1 induction. Sepsis may cause vascular injury not only via glycocalyx degradation, but also by impairing FGFR1/EXT1–mediated glycocalyx reconstitution. PMID:28187268

Rapid Mueller matrix polarimetry imaging based on four photoelastic modulators with no moving parts (Conference Presentation)

NASA Astrophysics Data System (ADS)

Gribble, Adam; Alali, Sanaz; Vitkin, Alex

2016-03-01

Polarized light has many applications in biomedical imaging. The interaction of a biological sample with polarized light reveals information about its composition, both structural and functional. For example, the polarimetry-derived metric of linear retardance (birefringence) is dependent on tissue structural organization (anisotropy) and can be used to diagnose myocardial infarct; circular birefringence (optical rotation) can measure glucose concentrations. The most comprehensive type of polarimetry analysis is to measure the Mueller matrix, a polarization transfer function that completely describes how a sample interacts with polarized light. To derive this 4x4 matrix it is necessary to observe how a tissue interacts with different polarizations. A well-suited approach for tissue polarimetry is to use photoelastic modulators (PEMs), which dynamically modulate the polarization of light. Previously, we have demonstrated a rapid time-gated Stokes imaging system that is capable of characterizing the state of polarized light (the Stokes vector) over a large field, after interacting with any turbid media. This was accomplished by synchronizing CCD camera acquisition times relative to two PEMs using a field-programmable gate array (FPGA). Here, we extend this technology to four PEMs, yielding a polarimetry system that is capable of rapidly measuring the complete sample Mueller matrix over a large field of view, with no moving parts and no beam steering. We describe the calibration procedure and evaluate the accuracy of the measurements. Results are shown for tissue-mimicking phantoms, as well as initial biological samples.

Synchronization properties of heterogeneous neuronal networks with mixed excitability type

NASA Astrophysics Data System (ADS)

Leone, Michael J.; Schurter, Brandon N.; Letson, Benjamin; Booth, Victoria; Zochowski, Michal; Fink, Christian G.

2015-03-01

We study the synchronization of neuronal networks with dynamical heterogeneity, showing that network structures with the same propensity for synchronization (as quantified by master stability function analysis) may develop dramatically different synchronization properties when heterogeneity is introduced with respect to neuronal excitability type. Specifically, we investigate networks composed of neurons with different types of phase response curves (PRCs), which characterize how oscillating neurons respond to excitatory perturbations. Neurons exhibiting type 1 PRC respond exclusively with phase advances, while neurons exhibiting type 2 PRC respond with either phase delays or phase advances, depending on when the perturbation occurs. We find that Watts-Strogatz small world networks transition to synchronization gradually as the proportion of type 2 neurons increases, whereas scale-free networks may transition gradually or rapidly, depending upon local correlations between node degree and excitability type. Random placement of type 2 neurons results in gradual transition to synchronization, whereas placement of type 2 neurons as hubs leads to a much more rapid transition, showing that type 2 hub cells easily "hijack" neuronal networks to synchronization. These results underscore the fact that the degree of synchronization observed in neuronal networks is determined by a complex interplay between network structure and the dynamical properties of individual neurons, indicating that efforts to recover structural connectivity from dynamical correlations must in general take both factors into account.

Dynamic Motion and Communication in the Streptococcal C1 Phage Lysin, PlyC

PubMed Central

Reboul, Cyril F.; Cowieson, Nathan P.; Costa, Mauricio G. S.; Kass, Itamar; Jackson, Colin; Perahia, David; Buckle, Ashley M.; McGowan, Sheena

2015-01-01

The growing problem of antibiotic resistance underlies the critical need to develop new treatments to prevent and control resistant bacterial infection. Exogenous application of bacteriophage lysins results in rapid and specific destruction of Gram-positive bacteria and therefore lysins represent novel antibacterial agents. The PlyC phage lysin is the most potent lysin characterized to date and can rapidly lyse Group A, C and E streptococci. Previously, we have determined the X-ray crystal structure of PlyC, revealing a complicated and unique arrangement of nine proteins. The scaffold features a multimeric cell-wall docking assembly bound to two catalytic domains that communicate and work synergistically. However, the crystal structure appeared to be auto-inhibited and raised important questions as to the mechanism underlying its extreme potency. Here we use small angle X-ray scattering (SAXS) and reveal that the conformational ensemble of PlyC in solution is different to that in the crystal structure. We also investigated the flexibility of the enzyme using both normal mode (NM) analysis and molecular dynamics (MD) simulations. Consistent with our SAXS data, MD simulations show rotational dynamics of both catalytic domains, and implicate inter-domain communication in achieving a substrate-ready conformation required for enzyme function. Our studies therefore provide insights into how the domains in the PlyC holoenzyme may act together to achieve its extraordinary potency. PMID:26470022

Dendritic growth and structure of undercooled nickel base alloys

NASA Technical Reports Server (NTRS)

Flemings, M. C.; Shiohara, Y.

1988-01-01

The principal objectives of this overall investigation are to: study means for obtaining high undercooling in levitation melted droplets, and study structures produced upon the solidification of these undercooled specimens. Thermal measurements are made of the undercooling, and of the rapid recalescence, to develop an understanding of the solidification mechanism. Comparison of results is made with the modeling studies. Characterization and metallographic work is done to gain an understanding of the relationship between rapid solidification variables and the structures so produced. In ground based work to date, solidification of undercooled Ni-25 wt percent Sn alloy was observed by high-speed cinematography and the results compared with optical temperature measurements. Also in ground based work, high-speed optical temperature measurements were made of the solidification behavior of levitated metal samples within a transparent glass medium. Two undercooled Ni-Sn alloys were examined. Measurements were carried out on samples at undercoolings up to 330 K. Microstructures of samples produced in ground based work were determined by optical metallography and by SEM, and microsegregation by electron microprobe measurements. A series of flight tests were planned to conduct experiments similar to the ground based experiments. The Space Shuttle Columbia carried an alloy undercooled experiment in the STS 61-C mission in January 1986. A sample of Ni-32.5 wt percent Sn eutectic was melted and solidified under microgravity conditions.

Human cortical organization for processing vocalizations indicates representation of harmonic structure as a signal attribute

PubMed Central

Lewis, James W.; Talkington, William J.; Walker, Nathan A.; Spirou, George A.; Jajosky, Audrey; Frum, Chris

2009-01-01

The ability to detect and rapidly process harmonic sounds, which in nature are typical of animal vocalizations and speech, can be critical for communication among conspecifics and for survival. Single-unit studies have reported neurons in auditory cortex sensitive to specific combinations of frequencies (e.g. harmonics), theorized to rapidly abstract or filter for specific structures of incoming sounds, where large ensembles of such neurons may constitute spectral templates. We studied the contribution of harmonic structure to activation of putative spectral templates in human auditory cortex by using a wide variety of animal vocalizations, as well as artificially constructed iterated rippled noises (IRNs). Both the IRNs and vocalization sounds were quantitatively characterized by calculating a global harmonics-to-noise ratio (HNR). Using fMRI we identified HNR-sensitive regions when presenting either artificial IRNs and/or recordings of natural animal vocalizations. This activation included regions situated between functionally defined primary auditory cortices and regions preferential for processing human non-verbal vocalizations or speech sounds. These results demonstrate that the HNR of sound reflects an important second-order acoustic signal attribute that parametrically activates distinct pathways of human auditory cortex. Thus, these results provide novel support for putative spectral templates, which may subserve a major role in the hierarchical processing of vocalizations as a distinct category of behaviorally relevant sound. PMID:19228981

Rapid Characterization of Spider Silk Genes via Exon Capture

DTIC Science & Technology

2015-03-28

SECURITY CLASSIFICATION OF: Spider silks are high-performance materials with an array of potential military and civilian applications. As such, there...is persistent demand for the mass production of silks, which requires knowledge of the underlying silk gene sequences. Spidroins ( spider fibroins...2015 1-May-2014 31-Jan-2015 Approved for Public Release; Distribution Unlimited Final Report: Rapid Characterization of Spider Silk Genes via Exon

Low-Dimensional Network Formation in Molten Sodium Carbonate

PubMed Central

Wilding, Martin C.; Wilson, Mark; Alderman, Oliver L. G.; Benmore, Chris; Weber, J. K. R.; Parise, John B.; Tamalonis, Anthony; Skinner, Lawrie

2016-01-01

Molten carbonates are highly inviscid liquids characterized by low melting points and high solubility of rare earth elements and volatile molecules. An understanding of the structure and related properties of these intriguing liquids has been limited to date. We report the results of a study of molten sodium carbonate (Na2CO3) which combines high energy X-ray diffraction, containerless techniques and computer simulation to provide insight into the liquid structure. Total structure factors (Fx(Q)) are collected on the laser-heated carbonate spheres suspended in flowing gases of varying composition in an aerodynamic levitation furnace. The respective partial structure factor contributions to Fx(Q) are obtained by performing molecular dynamics simulations treating the carbonate anions as flexible entities. The carbonate liquid structure is found to be heavily temperature-dependent. At low temperatures a low-dimensional carbonate chain network forms, at T = 1100 K for example ~55% of the C atoms form part of a chain. The mean chain lengths decrease as temperature is increased and as the chains become shorter the rotation of the carbonate anions becomes more rapid enhancing the diffusion of Na+ ions. PMID:27080401

Structural origin underlying poor glass forming ability of Al metallic glass

NASA Astrophysics Data System (ADS)

Li, F.; Liu, X. J.; Hou, H. Y.; Chen, G.; Chen, G. L.

2011-07-01

We performed molecular dynamics simulations to study the glass formation and local atomic structure of rapidly quenched Al. Both potential energy and structural parameters indicate that the glass transition temperature of amorphous Al is as low as 300 K, which may lead to the poor thermal stability of the amorphous Al as it is prone to crystallize even at room temperature. Voronoi polyhedra analysis reveals that the most popular polyhedron is the deformed body-centered cubic (bcc) cluster characterized by the index < 0, 3, 6, 4 > in the amorphous Al, while the icosahedron with the index < 0, 0, 12, 0 > is always predominant in bulk metallic glass formers with excellent glass forming ability (GFA). Moreover, these deformed-bcc short-range orders can make up medium-range orders via the linkage of vertex-, edge-, face-, intercrossed-shared atoms, which are believed to more easily transform into face-centered cubic (fcc) Al nanocrystal compared with the icosahedral clusters in terms of the symmetrical similarity between bcc and fcc structures. This finding could unveil the structural origin of poor GFA of Al-based alloys.

Structural characterization of ZnCl2 modified tellurite based glasses

NASA Astrophysics Data System (ADS)

Dhankhar, Sunil; Kundu, R. S.; Punia, R.; Sunita, Parmar, R.; Sanjay, Kishore, N.

2016-05-01

Glass composition 70 TeO2-(30-x) BaO - x ZnCl2; x = 5, 10, 15, 20 and 25 have been prepared by rapid melt quenching technique under controlled atmospheric conditions. Amorphous nature of the samples was confirmed by x-ray diffractogram. The glass transition temperature (Tg) has been determined using differential scanning calorimetry (DSC) and its value is observed to decrease with increase in ZnCl2 content. The peaks in the Raman and FTIR spectra have been estimated by deconvolutation of the spectra and each of deconvoluted spectra exhibits several peaks. IR and Raman spectra of the present glass system indicate that TeO2 exists as TeO3 trigonal pyramidal (tp), TeO4 trigonal bipyramidal (tbp) and TeO6 polyhedra structural units. With increase in zinc halide content, transformation of some of TeO4 structural units into TeO3 structural units is observed Increase in TeO3 structural units shows that non-bridging oxygen contribution increases which confirms the decrease in glass transition temperature.

A simple and effective approach towards biomimetic replication of photonic structures from butterfly wings.

PubMed

Zhu, Shenmin; Zhang, Di; Chen, Zhixin; Gu, Jiajun; Li, Wenfei; Jiang, Haibo; Zhou, Gang

2009-08-05

A general sonochemical process is reported for the replication of photonic structures from Morpho butterfly wings in several hours. By selecting appropriate precursors, we can achieve exact replications of photonic structures in a variety of transparent metal oxides, such as titania, tin oxide and silica. The exact replications at the micro- and nanoscales were characterized by a combination of FE-SEM, TEM, EDX and Raman measurements. The optical properties of the replicas were investigated by using reflectance spectroscopy, and it was found that the interesting chromaticity of the reflected light could be adjusted simply by tuning the replica materials. An ultrasensitive SnO(2)-based chemical sensor was prepared from the SnO(2) replica. The sensor has a sensitivity of 35.3-50 ppm ethanol at 300 degrees C, accompanied by a rapid response and recovery (around 8-15 s), owing to its large surface area and photonic structure. Thus, this process could be developed to produce photonic structural ceramics which could be used in many passive and active infrared devices, especially high performance optical components and sensors.

Effects of Accelerated Deglaciation on Chemical Characteristics of Sub-arctic Lakes and Rivers in South and West Iceland

NASA Astrophysics Data System (ADS)

Ritter, M.; Strock, K.; Edwards, B. R.

2017-12-01

Glaciers and their associated paraglacial landscapes have changed rapidly over the past century, and may see increased rates of melt as temperatures increase in high latitude environments. As glaciers recede, glacial meltwater subsidies increase to inland freshwater systems, influencing their structure and function. Evidence suggests melting ice influences the chemical characteristics of systems by providing nutrient subsidies, while inputs of glacial flour influence their physical structure by affecting temperature, reducing water clarity and increasing turbidity. Together, changes in physical and chemical structure of these systems have subsequent effects on biota, with the potential to lower taxonomic richness. This study characterized the chemistry of rivers and lakes fed by glacial meltwater in sub-arctic environments of Iceland, where there is limited limnological data. The survey characterized nutrient chemistry, dissolved organic carbon, and ion chemistry. We surveyed glacial meltwater from six glaciers in south and west Iceland, using the drainage basin of Gigjökull glacier along the southern coast as a detailed study area to examine the interactions between groundwater and surface runoff. The southern systems, within the Eastern Volcanic Zone, have minimal soil development and active volcanoes produce ash input to lakes. Lakes in the Western Volcanic Zone were more diverse, located in older bedrock with more extensively weathered soil. Key differences were observed between aquatic environments subsidized with glacial meltwater and those without. This included physical effects, such as lower temperatures and chemical effects such as lower conductivity and higher pH in glacially fed systems. In the drainage basin of Gigjökull glacier, lakes formed after the former lagoon was emptied and then partly refilled with debris from jokulhlaups during the 2010 Eyjafjallajökull eruption. These newly formed lakes resembled non-glacial melt systems despite receiving glacial melt via indirect pathways. The effects of changing glacial inputs to inland freshwater systems are complex, and will be felt over a wide range of time scales. The systems in Gigjökull basin suggest once systems no longer receive glacial surface water melt, they will experience rapid shifts in physical and chemical structure.

Structure Prediction and Analysis of DNA Transposon and LINE Retrotransposon Proteins*

PubMed Central

Abrusán, György; Zhang, Yang; Szilágyi, András

2013-01-01

Despite the considerable amount of research on transposable elements, no large-scale structural analyses of the TE proteome have been performed so far. We predicted the structures of hundreds of proteins from a representative set of DNA and LINE transposable elements and used the obtained structural data to provide the first general structural characterization of TE proteins and to estimate the frequency of TE domestication and horizontal transfer events. We show that 1) ORF1 and Gag proteins of retrotransposons contain high amounts of structural disorder; thus, despite their very low conservation, the presence of disordered regions and probably their chaperone function is conserved. 2) The distribution of SCOP classes in DNA transposons and LINEs indicates that the proteins of DNA transposons are more ancient, containing folds that already existed when the first cellular organisms appeared. 3) DNA transposon proteins have lower contact order than randomly selected reference proteins, indicating rapid folding, most likely to avoid protein aggregation. 4) Structure-based searches for TE homologs indicate that the overall frequency of TE domestication events is low, whereas we found a relatively high number of cases where horizontal transfer, frequently involving parasites, is the most likely explanation for the observed homology. PMID:23530042

Automated Recognition of RNA Structure Motifs by Their SHAPE Data Signatures.

PubMed

Radecki, Pierce; Ledda, Mirko; Aviran, Sharon

2018-06-14

High-throughput structure profiling (SP) experiments that provide information at nucleotide resolution are revolutionizing our ability to study RNA structures. Of particular interest are RNA elements whose underlying structures are necessary for their biological functions. We previously introduced patteRNA , an algorithm for rapidly mining SP data for patterns characteristic of such motifs. This work provided a proof-of-concept for the detection of motifs and the capability of distinguishing structures displaying pronounced conformational changes. Here, we describe several improvements and automation routines to patteRNA . We then consider more elaborate biological situations starting with the comparison or integration of results from searches for distinct motifs and across datasets. To facilitate such analyses, we characterize patteRNA ’s outputs and describe a normalization framework that regularizes results. We then demonstrate that our algorithm successfully discerns between highly similar structural variants of the human immunodeficiency virus type 1 (HIV-1) Rev response element (RRE) and readily identifies its exact location in whole-genome structure profiles of HIV-1. This work highlights the breadth of information that can be gleaned from SP data and broadens the utility of data-driven methods as tools for the detection of novel RNA elements.

Genomics and structure/function studies of Rhabdoviridae proteins involved in replication and transcription.

PubMed

Assenberg, R; Delmas, O; Morin, B; Graham, S C; De Lamballerie, X; Laubert, C; Coutard, B; Grimes, J M; Neyts, J; Owens, R J; Brandt, B W; Gorbalenya, A; Tucker, P; Stuart, D I; Canard, B; Bourhy, H

2010-08-01

Some mammalian rhabdoviruses may infect humans, and also infect invertebrates, dogs, and bats, which may act as vectors transmitting viruses among different host species. The VIZIER programme, an EU-funded FP6 program, has characterized viruses that belong to the Vesiculovirus, Ephemerovirus and Lyssavirus genera of the Rhabdoviridae family to perform ground-breaking research on the identification of potential new drug targets against these RNA viruses through comprehensive structural characterization of the replicative machinery. The contribution of VIZIER programme was of several orders. First, it contributed substantially to research aimed at understanding the origin, evolution and diversity of rhabdoviruses. This diversity was then used to obtain further structural information on the proteins involved in replication. Two strategies were used to produce recombinant proteins by expression of both full length or domain constructs in either E. coli or insect cells, using the baculovirus system. In both cases, parallel cloning and expression screening at small-scale of multiple constructs based on different viruses including the addition of fusion tags, was key to the rapid generation of expression data. As a result, some progress has been made in the VIZIER programme towards dissecting the multi-functional L protein into components suitable for structural and functional studies. However, the phosphoprotein polymerase co-factor and the structural matrix protein, which play a number of roles during viral replication and drives viral assembly, have both proved much more amenable to structural biology. Applying the multi-construct/multi-virus approach central to protein production processes in VIZIER has yielded new structural information which may ultimately be exploitable in the derivation of novel ways of intervening in viral replication. Copyright 2010 Elsevier B.V. All rights reserved.

Real-time subsecond voltammetric analysis of Pb in aqueous environmental samples.

PubMed

Yang, Yuanyuan; Pathirathna, Pavithra; Siriwardhane, Thushani; McElmurry, Shawn P; Hashemi, Parastoo

2013-08-06

Lead (Pb) pollution is an important environmental and public health concern. Rapid Pb transport during stormwater runoff significantly impairs surface water quality. The ability to characterize and model Pb transport during these events is critical to mitigating its impact on the environment. However, Pb analysis is limited by the lack of analytical methods that can afford rapid, sensitive measurements in situ. While electrochemical methods have previously shown promise for rapid Pb analysis, they are currently limited in two ways. First, because of Pb's limited solubility, test solutions that are representative of environmental systems are not typically employed in laboratory characterizations. Second, concerns about traditional Hg electrode toxicity, stability, and low temporal resolution have dampened opportunities for in situ analyses with traditional electrochemical methods. In this paper, we describe two novel methodological advances that bypass these limitations. Using geochemical models, we first create an environmentally relevant test solution that can be used for electrochemical method development and characterization. Second, we develop a fast-scan cyclic voltammetry (FSCV) method for Pb detection on Hg-free carbon fiber microelectrodes. We assess the method's sensitivity and stability, taking into account Pb speciation, and utilize it to characterize rapid Pb fluctuations in real environmental samples. We thus present a novel real-time electrochemical tool for Pb analysis in both model and authentic environmental solutions.

Mössbauer spectroscopy.

PubMed

Huynh, Boi Hanh

2011-01-01

Mössbauer spectroscopy has contributed significantly to the studies of Fe-containing proteins. Early applications yielded detailed electronic characterizations of hemeproteins, and thus enhanced our understanding of the chemical properties of this important class of proteins. The next stage of the applications was marked by major discoveries of several novel Fe clusters of complex structures, including the 8Fe7S P cluster and the mixed metal 1Mo7Fe M center in nitrogenase. Since early 1990 s, rapid kinetic techniques have been used to arrest enzymatic reactions for Mössbauer studies. A number of reaction intermediates were discovered and characterized, both spectroscopically and kinetically, providing unprecedented detailed molecular-level mechanistic information. This chapter gives a brief summary of the historical accounts and a concise description of some experimental and theoretical elements in Mössbauer spectroscopy that are essential for understanding Mössbauer spectra. Major biological applications are summarized at the end.

Characterizing Conformational Dynamics of Proteins Using Evolutionary Couplings.

PubMed

Feng, Jiangyan; Shukla, Diwakar

2018-01-25

Understanding of protein conformational dynamics is essential for elucidating molecular origins of protein structure-function relationship. Traditionally, reaction coordinates, i.e., some functions of protein atom positions and velocities have been used to interpret the complex dynamics of proteins obtained from experimental and computational approaches such as molecular dynamics simulations. However, it is nontrivial to identify the reaction coordinates a priori even for small proteins. Here, we evaluate the power of evolutionary couplings (ECs) to capture protein dynamics by exploring their use as reaction coordinates, which can efficiently guide the sampling of a conformational free energy landscape. We have analyzed 10 diverse proteins and shown that a few ECs are sufficient to characterize complex conformational dynamics of proteins involved in folding and conformational change processes. With the rapid strides in sequencing technology, we expect that ECs could help identify reaction coordinates a priori and enhance the sampling of the slow dynamical process associated with protein folding and conformational change.

How sailfish use their bills to capture schooling prey.

PubMed

Domenici, P; Wilson, A D M; Kurvers, R H J M; Marras, S; Herbert-Read, J E; Steffensen, J F; Krause, S; Viblanc, P E; Couillaud, P; Krause, J

2014-06-07

The istiophorid family of billfishes is characterized by an extended rostrum or 'bill'. While various functions (e.g. foraging and hydrodynamic benefits) have been proposed for this structure, until now no study has directly investigated the mechanisms by which billfishes use their rostrum to feed on prey. Here, we present the first unequivocal evidence of how the bill is used by Atlantic sailfish (Istiophorus albicans) to attack schooling sardines in the open ocean. Using high-speed video-analysis, we show that (i) sailfish manage to insert their bill into sardine schools without eliciting an evasive response and (ii) subsequently use their bill to either tap on individual prey targets or to slash through the school with powerful lateral motions characterized by one of the highest accelerations ever recorded in an aquatic vertebrate. Our results demonstrate that the combination of stealth and rapid motion make the sailfish bill an extremely effective feeding adaptation for capturing schooling prey.

Screening and characterization of novel bacteriocins from lactic acid bacteria.

PubMed

Zendo, Takeshi

2013-01-01

Bacteriocins produced by lactic acid bacteria (LAB) are expected to be safe antimicrobial agents. While the best studied LAB bacteriocin, nisin A, is widely utilized as a food preservative, various novel ones are required to control undesirable bacteria more effectively. To discover novel bacteriocins at the early step of the screening process, we developed a rapid screening system that evaluates bacteriocins produced by newly isolated LAB based on their antibacterial spectra and molecular masses. By means of this system, various novel bacteriocins were identified, including a nisin variant, nisin Q, a two-peptide bacteriocin, lactococcin Q, a leaderless bacteriocin, lacticin Q, and a circular bacteriocin, lactocyclicin Q. Moreover, some LAB isolates were found to produce multiple bacteriocins. They were characterized as to their structures, mechanisms of action, and biosynthetic mechanisms. Novel LAB bacteriocins and their biosynthetic mechanisms are expected for applications such as food preservation and peptide engineering.

Influence of carbon conductive additives on electrochemical double-layer supercapacitor parameters

NASA Astrophysics Data System (ADS)

Kiseleva, E. A.; Zhurilova, M. A.; Kochanova, S. A.; Shkolnikov, E. J.; Tarasenko, A. B.; Zaitseva, O. V.; Uryupina, O. V.; Valyano, G. V.

2018-01-01

Electrochemical double-layer capacitors (EDLC) offer energy storage technology, highly demanded for rapid transition processes in transport and stationary applications, concerned with fast power fluctuations. Rough structure of activated carbon, widely used as electrode material because of its high specific area, leads to poor electrode conductivity. Therefore there is the need for conductive additive to decrease internal resistance and to achieve high specific power and high specific energy. Usually carbon blacks are widely used as conductive additive. In this paper electrodes with different conductive additives—two types of carbon blacks and single-walled carbon nanotubes—were prepared and characterized in organic electrolyte-based EDLC cells. Electrodes are based on original wood derived activated carbon produced by potassium hydroxide high-temperature activation at Joint Institute for High Temperatures RAS. Electrodes were prepared from slurry by cold-rolling. For electrode characterization cyclic voltammetry, impedance spectra analysis, equivalent series resistance measurements and galvanostatic charge-discharge were used.

Nanomanipulation and nanofabrication with multi-probe scanning tunneling microscope: from individual atoms to nanowires.

PubMed

Qin, Shengyong; Kim, Tae-Hwan; Wang, Zhouhang; Li, An-Ping

2012-06-01

The wide variety of nanoscale structures and devices demands novel tools for handling, assembly, and fabrication at nanoscopic positioning precision. The manipulation tools should allow for in situ characterization and testing of fundamental building blocks, such as nanotubes and nanowires, as they are built into functional devices. In this paper, a bottom-up technique for nanomanipulation and nanofabrication is reported by using a 4-probe scanning tunneling microscope (STM) combined with a scanning electron microscope (SEM). The applications of this technique are demonstrated in a variety of nanosystems, from manipulating individual atoms to bending, cutting, breaking carbon nanofibers, and constructing nanodevices for electrical characterizations. The combination of the wide field of view of SEM, the atomic position resolution of STM, and the flexibility of multiple scanning probes is expected to be a valuable tool for rapid prototyping in the nanoscience and nanotechnology.

Physical interpretation and development of ultrasonic nondestructive evaluation techniques applied to the quantitative characterization of textile composite materials

NASA Technical Reports Server (NTRS)

Miller, James G.

1994-01-01

In this Progress Report, we describe our continuing research activities concerning the development and implementation of advanced ultrasonic nondestructive evaluation methods applied to the inspection and characterization of complex composite structures. We explore the feasibility of implementing medical linear array imaging technology as a viable ultrasonic-based nondestructive evaluation method to inspect and characterize complex materials. As an initial step toward the application of linear array imaging technology to the interrogation of a wide range of complex composite structures, we present images obtained using an unmodified medical ultrasonic imaging system of two epoxy-bonded aluminum plate specimens, each with intentionally disbonded regions. These images are compared with corresponding conventional ultrasonic contact transducer measurements in order to assess whether these images can detect disbonded regions and provide information regarding the nature of the disbonded region. We present a description of a standoff/delay fixture which has been designed, constructed, and implemented on a Hewlett-Packard SONOS 1500 medical imaging system. This standoff/delay fixture, when attached to a 7.5 MHz linear array probe, greatly enhances our ability to interrogate flat plate specimens. The final section of this Progress Report describes a woven composite plate specimen that has been specially machined to include intentional flaws. This woven composite specimen will allow us to assess the feasibility of applying linear array imaging technology to the inspection and characterization of complex textile composite materials. We anticipate the results of this on-going investigation may provide a step toward the development of a rapid, real-time, and portable method of ultrasonic inspection and characterization based on linear array technology.

Bioforensics: Characterization of biological weapons agents by NanoSIMS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weber, P K; Ghosal, S; Leighton, T J

2007-02-26

The anthrax attacks of Fall 2001 highlight the need to develop forensic methods based on multiple identifiers to determine the origin of biological weapons agents. Genetic typing methods (i.e., DNA and RNA-based) provide one attribution technology, but genetic information alone is not usually sufficient to determine the provenance of the material. Non-genetic identifiers, including elemental and isotopic signatures, provide complementary information that can be used to identify the means, geographic location and date of production. Under LDRD funding, we have successfully developed the techniques necessary to perform bioforensic characterization with the NanoSIMS at the individual spore level. We have developedmore » methods for elemental and isotopic characterization at the single spore scale. We have developed methods for analyzing spore sections to map elemental abundance within spores. We have developed rapid focused ion beam (FIB) sectioning techniques for spores to preserve elemental and structural integrity. And we have developed a high-resolution depth profiling method to characterize the elemental distribution in individual spores without sectioning. We used these newly developed methods to study the controls on elemental abundances in spores, characterize the elemental distribution of in spores, and to study elemental uptake by spores. Our work under this LDRD project attracted FBI and DHS funding for applied purposes.« less

Characterizing Sleep Structure Using the Hypnogram

PubMed Central

Swihart, Bruce J.; Caffo, Brian; Bandeen-Roche, Karen; Punjabi, Naresh M.

2008-01-01

Objectives: Research on the effects of sleep-disordered breathing (SDB) on sleep structure has traditionally been based on composite sleep-stage summaries. The primary objective of this investigation was to demonstrate the utility of log-linear and multistate analysis of the sleep hypnogram in evaluating differences in nocturnal sleep structure in subjects with and without SDB. Methods: A community-based sample of middle-aged and older adults with and without SDB matched on age, sex, race, and body mass index was identified from the Sleep Heart Health Study. Sleep was assessed with home polysomnography and categorized into rapid eye movement (REM) and non-REM (NREM) sleep. Log-linear and multistate survival analysis models were used to quantify the frequency and hazard rates of transitioning, respectively, between wakefulness, NREM sleep, and REM sleep. Results: Whereas composite sleep-stage summaries were similar between the two groups, subjects with SDB had higher frequencies and hazard rates for transitioning between the three states. Specifically, log-linear models showed that subjects with SDB had more wake-to-NREM sleep and NREM sleep-to-wake transitions, compared with subjects without SDB. Multistate survival models revealed that subjects with SDB transitioned more quickly from wake-to-NREM sleep and NREM sleep-to-wake than did subjects without SDB. Conclusions: The description of sleep continuity with log-linear and multistate analysis of the sleep hypnogram suggests that such methods can identify differences in sleep structure that are not evident with conventional sleep-stage summaries. Detailed characterization of nocturnal sleep evolution with event history methods provides additional means for testing hypotheses on how specific conditions impact sleep continuity and whether sleep disruption is associated with adverse health outcomes. Citation: Swihart BJ; Caffo B; Bandeen-Roche K; Punjabi NM. Characterizing sleep structure using the hypnogram. J Clin Sleep Med 2008;4(4):349–355. PMID:18763427

Rapid Characterization of Microorganisms by Mass Spectrometry—What Can Be Learned and How?

NASA Astrophysics Data System (ADS)

Fenselau, Catherine C.

2013-08-01

Strategies for the rapid and reliable analysis of microorganisms have been sought to meet national needs in defense, homeland security, space exploration, food and water safety, and clinical diagnosis. Mass spectrometry has long been a candidate technique because it is extremely rapid and can provide highly specific information. It has excellent sensitivity. Molecular and fragment ion masses provide detailed fingerprints, which can also be interpreted. Mass spectrometry is also a broad band method—everything has a mass—and it is automatable. Mass spectrometry is a physiochemical method that is orthogonal and complementary to biochemical and morphological methods used to characterize microorganisms.

Rapid characterization of microorganisms by mass spectrometry--what can be learned and how?

PubMed

Fenselau, Catherine C

2013-08-01

Strategies for the rapid and reliable analysis of microorganisms have been sought to meet national needs in defense, homeland security, space exploration, food and water safety, and clinical diagnosis. Mass spectrometry has long been a candidate technique because it is extremely rapid and can provide highly specific information. It has excellent sensitivity. Molecular and fragment ion masses provide detailed fingerprints, which can also be interpreted. Mass spectrometry is also a broad band method--everything has a mass--and it is automatable. Mass spectrometry is a physiochemical method that is orthogonal and complementary to biochemical and morphological methods used to characterize microorganisms.

Characterizing Rapidly Rotating Asteroids with Filtered Photometry

NASA Astrophysics Data System (ADS)

Arion, Douglas

2018-01-01

It is challenging to characterize rapidly rotating asteroids, as their aspect changes significantly between exposures using different filters. Indeed, small asteroids may very well be agglomerations of smaller components that may have differing compositions, and thus the shape and composition of the body may be incorrectly inferred. We have observed a number of smaller, rapidly rotating bodies to try to separate compositional and shape elements from light curves in B, V, R, and I. Results from these observations will be presented, as well as identifying the challenges in conducting this research will be discussed. This work has been supported by the Wisconsin Space Grant Consortium.

Multiscale Modeling: A Review

NASA Astrophysics Data System (ADS)

Horstemeyer, M. F.

This review of multiscale modeling covers a brief history of various multiscale methodologies related to solid materials and the associated experimental influences, the various influence of multiscale modeling on different disciplines, and some examples of multiscale modeling in the design of structural components. Although computational multiscale modeling methodologies have been developed in the late twentieth century, the fundamental notions of multiscale modeling have been around since da Vinci studied different sizes of ropes. The recent rapid growth in multiscale modeling is the result of the confluence of parallel computing power, experimental capabilities to characterize structure-property relations down to the atomic level, and theories that admit multiple length scales. The ubiquitous research that focus on multiscale modeling has broached different disciplines (solid mechanics, fluid mechanics, materials science, physics, mathematics, biological, and chemistry), different regions of the world (most continents), and different length scales (from atoms to autos).

Ultrastructural and biochemical characterization of the epidermal hairs of the seeds of Cuphea procumbens.

PubMed

Stubbs, J M; Slabas, A R

1982-09-01

Rehydration of desiccated Cuphea seeds results in a rapid morphological change in the seed. Within 20 min thread like epidermal hairs are present on the seed surface. The hairs, which are highly ordered helical structures, are present in the epidermal cells of the desiccated seed. Following emergence the hairs increase in length by means of an eversion process, the mechanism for which is proposed in the text. The hairs were purified to homogeneity and found to be composed of 55% carbohydrate and 45% protein. Following β-elimination of the carbohydrate using NaOH/NaBH4 one major protein of MW 31,000 was seen upon polacrylamide gel electrophoresis in the presence of sodium dodecylsulphate. The protein, here termed helexin, probably plays a major structural role in determining the helical shape of the hairs.

Pump spot size dependent lasing threshold in organic semiconductor DFB lasers fabricated via nanograting transfer.

PubMed

Liu, Xin; Klinkhammer, Sönke; Wang, Ziyao; Wienhold, Tobias; Vannahme, Christoph; Jakobs, Peter-Jürgen; Bacher, Andreas; Muslija, Alban; Mappes, Timo; Lemmer, Uli

2013-11-18

Optically excited organic semiconductor distributed feedback (DFB) lasers enable efficient lasing in the visible spectrum. Here, we report on the rapid and parallel fabrication of DFB lasers via transferring a nanograting structure from a flexible mold onto an unstructured film of the organic gain material. This geometrically well-defined structure allows for a systematic investigation of the laser threshold behavior. The laser thresholds for these devices show a strong dependence on the pump spot diameter. This experimental finding is in good qualitative agreement with calculations based on coupled-wave theory. With further investigations on various DFB laser geometries prepared by different routes and based on different organic gain materials, we found that these findings are quite general. This is important for the comparison of threshold values of various devices characterized under different excitation areas.

Controlling human corneal stromal stem cell contraction to mediate rapid cell and matrix organization of real architecture for 3-dimensional tissue equivalents.

PubMed

Mukhey, Dev; Phillips, James B; Daniels, Julie T; Kureshi, Alvena K

2018-02-01

The architecture of the human corneal stroma consists of a highly organized extracellular matrix (ECM) interspersed with keratocytes. Their progenitor cells; corneal stromal stem cells (CSSC) are located at the periphery, in the limbal stroma. A highly organized corneal ECM is critical for effective transmission of light but this structure may be compromised during injury or disease, resulting in loss of vision. Re-creating normal organization in engineered tissue equivalents for transplantation often involves lengthy culture times that are inappropriate for clinical use or utilisation of synthetic substrates that bring complications such as corneal melting. CSSC have great therapeutic potential owing to their ability to reorganize a disorganized matrix, restoring transparency in scarred corneas. We examined CSSC contractile behavior to assess whether this property could be exploited to rapidly generate cell and ECM organization in Real Architecture For 3D Tissues (RAFT) tissue equivalents (TE) for transplantation. Free-floating collagen gels were characterized to assess contractile behavior of CSSC and establish optimum cell density and culture times. To mediate cell and collagen organization, tethered collagen gels seeded with CSSC were cultured and subsequently stabilized with the RAFT process. We demonstrated rapid creation of biomimetic RAFT TE with tunable structural properties. These displayed three distinct regions of varying degrees of cellular and collagen organization. Interestingly, increased organization coincided with a dramatic loss of PAX6 expression in CSSC, indicating rapid differentiation into keratocytes. The organized RAFT TE system could be a useful bioengineering tool to rapidly create an organized ECM while simultaneously controlling cell phenotype. For the first time, we have demonstrated that human CSSC exhibit the phenomenon of cellular self-alignment in tethered collagen gels. We found this mediated rapid co-alignment of collagen fibrils and thus subsequently exploited this property in vitro to improve the architecture of engineered RAFT tissue equivalents of the corneal stroma. Existing techniques are extremely lengthy and carry significant risk and cost for GMP manufacture. This rapid and tunable technique takes just 8 h of culture and is therefore ideal for clinical manufacture, creating biomimetic tissue equivalents with both cellular and ECM organization. Thus, cellular self-alignment can be a useful bioengineering tool for the development of organized tissue equivalents in a variety of applications. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Generation and characterization of biological aerosols for laser measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheng, Yung-Sung; Barr, E.B.

1995-12-01

Concerns for proliferation of biological weapons including bacteria, fungi, and viruses have prompted research and development on methods for the rapid detection of biological aerosols in the field. Real-time instruments that can distinguish biological aerosols from background dust would be especially useful. Sandia National Laboratories (SNL) is developing a laser-based, real-time instrument for rapid detection of biological aerosols, and ITRI is working with SNL scientists and engineers to evaluate this technology for a wide range of biological aerosols. This paper describes methods being used to generate the characterize the biological aerosols for these tests. In summary, a biosafe system hasmore » been developed for generating and characterizing biological aerosols and using those aerosols to test the SNL laser-based real-time instrument. Such tests are essential in studying methods for rapid detection of airborne biological materials.« less

Reticulate Structures Reveal the Significance of Cell Motility in the Morphogenesis of Complex Microbial Structures in Pavilion Lake, British Columbia

NASA Astrophysics Data System (ADS)

Shepard, R.

2008-12-01

Microbial communities are architects of incredibly complex and diverse morphological structures. Each morphology is a snapshot that reflects the complex interactions within the microbial community and between the community and its environment. Characterizing morphology as an emergent property of microbial communities is thus relevant to understanding the evolution of multicellularity and complexity in developmental systems, to the identification of biosignatures, and to furthering our understanding of modern and ancient microbial ecology. Recently discovered cyanobacterial mats in Pavilion Lake, British Columbia construct unusual complex architecture on the scale of decimeters that incorporates significant void space. Fundamental mesoscale morphological elements include terraces, arches, bridges, depressions, domes, and pillars. The mats themselves also exhibit several microscale morphologies, with reticulate structures being the dominant example. The reticulate structures exhibit a diverse spectrum of morphologies with endmembers characterized by either angular or curvilinear ridges. In laboratory studies, aggregation into reticulate structures occurs as a result of the random gliding and colliding among motile cyanobacterial filaments. Likewise, when Pavilion reticulate mats were sampled and brought to the surface, cyanobacteria invariably migrated out of the mat onto surrounding surfaces. Filaments were observed to move rapidly in clumps, preferentially following paths of previous filaments. The migrating filaments organized into new angular and ropey reticulate biofilms within hours of sampling, demonstrating that cell motility is responsible for the reticulate patterns. Because the morphogenesis of reticulate structures can be linked to motility behaviors of filamentous cyanobacteria, the Willow Point mats provide a unique natural laboratory in which to elucidate the connections between a specific microbial behavior and the construction of complex microbial community morphology. To this end, we identified and characterized fundamental building blocks of the mesoscale morphologies, including bridges, anchors, and curved edges. These morphological building blocks were compared with the suite of motility behaviors and patterns observed in reticulate morphogenesis. Results of this comparison suggest that cyanobacterial motility plays a significant and often dominant role in the morphogenesis of the entire suite of morphologies observed in the microbial mats of Pavilion Lake.

Structural and biochemical characterization of N[superscript 5]-carboxyaminoimidazole ribonucleotide synthetase and N[superscript 5]-carboxyaminoimidazole ribonucleotide mutase from Staphylococcus aureus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brugarolas, Pedro; Duguid, Erica M.; Zhang, Wen

With the rapid rise of methicillin-resistant Staphylococcus aureus infections, new strategies against S. aureus are urgently needed. De novo purine biosynthesis is a promising yet unexploited target, insofar as abundant evidence has shown that bacteria with compromised purine biosynthesis are attenuated. Fundamental differences exist within the process by which humans and bacteria convert 5-aminoimidazole ribonucleotide (AIR) to 4-carboxy-5-aminoimidazole ribonucleotide (CAIR). In bacteria, this transformation occurs through a two-step conversion catalyzed by PurK and PurE; in humans, it is mediated by a one-step conversion catalyzed by class II PurE. Thus, these bacterial enzymes are potential targets for selective antibiotic development. Here,more » the first comprehensive structural and biochemical characterization of PurK and PurE from S. aureus is presented. Structural analysis of S. aureus PurK reveals a nonconserved phenylalanine near the AIR-binding site that occupies the putative position of the imidazole ring of AIR. Mutation of this phenylalanine to isoleucine or tryptophan reduced the enzyme efficiency by around tenfold. The K{sub m} for bicarbonate was determined for the first time for a PurK enzyme and was found to be {approx}18.8 mM. The structure of PurE is described in comparison to that of human class II PurE. It is confirmed biochemically that His38 is essential for function. These studies aim to provide foundations for future structure-based drug-discovery efforts against S. aureus purine biosynthesis.« less

Transfer-arm evaporator cell for rapid loading and deposition of organic thin films.

PubMed

Greiner, M T; Helander, M G; Wang, Z B; Lu, Z H

2009-12-01

Described herein is a transfer-arm evaporator cell (TAE-cell), which allows for rapid loading of materials into vacuum for low-temperature sublimation deposition of thin films. This design can be incorporated with an existing analysis system for convenient in situ thin film characterization. This evaporator is especially well suited for photoemission characterization of organic semiconductor interfaces. Photoemission is one of the most important techniques for characterizing such, however, it generally requires in situ sample preparation. The ease with which materials can be loaded and evaporated with this design increases the throughput of in situ photoemission characterization, and broadens the research scope of the technique. Here, we describe the design, operation, and performance of the TAE-cell.

Development of an endoscopic fluorescence image-guided OCT probe for oral cancer detection

NASA Astrophysics Data System (ADS)

McNichols, Roger J.; Gowda, Ashok; Bell, Brent A.; Johnigan, Richard M.; Calhoun, Karen H.; Motamedi, Massoud

2001-06-01

Oral squamous cell carcinoma is a disease which progresses through a number of well-defined morphological and biochemical changes. Optical coherence tomography (OCT) is a rapidly-evolving, non-invasive imaging modality which allows detailed probing of subsurface tissue structures with resolution on the order of microns. While this technique offers tremendous potential as a diagnostic tool for detection and characterization of oral cancer, OCT imaging is presently associated with a field of view on the order of millimeters, and acquisition time on the order of seconds. Thus, OCT's utility as a rapid cancer screening technique is presently limited. On the other hand, imaging of tissue autofluorescence provides a very rapid, high-throughput method for cancer screening. However, while autofluorescence measures may be sensitive to cancer, they are often non- specific and lead to a large number of false positives. In the present work, we have developed a fluorescence image guided optical coherence tomographic (FIG-OCT) probe in which tissue autofluorescence images are simultaneously used to guide OCT image acquisition of suspicious regions in real time. We have begun pre-clinical pilot studies with this instrument in a DMBA-induced model of oral cancer in the hamster cheek pouch. Initial results indicate that the FIG- OCT approach shows promise as a rapid and effective tool for screening of oral cancer.

Bicuspid aortic valve hemodynamics: a fluid-structure interaction study

NASA Astrophysics Data System (ADS)

Chandra, Santanu; Seaman, Clara; Sucosky, Philippe

2011-11-01

The bicuspid aortic valve (BAV) is a congenital defect in which the aortic valve forms with two leaflets instead of three. While calcific aortic valve disease (CAVD) also develops in the normal tricuspid aortic valve (TAV), its progression in the BAV is more rapid. Although studies have suggested a mechano-potential root for the disease, the native BAV hemodynamics remains largely unknown. This study aimed at characterizing BAV hemodynamics and quantifying the degree of wall-shear stress (WSS) abnormality on BAV leaflets. Fluid-structure interaction models validated with particle-image velocimetry were designed to predict the flow and leaflet dynamics in idealized TAV and BAV anatomies. Valvular function was quantified in terms of the effective orifice area. The regional leaflet WSS was characterized in terms of oscillatory shear index, temporal shear magnitude and temporal shear gradient. The predictions indicate the intrinsic degree of stenosis of the BAV anatomy, reveal drastic differences in shear stress magnitude and pulsatility on BAV and TAV leaflets and confirm the side- and site-specificity of the leaflet WSS. Given the ability of abnormal fluid shear stress to trigger valvular inflammation, these results support the existence of a mechano-etiology of CAVD in the BAV.

Polymer planar waveguide Bragg gratings: fabrication, characterization, and sensing applications

NASA Astrophysics Data System (ADS)

Rosenberger, M.; Hessler, S.; Pauer, H.; Girschikofsky, M.; Roth, G. L.; Adelmann, B.; Woern, H.; Schmauss, B.; Hellmann, R.

2017-02-01

In this contribution, we give a comprehensive overview of the fabrication, characterization, and application of integrated planar waveguide Bragg gratings (PPBGs) in cyclo-olefin copolymers (COC). Starting with the measurement of the refractive index depth profile of integrated UV-written structures in COC by phase shifting Mach-Zehnder- Interferometry, we analyze the light propagation using numerical simulations. Furthermore, we show the rapid fabrication of humidity insensitive polymer waveguide Bragg gratings in cyclo-olefin copolymers and discuss the influence of the UV-dosage onto the spectral characteristics and the transmission behavior of the waveguide. Based on these measurements we exemplify that our Bragg gratings exhibit a reflectivity of over 99 % and are highly suitable for sensing applications. With regard to a negligible affinity to absorb water and in conjunction with high temperature stability these polymer devices are ideal for mechanical deformation sensing. Since planar structures are not limited to tensile but can also be applied for measuring compressive strain, we manufacture different functional devices and corroborate their applicability as optical sensors. Exemplarily, we highlight a temperature referenced PPBG sensor written into a femtosecond-laser cut tensile test geometry for tensile and compressive strain sensing. Furthermore, a flexible polymer planar shape sensor is presented.

Enhanced Mass Defect Filtering To Simplify and Classify Complex Mixtures of Lignin Degradation Products.

PubMed

Dier, Tobias K F; Egele, Kerstin; Fossog, Verlaine; Hempelmann, Rolf; Volmer, Dietrich A

2016-01-19

High resolution mass spectrometry was utilized to study the highly complex product mixtures resulting from electrochemical breakdown of lignin. As most of the chemical structures of the degradation products were unknown, enhanced mass defect filtering techniques were implemented to simplify the characterization of the mixtures. It was shown that the implemented ionization techniques had a major impact on the range of detectable breakdown products, with atmospheric pressure photoionization in negative ionization mode providing the widest coverage in our experiments. Different modified Kendrick mass plots were used as a basis for mass defect filtering, where Kendrick mass defect and the mass defect of the lignin-specific guaiacol (C7H7O2) monomeric unit were utilized, readily allowing class assignments independent of the oligomeric state of the product. The enhanced mass defect filtering strategy therefore provided rapid characterization of the sample composition. In addition, the structural similarities between the compounds within a degradation sequence were determined by comparison to a tentatively identified product of this compound series. In general, our analyses revealed that primarily breakdown products with low oxygen content were formed under electrochemical conditions using protic ionic liquids as solvent for lignin.

Specific noncovalent interactions at protein-ligand interface: implications for rational drug design.

PubMed

Zhou, P; Huang, J; Tian, F

2012-01-01

Specific noncovalent interactions that are indicative of attractive, directional intermolecular forces have always been of key interest to medicinal chemists in their search for the "glue" that holds drugs and their targets together. With the rapid increase in the number of solved biomolecular structures as well as the performance enhancement of computer hardware and software in recent years, it is now possible to give more comprehensive insight into the geometrical characteristics and energetic landscape of certain sophisticated noncovalent interactions present at the binding interface of protein receptors and small ligands based on accumulated knowledge gaining from the combination of two quite disparate but complementary approaches: crystallographic data analysis and quantum-mechanical ab initio calculation. In this perspective, we survey massive body of published works relating to structural characterization and theoretical investigation of three kinds of strong, specific, direct, enthalpy-driven intermolecular forces, including hydrogen bond, halogen bond and salt bridge, involved in the formation of protein-ligand complex architecture in order to characterize their biological functions in conferring affinity and specificity for ligand recognition by host protein. In particular, the biomedical implications of raised knowledge are discussed with respect to potential applications in rational drug design.

Novel synthesis and characterization of pristine Cu nanoparticles for the non-enzymatic glucose biosensor.

PubMed

Dayakar, T; Rao, K Venkateswara; Bikshalu, K; Rajendar, V; Park, Si-Hyun

2017-07-01

Non enzymatic electrochemical glucose sensing was developed based on pristine Cu Nanopartilces (NPs)/Glassy Carbon Electrode (GCE) which can be accomplished by simple green method via ocimum tenuiflorum leaf extract. Then, the affect of leaf extract addition on improving Structural, Optical and electrochemical properties of pristine cu NPs was investigated. The synthesized Cu NPs were characterized with X-ray diffraction (X-ray), Uv-Visible spectroscopy (Uv-Vis), Fourier transformation infrared spectroscopy (FTIR), Particle size distribution (PSA), Scanning electron microscopy (SEM), Energy dispersive X-ray spectroscopy (EDS), Transmission electron microscopy (TEM) for structural optical and morphological studies respectively. The synthesized Cu NPs were coated over glassy carbon electrode (GCE) to study the electrochemical response of glucose by cyclic voltammetry and ampherometer. The results indicates that the modified biosensor shows a remarkable sensitivity (1065.21 μA mM -1  cm -2 ), rapid response time (<3s), wide linear range (1 to 7.2 mM), low detection limit (0.038 μM at S/N = 3). Therefore, the prepared Cu NPs by the Novel Bio-mediated route were exploited to construct a non-enzymatic glucose biosensor for sustainable clinical field applications.

Mechanical and biocompatible characterizations of a readily available multilayer vascular graft

PubMed Central

Madhavan, Krishna; Elliott, Winston H; Bonani, Walter; Monnet, Eric; Tan, Wei

2013-01-01

There is always a considerable clinical need for vascular grafts. Considering the availability, physical and mechanical properties, and regenerative potential, we have developed and characterized readily available, strong, and compliant multilayer grafts that support cell culture and ingrowth. The grafts were made from heterogeneous materials and structures, including a thin, dense, nanofibrous core composed of poly-ε-caprolactone (PCL), and a thick, porous, hydrogel sleeve composed of genipin-crosslinked collagen–chitosan (GCC). Because the difference in physicochemical properties between PCL and GCC caused layer separation, the layer adhesion was identified as a determinant to graft property and integrity under physiological conditions. Thus, strategies to modify the layer interface, including increasing porosity of the PCL surface, decreasing hydrophobicity, and increasing interlayer crosslinking, were developed. Results from microscopic images showed that increasing PCL porosity was characterized by improved layer adhesion. The resultant graft was characterized by high compliance (4.5%), and desired permeability (528 mL/cm2/min), burst strength (695 mmHg), and suture strength (2.38 N) for readily grafting. Results also showed that PCL mainly contributed to the graft mechanical properties, whereas GCC reduced the water permeability. In addition to their complementary contributions to physical and mechanical properties, the distinct graft layers also provided layer-specific structures for seeding and culture of vascular endothelial and smooth muscle cells in vitro. Acellular graft constructs were readily used to replace abdominal aorta of rabbits, resulting in rapid cell ingrowth and flow reperfusion. The multilayer constructs capable of sustaining physiological conditions and promoting cellular activities could serve as a platform for future development of regenerative vascular grafts. PMID:23165922

Preclinical Characterization of the Phosphodiesterase 10A PET Tracer [(11)C]MK-8193.

PubMed

Hostetler, Eric D; Fan, Hong; Joshi, Aniket D; Zeng, Zhizhen; Eng, Waisi; Gantert, Liza; Holahan, Marie; Meng, Xianjun; Miller, Patricia; O'Malley, Stacey; Purcell, Mona; Riffel, Kerry; Salinas, Cristian; Williams, Mangay; Ma, Bennett; Buist, Nicole; Smith, Sean M; Coleman, Paul J; Cox, Christopher D; Flores, Brock A; Raheem, Izzat T; Cook, Jacquelynn J; Evelhoch, Jeffrey L

2016-08-01

A positron emission tomography (PET) tracer for the enzyme phosphodiesterase 10A (PDE10A) is desirable to guide the discovery and development of PDE10A inhibitors as potential therapeutics. The preclinical characterization of the PDE10A PET tracer [(11)C]MK-8193 is described. In vitro binding studies with [(3)H]MK-8193 were conducted in rat, monkey, and human brain tissue. PET studies with [(11)C]MK-8193 were conducted in rats and rhesus monkeys at baseline and following administration of a PDE10A inhibitor. [(3)H]MK-8193 is a high-affinity, selective PDE10A radioligand in rat, monkey, and human brain tissue. In vivo, [(11)C]MK-8193 displays rapid kinetics, low test-retest variability, and a large specific signal that is displaced by a structurally diverse PDE10A inhibitor, enabling the determination of pharmacokinetic/enzyme occupancy relationships. [(11)C]MK-8193 is a useful PET tracer for the preclinical characterization of PDE10A therapeutic candidates in rat and monkey. Further evaluation of [(11)C]MK-8193 in humans is warranted.

Unravelling the mysteries of sub-second biochemical processes using time-resolved mass spectrometry.

PubMed

Lento, Cristina; Wilson, Derek J

2017-05-21

Many important chemical and biochemical phenomena proceed on sub-second time scales before entering equilibrium. In this mini-review, we explore the history and recent advancements of time-resolved mass spectrometry (TRMS) for the characterization of millisecond time-scale chemical reactions and biochemical processes. TRMS allows for the simultaneous tracking of multiple reactants, intermediates and products with no chromophoric species required, high sensitivity and temporal resolution. The method has most recently been used for the characterization of several short-lived reaction intermediates in rapid chemical reactions. Most of the reactions that occur in living organisms are accelerated by enzymes, with pre-steady state kinetics only attainable using time-resolved methods. TRMS has been increasingly used to monitor the conversion of substrates to products and the resulting changes to the enzyme during catalytic turnover. Early events in protein folding systems have also been elucidated, along with the characterization of dynamics and transient secondary structures in intrinsically disordered proteins. In this review, we will highlight representative examples where TRMS has been applied to study these phenomena.

Fabrication and characterization of Gd2O2SO4:Tb3+ phosphors by sol-gel method

NASA Astrophysics Data System (ADS)

Aritman, I.; Yildirim, S.; Kisa, A.; Guleryuz, L. F.; Yurddaskal, M.; Dikici, T.; Celik, E.

2017-02-01

The objective of the innovative approaches of the scintillation materials to be used in the digital portal imaging systems in the radiotherapy applications is to research the GOS material production that has been activated with the rare earth elements (RE), to produce the scintillation detectors that have a rapid imaging process with a lesser radiation and higher image quality from these materials and to apply the radiographic imaging systems. The GOS: Tb3+ showed high emission peak and high x-ray absorption properties which have been determined for application to mammography and dental radiography. In this study, Gd2O2SO4:Tb3+ phosphors were fabricated by the sol-gel method that is a unique technique and not previously applied. Besides, the structural characterization of GOS: Tb3+ has been investigated. The strongest emission peak located at 549 nm under 312 nm UV light excitation was appeared on the GOS: Tb3+ phosphor particles. The characterization processing optimized by using FTIR, DTA-TG, XRD, XPS, SEM and the luminescence spectroscopy.

Time-Resolved CubeSat Photometry with a Low Cost Electro-Optics System

NASA Astrophysics Data System (ADS)

Gasdia, F.; Barjatya, A.; Bilardi, S.

2016-09-01

Once the orbits of small debris or CubeSats are determined, optical rate-track follow-up observations can provide information for characterization or identification of these objects. Using the Celestron 11" RASA telescope and an inexpensive CMOS machine vision camera, we have obtained time-series photometry from dozens of passes of small satellites and CubeSats over sites in Florida and Massachusetts. The fast readout time of the CMOS detector allows temporally resolved sampling of glints from small wire antennae and structural facets of rapidly tumbling objects. Because the shape of most CubeSats is known, these light curves can be used in a mission support function for small satellite operators to diagnose or verify the proper functioning of an attitude control system or deployed antenna or instrument. We call this telescope system and the accompanying analysis tools OSCOM for Optical tracking and Spectral characterization of CubeSats for Operational Missions. We introduce the capability of OSCOM for space object characterization, and present photometric observations demonstrating the potential of high frame rate small satellite photometry.

Computational Amide I Spectroscopy for Refinement of Disordered Peptide Ensembles: Maximum Entropy and Related Approaches

NASA Astrophysics Data System (ADS)

Reppert, Michael; Tokmakoff, Andrei

The structural characterization of intrinsically disordered peptides (IDPs) presents a challenging biophysical problem. Extreme heterogeneity and rapid conformational interconversion make traditional methods difficult to interpret. Due to its ultrafast (ps) shutter speed, Amide I vibrational spectroscopy has received considerable interest as a novel technique to probe IDP structure and dynamics. Historically, Amide I spectroscopy has been limited to delivering global secondary structural information. More recently, however, the method has been adapted to study structure at the local level through incorporation of isotope labels into the protein backbone at specific amide bonds. Thanks to the acute sensitivity of Amide I frequencies to local electrostatic interactions-particularly hydrogen bonds-spectroscopic data on isotope labeled residues directly reports on local peptide conformation. Quantitative information can be extracted using electrostatic frequency maps which translate molecular dynamics trajectories into Amide I spectra for comparison with experiment. Here we present our recent efforts in the development of a rigorous approach to incorporating Amide I spectroscopic restraints into refined molecular dynamics structural ensembles using maximum entropy and related approaches. By combining force field predictions with experimental spectroscopic data, we construct refined structural ensembles for a family of short, strongly disordered, elastin-like peptides in aqueous solution.

Function does not follow form in gene regulatory circuits.

PubMed

Payne, Joshua L; Wagner, Andreas

2015-08-20

Gene regulatory circuits are to the cell what arithmetic logic units are to the chip: fundamental components of information processing that map an input onto an output. Gene regulatory circuits come in many different forms, distinct structural configurations that determine who regulates whom. Studies that have focused on the gene expression patterns (functions) of circuits with a given structure (form) have examined just a few structures or gene expression patterns. Here, we use a computational model to exhaustively characterize the gene expression patterns of nearly 17 million three-gene circuits in order to systematically explore the relationship between circuit form and function. Three main conclusions emerge. First, function does not follow form. A circuit of any one structure can have between twelve and nearly thirty thousand distinct gene expression patterns. Second, and conversely, form does not follow function. Most gene expression patterns can be realized by more than one circuit structure. And third, multifunctionality severely constrains circuit form. The number of circuit structures able to drive multiple gene expression patterns decreases rapidly with the number of these patterns. These results indicate that it is generally not possible to infer circuit function from circuit form, or vice versa.

Structure and backbone dynamics of a microcrystalline metalloprotein by solid-state NMR.

PubMed

Knight, Michael J; Pell, Andrew J; Bertini, Ivano; Felli, Isabella C; Gonnelli, Leonardo; Pierattelli, Roberta; Herrmann, Torsten; Emsley, Lyndon; Pintacuda, Guido

2012-07-10

We introduce a new approach to improve structural and dynamical determination of large metalloproteins using solid-state nuclear magnetic resonance (NMR) with (1)H detection under ultrafast magic angle spinning (MAS). The approach is based on the rapid and sensitive acquisition of an extensive set of (15)N and (13)C nuclear relaxation rates. The system on which we demonstrate these methods is the enzyme Cu, Zn superoxide dismutase (SOD), which coordinates a Cu ion available either in Cu(+) (diamagnetic) or Cu(2+) (paramagnetic) form. Paramagnetic relaxation enhancements are obtained from the difference in rates measured in the two forms and are employed as structural constraints for the determination of the protein structure. When added to (1)H-(1)H distance restraints, they are shown to yield a twofold improvement of the precision of the structure. Site-specific order parameters and timescales of motion are obtained by a gaussian axial fluctuation (GAF) analysis of the relaxation rates of the diamagnetic molecule, and interpreted in relation to backbone structure and metal binding. Timescales for motion are found to be in the range of the overall correlation time in solution, where internal motions characterized here would not be observable.

Deciphering the glycosaminoglycan code with the help of microarrays.

PubMed

de Paz, Jose L; Seeberger, Peter H

2008-07-01

Carbohydrate microarrays have become a powerful tool to elucidate the biological role of complex sugars. Microarrays are particularly useful for the study of glycosaminoglycans (GAGs), a key class of carbohydrates. The high-throughput chip format enables rapid screening of large numbers of potential GAG sequences produced via a complex biosynthesis while consuming very little sample. Here, we briefly highlight the most recent advances involving GAG microarrays built with synthetic or naturally derived oligosaccharides. These chips are powerful tools for characterizing GAG-protein interactions and determining structure-activity relationships for specific sequences. Thereby, they contribute to decoding the information contained in specific GAG sequences.

Strengthening of ferrous binder jet 3D printed components through bronze infiltration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cordero, Zachary C.; Siddel, Derek H.; Peter, William H.

Fully-dense, net shape objects have been fabricated from a rapidly-solidified ferrous powder using binder-jet 3D printing and molten bronze infiltration. X-ray diffraction, scanning electron microscopy, and differential thermal analysis were used to characterize the structural evolution of the powder feedstock during an infiltration heating cycle. Microindentation and bend tests were performed on the infiltrated material to evaluate its mechanical properties. The infiltrated material had an 11 GPa hardness and moderate damage tolerance. It was found that infiltration improved both the ductility and strength of the sintered preforms by eliminating the stress concentration at the interparticle necks.

Strengthening of ferrous binder jet 3D printed components through bronze infiltration

DOE PAGES

Cordero, Zachary C.; Siddel, Derek H.; Peter, William H.; ...

2017-04-08

Fully-dense, net shape objects have been fabricated from a rapidly-solidified ferrous powder using binder-jet 3D printing and molten bronze infiltration. X-ray diffraction, scanning electron microscopy, and differential thermal analysis were used to characterize the structural evolution of the powder feedstock during an infiltration heating cycle. Microindentation and bend tests were performed on the infiltrated material to evaluate its mechanical properties. The infiltrated material had an 11 GPa hardness and moderate damage tolerance. It was found that infiltration improved both the ductility and strength of the sintered preforms by eliminating the stress concentration at the interparticle necks.

Preparation of In2S3 nanopraricle by ultrasonic dispersion and its tribology property.

PubMed

Li, Zhiwei; Tao, Xiaojun; Wu, Zhishen; Zhang, Pingyu; Zhang, Zhijun

2009-02-01

In this paper, we describe a facile and rapid method for preparing In2S3 nanoparticles via ultrasound dispersion. This method allows us to prepare In2S3 nanoparticles from bulk indium and sulfur with ease and without using expensive agents and in a short time. The possible growing mechanism of the In2S3 nanoparticles was presented. In addition, we provide detailed characterizations including TEM, XRD, TG-DTA, and XPS to study the shape, composition and structure of In2S3 nanoparticles. We also studied the tribology property of In2S3 nanoparticles made using this novel recipe.

Which future for traumatology in Europe?

PubMed

Rommens, P M

2014-01-01

The last decades have been characterized by rapid changes in society, medicine and surgery. There is a distinct evolution towards specialization and super-specialization. Trauma surgery also evolves towards a specialty, focused on the care of the injured. To optimize the quality of care and meet the needs of patients and care providers, a well-structured trauma surgery training program as well as the regionalization of trauma care with the implementation of Level I trauma centers are needed. The core competence of the European trauma surgeon is the coordination of the early management of the severely injured and the treatment of muskuloskeletal trauma, which represent the most common pathologies in our countries.

Efficient and optimized identification of generalized Maxwell viscoelastic relaxation spectra.

PubMed

Babaei, Behzad; Davarian, Ali; Pryse, Kenneth M; Elson, Elliot L; Genin, Guy M

2015-03-01

Viscoelastic relaxation spectra are essential for predicting and interpreting the mechanical responses of materials and structures. For biological tissues, these spectra must usually be estimated from viscoelastic relaxation tests. Interpreting viscoelastic relaxation tests is challenging because the inverse problem is expensive computationally. We present here an efficient algorithm that enables rapid identification of viscoelastic relaxation spectra. The algorithm was tested against trial data to characterize its robustness and identify its limitations and strengths. The algorithm was then applied to identify the viscoelastic response of reconstituted collagen, revealing an extensive distribution of viscoelastic time constants. Copyright © 2015 Elsevier Ltd. All rights reserved.

Neuroimaging of Narcolepsy and Kleine-Levin Syndrome.

PubMed

Hong, Seung Bong

2017-09-01

Narcolepsy is a chronic neurologic disorder with the abnormal regulation of the sleep-wake cycle, resulting in excessive daytime sleepiness, disturbed nocturnal sleep, and manifestations related to rapid eye movement sleep, such as cataplexy, sleep paralysis, and hypnagogic hallucination. Over the past decade, numerous neuroimaging studies have been performed to characterize the pathophysiology and various clinical features of narcolepsy. This article reviews structural and functional brain imaging findings in narcolepsy and Kleine-Levin syndrome. Based on the current state of research, brain imaging is a useful tool to investigate and understand the neuroanatomic correlates and brain abnormalities of narcolepsy and other hypersomnia. Copyright © 2017 Elsevier Inc. All rights reserved.

Jellyfish modulate bacterial dynamic and community structure.

PubMed

Tinta, Tinkara; Kogovšek, Tjaša; Malej, Alenka; Turk, Valentina

2012-01-01

Jellyfish blooms have increased in coastal areas around the world and the outbreaks have become longer and more frequent over the past few decades. The Mediterranean Sea is among the heavily affected regions and the common bloom-forming taxa are scyphozoans Aurelia aurita s.l., Pelagia noctiluca, and Rhizostoma pulmo. Jellyfish have few natural predators, therefore their carcasses at the termination of a bloom represent an organic-rich substrate that supports rapid bacterial growth, and may have a large impact on the surrounding environment. The focus of this study was to explore whether jellyfish substrate have an impact on bacterial community phylotype selection. We conducted in situ jellyfish-enrichment experiment with three different jellyfish species. Bacterial dynamic together with nutrients were monitored to assess decaying jellyfish-bacteria dynamics. Our results show that jellyfish biomass is characterized by protein rich organic matter, which is highly bioavailable to 'jellyfish-associated' and 'free-living' bacteria, and triggers rapid shifts in bacterial population dynamics and composition. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE) analysis, we observed a rapid shift in community composition from unculturable Alphaproteobacteria to culturable species of Gammaproteobacteria and Flavobacteria. The results of sequence analyses of bacterial isolates and of total bacterial community determined by culture independent genetic analysis showed the dominance of the Pseudoalteromonadaceae and the Vibrionaceae families. Elevated levels of dissolved proteins, dissolved organic and inorganic nutrient release, bacterial abundance and carbon production as well as ammonium concentrations characterized the degradation process. The biochemical composition of jellyfish species may influence changes in the amount of accumulated dissolved organic and inorganic nutrients. Our results can contribute insights into possible changes in bacterial population dynamics and nutrient pathways following jellyfish blooms which have important implications for ecology of coastal waters.

Georgia Basin-Puget Sound Airshed Characterization Report 2014

EPA Science Inventory

The Georgia Basin - Puget Sound Airshed Characterization Report, 2012 was undertaken to characterize the air quality within the Georgia Basin/Puget Sound region,a vibrant, rapidly growing, urbanized area of the Pacific Northwest. The Georgia Basin - Puget Sound Airshed Characteri...

Human long intrinsically disordered protein regions are frequent targets of positive selection.

PubMed

Afanasyeva, Arina; Bockwoldt, Mathias; Cooney, Christopher R; Heiland, Ines; Gossmann, Toni I

2018-06-01

Intrinsically disordered regions occur frequently in proteins and are characterized by a lack of a well-defined three-dimensional structure. Although these regions do not show a higher order of structural organization, they are known to be functionally important. Disordered regions are rapidly evolving, largely attributed to relaxed purifying selection and an increased role of genetic drift. It has also been suggested that positive selection might contribute to their rapid diversification. However, for our own species, it is currently unknown whether positive selection has played a role during the evolution of these protein regions. Here, we address this question by investigating the evolutionary pattern of more than 6600 human proteins with intrinsically disordered regions and their ordered counterparts. Our comparative approach with data from more than 90 mammalian genomes uses a priori knowledge of disordered protein regions, and we show that this increases the power to detect positive selection by an order of magnitude. We can confirm that human intrinsically disordered regions evolve more rapidly, not only within humans but also across the entire mammalian phylogeny. They have, however, experienced substantial evolutionary constraint, hinting at their fundamental functional importance. We find compelling evidence that disordered protein regions are frequent targets of positive selection and estimate that the relative rate of adaptive substitutions differs fourfold between disordered and ordered protein regions in humans. Our results suggest that disordered protein regions are important targets of genetic innovation and that the contribution of positive selection in these regions is more pronounced than in other protein parts. © 2018 Afanasyeva et al.; Published by Cold Spring Harbor Laboratory Press.

Automatic and rapid identification of glycopeptides by nano-UPLC-LTQ-FT-MS and proteomic search engine.

PubMed

Giménez, Estela; Gay, Marina; Vilaseca, Marta

2017-01-30

Here we demonstrate the potential of nano-UPLC-LTQ-FT-MS and the Byonic™ proteomic search engine for the separation, detection, and identification of N- and O-glycopeptide glycoforms in standard glycoproteins. The use of a BEH C18 nanoACQUITY column allowed the separation of the glycopeptides present in the glycoprotein digest and a baseline-resolution of the glycoforms of the same glycopeptide on the basis of the number of sialic acids. Moreover, we evaluated several acquisition strategies in order to improve the detection and characterization of glycopeptide glycoforms with the maximum number of identification percentages. The proposed strategy is simple to set up with the technology platforms commonly used in proteomic labs. The method allows the straightforward and rapid obtention of a general glycosylated map of a given protein, including glycosites and their corresponding glycosylated structures. The MS strategy selected in this work, based on a gas phase fractionation approach, led to 136 unique peptides from four standard proteins, which represented 78% of the total number of peptides identified. Moreover, the method does not require an extra glycopeptide enrichment step, thus preventing the bias that this step could cause towards certain glycopeptide species. Data are available via ProteomeXchange with identifier PXD003578. We propose a simple and high-throughput glycoproteomics-based methodology that allows the separation of glycopeptide glycoforms on the basis of the number of sialic acids, and their automatic and rapid identification without prior knowledge of protein glycosites or type and structure of the glycans. Copyright © 2016 Elsevier B.V. All rights reserved.

Autonomous Metabolomics for Rapid Metabolite Identification in Global Profiling

DOE PAGES

Benton, H. Paul; Ivanisevic, Julijana; Mahieu, Nathaniel G.; ...

2014-12-12

An autonomous metabolomic workflow combining mass spectrometry analysis with tandem mass spectrometry data acquisition was designed to allow for simultaneous data processing and metabolite characterization. Although previously tandem mass spectrometry data have been generated on the fly, the experiments described herein combine this technology with the bioinformatic resources of XCMS and METLIN. We can analyze large profiling datasets and simultaneously obtain structural identifications, as a result of this unique integration. Furthermore, validation of the workflow on bacterial samples allowed the profiling on the order of a thousand metabolite features with simultaneous tandem mass spectra data acquisition. The tandem mass spectrometrymore » data acquisition enabled automatic search and matching against the METLIN tandem mass spectrometry database, shortening the current workflow from days to hours. Overall, the autonomous approach to untargeted metabolomics provides an efficient means of metabolomic profiling, and will ultimately allow the more rapid integration of comparative analyses, metabolite identification, and data analysis at a systems biology level.« less

Design of rapid hardening engineered cementitious composites for sustainable construction

NASA Astrophysics Data System (ADS)

Marushchak, Uliana; Sanytsky, Myroslav; Sydor, Nazar

2017-12-01

This paper deals with design of environmentally friendly Rapid Hardening Engineered Cementitious Composite (RHECC) nanomodified with ultrafine mineral additives, polycarboxylate ether based superplasticizer, calcium hydrosilicate nanoparticles and dispersal reinforced by fibers. The incremental coefficient of surface activity was proposed in order to estimation of ultrafine supplementary materials (fly ash, methakaolin, microsilica) efficiency. A characterization of RHECC's compressive and flexural properties at different ages is reported in this paper. Early compressive strength of ECC is 45-50 MPa, standard strength - 84-95 MPa and parameter Rc2/Rc28 - 65-70%. The microstructure of the cement matrix and RHECC was investigated. The use of ultrafine mineral supplementary materials provides reinforcement of structure on micro- and nanoscale level (cementing matrix) due to formation of sub-microreinforcing hydrate phase as AFt- and C-S-H phases in unclinker part of cement matrix, resulting in the phenomena of "self-reinforcement" on the microstructure level. Designed RHECC may be regarded as lower brittle since the crack resistance coefficient is higher comparison to conventional fine grain concrete.

Thalamic reticular nucleus induces fast and local modulation of arousal state

PubMed Central

Lewis, Laura D; Voigts, Jakob; Flores, Francisco J; Schmitt, L Ian; Wilson, Matthew A

2015-01-01

During low arousal states such as drowsiness and sleep, cortical neurons exhibit rhythmic slow wave activity associated with periods of neuronal silence. Slow waves are locally regulated, and local slow wave dynamics are important for memory, cognition, and behaviour. While several brainstem structures for controlling global sleep states have now been well characterized, a mechanism underlying fast and local modulation of cortical slow waves has not been identified. Here, using optogenetics and whole cortex electrophysiology, we show that local tonic activation of thalamic reticular nucleus (TRN) rapidly induces slow wave activity in a spatially restricted region of cortex. These slow waves resemble those seen in sleep, as cortical units undergo periods of silence phase-locked to the slow wave. Furthermore, animals exhibit behavioural changes consistent with a decrease in arousal state during TRN stimulation. We conclude that TRN can induce rapid modulation of local cortical state. DOI: http://dx.doi.org/10.7554/eLife.08760.001 PMID:26460547

Space-time asymptotics of the two dimensional Navier-Stokes flow in the whole plane

NASA Astrophysics Data System (ADS)

Okabe, Takahiro

2018-01-01

We consider the space-time behavior of the two dimensional Navier-Stokes flow. Introducing some qualitative structure of initial data, we succeed to derive the first order asymptotic expansion of the Navier-Stokes flow without moment condition on initial data in L1 (R2) ∩ Lσ2 (R2). Moreover, we characterize the necessary and sufficient condition for the rapid energy decay ‖ u (t) ‖ 2 = o (t-1) as t → ∞ motivated by Miyakawa-Schonbek [21]. By weighted estimated in Hardy spaces, we discuss the possibility of the second order asymptotic expansion of the Navier-Stokes flow assuming the first order moment condition on initial data. Moreover, observing that the Navier-Stokes flow u (t) lies in the Hardy space H1 (R2) for t > 0, we consider the asymptotic expansions in terms of Hardy-norm. Finally we consider the rapid time decay ‖ u (t) ‖ 2 = o (t - 3/2 ) as t → ∞ with cyclic symmetry introduced by Brandolese [2].

Measuring the Global Substrate Specificity of Mycobacterial Serine Hydrolases Using a Library of Fluorogenic Ester Substrates.

PubMed

Bassett, Braden; Waibel, Brent; White, Alex; Hansen, Heather; Stephens, Dominique; Koelper, Andrew; Larsen, Erik M; Kim, Charles; Glanzer, Adam; Lavis, Luke D; Hoops, Geoffrey C; Johnson, R Jeremy

2018-04-16

Among the proteins required for lipid metabolism in Mycobacterium tuberculosis are a significant number of uncharacterized serine hydrolases, especially lipases and esterases. Using a streamlined synthetic method, a library of immolative fluorogenic ester substrates was expanded to better represent the natural lipidomic diversity of Mycobacterium. This expanded fluorogenic library was then used to rapidly characterize the global structure activity relationship (SAR) of mycobacterial serine hydrolases in M. smegmatis under different growth conditions. Confirmation of fluorogenic substrate activation by mycobacterial serine hydrolases was performed using nonspecific serine hydrolase inhibitors and reinforced the biological significance of the SAR. The hydrolases responsible for the global SAR were then assigned using gel-resolved activity measurements, and these assignments were used to rapidly identify the relative substrate specificity of previously uncharacterized mycobacterial hydrolases. These measurements provide a global SAR of mycobacterial hydrolase activity, a picture of cycling hydrolase activity, and a detailed substrate specificity profile for previously uncharacterized hydrolases.

Pedestal bifurcation and resonant field penetration at the threshold of edge-localized mode suppression in the DIII-D Tokamak.

PubMed

Nazikian, R; Paz-Soldan, C; Callen, J D; deGrassie, J S; Eldon, D; Evans, T E; Ferraro, N M; Grierson, B A; Groebner, R J; Haskey, S R; Hegna, C C; King, J D; Logan, N C; McKee, G R; Moyer, R A; Okabayashi, M; Orlov, D M; Osborne, T H; Park, J-K; Rhodes, T L; Shafer, M W; Snyder, P B; Solomon, W M; Strait, E J; Wade, M R

2015-03-13

Rapid bifurcations in the plasma response to slowly varying n=2 magnetic fields are observed as the plasma transitions into and out of edge-localized mode (ELM) suppression. The rapid transition to ELM suppression is characterized by an increase in the toroidal rotation and a reduction in the electron pressure gradient at the top of the pedestal that reduces the perpendicular electron flow there to near zero. These events occur simultaneously with an increase in the inner-wall magnetic response. These observations are consistent with strong resonant field penetration of n=2 fields at the onset of ELM suppression, based on extended MHD simulations using measured plasma profiles. Spontaneous transitions into (and out of) ELM suppression with a static applied n=2 field indicate competing mechanisms of screening and penetration of resonant fields near threshold conditions. Magnetic measurements reveal evidence for the unlocking and rotation of tearinglike structures as the plasma transitions out of ELM suppression.

Complementation of biotransformations with chemical C-H oxidation: copper-catalyzed oxidation of tertiary amines in complex pharmaceuticals.

PubMed

Genovino, Julien; Lütz, Stephan; Sames, Dalibor; Touré, B Barry

2013-08-21

The isolation, quantitation, and characterization of drug metabolites in biological fluids remain challenging. Rapid access to oxidized drugs could facilitate metabolite identification and enable early pharmacology and toxicity studies. Herein, we compared biotransformations to classical and new chemical C-H oxidation methods using oxcarbazepine, naproxen, and an early compound hit (phthalazine 1). These studies illustrated the low preparative efficacy of biotransformations and the inability of chemical methods to oxidize complex pharmaceuticals. We also disclose an aerobic catalytic protocole (CuI/air) to oxidize tertiary amines and benzylic CH's in drugs. The reaction tolerates a broad range of functionalities and displays a high level of chemoselectivity, which is not generally explained by the strength of the C-H bonds but by the individual structural chemotype. This study represents a first step toward establishing a chemical toolkit (chemotransformations) that can selectively oxidize C-H bonds in complex pharmaceuticals and rapidly deliver drug metabolites.

Transition to turbulence under low-pressure turbine conditions.

PubMed

Simon, T W; Kaszeta, R W

2001-05-01

In this paper, the topic of laminar to turbulent flow transition, as applied to the design of gas turbines, is discussed. Transition comes about when a flow becomes sufficiently unstable that the orderly vorticity structure of the laminar layer becomes randomly oriented. Vorticity with a streamwise component leads to rapid growth of eddies of a wide range of sizes and eventually to turbulent flow. Under "natural" transition, infinitesimal disturbances of selected frequencies grow. "Bypass transition" is a term coined to describe a similar process, but one driven by strong external disturbances. Transition proceeds so rapidly that the processes associated with "natural" transition seem to be "bypassed." Because the flow environment in the turbine is disturbed by wakes from upstream airfoils, eddies from combustor flows, jets from film cooling, separation zones on upstream airfoils and steps in the duct walls, transition is of the bypass mode. In this paper, we discuss work that has been done to characterize and model bypass transition, as applied to the turbine environment.

Multiscale Analysis of Rapidly Rotating Dynamo Simulations

NASA Astrophysics Data System (ADS)

Orvedahl, Ryan; Calkins, Michael; Featherstone, Nicholas

2017-11-01

The magnetic field of the planets and stars are generated by dynamo action in their electrically conducting fluid interiors. Numerical models of this process solve the fundamental equations of magnetohydrodynamics driven by convection in a rotating spherical shell. Rotation plays an important role in modifying the resulting convective flows and the self-generated magnetic field. We present results of simulating rapidly rotating systems that are unstable to dynamo action. We use the pseudo-spectral code Rayleigh to generate a suite of direct numerical simulations. Each simulation uses the Boussinesq approximation and is characterized by an Ekman number (Ek = ν / ΩL2) of 10-5. We vary the degree of convective forcing to obtain a range of convective Rossby numbers. The resulting flows and magnetic structures are analyzed using a Reynolds decomposition. We determine the relative importance of each term in the scale-separated governing equations and estimate the relevant spatial scales responsible for generating the mean magnetic field.

Rapid estimation of glucosinolate thermal degradation rate constants in leaves of Chinese kale and broccoli (Brassica oleracea) in two seasons.

PubMed

Hennig, Kristin; Verkerk, Ruud; Bonnema, Guusje; Dekker, Matthijs

2012-08-15

Kinetic modeling was used as a tool to quantitatively estimate glucosinolate thermal degradation rate constants. Literature shows that thermal degradation rates differ in different vegetables. Well-characterized plant material, leaves of broccoli and Chinese kale plants grown in two seasons, was used in the study. It was shown that a first-order reaction is appropriate to model glucosinolate degradation independent from the season. No difference in degradation rate constants of structurally identical glucosinolates was found between broccoli and Chinese kale leaves when grown in the same season. However, glucosinolate degradation rate constants were highly affected by the season (20-80% increase in spring compared to autumn). These results suggest that differences in glucosinolate degradation rate constants can be due to variation in environmental as well as genetic factors. Furthermore, a methodology to estimate rate constants rapidly is provided to enable the analysis of high sample numbers for future studies.

Production of new 3D scaffolds for bone tissue regeneration by rapid prototyping.

PubMed

Fradique, R; Correia, T R; Miguel, S P; de Sá, K D; Figueira, D R; Mendonça, A G; Correia, I J

2016-04-01

The incidence of bone disorders, whether due to trauma or pathology, has been trending upward with the aging of the worldwide population. The currently available treatments for bone injuries are rather limited, involving mainly bone grafts and implants. A particularly promising approach for bone regeneration uses rapid prototyping (RP) technologies to produce 3D scaffolds with highly controlled structure and orientation, based on computer-aided design models or medical data. Herein, tricalcium phosphate (TCP)/alginate scaffolds were produced using RP and subsequently their physicochemical, mechanical and biological properties were characterized. The results showed that 60/40 of TCP and alginate formulation was able to match the compression and present a similar Young modulus to that of trabecular bone while presenting an adequate biocompatibility. Moreover, the biomineralization ability, roughness and macro and microporosity of scaffolds allowed cell anchoring and proliferation at their surface, as well as cell migration to its interior, processes that are fundamental for osteointegration and bone regeneration.

Pedestal Bifurcation and Resonant Field Penetration at the Threshold of Edge-Localized Mode Suppression in the DIII-D Tokamak

DOE PAGES

Nazikian, Raffi; Paz-Soldan, Carlos; Callen, James D.; ...

2015-03-12

Rapid bifurcations in the plasma response to slowly varying n=2 magnetic fields are observed as the plasma transitions into and out of edge localized mode (ELM) suppression. The rapid transition to ELM suppression is characterized by an increase in the toroidal rotation and a reduction in the electron pressure gradient at the top of the pedestal which reduces the perpendicular electron flow to near zero. These events occur simultaneously with an increase in the inner wall magnetic response. These observations are consistent strong resonant field penetration of n=2 fields at the onset of ELM suppression, based on extended MHD simulationsmore » using measured plasma profiles. Spontaneous transitions into (and out of) ELM suppression with a static applied n=2 field indicate competing mechanisms of screening and penetration of resonant fields near threshold conditions. Magnetic measurements reveal evidence for the unlocking and rotation of tearing-like structures as the plasma transitions out of ELM suppression.« less

Application of a three-tier framework to assess ecological ...

EPA Pesticide Factsheets

A multi‐level coastal wetland assessment strategy was applied to wetlands in the northern Gulf of Mexico (GOM) to evaluate the feasibility of this approach for a broad national scale wetland condition assessment (U.S. Environmental Protection Agency’s National Wetlands Condition Assessment). Landscape‐scale assessment indicators (Tier 1) were developed and applied at the sub‐watershed (12‐digit Hydrologic Unit) level within the GOM coastal wetland sample frame with scores calculated using land‐use maps and GIS. Rapid assessment protocols (Tier‐2), using a combination of office and field work, evaluated metrics associated with landscape context, hydrology, physical structure, and biological structure. Intensive site monitoring (Tier‐3) included measures of soil chemistry and composition, water column and pore‐water chemistry, and dominant macrophyte community composition and tissue chemistry. Relationships within and among assessment levels were evaluated using multivariate and principal component analyses with few significant correlations were found. More detailed measures of hydrology, soils, and macrophyte species composition from sites across a known condition gradient, in conjunction with validation of standardized rapid assessment method, may be necessary to fully characterize coastal wetlands across the region This manuscript describes the application of a multi-level coastal wetland assessment strategy to wetlands in the northern Gulf of

Microstructural and mechanical characterization of laser deposited advanced materials

NASA Astrophysics Data System (ADS)

Sistla, Harihar Rakshit

Additive manufacturing in the form of laser deposition is a unique way to manufacture near net shape metallic components from advanced materials. Rapid solidification facilitates the extension of solid solubility, compositional flexibility and decrease in micro-segregation in the melt among other advantages. The current work investigates the employment of laser deposition to fabricate the following: 1. Functionally gradient materials: This allows grading dissimilar materials compositionally to tailor specific properties of both these materials into a single component. Specific compositions of the candidate materials (SS 316, Inconel 625 and Ti64) were blended and deposited to study the brittle intermetallics reported in these systems. 2. High entropy alloys: These are multi- component alloys with equiatomic compositions of 5 or more elements. The ratio of Al to Ni was decreased to observe the transition of solid solution from a BCC to an FCC crystal structure in the AlFeCoCrNi system. 3. Structurally amorphous alloys: Zr-based metallic glasses have been reported to have high glass forming ability. These alloys have been laser deposited so as to rapidly cool them from the melt into an amorphous state. Microstructural analysis and X-ray diffraction were used to study the phase formation, and hardness was measured to estimate the mechanical properties.

Peroxide Activation for Electrophilic Reactivity by the Binuclear Non-heme Iron Enzyme AurF

DOE PAGES

Park, Kiyoung; Li, Ning; Kwak, Yeonju; ...

2017-05-01

Binuclear non-heme iron enzymes activate O 2 for diverse chemistries that include oxygenation of organic substrates and hydrogen atom abstraction. This process often involves the formation of peroxo-bridged biferric intermediates, only some of which can perform electrophilic reactions. To elucidate the geometric and electronic structural requirements to activate peroxo reactivity, the active peroxo intermediate in 4-aminobenzoate N-oxygenase (AurF) has been characterized spectroscopically and computationally. A magnetic circular dichroism study of reduced AurF shows that its electronic and geometric structures are poised to react rapidly with O 2. Nuclear resonance vibrational spectroscopic definition of the peroxo intermediate formed in this reactionmore » shows that the active intermediate has a protonated peroxo bridge. Density functional theory computations on the structure established here show that the protonation activates peroxide for electrophilic/single-electron-transfer reactivity. As a result, this activation of peroxide by protonation is likely also relevant to the reactive peroxo intermediates in other binuclear non-heme iron enzymes.« less

CFD Fuel Slosh Modeling of Fluid-Structure Interaction in Spacecraft Propellant Tanks with Diaphragms

NASA Technical Reports Server (NTRS)

Sances, Dillon J.; Gangadharan, Sathya N.; Sudermann, James E.; Marsell, Brandon

2010-01-01

Liquid sloshing within spacecraft propellant tanks causes rapid energy dissipation at resonant modes, which can result in attitude destabilization of the vehicle. Identifying resonant slosh modes currently requires experimental testing and mechanical pendulum analogs to characterize the slosh dynamics. Computational Fluid Dynamics (CFD) techniques have recently been validated as an effective tool for simulating fuel slosh within free-surface propellant tanks. Propellant tanks often incorporate an internal flexible diaphragm to separate ullage and propellant which increases modeling complexity. A coupled fluid-structure CFD model is required to capture the damping effects of a flexible diaphragm on the propellant. ANSYS multidisciplinary engineering software employs a coupled solver for analyzing two-way Fluid Structure Interaction (FSI) cases such as the diaphragm propellant tank system. Slosh models generated by ANSYS software are validated by experimental lateral slosh test results. Accurate data correlation would produce an innovative technique for modeling fuel slosh within diaphragm tanks and provide an accurate and efficient tool for identifying resonant modes and the slosh dynamic response.

On-the-fly machine-learning for high-throughput experiments: search for rare-earth-free permanent magnets

PubMed Central

Kusne, Aaron Gilad; Gao, Tieren; Mehta, Apurva; Ke, Liqin; Nguyen, Manh Cuong; Ho, Kai-Ming; Antropov, Vladimir; Wang, Cai-Zhuang; Kramer, Matthew J.; Long, Christian; Takeuchi, Ichiro

2014-01-01

Advanced materials characterization techniques with ever-growing data acquisition speed and storage capabilities represent a challenge in modern materials science, and new procedures to quickly assess and analyze the data are needed. Machine learning approaches are effective in reducing the complexity of data and rapidly homing in on the underlying trend in multi-dimensional data. Here, we show that by employing an algorithm called the mean shift theory to a large amount of diffraction data in high-throughput experimentation, one can streamline the process of delineating the structural evolution across compositional variations mapped on combinatorial libraries with minimal computational cost. Data collected at a synchrotron beamline are analyzed on the fly, and by integrating experimental data with the inorganic crystal structure database (ICSD), we can substantially enhance the accuracy in classifying the structural phases across ternary phase spaces. We have used this approach to identify a novel magnetic phase with enhanced magnetic anisotropy which is a candidate for rare-earth free permanent magnet. PMID:25220062

Scanning electron microscopical and cross-sectional analysis of extraterrestrial carbonaceous nanoglobules

NASA Astrophysics Data System (ADS)

Garvie, Laurence A. J.; Baumgardner, Grant; Buseck, Peter R.

2008-05-01

Carbonaceous nanoglobules are ubiquitous in carbonaceous chondrite (CC) meteorites. The Tagish Lake (C2) meteorite is particularly intriguing in containing an abundance of nanoglobules, with a wider range of forms and sizes than encountered in other CC meteorites. Previous studies by transmission electron microscopy (TEM) have provided a wealth of information on chemistry and structure. In this study low voltage scanning electron microscopy (SEM) was used to characterize the globule forms and external structures. The internal structure of the globules was investigated after sectioning by focused ion beam (FIB) milling. The FIB-SEM analysis shows that the globules range from solid to hollow. Some hollow globules show a central open core, with adjoining smaller cores. The FIB with an SEM is a valuable tool for the analysis of extraterrestrial materials, even of sub-micron-sized "soft" carbonaceous particles. The rapid site-specific cross-sectioning capabilities of the FIB allow the preservation of the internal morphology of the nanoglobules, with minimal damage or alteration of the unsectioned areas.

Peroxide Activation for Electrophilic Reactivity by the Binuclear Non-heme Iron Enzyme AurF

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, Kiyoung; Li, Ning; Kwak, Yeonju

Binuclear non-heme iron enzymes activate O 2 for diverse chemistries that include oxygenation of organic substrates and hydrogen atom abstraction. This process often involves the formation of peroxo-bridged biferric intermediates, only some of which can perform electrophilic reactions. To elucidate the geometric and electronic structural requirements to activate peroxo reactivity, the active peroxo intermediate in 4-aminobenzoate N-oxygenase (AurF) has been characterized spectroscopically and computationally. A magnetic circular dichroism study of reduced AurF shows that its electronic and geometric structures are poised to react rapidly with O 2. Nuclear resonance vibrational spectroscopic definition of the peroxo intermediate formed in this reactionmore » shows that the active intermediate has a protonated peroxo bridge. Density functional theory computations on the structure established here show that the protonation activates peroxide for electrophilic/single-electron-transfer reactivity. As a result, this activation of peroxide by protonation is likely also relevant to the reactive peroxo intermediates in other binuclear non-heme iron enzymes.« less

Modeling structure and resilience of the dark network.

PubMed

De Domenico, Manlio; Arenas, Alex

2017-02-01

While the statistical and resilience properties of the Internet are no longer changing significantly across time, the Darknet, a network devoted to keep anonymous its traffic, still experiences rapid changes to improve the security of its users. Here we study the structure of the Darknet and find that its topology is rather peculiar, being characterized by a nonhomogeneous distribution of connections, typical of scale-free networks; very short path lengths and high clustering, typical of small-world networks; and lack of a core of highly connected nodes. We propose a model to reproduce such features, demonstrating that the mechanisms used to improve cybersecurity are responsible for the observed topology. Unexpectedly, we reveal that its peculiar structure makes the Darknet much more resilient than the Internet (used as a benchmark for comparison at a descriptive level) to random failures, targeted attacks, and cascade failures, as a result of adaptive changes in response to the attempts of dismantling the network across time.

Modeling our understanding of the His-Purkinje system.

PubMed

Vigmond, Edward J; Stuyvers, Bruno D

2016-01-01

The His-Purkinje System (HPS) is responsible for the rapid electric conduction in the ventricles. It relays electrical impulses from the atrioventricular node to the muscle cells and, thus, coordinates the contraction of ventricles in order to ensure proper cardiac pump function. The HPS has been implicated in the genesis of ventricular tachycardia and fibrillation as a source of ectopic beats, as well as forming distinct portions of reentry circuitry. Despite its importance, it remains much less well characterized, structurally and functionally, than the myocardium. Notably, important differences exist with regard to cell structure and electrophysiology, including ion channels, intracellular calcium handling, and gap junctions. Very few computational models address the HPS, and the majority of organ level modeling studies omit it. This review will provide an overview of our current knowledge of structure and function (including electrophysiology) of the HPS. We will review the most recent advances in modeling of the system from the single cell to the organ level, with considerations for relevant interspecies distinctions. Copyright © 2015 Elsevier Ltd. All rights reserved.

Modeling structure and resilience of the dark network

NASA Astrophysics Data System (ADS)

De Domenico, Manlio; Arenas, Alex

2017-02-01

While the statistical and resilience properties of the Internet are no longer changing significantly across time, the Darknet, a network devoted to keep anonymous its traffic, still experiences rapid changes to improve the security of its users. Here we study the structure of the Darknet and find that its topology is rather peculiar, being characterized by a nonhomogeneous distribution of connections, typical of scale-free networks; very short path lengths and high clustering, typical of small-world networks; and lack of a core of highly connected nodes. We propose a model to reproduce such features, demonstrating that the mechanisms used to improve cybersecurity are responsible for the observed topology. Unexpectedly, we reveal that its peculiar structure makes the Darknet much more resilient than the Internet (used as a benchmark for comparison at a descriptive level) to random failures, targeted attacks, and cascade failures, as a result of adaptive changes in response to the attempts of dismantling the network across time.

Sandwich-structured C/C-SiC composites fabricated by electromagnetic-coupling chemical vapor infiltration.

PubMed

Hu, Chenglong; Hong, Wenhu; Xu, Xiaojing; Tang, Sufang; Du, Shanyi; Cheng, Hui-Ming

2017-10-13

Carbon fiber (CF) reinforced carbon-silicon carbide (C/C-SiC) composites are one of the most promising lightweight materials for re-entry thermal protection, rocket nozzles and brake discs applications. In this paper, a novel sandwich-structured C/C-SiC composite, containing two exterior C/SiC layers, two gradient C/C-SiC layers and a C/C core, has been designed and fabricated by two-step electromagnetic-coupling chemical vapor infiltration (E-CVI) for a 20-hour deposition time. The cross-section morphologies, interface microstructures and SiC-matrix growth characteristics and compositions of the composites were characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM) and X-ray diffraction (XRD), respectively. Microstructure characterization indicates that the SiC growth includes an initial amorphous SiC zone, a gradual crystallization of SiC and grow-up of nano-crystal, and a columnar grain region. The sandwich structure, rapid deposition rate and growth characteristics are attributed to the formation of thermal gradient and the establishment of electromagnetic field in the E-CVI process. The composite possesses low density of 1.84 g/cm 3 , high flexural strength of 325 MPa, and low linear ablation rate of 0.38 μm/s under exposure to 5-cycle oxyacetylene flame for 1000 s at ~1700 °C.

In situ characterization of charge rate dependent stress and structure changes in V2O5 cathode prepared by atomic layer deposition

NASA Astrophysics Data System (ADS)

Jung, Hyun; Gerasopoulos, Konstantinos; Talin, A. Alec; Ghodssi, Reza

2017-02-01

The insertion/extraction of lithium into/from various host materials is the basic process by which lithium-ion batteries reversible store charge. This process is generally accompanied by strain in the host material, inducing stress which can lead to capacity loss. Therefore, understanding of both the structural changes and the associated stress - investigated almost exclusively separate to date - is a critical factor for developing high-performance batteries. Here, we report an in situ method, which utilizes Raman spectroscopy in parallel with optical interferometry to study effects of varying charging rates (C-rates) on the structure and stress in a V2O5 thin film cathode. Abrupt stress changes at specific crystal phase transitions in the Lisbnd Vsbnd O system are observed and the magnitude of the stress changes with the amount of lithium inserted into the electrode are correlated. A linear increase in the stress as a function of x in LixV2O5 is observed, indicating that C-rate does not directly contribute to larger intercalation stress. However, a more rapid increase in disorder within the LixV2O5 layers is correlated with higher C-rate. Ultimately, these experiments demonstrate how the simultaneous stress/Raman in situ approach can be utilized as a characterization platform for investigating various critical factors affecting lithium-ion battery performance.

The magnetodynamic filters in monitoring the contaminants from polluted water systems (abstract)

NASA Astrophysics Data System (ADS)

Swarup, R.; Singh, Bharat

1994-05-01

The magnetic interaction seems to influence the ``structural memory'' of water systems which is quenched in ideally pure water. The sedentary lifetime of each water molecule is extremely short (10-10 s) and its molecular structures may be influenced by some physical effect like magnetic field treatment, it's space time gradients, water velocity, pressure drop, etc. in the interpolar space, so as to yield a noticeable temporal magnetopotential development characterizing the properties of homogeneous and heterogeneous water systems. This principle is also extended to prevailing water systems which always contain various impurities, gas, molecules, ions, microscopic particles in random order. Still the existence of structural memory may be verified by reliable experimental data. The magnetopotential curves of different water systems depict the design and develop-software package for constructing the magnetodynamic-filters superior to the existing techniques on pollution studies like remote sensing, muon spin resonance, laser spectroscopy, nuclear techniques, the gamma ray peak efficiency method, trace elemental characterization due to NBS, neutron activation analysis, and graphite furnance atomic absorption spectrometer. The physiochemical characteristics of water calibrated in terms of magnetopotential curves change with the removal of dissolved gasses, impurities, thermal activation, etc. and the algae, bacteria, phosphates, etc. have been removed at a rapid rate. The magnetodynamic study of ganga water proves it to be an extremely pure and highly resourced fluid.

Mutational Analysis of the Stability of the H2A and H2B Histone Monomers

PubMed Central

Stump, Matthew R.; Gloss, Lisa M.

2008-01-01

The eukaryotic histone heterodimer H2A-H2B folds through an obligatory dimeric intermediate that forms in a nearly diffusion-limited association reaction in the stopped-flow dead time. It is unclear whether there is partial folding of the isolated monomers before association. To address the possible contributions of structure in the monomers to the rapid association, we characterized H2A and H2B monomers in the absence of their heterodimeric partner. By far-UV circular dichroism, the H2A and H2B monomers are 15% and 31% helical, respectively—significantly less than observed in X-ray crystal structures. Acrylamide quenching of the intrinsic Tyr fluorescence was indicative of tertiary structure. The H2A and H2B monomers exhibit free energies of unfolding of 2.5 and 2.9 kcal mol−1, respectively; at 10 μM, the sum of the stability of the monomers is ~60% of the stability of the native dimer. The helical content, stability and m values indicate that H2B has a more stable, compact structure than H2A. The monomer m values are larger than expected for the extended histone fold motif, suggesting that the monomers adopt an overly-collapsed structure. Stopped-flow refolding—initiated from urea-denatured monomers or the partially folded monomers populated at low denaturant concentrations—yielded essentially identical rates, indicating that monomer folding is productive in the rapid association and folding of the heterodimer. A series of Ala and Gly mutations were introduced into H2A and H2B to probe the importance of helix propensity on the structure and stability of the monomers. The mutational studies show that the central α-helix of the histone fold, which makes extensive inter-monomer contacts, is structured in H2B but only partially folded in H2A. PMID:18976667

A programmable nanoreplica molding for the fabrication of nanophotonic devices.

PubMed

Liu, Longju; Zhang, Jingxiang; Badshah, Mohsin Ali; Dong, Liang; Li, Jingjing; Kim, Seok-min; Lu, Meng

2016-03-01

The ability to fabricate periodic structures with sub-wavelength features has a great potential for impact on integrated optics, optical sensors, and photovoltaic devices. Here, we report a programmable nanoreplica molding process to fabricate a variety of sub-micrometer periodic patterns using a single mold. The process utilizes a stretchable mold to produce the desired periodic structure in a photopolymer on glass or plastic substrates. During the replica molding process, a uniaxial force is applied to the mold and results in changes of the periodic structure, which resides on the surface of the mold. Direction and magnitude of the force determine the array geometry, including the lattice constant and arrangement. By stretching the mold, 2D arrays with square, rectangular, and triangular lattice structures can be fabricated. As one example, we present a plasmonic crystal device with surface plasmon resonances determined by the force applied during molding. In addition, photonic crystal slabs with different array patterns are fabricated and characterized. This unique process offers the capability of generating various periodic nanostructures rapidly and inexpensively.

Optical and structural characterization of Ge clusters embedded in ZrO2

NASA Astrophysics Data System (ADS)

Agocs, E.; Zolnai, Z.; Rossall, A. K.; van den Berg, J. A.; Fodor, B.; Lehninger, D.; Khomenkova, L.; Ponomaryov, S.; Gudymenko, O.; Yukhymchuk, V.; Kalas, B.; Heitmann, J.; Petrik, P.

2017-11-01

The change of optical and structural properties of Ge nanoclusters in ZrO2 matrix have been investigated by spectroscopic ellipsometry versus annealing temperatures. Radio-frequency top-down magnetron sputtering approach was used to produce the samples of different types, i.e. single-layers of pure Ge, pure ZrO2 and Ge-rich-ZrO2 as well as multi-layers stacked of 40 periods of 5-nm-Ge-rich-ZrO2 layers alternated by 5-nm-ZrO2 ones. Germanium nanoclusters in ZrO2 host were formed by rapid-thermal annealing at 600-800 °C during 30 s in nitrogen atmosphere. Reference optical properties for pure ZrO2 and pure Ge have been extracted using single-layer samples. As-deposited multi-layer structures can be perfectly modeled using the effective medium theory. However, annealed multi-layers demonstrated a significant diffusion of elements that was confirmed by medium energy ion scattering measurements. This fact prevents fitting of such annealed structure either by homogeneous or by periodic multi-layer models.

A programmable nanoreplica molding for the fabrication of nanophotonic devices

PubMed Central

Liu, Longju; Zhang, Jingxiang; Badshah, Mohsin Ali; Dong, Liang; Li, Jingjing; Kim, Seok-min; Lu, Meng

2016-01-01

The ability to fabricate periodic structures with sub-wavelength features has a great potential for impact on integrated optics, optical sensors, and photovoltaic devices. Here, we report a programmable nanoreplica molding process to fabricate a variety of sub-micrometer periodic patterns using a single mold. The process utilizes a stretchable mold to produce the desired periodic structure in a photopolymer on glass or plastic substrates. During the replica molding process, a uniaxial force is applied to the mold and results in changes of the periodic structure, which resides on the surface of the mold. Direction and magnitude of the force determine the array geometry, including the lattice constant and arrangement. By stretching the mold, 2D arrays with square, rectangular, and triangular lattice structures can be fabricated. As one example, we present a plasmonic crystal device with surface plasmon resonances determined by the force applied during molding. In addition, photonic crystal slabs with different array patterns are fabricated and characterized. This unique process offers the capability of generating various periodic nanostructures rapidly and inexpensively. PMID:26925828

Crystal morphology variation in inkjet-printed organic materials

NASA Astrophysics Data System (ADS)

Ihnen, Andrew C.; Petrock, Anne M.; Chou, Tsengming; Samuels, Phillip J.; Fuchs, Brian E.; Lee, Woo Y.

2011-11-01

The recent commercialization of piezoelectric-based drop-on-demand inkjet printers provides an additive processing platform for producing and micropatterning organic crystal structures. We report an inkjet printing approach where macro- and nano-scale energetic composites composed of cyclotrimethylenetrinitramine (RDX) crystals dispersed in a cellulose acetate butyrate (CAB) matrix are produced by direct phase transformation from organic solvent-based all-liquid inks. The characterization of printed composites illustrates distinct morphological changes dependent on ink deposition parameters. When 10 pL ink droplets rapidly formed a liquid pool, a coffee ring structure containing dendritic RDX crystals was produced. By increasing the substrate temperature, and consequently the evaporation rate of the pooled ink, the coffee ring structure was mitigated and shorter dendrites from up to ∼1 to 0.2 mm with closer arm spacing from ∼15 to 1 μm were produced. When the nucleation and growth of RDX and CAB were confined within the evaporating droplets, a granular structure containing nanoscale RDX crystals was produced. The results suggest that evaporation rate and microfluidic droplet confinement can effectively be used to tailor the morphology of inkjet-printed energetic composites.

Surface reconstruction of GaAs(001) nitrided under the controlled As partial pressure [rapid communication

NASA Astrophysics Data System (ADS)

Imayoshi, Takahiro; Oigawa, Haruhiro; Shigekawa, Hidemi; Tokumoto, Hiroshi

2003-08-01

Under the controlled As partial pressure, the nitridation process of GaAs(0 0 1)-(2 × 4) surface was studied using a scanning tunneling microscope (STM) combined with an electron cyclotron resonance plasma-assisted molecular beam epitaxy system. With either prolonging the nitridation time or decreasing the As partial pressure, the previously reported (3 × 3) structure with two dimers per surface cell ((3 × 3)-2D) was found to progressively convert into a new (3 × 3) structure characterized by one dimer per surface cell ((3 × 3)-1D). Reversely the exposure to arsenic transformed the structure from (3 × 3)-1D to (3 × 3)-2D, suggesting that the topmost layer is composed of As 2-dimers. Based on these STM images together with the X-ray photoelectron spectroscopy data, we propose the new As 2-dimer coverage models to explain both (3 × 3)-1D and -2D structures involving the exchange reaction of arsenic with nitrogen in the subsurface region of GaAs.

Two-dimensional phase separated structures of block copolymers on solids

NASA Astrophysics Data System (ADS)

Sen, Mani; Jiang, Naisheng; Endoh, Maya; Koga, Tadanori; Ribbe, Alexander

The fundamental, yet unsolved question in block copolymer (BCP) thin films is the self-organization process of BCPs at the solid-polymer melt interface. We here focus on the self-organization processes of cylinder-forming polystyrene-block-poly (4-vinylpyridine) diblock copolymer and lamellar-forming poly (styrene-block-butadiene-block-styrene) triblock copolymer on Si substrates as model systems. In order to reveal the buried interfacial structures, the following experimental protocols were utilized: the BCP monolayer films were annealed under vacuum at T>Tg of the blocks (to equilibrate the melts); vitrification of the annealed BCP films via rapid quench to room temperature; subsequent intensive solvent leaching (to remove unadsorbed chains) with chloroform, a non-selective good solvent for the blocks. The strongly bound BCP layers were then characterized by using atomic force microscopy, scanning electron microscopy, grazing incidence small angle X-ray scattering, and X-ray reflectivity. The results showed that both blocks lie flat on the substrate, forming the two-dimensional, randomly phase-separated structure irrespective of their microdomain structures and interfacial energetics. Acknowledgement of financial support from NSF Grant (CMMI -1332499).

Chemical synthesis and NMR characterization of structured polyunsaturated triacylglycerols.

PubMed

Fauconnot, Laëtitia; Robert, Fabien; Villard, Renaud; Dionisi, Fabiola

2006-02-01

The chemical synthesis of pure triacylglycerol (TAG) regioisomers, that contain long chain polyunsaturated fatty acids, such as arachidonic acid (AA) or docosahexaenoic acid (DHA), and saturated fatty acids, such as lauric acid (La) or palmitic acid (P), at defined positions, is described. A single step methodology using (benzotriazol-1-yloxy)-tripyrrolidinophosphonium hexafluorophosphate (PyBOP), an activator of carboxyl group commonly used in peptide synthesis and occasionally used in carboxylic acid esterification, has been developed for structured TAG synthesis. Identification of the fatty acyl chains for each TAG species was confirmed by atmospheric pressure chemical ionisation mass spectrometry (APCI-MS) and fatty acid positional distribution was determined by (1)H and (13)C NMR spectra. The generic described procedures can be applied to a large variety of substrates and was used for the production of specific triacylglycerols of defined molecular structures, with high regioisomeric purity. Combination of MS and NMR was shown to be an efficient tool for structural analysis of TAG. In particular, some NMR signals were demonstrated to be regioisomer specific, allowing rapid positional analysis of LC-PUFA containing TAG.

Bulk combinatorial synthesis and high throughput characterization for rapid assessment of magnetic materials: Application of laser engineered net shaping (LENS)

DOE PAGES

Geng, J.; Nlebedim, I. C.; Besser, M. F.; ...

2016-04-15

A bulk combinatorial approach for synthesizing alloy libraries using laser engineered net shaping (LENS; i.e., 3D printing) was utilized to rapidly assess material systems for magnetic applications. The LENS system feeds powders in different ratios into a melt pool created by a laser to synthesize samples with bulk (millimeters) dimensions. By analyzing these libraries with autosampler differential scanning calorimeter/thermal gravimetric analysis and vibrating sample magnetometry, we are able to rapidly characterize the thermodynamic and magnetic properties of the libraries. Furthermore, the Fe-Co binary alloy was used as a model system and the results were compared with data in the literature.

Rapid three-dimensional microfluidic mixer for high viscosity solutions to unravel earlier folding kinetics of G-quadruplex under molecular crowding conditions.

PubMed

Liu, Chao; Li, Ying; Li, Yiwei; Chen, Peng; Feng, Xiaojun; Du, Wei; Liu, Bi-Feng

2016-01-01

Rapid mixing of highly viscous solutions is a great challenge, which helps to analyze the reaction kinetics in viscous liquid phase, particularly to discover the folding kinetics of macromolecules under molecular crowding conditions mimicking the conditions inside cells. Here, we demonstrated a novel microfluidic mixer based on Dean flows with three-dimensional (3D) microchannel configuration for fast mixing of high-viscosity fluids. The main structure contained three consecutive subunits, each consisting of a "U"-type channel followed by a chamber with different width and height. Thus, the two solutions injected from the two inlets would undergo a mixing in the first "U"-type channel due to the Dean flow effect, and simultaneous vortices expansions in both horizontal and vertical directions in the following chamber. Numerical simulations and experimental characterizations confirmed that the micromixer could achieve a mixing time of 122.4μs for solutions with viscosities about 33.6 times that of pure water. It was the fastest micromixer for high viscosity solutions compared with previous reports. With this highly efficient 3D microfluidic mixer, we further characterized the early folding kinetics of human telomere G-quadruplex under molecular crowding conditions, and unravelled a new folding process within 550μs. Copyright © 2015 Elsevier B.V. All rights reserved.

Noise Rating Criteria for Elevated Rapid Transit Structures

DOT National Transportation Integrated Search

1980-05-01

The purpose of this report is to recommend criteria for rating the noise radiated from elevated rapid transit structures during train passages, so that different types of structures can be inter-compared with respect to their noise impact on the imme...

Hepatoselective Nitric Oxide (NO) Donors, V-PYRRO/NO and V-PROLI/NO, in Nonalcoholic Fatty Liver Disease: A Comparison of Antisteatotic Effects with the Biotransformation and Pharmacokinetics.

PubMed

Kus, Kamil; Walczak, Maria; Maslak, Edyta; Zakrzewska, Agnieszka; Gonciarz-Dytman, Anna; Zabielski, Piotr; Sitek, Barbara; Wandzel, Krystyna; Kij, Agnieszka; Chabowski, Adrian; Holland, Ryan J; Saavedra, Joseph E; Keefer, Larry K; Chlopicki, Stefan

2015-07-01

V-PYRRO/NO [O(2)-vinyl-1-(pyrrolidin-1-yl)diazen-1-ium-1,2-diolate] and V-PROLI/NO (O2-vinyl-[2-(carboxylato)pyrrolidin-1-yl]diazen-1-ium-1,2-diolate), two structurally similar diazeniumdiolate derivatives, were designed as liver-selective prodrugs that are metabolized by cytochrome P450 isoenzymes, with subsequent release of nitric oxide (NO). Yet, their efficacy in the treatment of nonalcoholic fatty liver disease (NAFLD) and their comparative pharmacokinetic and metabolic profiles have not been characterized. The aim of the present work was to compare the effects of V-PYRRO/NO and V-PROLI/NO on liver steatosis, glucose tolerance, and liver fatty acid composition in C57BL/6J mice fed a high-fat diet, as well as to comprehensively characterize the ADME (absorption, distribution, metabolism and excretion) profiles of both NO donors. Despite their similar structure, V-PYRRO/NO and V-PROLI/NO showed differences in pharmacological efficacy in the murine model of NAFLD. V-PYRRO/NO, but not V-PROLI/NO, attenuated liver steatosis, improved glucose tolerance, and favorably modified fatty acid composition in the liver. Both compounds were characterized by rapid absorption following i.p. administration, rapid elimination from the body, and incomplete bioavailability. However, V-PYRRO/NO was eliminated mainly by the liver, whereas V-PROLI/NO was excreted mostly in unchanged form by the kidney. V-PYRRO/NO was metabolized by CYP2E1, CYP2C9, CYP1A2, and CYP3A4, whereas V-PROLI/NO was metabolized mainly by CYP1A2. Importantly, V-PYRRO/NO was a better NO releaser in vivo and in the isolated, perfused liver than V-PROLI/NO, an effect compatible with the superior antisteatotic activity of V-PYRRO/NO. In conclusion, V-PYRRO/NO displayed a pronounced antisteatotic effect associated with liver-targeted NO release, whereas V-PROLI/NO showed low effectiveness, was not taken up by the liver, and was eliminated mostly in unchanged form by the kidney. U.S. Government work not protected by U.S. copyright.

Changes in Sensory Evoked Responses Coincide with Rapid Improvement in Speech Identification Performance

ERIC Educational Resources Information Center

Alain, Claude; Campeanu, Sandra; Tremblay, Kelly

2010-01-01

Perceptual learning is sometimes characterized by rapid improvements in performance within the first hour of training (fast perceptual learning), which may be accompanied by changes in sensory and/or response pathways. Here, we report rapid physiological changes in the human auditory system that coincide with learning during a 1-hour test session…

From functional structure to packaging: full-printing fabrication of a microfluidic chip.

PubMed

Zheng, Fengyi; Pu, Zhihua; He, Enqi; Huang, Jiasheng; Yu, Bocheng; Li, Dachao; Li, Zhihong

2018-05-24

This paper presents a concept of a full-printing methodology aiming at convenient and fast fabrication of microfluidic devices. For the first time, we achieved a microfluidic biochemical sensor with all functional structures fabricated by inkjet printing, including electrodes, immobilized enzymes, microfluidic components and packaging. With the cost-effective and rapid process, this method provides the possibility of quick model validation of a novel lab-on-chip system. In this study, a three-electrode electrochemical system was integrated successfully with glucose oxidase immobilization gel and sealed in an ice channel, forming a disposable microfluidic sensor for glucose detection. This fully-printed chip was characterized and showed good sensitivity and a linear section at a low-level concentration of glucose (0-10 mM). With the aid of automatic equipment, the fully-printed sensor can be massively produced with low cost.

In vivo imaging of coral tissue and skeleton with optical coherence tomography

PubMed Central

Wentzel, Camilla; Jacques, Steven L.; Wagner, Michael

2017-01-01

Application of optical coherence tomography (OCT) for in vivo imaging of tissue and skeleton structure of intact living corals enabled the non-invasive visualization of coral tissue layers (endoderm versus ectoderm), skeletal cavities and special structures such as mesenterial filaments and mucus release from intact living corals. Coral host chromatophores containing green fluorescent protein-like pigment granules appeared hyper-reflective to near-infrared radiation allowing for excellent optical contrast in OCT and a rapid characterization of chromatophore size, distribution and abundance. In vivo tissue plasticity could be quantified by the linear contraction velocity of coral tissues upon illumination resulting in dynamic changes in the live coral tissue surface area, which varied by a factor of 2 between the contracted and expanded state of a coral. Our study provides a novel view on the in vivo organization of coral tissue and skeleton and highlights the importance of microstructural dynamics for coral ecophysiology. PMID:28250104

Listeria phospholipases subvert host autophagic defenses by stalling pre-autophagosomal structures

PubMed Central

Tattoli, Ivan; Sorbara, Matthew T; Yang, Chloe; Tooze, Sharon A; Philpott, Dana J; Girardin, Stephen E

2013-01-01

Listeria can escape host autophagy defense pathways through mechanisms that remain poorly understood. We show here that in epithelial cells, Listeriolysin (LLO)-dependent cytosolic escape of Listeria triggered a transient amino-acid starvation host response characterized by GCN2 phosphorylation, ATF3 induction and mTOR inhibition, the latter favouring a pro-autophagic cellular environment. Surprisingly, rapid recovery of mTOR signalling was neither sufficient nor necessary for Listeria avoidance of autophagic targeting. Instead, we observed that Listeria phospholipases PlcA and PlcB reduced autophagic flux and phosphatidylinositol 3-phosphate (PI3P) levels, causing pre-autophagosomal structure stalling and preventing efficient targeting of cytosolic bacteria. In co-infection experiments, wild-type Listeria protected PlcA/B-deficient bacteria from autophagy-mediated clearance. Thus, our results uncover a critical role for Listeria phospholipases C in the inhibition of autophagic flux, favouring bacterial escape from host autophagic defense. PMID:24162724

NDE of polymeric composite material bridge components

NASA Astrophysics Data System (ADS)

Duke, John C., Jr.; Horne, Michael R.

1998-03-01

Rapid advancements with respect to utilization of polymeric composite materials for bridge components is occurring. This situation is driven primarily by the potential improvements offered by these materials with respect to long term durability. However, because of the developmental nature of these materials much of the materials characterization has involved short term testing without the synergistic effects of environmental exposure. Efforts to develop nondestructive evaluation procedures, essential for any wide spread use in critical structural applications, have been consequently limited. This paper discuses the effort to develop NDE methods for field inspection of hybrid glass and carbon fiber reinforced vinyl ester pultruded 'double box' I beams that are installed in a small bridge over Tom's Creek, in Blacksburg, Virginia. Integrated structural element sensors, dormant infrared devices, as well as acousto-ultrasonic methods are under development for detecting and monitoring the occurrence and progression of life limiting deterioration mechanisms.

Oxidation-induced structural changes in sub-nanometer platinum supported on alumina

DOE PAGES

DeBusk, Melanie Moses; Allard, Jr, Lawrence Frederick; Blom, Douglas Allen; ...

2015-06-26

Platinum supported on alumina is an essential component of emission treatment catalysts used in transportation. Theoretical, experimental, and mechanistic aspects of platinum particles supported on a variety of supports have been extensively studied; however, available experimental information on the behavior of single vs. sub-nanometer platinum is extremely limited. To bridge the knowledge gap between single supported platinum and well-formed supported platinum nanoparticles, we have carried out synthesis, characterization, and CO and NO oxidation studies of sub-nanometer platinum supported on α, θ, and γ-Al 2O 3 and monitored changes in structure upon exposure to CO and NO oxidation conditions. Furthermore, wemore » find that sub-nanometer Pt is highly effective for CO oxidation due to high platinum dispersion but is not very efficient as NO oxidation catalyst. Lastly, sub-nanometer platinum agglomerates rapidly under CO or NO oxidation conditions to form nanoparticles.« less

The State of the Summer: a Review of Child Summer Weight Gain and Efforts to Prevent It.

PubMed

Tanskey, Lindsay A; Goldberg, Jeanne; Chui, Kenneth; Must, Aviva; Sacheck, Jennifer

2018-06-01

Accumulating evidence shows that children in the USA gain weight more rapidly during the summer, when school is not in session. This narrative review spanning 2007 to 2017 summarizes efforts to characterize the problem, identify key determinants, and intervene to prevent excess summer weight gain. Summer weight gain remains a concern for elementary-age youth. Few studies have examined its determinants, but unfavorable summertime shifts in diet, physical activity, sedentary time, screen media use, and sleep have been reported. Increased structure is thought to protect against summer weight gain. Interventions to support physical activity and nutrition during the summer show promise, though large-scale impact on weight outcomes remains to be seen. Supporting health behaviors during the summer remains a priority for obesity prevention researchers, practitioners, and policymakers. Strategies to expand access to structured programs and reach beyond such programs to improve behaviors at home are of particular importance.

Rapid screening and structural elucidation of a novel sibutramine analogue in a weight loss supplement: 11-desisobutyl-11-benzylsibutramine.

PubMed

Mans, Daniel J; Gucinski, Ashley C; Dunn, Jamie D; Gryniewicz-Ruzicka, Connie M; Mecker-Pogue, Laura C; Kao, Jeff L-F; Ge, Xia

2013-09-01

A novel analogue of sibutramine, 11-desisobutyl-11-benzylsibutramine, has been discovered. During routine ion mobility spectrometry (IMS) screening of a weight loss supplement collected at an US FDA import operation facility an unknown peak was observed. Further analysis of the supplement by liquid chromatography-mass spectrometry (LC-MS) and high resolution mass spectrometry revealed an unknown peak with a relative retention time of 1.04 with respect to sibutramine and a predicted formula of C20H24NCl. In order to elucidate the analogue's structure, it was isolated from the supplement and characterized by tandem mass spectrometry and nuclear magnetic resonance (NMR), which revealed the analogue possessed a benzyl moiety at the 11 position in place of the isobutyl group associated with sibutramine. Copyright © 2013. Published by Elsevier B.V.

Ballistic Analysis of New Military Grade Magnesium Alloys for Armor Applications

NASA Astrophysics Data System (ADS)

Jones, Tyrone L.; Kondoh, Katsuyoshi

Since 2006, the U.S. Army has been evaluating magnesium (Mg) alloys for ballistic structural applications. While Mg-alloys have been used in military structural applications since WWII, very little research has been done to improve its mediocre ballistic performance. The Army's need for ultra-lightweight armor systems has led to research and development of high strength, high ductility Mg-alloys. The U.S. Army Research Laboratory contracted through International Technology Center-Pacific Contract Number FA-5209-09-P-0158 with the Joining and Welding Research Instituteof Osaka University to develop the next generation of high strength, high ductility Mg-alloys using a novel Spinning Water Atomization Process for rapid solidification. New alloys AMX602 and ZAXE1711 in extruded bar form were characterized for microstructure, mechanical, and ballistic response. Significant increases in ballistic performance were evident when compared to the baseline alloy AZ31B.

Computer-Aided Screening of Conjugated Polymers for Organic Solar Cell: Classification by Random Forest.

PubMed

Nagasawa, Shinji; Al-Naamani, Eman; Saeki, Akinori

2018-05-17

Owing to the diverse chemical structures, organic photovoltaic (OPV) applications with a bulk heterojunction framework have greatly evolved over the last two decades, which has produced numerous organic semiconductors exhibiting improved power conversion efficiencies (PCEs). Despite the recent fast progress in materials informatics and data science, data-driven molecular design of OPV materials remains challenging. We report a screening of conjugated molecules for polymer-fullerene OPV applications by supervised learning methods (artificial neural network (ANN) and random forest (RF)). Approximately 1000 experimental parameters including PCE, molecular weight, and electronic properties are manually collected from the literature and subjected to machine learning with digitized chemical structures. Contrary to the low correlation coefficient in ANN, RF yields an acceptable accuracy, which is twice that of random classification. We demonstrate the application of RF screening for the design, synthesis, and characterization of a conjugated polymer, which facilitates a rapid development of optoelectronic materials.

Characterization of LaF 3 coatings prepared at different temperatures and rates

NASA Astrophysics Data System (ADS)

Yu, Hua; Shen, Yanming; Cui, Yun; Qi, Hongji; Shao, JianDa; Fan, ZhengXiu

2008-01-01

LaF 3 thin films were prepared by thermal boat evaporation at different substrate temperatures and various deposition rates. X-ray diffraction (XRD), Lambda 900 spectrophotometer and X-ray photoelectron spectroscopy (XPS) were employed to study crystal structure, transmittance and chemical composition of the coatings, respectively. Laser-induce damage threshold (LIDT) was determined by a tripled Nd:YAG laser system with a pulse width of 8 ns. It is found that the crystal structure became more perfect and the refractive index increased gradually with the temperature rising. The LIDT was comparatively high at high temperature. In the other hand, the crystallization status also became better and the refractive index increased when the deposition rate enhanced at a low level. If the rate was super rapid, the crystallization worsened instead and the refractive index would lessen greatly. On the whole, the LIDT decreased with increasing rate.

Workers' Housing Estates In Postindustrial Cities - Modernization Or Revitalization?

NASA Astrophysics Data System (ADS)

Gaweł, Dariusz

2015-09-01

The article presents a part of the results on the physiognomy of a postindustrial city under conditions of economic transformation in Poland. The study area encompasses industrial centers located in the region of the Central Industrial District (Centralny Okręg Przemysłowy - COP) in the Świętokrzystkie and Mazowieckie voivodeships (districts). The specific urban structure of the industrial city and unemployment among its inhabitants resulting from ownership transformations generate various problems. The workers' neighborhoods and colonies, which sprouted up so quickly at the beginning of the XX century, were a supply base for the rapidly developing industrial centers. Their clear urban structure and cultural potential they possess predispose them to developing necessary repair programs. Thus, the article draws attention to this form of settlement on the one hand, and on the other characterizes the activities assumed by gminas (municipalities) in the scope of modernizing and revitalizing these areas.

Modulation of Small-scale Turbulence Structure by Large-scale Motions in the Absence of Direct Energy Transfer.

NASA Astrophysics Data System (ADS)

Brasseur, James G.; Juneja, Anurag

1996-11-01

Previous DNS studies indicate that small-scale structure can be directly altered through ``distant'' dynamical interactions by energetic forcing of the large scales. To remove the possibility of stimulating energy transfer between the large- and small-scale motions in these long-range interactions, we here perturb the large scale structure without altering its energy content by suddenly altering only the phases of large-scale Fourier modes. Scale-dependent changes in turbulence structure appear as a non zero difference field between two simulations from identical initial conditions of isotropic decaying turbulence, one perturbed and one unperturbed. We find that the large-scale phase perturbations leave the evolution of the energy spectrum virtually unchanged relative to the unperturbed turbulence. The difference field, on the other hand, is strongly affected by the perturbation. Most importantly, the time scale τ characterizing the change in in turbulence structure at spatial scale r shortly after initiating a change in large-scale structure decreases with decreasing turbulence scale r. Thus, structural information is transferred directly from the large- to the smallest-scale motions in the absence of direct energy transfer---a long-range effect which cannot be explained by a linear mechanism such as rapid distortion theory. * Supported by ARO grant DAAL03-92-G-0117

Fabrication and Optimal Design of Biodegradable Polymeric Stents for Aneurysms Treatments

PubMed Central

Han, Xue; Wu, Xia; Kelly, Michael; Chen, Xiongbiao

2017-01-01

An aneurysm is a balloon-like bulge in the wall of blood vessels, occurring in major arteries of the heart and brain. Biodegradable polymeric stent-assisted coiling is expected to be the ideal treatment of wide-neck complex aneurysms. This paper presents the development of methods to fabricate and optimally design biodegradable polymeric stents for aneurysms treatment. Firstly, a dispensing-based rapid prototyping (DBRP) system was developed to fabricate coil and zigzag structures of biodegradable polymeric stents. Then, compression testing was carried out to characterize the radial deformation of the stents fabricated with the coil or zigzag structure. The results illustrated the stent with a zigzag structure has a stronger radial stiffness than the one with a coil structure. On this basis, the stent with a zigzag structure was chosen for the development of a finite element model for simulating the real compression tests. The result showed the finite element model of biodegradable polymeric stents is acceptable within a range of radial deformation around 20%. Furthermore, the optimization of the zigzag structure was performed with ANSYS DesignXplorer, and the results indicated that the total deformation could be decreased by 35.7% by optimizing the structure parameters, which would represent a significant advance of the radial stiffness of biodegradable polymeric stents. PMID:28264515

Protoplast isolation, transient transformation of leaf mesophyll protoplasts and improved Agrobacterium-mediated leaf disc infiltration of Phaseolus vulgaris: tools for rapid gene expression analysis.

PubMed

Nanjareddy, Kalpana; Arthikala, Manoj-Kumar; Blanco, Lourdes; Arellano, Elizabeth S; Lara, Miguel

2016-06-24

Phaseolus vulgaris is one of the most extensively studied model legumes in the world. The P. vulgaris genome sequence is available; therefore, the need for an efficient and rapid transformation system is more imperative than ever. The functional characterization of P. vulgaris genes is impeded chiefly due to the non-amenable nature of Phaseolus sp. to stable genetic transformation. Transient transformation systems are convenient and versatile alternatives for rapid gene functional characterization studies. Hence, the present work focuses on standardizing methodologies for protoplast isolation from multiple tissues and transient transformation protocols for rapid gene expression analysis in the recalcitrant grain legume P. vulgaris. Herein, we provide methodologies for the high-throughput isolation of leaf mesophyll-, flower petal-, hypocotyl-, root- and nodule-derived protoplasts from P. vulgaris. The highly efficient polyethylene glycol-mannitol magnesium (PEG-MMG)-mediated transformation of leaf mesophyll protoplasts was optimized using a GUS reporter gene. We used the P. vulgaris SNF1-related protein kinase 1 (PvSnRK1) gene as proof of concept to demonstrate rapid gene functional analysis. An RT-qPCR analysis of protoplasts that had been transformed with PvSnRK1-RNAi and PvSnRK1-OE vectors showed the significant downregulation and ectopic constitutive expression (overexpression), respectively, of the PvSnRK1 transcript. We also demonstrated an improved transient transformation approach, sonication-assisted Agrobacterium-mediated transformation (SAAT), for the leaf disc infiltration of P. vulgaris. Interestingly, this method resulted in a 90 % transformation efficiency and transformed 60-85 % of the cells in a given area of the leaf surface. The constitutive expression of YFP further confirmed the amenability of the system to gene functional characterization studies. We present simple and efficient methodologies for protoplast isolation from multiple P. vulgaris tissues. We also provide a high-efficiency and amenable method for leaf mesophyll transformation for rapid gene functional characterization studies. Furthermore, a modified SAAT leaf disc infiltration approach aids in validating genes and their functions. Together, these methods help to rapidly unravel novel gene functions and are promising tools for P. vulgaris research.

A review of whole cell wall NMR by the direct-dissolution of biomass

DOE PAGES

Foston, Marcus B.; Samuel, Reichel; He, Jian; ...

2016-01-19

To fully realize the potential of lignocellulosic biomass as a renewable resource for the production of fuels, chemicals, and materials, an improved understanding of the chemical and molecular structures within biomass and how those structures are formed during biosynthesis and transformed during (thermochemical and biological) conversion must be developed. This effort will require analytical techniques which are not only in-depth, rapid, and cost-effective, but also leave native cell wall features intact. Whole plant cell wall nuclear magnetic resonance (NMR) analysis facilitates unparalleled structural characterization of lignocellulosic biomass without causing (or with minimal) structural modification. The objective of this review ismore » to summarize research pertaining to solution- or gel-state whole plant cell wall NMR analysis of biomass, demonstrating the capability of NMR to delineate the structural features and transformations of biomass. In particular, this review will focus on the application of a two-dimensional solution-state NMR technique and perdeuterated ionic liquid based organic electrolyte solvents for the direct dissolution and analysis of biomass. Furthermore, we believe this type of analysis will be critical to advancing biofuel research, improving bioprocessing methodology, and enhancing plant bioengineering efforts.« less

A review of whole cell wall NMR by the direct-dissolution of biomass

DOE Office of Scientific and Technical Information (OSTI.GOV)

Foston, Marcus B.; Samuel, Reichel; He, Jian

To fully realize the potential of lignocellulosic biomass as a renewable resource for the production of fuels, chemicals, and materials, an improved understanding of the chemical and molecular structures within biomass and how those structures are formed during biosynthesis and transformed during (thermochemical and biological) conversion must be developed. This effort will require analytical techniques which are not only in-depth, rapid, and cost-effective, but also leave native cell wall features intact. Whole plant cell wall nuclear magnetic resonance (NMR) analysis facilitates unparalleled structural characterization of lignocellulosic biomass without causing (or with minimal) structural modification. The objective of this review ismore » to summarize research pertaining to solution- or gel-state whole plant cell wall NMR analysis of biomass, demonstrating the capability of NMR to delineate the structural features and transformations of biomass. In particular, this review will focus on the application of a two-dimensional solution-state NMR technique and perdeuterated ionic liquid based organic electrolyte solvents for the direct dissolution and analysis of biomass. Furthermore, we believe this type of analysis will be critical to advancing biofuel research, improving bioprocessing methodology, and enhancing plant bioengineering efforts.« less

Low-Dimensional Network Formation in Molten Sodium Carbonate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilding, Martin C.; Wilson, Mark; Alderman, Oliver L. G.

2016-04-15

Molten carbonates are highly inviscid liquids characterized by low melting points and high solubility of rare earth elements and volatile molecules. An understanding of the structure and related properties of these intriguing liquids has been limited to date. We report the results of a study of molten sodium carbonate (Na2CO3) which combines high energy X-ray diffraction, containerless techniques and computer simulation to provide insight into the liquid structure. Total structure factors (F-x(Q)) are collected on the laser-heated carbonate spheres suspended in flowing gases of varying composition in an aerodynamic levitation furnace. The respective partial structure factor contributions to Fx(Q) aremore » obtained by performing molecular dynamics simulations treating the carbonate anions as flexible entities. The carbonate liquid structure is found to be heavily temperature-dependent. At low temperatures a low-dimensional carbonate chain network forms, at T = 1100 K for example similar to 55% of the C atoms form part of a chain. The mean chain lengths decrease as temperature is increased and as the chains become shorter the rotation of the carbonate anions becomes more rapid enhancing the diffusion of Na+ ions.« less

Mechanism of drug release from silica-gelatin aerogel-Relationship between matrix structure and release kinetics.

PubMed

Veres, Péter; Kéri, Mónika; Bányai, István; Lázár, István; Fábián, István; Domingo, Concepción; Kalmár, József

2017-04-01

Specific features of a silica-gelatin aerogel (3 wt.% gelatin content) in relation to drug delivery has been studied. It was confirmed that the release of both ibuprofen (IBU) and ketoprofen (KET) is about tenfold faster from loaded silica-gelatin aerogel than from pure silica aerogel, although the two matrices are structurally very similar. The main goal of the study was to understand the mechanistic background of the striking difference between the delivery properties of these closely related porous materials. Hydrated and dispersed silica-gelatin aerogel has been characterized by NMR cryoporometry, diffusiometry and relaxometry. The pore structure of the silica aerogel remains intact when it disintegrates in water. In contrast, dispersed silica-gelatin aerogel develops a strong hydration sphere, which reshapes the pore walls and deforms the pore structure. The drug release kinetics was studied on a few minutes time scale with 1s time resolution. Simultaneous evaluation of all relevant kinetic and structural information confirmed that strong hydration of the silica-gelatin skeleton facilitates the rapid desorption and dissolution of the drugs from the loaded aerogel. Such a driving force is not operative in pure silica aerogels. Copyright © 2017 Elsevier B.V. All rights reserved.

Sensory processing and corollary discharge effects in posterior caudal lobe Purkinje cells in a weakly electric mormyrid fish.

PubMed

Alviña, Karina; Sawtell, Nathaniel B

2014-07-15

Although it has been suggested that the cerebellum functions to predict the sensory consequences of motor commands, how such predictions are implemented in cerebellar circuitry remains largely unknown. A detailed and relatively complete account of predictive mechanisms has emerged from studies of cerebellum-like sensory structures in fish, suggesting that comparisons of the cerebellum and cerebellum-like structures may be useful. Here we characterize electrophysiological response properties of Purkinje cells in a region of the cerebellum proper of weakly electric mormyrid fish, the posterior caudal lobe (LCp), which receives the same mossy fiber inputs and projects to the same target structures as the electrosensory lobe (ELL), a well-studied cerebellum-like structure. We describe patterns of simple spike and climbing fiber activation in LCp Purkinje cells in response to motor corollary discharge, electrosensory, and proprioceptive inputs and provide evidence for two functionally distinct Purkinje cell subtypes within LCp. Protocols that induce rapid associative plasticity in ELL fail to induce plasticity in LCp, suggesting differences in the adaptive functions of the two structures. Similarities and differences between LCp and ELL are discussed in light of these results. Copyright © 2014 the American Physiological Society.

Photothermal imaging scanning microscopy

DOEpatents

Chinn, Diane [Pleasanton, CA; Stolz, Christopher J [Lathrop, CA; Wu, Zhouling [Pleasanton, CA; Huber, Robert [Discovery Bay, CA; Weinzapfel, Carolyn [Tracy, CA

2006-07-11

Photothermal Imaging Scanning Microscopy produces a rapid, thermal-based, non-destructive characterization apparatus. Also, a photothermal characterization method of surface and subsurface features includes micron and nanoscale spatial resolution of meter-sized optical materials.

Development of a proto-typology of opiate overdose onset.

PubMed

Neale, Joanne; Bradford, Julia; Strang, John

2017-01-01

The time available to act is a crucial factor affecting the probable success of interventions to manage opiate overdose. We analyse opiate users' accounts of non-fatal overdose incidents to (i) construct a proto-typology of non-fatal opiate overdose onset and (ii) assess the implications for overdose management and prevention of fatalities. Re-analysis of a subset of data from a large qualitative study of non-fatal opiate overdose conducted from 1997 to 1999. Data were generated from semi-structured interviews undertaken with opiate users who had experienced a non-fatal overdose in the previous 24 hours. Forty-four participants (30 men; 14 women; aged 16-47 years) provided sufficient information for in-depth analysis. Data relating to 'memory of the moment of overdose', 'time to loss of consciousness' and 'subjective description of the overdose experience' were scrutinised using iterative categorization. Four types of overdose onset were identified: type A 'amnesic' (n = 8), characterized by no memory, rapid loss of consciousness and no description of the overdose experience; type B 'conscious' (n = 17), characterized by some memory, sustained consciousness and a description of the overdose in terms of feeling unwell and symptomatic; type C 'instant' (n = 14), characterized by some memory, immediate loss of consciousness and no description of the overdose experience; and type D 'enjoyable' (n = 5), characterized by some memory, rapid loss of consciousness and a description of the overdose experience as pleasant or positive. The identification of different types of overdose onset highlights the complexity of overdose events, the need for a range of interventions and the challenges faced in managing incidents and preventing fatalities. Opiate overdose victims who retain consciousness for a sustained period and recognize the negative signs and symptoms of overdosing could summon help or self-administer naloxone, thus indicating that opiate overdose training should incorporate self-management strategies. © 2016 Society for the Study of Addiction.

Rapid Assessment of Aircraft Structural Topologies for Multidisciplinary Optimization and Weight Estimation

NASA Technical Reports Server (NTRS)

Samareh, Jamshid A.; Sensmeier, mark D.; Stewart, Bret A.

2006-01-01

Algorithms for rapid generation of moderate-fidelity structural finite element models of air vehicle structures to allow more accurate weight estimation earlier in the vehicle design process have been developed. Application of these algorithms should help to rapidly assess many structural layouts before the start of the preliminary design phase and eliminate weight penalties imposed when actual structure weights exceed those estimated during conceptual design. By defining the structural topology in a fully parametric manner, the structure can be mapped to arbitrary vehicle configurations being considered during conceptual design optimization. Recent enhancements to this approach include the porting of the algorithms to a platform-independent software language Python, and modifications to specifically consider morphing aircraft-type configurations. Two sample cases which illustrate these recent developments are presented.

ZP Domain Proteins in the Abalone Egg Coat Include a Paralog of VERL under Positive Selection That Binds Lysin and 18-kDa Sperm Proteins

PubMed Central

Aagaard, Jan E.; Vacquier, Victor D.; MacCoss, Michael J.; Swanson, Willie J.

2010-01-01

Identifying fertilization molecules is key to our understanding of reproductive biology, yet only a few examples of interacting sperm and egg proteins are known. One of the best characterized comes from the invertebrate archeogastropod abalone (Haliotis spp.), where sperm lysin mediates passage through the protective egg vitelline envelope (VE) by binding to the VE protein vitelline envelope receptor for lysin (VERL). Rapid adaptive divergence of abalone lysin and VERL are an example of positive selection on interacting fertilization proteins contributing to reproductive isolation. Previously, we characterized a subset of the abalone VE proteins that share a structural feature, the zona pellucida (ZP) domain, which is common to VERL and the egg envelopes of vertebrates. Here, we use additional expressed sequence tag sequencing and shotgun proteomics to characterize this family of proteins in the abalone egg VE. We expand 3-fold the number of known ZP domain proteins present within the VE (now 30 in total) and identify a paralog of VERL (vitelline envelope zona pellucida domain protein [VEZP] 14) that contains a putative lysin-binding motif. We find that, like VERL, the divergence of VEZP14 among abalone species is driven by positive selection on the lysin-binding motif alone and that these paralogous egg VE proteins bind a similar set of sperm proteins including a rapidly evolving 18-kDa paralog of lysin, which may mediate sperm–egg fusion. This work identifies an egg coat paralog of VERL under positive selection and the candidate sperm proteins with which it may interact during abalone fertilization. PMID:19767347

Characterizing of tissue microstructure with single-detector polarization-sensitive optical coherence tomography

NASA Astrophysics Data System (ADS)

Liu, Bin; Harman, Michelle; Giattina, Susanne; Stamper, Debra L.; Demakis, Charles; Chilek, Mark; Raby, Stephanie; Brezinski, Mark E.

2006-06-01

Assessing tissue birefringence with imaging modality polarization-sensitive optical coherence tomography (PS-OCT) could improve the characterization of in vivo tissue pathology. Among the birefringent components, collagen may provide invaluable clinical information because of its alteration in disorders ranging from myocardial infarction to arthritis. But the features required of clinical imaging modality in these areas usually include the ability to assess the parameter of interest rapidly and without extensive data analysis, the characteristics that single-detector PS-OCT demonstrates. But beyond detecting organized collagen, which has been previously demonstrated and confirmed with the appropriate histological techniques, additional information can potentially be gained with PS-OCT, including collagen type, form versus intrinsic birefringence, the collagen angle, and the presence of multiple birefringence materials. In part I, we apply the simple but powerful fast-Fourier transform (FFT) to both PS-OCT mathematical modeling and in vitro bovine meniscus for improved PS-OCT data analysis. The FFT analysis yields, in a rapid, straightforward, and easily interpreted manner, information on the presence of multiple birefringent materials, distinguishing the true anatomical structure from patterns in image resulting from alterations in the polarization state and identifying the tissue/phantom optical axes. Therefore the use of the FFT analysis of PS-OCT data provides information on tissue composition beyond identifying the presence of organized collagen in real time and directly from the image without extensive mathematical manipulation or data analysis. In part II, Helistat phantoms (collagen type I) are analyzed with the ultimate goal of improved tissue characterization. This study, along with the data in part I, advance the insights gained from PS-OCT images beyond simply determining the presence or absence of birefringence.

Molecular Cytogenetics Guides Massively Parallel Sequencing of a Radiation-Induced Chromosome Translocation in Human Cells.

PubMed

Cornforth, Michael N; Anur, Pavana; Wang, Nicholas; Robinson, Erin; Ray, F Andrew; Bedford, Joel S; Loucas, Bradford D; Williams, Eli S; Peto, Myron; Spellman, Paul; Kollipara, Rahul; Kittler, Ralf; Gray, Joe W; Bailey, Susan M

2018-05-11

Chromosome rearrangements are large-scale structural variants that are recognized drivers of oncogenic events in cancers of all types. Cytogenetics allows for their rapid, genome-wide detection, but does not provide gene-level resolution. Massively parallel sequencing (MPS) promises DNA sequence-level characterization of the specific breakpoints involved, but is strongly influenced by bioinformatics filters that affect detection efficiency. We sought to characterize the breakpoint junctions of chromosomal translocations and inversions in the clonal derivatives of human cells exposed to ionizing radiation. Here, we describe the first successful use of DNA paired-end analysis to locate and sequence across the breakpoint junctions of a radiation-induced reciprocal translocation. The analyses employed, with varying degrees of success, several well-known bioinformatics algorithms, a task made difficult by the involvement of repetitive DNA sequences. As for underlying mechanisms, the results of Sanger sequencing suggested that the translocation in question was likely formed via microhomology-mediated non-homologous end joining (mmNHEJ). To our knowledge, this represents the first use of MPS to characterize the breakpoint junctions of a radiation-induced chromosomal translocation in human cells. Curiously, these same approaches were unsuccessful when applied to the analysis of inversions previously identified by directional genomic hybridization (dGH). We conclude that molecular cytogenetics continues to provide critical guidance for structural variant discovery, validation and in "tuning" analysis filters to enable robust breakpoint identification at the base pair level.

Understanding of the Formation of Micro/Nanoscale Structures on Metal Surfaces by Ultrafast Pulse Laser Processing

NASA Astrophysics Data System (ADS)

Peng, Edwin

In the recent decades, there has been much interest in functionalized surfaces produced by ultrafast laser processing. Using pulse lasers with nanosecond to femtosecond time scale, a wide range of micro/nanoscale structures can be produced on virtually all metal surfaces. These surface structures create special optoelectronic, wetting, and tribological properties with a diverse range of potential applications. The formation mechanisms of these surface structures, especially microscale, mound-like structures, are not fully understood. There has been wide study of ultrafast laser processing of metals. Yet, the proposed formation models present in current literature often lack sufficient experimental verification. Specifically, many studies are limited to surface characterization, e.g. scanning electron microscopy of the surfaces of these micro/nanoscale structures. Valuable insight into the physical processes responsible for formation can be obtained if standard material science characterization methods are performed across the entire mound. In our study, we examined mound-like structures formed on three metal alloys. Using cross section and 3D slice and view operations by a dual beam scanning electron microscope-focused ion beam, the interior microstructures of these mounds are revealed. Taking advantage of amorphous phase formation during laser processing of Ni60Nb40, we verified the fluence-dependent formation model: mounds formed at low fluence are primarily the result of ablation while mounds formed at high fluence are formed by both ablation and rapid resolidification by hydrodynamical fluid flow. For the first time, we revealed the cross section of a wide variety of mound-like structures on titanium surfaces. The increased contribution to mound formation by fluid flow with increasing fluence was observed. Finally, a 3D scanning electron microscopy technique was applied for mounds produced on silver surface by delayed-pulse laser processing. The interior microstructure demonstrated that most of the volume comprised of resolidified silver grains with 1% porosity.

Suspect Screening of Chemicals in Consumer Products

EPA Science Inventory

This presentation details a pilot suspect screening analysis (SSA) of common consumer products done under the Rapid Exposure and Dosimetry project of CSS. This work presents methods which can rapidly characterize chemicals identified in consumer products including formulations (s...

Challenges and Solutions for GNSS Receivers onboard LEO Satellites Traveling through the Ionosphere during Space Weather Events

NASA Astrophysics Data System (ADS)

Morton, Y.; Xu, D.; Yang, R.; Jiao, Y.; Rino, C.; Carrano, C. S.

2017-12-01

This presentation discusses challenges imposed on GNSS receiver carrier-tracking loop for receivers onboard LEO satellites traveling through ionosphere during space weather events and techniques that mitigate the effects. Recent studies show that the ESA's swarm satellites experienced a total loss of GPS signals in areas known for frequent occurrence of ionosphere plasma irregularities. The same phenomena have been observed in other satellite missions. More robust GNSS receiver technologies are needed to improve the navigation capabilities for future LEO satellite missions. A major challenge to characterize GNSS signals traversing ionospheric plasma structures to reach a LEO satellite is the lack of data. To overcome this challenge, we utilized a physics-based GNSS scintillation signal simulator to generate simulated data for analysis and algorithm development. The simulator relies on real scintillation data collected by ground-based receivers as the initializer to generate a realization of ionosphere irregularity structure statistical distribution. A user specifies desired satellite orbit, signal modulation scheme, receiver platform dynamics, and receiver front-end hardware design. These inputs are used to establish the signal propagation geometry to allow interception of the disturbed signal by a realistic GNSS receiver. The simulator results showed that plasma structures lead to strong disturbances on GNSS signals reaching a LEO platform. The disturbances are characterized by simultaneous deep amplitude fades and extremely rapid carrier phase fluctuations. The carrier phase rate is orders of magnitude higher than the ones experienced by receivers on the ground. Such high carrier dynamics far exceeds the range that can be tolerated by the bandwidth of a typical GNSS receiver. The deep amplitude fades further exacerbate the problem. Based on the simulator outputs, we established models of the disturbed signal parameters. These models are used in an adaptive carrier-tracking algorithm that demonstrated improved performances when applied to various simulated scenarios of plasma structures and receiver trajectories. The presentation will discuss the simulator, disturbed signal characterization, and the adaptive algorithm architecture and performances.

High precision optical spectroscopy and quantum state selected photodissociation of ultracold 88Sr2 molecules in an optical lattice

NASA Astrophysics Data System (ADS)

McDonald, Mickey Patrick

Over the past several decades, rapid progress has been made toward the accurate characterization and control of atoms, made possible largely by the development of narrow-linewidth lasers and techniques for trapping and cooling at ultracold temperatures. Extending this progress to molecules will have exciting implications for chemistry, condensed matter physics, and precision tests of physics beyond the Standard Model. These possibilities are all consequences of the richness of molecular structure, which is governed by physics substantially different from that characterizing atomic structure. This same richness of structure, however, increases the complexity of any molecular experiment manyfold over its atomic counterpart, magnifying the difficulty of everything from trapping and cooling to the comparison of theory with experiment. This thesis describes work performed over the past six years to establish the state of the art in manipulation and quantum control of ultracold molecules. Our molecules are produced via photoassociation of ultracold strontium atoms followed by spontaneous decay to a stable ground state. We describe a thorough set of measurements characterizing the rovibrational structure of very weakly bound (and therefore very large) 88Sr2 molecules from several different perspectives, including determinations of binding energies; linear, quadratic, and higher order Zeeman shifts; transition strengths between bound states; and lifetimes of narrow subradiant states. The physical intuition gained in these experiments applies generally to weakly bound diatomic molecules, and suggests extensive applications in precision measurement and metrology. In addition, we present a detailed analysis of the thermally broadened spectroscopic lineshape of molecules in a non-magic optical lattice trap, showing how such lineshapes can be used to directly determine the temperature of atoms or molecules in situ, addressing a long-standing problem in ultracold physics. Finally, we discuss the measurement of photofragment angular distributions produced by photodissociation, leading to an exploration of quantum-state-resolved ultracold chemistry.

Exploiting genotyping by sequencing to characterize the genomic structure of the American cranberry through high-density linkage mapping.

PubMed

Covarrubias-Pazaran, Giovanny; Diaz-Garcia, Luis; Schlautman, Brandon; Deutsch, Joseph; Salazar, Walter; Hernandez-Ochoa, Miguel; Grygleski, Edward; Steffan, Shawn; Iorizzo, Massimo; Polashock, James; Vorsa, Nicholi; Zalapa, Juan

2016-06-13

The application of genotyping by sequencing (GBS) approaches, combined with data imputation methodologies, is narrowing the genetic knowledge gap between major and understudied, minor crops. GBS is an excellent tool to characterize the genomic structure of recently domesticated (~200 years) and understudied species, such as cranberry (Vaccinium macrocarpon Ait.), by generating large numbers of markers for genomic studies such as genetic mapping. We identified 10842 potentially mappable single nucleotide polymorphisms (SNPs) in a cranberry pseudo-testcross population wherein 5477 SNPs and 211 short sequence repeats (SSRs) were used to construct a high density linkage map in cranberry of which a total of 4849 markers were mapped. Recombination frequency, linkage disequilibrium (LD), and segregation distortion at the genomic level in the parental and integrated linkage maps were characterized for first time in cranberry. SSR markers, used as the backbone in the map, revealed high collinearity with previously published linkage maps. The 4849 point map consisted of twelve linkage groups spanning 1112 cM, which anchored 2381 nuclear scaffolds accounting for ~13 Mb of the estimated 470 Mb cranberry genome. Bin mapping identified 592 and 672 unique bins in the parentals and a total of 1676 unique marker positions in the integrated map. Synteny analyses comparing the order of anchored cranberry scaffolds to their homologous positions in kiwifruit, grape, and coffee genomes provided initial evidence of homology between cranberry and closely related species. GBS data was used to rapidly saturate the cranberry genome with markers in a pseudo-testcross population. Collinearity between the present saturated genetic map and previous cranberry SSR maps suggests that the SNP locations represent accurate marker order and chromosome structure of the cranberry genome. SNPs greatly improved current marker genome coverage, which allowed for genome-wide structure investigations such as segregation distortion, recombination, linkage disequilibrium, and synteny analyses. In the future, GBS can be used to accelerate cranberry molecular breeding through QTL mapping and genome-wide association studies (GWAS).

Systematic analytical characterization of new psychoactive substances: A case study.

PubMed

Lobo Vicente, Joana; Chassaigne, Hubert; Holland, Margaret V; Reniero, Fabiano; Kolář, Kamil; Tirendi, Salvatore; Vandecasteele, Ine; Vinckier, Inge; Guillou, Claude

2016-08-01

New psychoactive substances (NPS) are synthesized compounds that are not usually covered by European and/or international laws. With a slight alteration in the chemical structure of existing illegal substances registered in the European Union (EU), these NPS circumvent existing controls and are thus referred to as "legal highs". They are becoming increasingly available and can easily be purchased through both the internet and other means (smart shops). Thus, it is essential that the identification of NPS keeps up with this rapidly evolving market. In this case study, the Belgian Customs authorities apprehended a parcel, originating from China, containing two samples, declared as being "white pigments". For routine identification, the Belgian Customs Laboratory first analysed both samples by gas-chromatography mass-spectrometry and Fourier-Transform Infrared spectroscopy. The information obtained by these techniques is essential and can give an indication of the chemical structure of an unknown substance but not the complete identification of its structure. To bridge this gap, scientific and technical support is ensured by the Joint Research Centre (JRC) to the European Commission Directorate General for Taxation and Customs Unions (DG TAXUD) and the Customs Laboratory European Network (CLEN) through an Administrative Arrangement for fast recognition of NPS and identification of unknown chemicals. The samples were sent to the JRC for a complete characterization using advanced techniques and chemoinformatic tools. The aim of this study was also to encourage the development of a science-based policy driven approach on NPS. These samples were fully characterized and identified as 5F-AMB and PX-3 using (1)H and (13)C nuclear magnetic resonance (NMR), high-resolution tandem mass-spectrometry (HR-MS/MS) and Raman spectroscopy. A chemoinformatic platform was used to manage, unify analytical data from multiple techniques and instruments, and combine it with chemical and structural information. Copyright © 2016 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Rapid Synthesis and Formation Mechanism of Core-Shell-Structured La-Doped SrTiO3 with a Nb-Doped Shell

PubMed Central

Park, Nam-Hee; Akamatsu, Takafumi; Itoh, Toshio; Izu, Noriya; Shin, Woosuck

2015-01-01

To provide a convenient and practical synthesis process for metal ion doping on the surface of nanoparticles in an assembled nanostructure, core-shell-structured La-doped SrTiO3 nanocubes with a Nb-doped surface layer were synthesized via a rapid synthesis combining a rapid sol-precipitation and hydrothermal process. The La-doped SrTiO3 nanocubes were formed at room temperature by a rapid dissolution of NaOH pellets during the rapid sol-precipitation process, and the Nb-doped surface (shell) along with Nb-rich edges formed on the core nanocubes via the hydrothermal process. The formation mechanism of the core-shell-structured nanocubes and their shape evolution as a function of the Nb doping level were investigated. The synthesized core-shell-structured nanocubes could be arranged face-to-face on a SiO2/Si substrate by a slow evaporation process, and this nanostructured 10 μm thick thin film showed a smooth surface. PMID:28793420

Metabolite identification of triptolide by data-dependent accurate mass spectrometric analysis in combination with online hydrogen/deuterium exchange and multiple data-mining techniques.

PubMed

Du, Fuying; Liu, Ting; Liu, Tian; Wang, Yongwei; Wan, Yakun; Xing, Jie

2011-10-30

Triptolide (TP), the primary active component of the herbal medicine Tripterygium wilfordii Hook F, has shown promising antileukemic and anti-inflammatory activity. The pharmacokinetic profile of TP indicates an extensive metabolic elimination in vivo; however, its metabolic data is rarely available partly because of the difficulty in identifying it due to the absence of appropriate ultraviolet chromophores in the structure and the presence of endogenous interferences in biological samples. In the present study, the biotransformation of TP was investigated by improved data-dependent accurate mass spectrometric analysis, using an LTQ/Orbitrap hybrid mass spectrometer in conjunction with the online hydrogen (H)/deuterium (D) exchange technique for rapid structural characterization. Accurate full-scan MS and MS/MS data were processed with multiple post-acquisition data-mining techniques, which were complementary and effective in detecting both common and uncommon metabolites from biological matrices. As a result, 38 phase I, 9 phase II and 8 N-acetylcysteine (NAC) metabolites of TP were found in rat urine. Accurate MS/MS data were used to support assignments of metabolite structures, and online H/D exchange experiments provided additional evidence for exchangeable hydrogen atoms in the structure. The results showed the main phase I metabolic pathways of TP are hydroxylation, hydrolysis and desaturation, and the resulting metabolites subsequently undergo phase II processes. The presence of NAC conjugates indicated the capability of TP to form reactive intermediate species. This study also demonstrated the effectiveness of LC/HR-MS(n) in combination with multiple post-acquisition data-mining methods and the online H/D exchange technique for the rapid identification of drug metabolites. Copyright © 2011 John Wiley & Sons, Ltd.

An overview of the antiretroviral market.

PubMed

Camponeschi, Geannan; Fast, Jessica; Gauval, Marianne; Guerra, Katherine; Moore, Meredith; Ravinutala, Siddharth; Ripin, David; Shepel, Vadim

2013-11-01

An understanding of the current state of the antiretroviral marketplace is an important context in which to consider drug optimization work. The antiretroviral marketplace has undergone a remarkable evolution over the past 11 years, expanding from serving less than 300 000 patients in low and middle-income countries in 2002 to almost 10 million patients today. In addition to dramatic growth, a steady and rapid improvement in the drugs and drug regimens used to treat patients has characterized a rapidly changing market. The antiretroviral marketplace has been characterized by rapid growth and a succession of improving drugs and regimens over the past 11 years. The dynamic and innovative marketplace provides a strong platform from which to introduce new, optimized drugs and regimens to better serve patients' health needs.

Soil structural quality assessment for soil protection regulation

NASA Astrophysics Data System (ADS)

Johannes, Alice; Boivin, Pascal

2017-04-01

Soil quality assessment is rapidly developing worldwide, though mostly focused on the monitoring of arable land and soil fertility. Soil protection regulations assess soil quality differently, focusing on priority pollutants and threshold values. The soil physical properties are weakly considered, due to lack of consensus and experimental difficulties faced with characterization. Non-disputable, easy to perform and inexpensive methods should be available for environmental regulation to be applied, which is unfortunately not the case. As a consequence, quantitative soil physical protection regulation is not applied, and inexpensive soil physical quality indicators for arable soil management are not available. Overcoming these limitations was the objective of a research project funded by the Swiss federal office for environment (FOEN). The main results and the perspectives of application are given in this presentation. A first step of the research was to characterize soils in a good structural state (reference soils) under different land use. The structural quality was assessed with field expertise and Visual Evaluation of the Soil Structure (VESS), and the physical properties were assessed with Shrinkage analysis. The relationships between the physical properties and the soil constituents were linear and highly determined. They represent the reference properties of the corresponding soils. In a second step, the properties of physically degraded soils were analysed and compared to the reference properties. This allowed defining the most discriminant parameters departing the different structure qualities and their threshold limits. Equivalent properties corresponding to these parameters but inexpensive and easy to determine were defined and tested. More than 90% of the samples were correctly classed with this method, which meets, therefore, the requirements for practical application in regulation. Moreover, result-oriented agri-environmental schemes for soil quality are now proposed to farmers based on these indicators.

Analysis of Functional Dynamics of Modular Multidomain Proteins by SAXS and NMR.

PubMed

Thompson, Matthew K; Ehlinger, Aaron C; Chazin, Walter J

2017-01-01

Multiprotein machines drive virtually all primary cellular processes. Modular multidomain proteins are widely distributed within these dynamic complexes because they provide the flexibility needed to remodel structure as well as rapidly assemble and disassemble components of the machinery. Understanding the functional dynamics of modular multidomain proteins is a major challenge confronting structural biology today because their structure is not fixed in time. Small-angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy have proven particularly useful for the analysis of the structural dynamics of modular multidomain proteins because they provide highly complementary information for characterizing the architectural landscape accessible to these proteins. SAXS provides a global snapshot of all architectural space sampled by a molecule in solution. Furthermore, SAXS is sensitive to conformational changes, organization and oligomeric states of protein assemblies, and the existence of flexibility between globular domains in multiprotein complexes. The power of NMR to characterize dynamics provides uniquely complementary information to the global snapshot of the architectural ensemble provided by SAXS because it can directly measure domain motion. In particular, NMR parameters can be used to define the diffusion of domains within modular multidomain proteins, connecting the amplitude of interdomain motion to the architectural ensemble derived from SAXS. Our laboratory has been studying the roles of modular multidomain proteins involved in human DNA replication using SAXS and NMR. Here, we present the procedure for acquiring and analyzing SAXS and NMR data, using DNA primase and replication protein A as examples. © 2017 Elsevier Inc. All rights reserved.

Design and implementation of handheld and desktop software for the structured reporting of hepatic masses using the LI-RADS schema.

PubMed

Clark, Toshimasa J; McNeeley, Michael F; Maki, Jeffrey H

2014-04-01

The Liver Imaging Reporting and Data System (LI-RADS) can enhance communication between radiologists and clinicians if applied consistently. We identified an institutional need to improve liver imaging report standardization and developed handheld and desktop software to serve this purpose. We developed two complementary applications that implement the LI-RADS schema. A mobile application for iOS devices written in the Objective-C language allows for rapid characterization of hepatic observations under a variety of circumstances. A desktop application written in the Java language allows for comprehensive observation characterization and standardized report text generation. We chose the applications' languages and feature sets based on the computing resources of target platforms, anticipated usage scenarios, and ease of application installation, deployment, and updating. Our primary results are the publication of the core source code implementing the LI-RADS algorithm and the availability of the applications for use worldwide via our website, http://www.liradsapp.com/. The Java application is free open-source software that can be integrated into nearly any vendor's reporting system. The iOS application is distributed through Apple's iTunes App Store. Observation categorizations of both programs have been manually validated to be correct. The iOS application has been used to characterize liver tumors during multidisciplinary conferences of our institution, and several faculty members, fellows, and residents have adopted the generated text of Java application into their diagnostic reports. Although these two applications were developed for the specific reporting requirements of our liver tumor service, we intend to apply this development model to other diseases as well. Through semiautomated structured report generation and observation characterization, we aim to improve patient care while increasing radiologist efficiency. Published by Elsevier Inc.

Contrasting coordination behavior of Group 12 perchlorate salts with an acyclic N3O2 donor ligand by X-ray crystallography and (1)H NMR.

PubMed

Tice, Daniel B; Pike, Robert D; Bebout, Deborah C

2016-08-09

An unbranched N3O2 ligand 2,6-bis[((2-pyridinylmethyl)oxy)methyl]pyridine (L1) was used to prepare new mononuclear heteroleptic Group 12 perchlorate complexes characterized by IR, (1)H NMR and X-ray crystallography. Racemic complexes with pentadentate L1 and one to four oxygens from either water or perchlorate bound to a metal ion were structurally characterized. Octahedral [Zn(L1)(OH2)](ClO4)2 (1) and pentagonal bipyramidal [Cd(L1)(OH2)(OClO3)]ClO4 (2) structures were found with lighter congeners. The polymorphic forms of [Hg(L1)(ClO4)2] characterized (3 in P1[combining macron] and 4 in P21/c) had a mix of monodentate, anisobidentate and bidentate perchlorates, providing the first examples of a tricapped trigonal prismatic Hg(ii) coordination geometry, as well as additional examples of a rare square antiprismatic Hg(ii) coordination geometry. Solution state (1)H NMR characterization of the Group 12 complexes in CD3CN indicated intramolecular reorganization remained rapid under conditions where intermolecular M-L1 exchange was slow on the chemical shift time scale for Zn(ii) and on the J(M(1)H) time scale for Cd(ii) and Hg(ii). Solution studies with more than one equivalent of ligand also suggested that a complex with a 1 : 2 ratio of M : L1 contributed significantly to solution equilibria with Hg(ii) but not the other metal ions. The behavior of related linear pentadentate ligands with Group 12 perchlorate salts is discussed.

SFG analysis of surface bound proteins: a route towards structure determination.

PubMed

Weidner, Tobias; Castner, David G

2013-08-14

The surface of a material is rapidly covered with proteins once that material is placed in a biological environment. The structure and function of these bound proteins play a key role in the interactions and communications of the material with the biological environment. Thus, it is crucial to gain a molecular level understanding of surface bound protein structure. While X-ray diffraction and solution phase NMR methods are well established for determining the structure of proteins in the crystalline or solution phase, there is not a corresponding single technique that can provide the same level of structural detail about proteins at surfaces or interfaces. However, recent advances in sum frequency generation (SFG) vibrational spectroscopy have significantly increased our ability to obtain structural information about surface bound proteins and peptides. A multi-technique approach of combining SFG with (1) protein engineering methods to selectively introduce mutations and isotopic labels, (2) other experimental methods such as time-of-flight secondary ion mass spectrometry (ToF-SIMS) and near edge X-ray absorption fine structure (NEXAFS) to provide complementary information, and (3) molecular dynamic (MD) simulations to extend the molecular level experimental results is a particularly promising route for structural characterization of surface bound proteins and peptides. By using model peptides and small proteins with well-defined structures, methods have been developed to determine the orientation of both backbone and side chains to the surface.

SFG analysis of surface bound proteins: A route towards structure determination

PubMed Central

Weidner, Tobias; Castner, David G.

2013-01-01

The surface of a material is rapidly covered with proteins once that material is placed in a biological environment. The structure and function of these bound proteins play a key role in the interactions and communications of the material with the biological environment. Thus, it is crucial to gain a molecular level understanding of surface bound protein structure. While X-ray diffraction and solution phase NMR methods are well established for determining the structure of proteins in the crystalline or solution phase, there is not a corresponding single technique that can provide the same level of structural detail about proteins at surfaces or interfaces. However, recent advances in sum frequency generation (SFG) vibrational spectroscopy have significantly increased our ability to obtain structural information about surface bound proteins and peptides. A multi-technique approach of combining SFG with (1) protein engineering methods to selectively introduce mutations and isotopic labels, (2) other experimental methods such as time-of-flight secondary ion mass spectrometry (ToF-SIMS) and near edge x-ray absorption fine structure (NEXAFS) to provide complementary information, and (3) molecular dynamic (MD) simulations to extend the molecular level experimental results is a particularly promising route for structural characterization of surface bound proteins and peptides. By using model peptides and small proteins with well-defined structures, methods have been developed to determine the orientation of both backbone and side chains to the surface. PMID:23727992

Using in-cell SHAPE-Seq and simulations to probe structure-function design principles of RNA transcriptional regulators.

PubMed

Takahashi, Melissa K; Watters, Kyle E; Gasper, Paul M; Abbott, Timothy R; Carlson, Paul D; Chen, Alan A; Lucks, Julius B

2016-06-01

Antisense RNA-mediated transcriptional regulators are powerful tools for controlling gene expression and creating synthetic gene networks. RNA transcriptional repressors derived from natural mechanisms called attenuators are particularly versatile, though their mechanistic complexity has made them difficult to engineer. Here we identify a new structure-function design principle for attenuators that enables the forward engineering of new RNA transcriptional repressors. Using in-cell SHAPE-Seq to characterize the structures of attenuator variants within Escherichia coli, we show that attenuator hairpins that facilitate interaction with antisense RNAs require interior loops for proper function. Molecular dynamics simulations of these attenuator variants suggest these interior loops impart structural flexibility. We further observe hairpin flexibility in the cellular structures of natural RNA mechanisms that use antisense RNA interactions to repress translation, confirming earlier results from in vitro studies. Finally, we design new transcriptional attenuators in silico using an interior loop as a structural requirement and show that they function as desired in vivo. This work establishes interior loops as an important structural element for designing synthetic RNA gene regulators. We anticipate that the coupling of experimental measurement of cellular RNA structure and function with computational modeling will enable rapid discovery of structure-function design principles for a diverse array of natural and synthetic RNA regulators. © 2016 Takahashi et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Rapid Development of Gossamer Propulsion for NASA Inner Solar System Science Missions

NASA Technical Reports Server (NTRS)

Young, Roy M.; Montgomery, Edward E.

2006-01-01

Over a two and one-half year period dating from 2003 through 2005, NASA s In-Space Propulsion Program matured solar sail technology from laboratory components to full systems, demonstrated in as relevant a space environment as could feasibly be simulated on the ground. This paper describes the challenges identified; as well as the approaches taken toward solving a broad set of issues spanning material science, manufacturing technology, and interplanetary trajectory optimization. Revolutionary advances in system structural predictive analysis and characterization testing occurred. Also addressed are the remaining technology challenges that might be resolved with further ground technology research, geared toward reducing technical risks associated with future space validation and science missions.

Health Care System Transformation and Integration: A Call to Action for Public Health.

PubMed

Wiley, Lindsay F; Matthews, Gene W

2017-03-01

Restructured health care reimbursement systems and new requirements for nonprofit hospitals are transforming the U.S. health system, creating opportunities for enhanced integration of public health and health care goals. This article explores the role of public health practitioners and lawyers in this moment of transformation. We argue that the population perspective and structural strategies that characterize public health can add value to the health care system but could get lost in translation as changes to tax requirements and payment systems are rapidly implemented. We urge public health leaders to take a more active role in hospital assessments of community health needs and evaluation of the patient outcomes for which providers are accountable.

Solid-state NMR as an effective method of polymorphic analysis: solid dosage forms of clopidogrel hydrogensulfate.

PubMed

Pindelska, Edyta; Szeleszczuk, Lukasz; Pisklak, Dariusz Maciej; Mazurek, Andrzej; Kolodziejski, Waclaw

2015-01-01

Clopidogrel hydrogensulfate (HSCL) is an antiplatelet agent, one of top-selling drugs in the world. In this paper, we have described a rapid and convenient method of verification which polymorph of HSCL is present in its final solid dosage form. Our methodology based on solid-state NMR spectroscopy and ab initio gauge-including projector-augmented wave calculations of NMR shielding constants is appropriate for currently available commercial solid dosage forms of HSCL. Furthermore, such structural characterization can assist with the development of new pharmaceutical products containing HSCL and also be useful in the identification of counterfeit drugs. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

An assessment of seismic monitoring in the United States; requirement for an Advanced National Seismic System

USGS Publications Warehouse

,

1999-01-01

This report assesses the status, needs, and associated costs of seismic monitoring in the United States. It sets down the requirement for an effective, national seismic monitoring strategy and an advanced system linking national, regional, and urban monitoring networks. Modernized seismic monitoring can provide alerts of imminent strong earthquake shaking; rapid assessment of distribution and severity of earthquake shaking (for use in emergency response); warnings of a possible tsunami from an offshore earthquake; warnings of volcanic eruptions; information for correctly characterizing earthquake hazards and for improving building codes; and data on response of buildings and structures during earthquakes, for safe, cost-effective design, engineering, and construction practices in earthquake-prone regions.

Update of sleep alterations in depression

PubMed Central

Medina, Andrés Barrera; Lechuga, DeboraYoaly Arana; Escandón, Oscar Sánchez; Moctezuma, Javier Velázquez

2014-01-01

Sleep disturbances in depression are up to 70%. Patients frequently have difficulty in falling asleep, frequent awakenings during the night and non-restorative sleep. Sleep abnormalities in depression are mainly characterized by increased rapid eye movement (REM) sleep and reduced slow wave sleep. Among the mechanisms of sleep disturbances in depression are hyperactivation of the hypothalamic-pituitary-adrenal axis, CLOCK gene polymorphism and primary sleep disorders. The habenula is a structure regulating the activities of monoaminergic neurons in the brain. The hyperactivation of the habenula has also been implicated, together with sleep disturbances, in depression. The presence of depression in primary sleep disorders is common. Sleep disturbances treatment include pharmacotherapy or Cognitive Behavioral Therapy. PMID:26483922

Media framing of complex issues: The case of endangered languages.

PubMed

Rivenburgh, Nancy K

2013-08-01

This study investigates how media frame a global trend that is complex in nature, emergent in terms of scientific understanding, and has public policy implications: the rapid disappearance of languages. It analyzes how English-language media from 15 western, industrialized countries frame the causes and implications of endangered languages over 35 years (1971-2006) - a time period notable for growing, interdisciplinary concerns over the potential negative impacts of losing the world's linguistic diversity. The results reveal a media discourse characterized by three complementary frames that are sympathetic to the plight of endangered languages, but that present the problem, its cause, and societal implications in a logical structure that would promote public complacency.

Sensitivity and rapidity of vegetational response to abrupt climate change

NASA Technical Reports Server (NTRS)

Peteet, D.

2000-01-01

Rapid climate change characterizes numerous terrestrial sediment records during and since the last glaciation. Vegetational response is best expressed in terrestrial records near ecotones, where sensitivity to climate change is greatest, and response times are as short as decades.

Academic Librarians' Perceptions of Teamwork and Organizational Structure in a Time of Rapid Technological Change

ERIC Educational Resources Information Center

Strecker, Beth L.

2010-01-01

The purpose of this study was to explore the perceptions of academic librarians on two topics: the delivery of services to students and faculty in a time of rapid technological changes and an organizational structure appropriate for delivering services to students in a time of rapid technological changes. Several researchers agree that to…

Entropic Anomaly Observed in Lipid Polymorphisms Induced by Surfactant Peptide SP-B(1-25).

PubMed

Tran, Nhi; Kurian, Justin; Bhatt, Avni; McKenna, Robert; Long, Joanna R

2017-10-05

The N-terminal 25 amino-acid residues of pulmonary surfactant protein B (SP-B 1-25 ) induces unusual lipid polymorphisms in a model lipid system, 4:1 DPPC/POPG, mirroring the lipid composition of native pulmonary surfactant. It is widely suggested that SP-B 1-25 -induced lipid polymorphisms within the alveolar aqueous subphase provide a structural platform for rapid lipid adsorption to the air-water interface. Here, we characterize in detail the phase behavior of DPPC and POPG in hydrated lipid assemblies containing therapeutic levels of SP-B 1-25 using 2 H and 31 P solid state NMR spectroscopy. The appearance of a previously observed isotropic lipid phase is found to be highly dependent on the thermal cycling of the samples. Slow heating of frozen samples leads to phase separation of DPPC into a lamellar phase whereas POPG lipids interact with the peptide to form an isotropic phase at physiologic temperature. Rapid heating of frozen samples to room temperature leads to strongly isotropic phase behavior for both DPPC and POPG lipids, with DPPC in exchange between isotropic and interdigitated phases. 31 P T 2 relaxation times confirm the isotropic phase to be consistent with a lipid cubic phase. The observed phases exhibit thermal stability up to physiologic temperature (37 °C) and are consistent with the formation of a ripple phase containing a large number of peptide-induced membrane structural defects enabling rapid transit of lipids between lipid lamellae. The coexistance of a lipid cubic phase with interdigitated lipids suggests a specific role for the highly conserved N-terminus of SP-B in stabilizing this unusual lipid polymorphism.

Engineering a horseradish peroxidase C stable to radical attacks by mutating multiple radical coupling sites.

PubMed

Kim, Su Jin; Joo, Jeong Chan; Song, Bong Keun; Yoo, Young Je; Kim, Yong Hwan

2015-04-01

Peroxidases have great potential as industrial biocatalysts. In particular, the oxidative polymerization of phenolic compounds catalyzed by peroxidases has been extensively examined because of the advantage of this method over other conventional chemical methods. However, the industrial application of peroxidases is often limited because of their rapid inactivation by phenoxyl radicals during oxidative polymerization. In this work, we report a novel protein engineering approach to improve the radical stability of horseradish peroxidase isozyme C (HRPC). Phenylalanine residues that are vulnerable to modification by the phenoxyl radicals were identified using mass spectrometry analysis. UV-Vis and CD spectra showed that radical coupling did not change the secondary structure or the active site of HRPC. Four phenylalanine (Phe) residues (F68, F142, F143, and F179) were each mutated to alanine residues to generate single mutants to examine the role of these sites in radical coupling. Despite marginal improvement of radical stability, each single mutant still exhibited rapid radical inactivation. To further reduce inactivation by radical coupling, the four substitution mutations were combined in F68A/F142A/F143A/F179A. This mutant demonstrated dramatic enhancement of radical stability by retaining 41% of its initial activity compared to the wild-type, which was completely inactivated. Structure and sequence alignment revealed that radical-vulnerable Phe residues of HPRC are conserved in homologous peroxidases, which showed the same rapid inactivation tendency as HRPC. Based on our site-directed mutagenesis and biochemical characterization, we have shown that engineering radical-vulnerable residues to eliminate multiple radical coupling can be a good strategy to improve the stability of peroxidases against radical attack. © 2014 Wiley Periodicals, Inc.

On-line characterization of monoclonal antibody variants by liquid chromatography-mass spectrometry operating in a two-dimensional format.

PubMed

Alvarez, Melissa; Tremintin, Guillaume; Wang, Jennifer; Eng, Marian; Kao, Yung-Hsiang; Jeong, Justin; Ling, Victor T; Borisov, Oleg V

2011-12-01

Recombinant monoclonal antibodies (MAbs) have become one of the most rapidly growing classes of biotherapeutics in the treatment of human disease. MAbs are highly heterogeneous proteins, thereby requiring a battery of analytical technologies for their characterization. However, incompatibility between separation and subsequent detection is often encountered. Here we demonstrate the utility of a generic on-line liquid chromatography-mass spectrometry (LC-MS) method operated in a two-dimensional format toward the rapid characterization of MAb charge and size variants. Using a single chromatographic system capable of running two independent gradients, up to six fractions of interest from an ion exchange (IEC) or size exclusion (SEC) separation can be identified by trapping and desalting the fractions onto a series of reversed phase trap cartridges with subsequent on-line analysis by mass spectrometry. Analysis of poorly resolved and low-level peaks in the IEC or SEC profile was facilitated by preconcentrating fractions on the traps using multiple injections. An on-line disulfide reduction step was successfully incorporated into the workflow, allowing more detailed characterization of modified MAbs by providing chain-specific information. The system is fully automated, thereby enabling high-throughput analysis with minimal sample handling. This technology provides rapid data turnaround time, a much needed feature during product characterization and development of multiple biotherapeutic proteins. Copyright © 2011 Elsevier Inc. All rights reserved.

Using in-cell SHAPE-Seq and simulations to probe structure–function design principles of RNA transcriptional regulators

PubMed Central

Takahashi, Melissa K.; Watters, Kyle E.; Gasper, Paul M.; Abbott, Timothy R.; Carlson, Paul D.; Chen, Alan A.

2016-01-01

Antisense RNA-mediated transcriptional regulators are powerful tools for controlling gene expression and creating synthetic gene networks. RNA transcriptional repressors derived from natural mechanisms called attenuators are particularly versatile, though their mechanistic complexity has made them difficult to engineer. Here we identify a new structure–function design principle for attenuators that enables the forward engineering of new RNA transcriptional repressors. Using in-cell SHAPE-Seq to characterize the structures of attenuator variants within Escherichia coli, we show that attenuator hairpins that facilitate interaction with antisense RNAs require interior loops for proper function. Molecular dynamics simulations of these attenuator variants suggest these interior loops impart structural flexibility. We further observe hairpin flexibility in the cellular structures of natural RNA mechanisms that use antisense RNA interactions to repress translation, confirming earlier results from in vitro studies. Finally, we design new transcriptional attenuators in silico using an interior loop as a structural requirement and show that they function as desired in vivo. This work establishes interior loops as an important structural element for designing synthetic RNA gene regulators. We anticipate that the coupling of experimental measurement of cellular RNA structure and function with computational modeling will enable rapid discovery of structure–function design principles for a diverse array of natural and synthetic RNA regulators. PMID:27103533

Structure-guided Protein Transition Modeling with a Probabilistic Roadmap Algorithm.

PubMed

Maximova, Tatiana; Plaku, Erion; Shehu, Amarda

2016-07-07

Proteins are macromolecules in perpetual motion, switching between structural states to modulate their function. A detailed characterization of the precise yet complex relationship between protein structure, dynamics, and function requires elucidating transitions between functionally-relevant states. Doing so challenges both wet and dry laboratories, as protein dynamics involves disparate temporal scales. In this paper we present a novel, sampling-based algorithm to compute transition paths. The algorithm exploits two main ideas. First, it leverages known structures to initialize its search and define a reduced conformation space for rapid sampling. This is key to address the insufficient sampling issue suffered by sampling-based algorithms. Second, the algorithm embeds samples in a nearest-neighbor graph where transition paths can be efficiently computed via queries. The algorithm adapts the probabilistic roadmap framework that is popular in robot motion planning. In addition to efficiently computing lowest-cost paths between any given structures, the algorithm allows investigating hypotheses regarding the order of experimentally-known structures in a transition event. This novel contribution is likely to open up new venues of research. Detailed analysis is presented on multiple-basin proteins of relevance to human disease. Multiscaling and the AMBER ff14SB force field are used to obtain energetically-credible paths at atomistic detail.

Observables for anticipating tornadogenesis in mesocyclones

NASA Technical Reports Server (NTRS)

Carrier, G.; Fendell, F.; Mitchell, J.; Bronstein, M.

1992-01-01

We seek to identify an observable for anticipating tornadogenesis in mesocyclones, because such tornadoes are characterized by particularly long life, long and wide path, and high wind speed. We associate tornadogenesis with the transition from a one-cell vortex to a two-cell vortex. In such a transition, 'insertion' of a virtually nonrotating, slowly recirculating core displaces that high-swirl-speed air which is rapidly ascending along a moist-adiabatic locus of thermodynamic states, to an annulus at small but finite distance from the axis of rotation. Such a transition, on a vastly larger lateral scale, is known to characterize intensification of a tropical storm to a typhoon. We examine analytically a quasisteady axisymmetric model of a four-part vortex structure consisting of a bulk potential vortex, near-ground inflow layer, 'eyewall', and 'eye'. We inquire whether such a four-part intense vortex, formed in convectively unstably stratified air, is self-sustaining. In particular, we inquire whether the vertical profile of the angular momentum at the periphery is a discriminant for identifying self-sustaining vortices.

How sailfish use their bills to capture schooling prey

PubMed Central

Domenici, P.; Wilson, A. D. M.; Kurvers, R. H. J. M.; Marras, S.; Herbert-Read, J. E.; Steffensen, J. F.; Krause, S.; Viblanc, P. E.; Couillaud, P.; Krause, J.

2014-01-01

The istiophorid family of billfishes is characterized by an extended rostrum or ‘bill’. While various functions (e.g. foraging and hydrodynamic benefits) have been proposed for this structure, until now no study has directly investigated the mechanisms by which billfishes use their rostrum to feed on prey. Here, we present the first unequivocal evidence of how the bill is used by Atlantic sailfish (Istiophorus albicans) to attack schooling sardines in the open ocean. Using high-speed video-analysis, we show that (i) sailfish manage to insert their bill into sardine schools without eliciting an evasive response and (ii) subsequently use their bill to either tap on individual prey targets or to slash through the school with powerful lateral motions characterized by one of the highest accelerations ever recorded in an aquatic vertebrate. Our results demonstrate that the combination of stealth and rapid motion make the sailfish bill an extremely effective feeding adaptation for capturing schooling prey. PMID:24759865

Characterization of the ribonuclease activity on the skin surface

PubMed Central

Probst, Jochen; Brechtel, Sonja; Scheel, Birgit; Hoerr, Ingmar; Jung, Günther; Rammensee, Hans-Georg; Pascolo, Steve

2006-01-01

The rapid degradation of ribonucleic acids (RNA) by ubiquitous ribonucleases limits the efficacy of new therapies based on RNA molecules. Therefore, our aim was to characterize the natural ribonuclease activities on the skin and in blood plasma i.e. at sites where many drugs in development are applied. On the skin surfaces of Homo sapiens and Mus musculus we observed dominant pyrimidine-specific ribonuclease activity. This activity is not prevented by a cap structure at the 5'-end of messenger RNA (mRNA) and is not primarily of a 5'- or 3'-exonuclease type. Moreover, the ribonuclease activity on the skin or in blood plasma is not inhibited by chemical modifications introduced at the 2'OH group of cytidine or uridine residues. It is, however, inhibited by the ribonuclease inhibitor RNasin® although not by the ribonuclease inhibitor SUPERase· In™. The application of our findings in the field of medical science may result in an improved efficiency of RNA-based therapies that are currently in development. PMID:16732888

79/81Br nuclear quadrupole resonance spectroscopic characterization of halogen bonds in supramolecular assemblies.

PubMed

Cerreia Vioglio, P; Szell, P M J; Chierotti, M R; Gobetto, R; Bryce, D L

2018-05-28

Despite the applicability of solid-state NMR to study the halogen bond, the direct NMR detection of 79/81 Br covalently bonded to carbon remains impractical due to extremely large spectral widths, even at ultra-high magnetic fields. In contrast, nuclear quadrupole resonance (NQR) offers comparatively sharp resonances. Here, we demonstrate the abilities of 79/81 Br NQR to characterize the electronic changes in the C-Br···N halogen bonding motifs found in supramolecular assemblies constructed from 1,4-dibromotetrafluorobenzene and nitrogen-containing heterocycles. An increase in the bromine quadrupolar coupling constant is observed, which correlates linearly with the halogen bond distance ( d Br···N ). Notably, 79/81 Br NQR is able to distinguish between two symmetry-independent halogen bonds in the same crystal structure. This approach offers a rapid and reliable indication for the occurrence of a halogen bond, with experimental times limited only by the observation of 79/81 Br NQR resonances.

Evaluation of Commercially-Available Equipment for the ...

EPA Pesticide Factsheets

Report The Underground Transport Restoration (UTR) project is an inter-agency effort. This effort aims to improve the capability for transit systems to quickly and efficiently recover from a biological contamination incident by refining existing methods, tools and protocols for characterization, clean-up, and clearance of contamination in physical structures (i.e., tunnels, stations) and rolling stock (i.e., subway trains). The aim was to evaluate existing sampling, characterization, and decontamination technologies through experimentation, table-top exercises and operational demonstrations to develop guidance and decision frameworks and support tools through interactions of local, state and federal partners. In this investigation, a survey of commercially-available or fielded equipment was conducted and resulted in three pieces of identified equipment that could be used or rapidly modified for use in dispensing liquid chemicals to decontaminate surfaces following a biological contamination incident. documenting lab-scale testing, field-scale testing, and an equipment demonstration of commercial equipment used to decontaminate subway infrastructure following a biological incident.

The Art and Science of Polymer Brushes: Recent Developments in Patterning and Characterization Approaches.

PubMed

Panzarasa, Guido

2017-06-28

Polymer brushes are dense arrays of macromolecular chains tethered by one end at a surface. They are at the cutting edge of polymer nanotechnology since the dawn of controlled surface-initiated polymerization techniques unlocked new prospects for the synthesis of polymer brushes with tailorable properties. More recently, thanks to the growing interest in the use of brushes for the generation of functional surfaces, the need for advanced patterning and characterization approaches rapidly increased. Meeting these needs requires the contribution of experts from different disciplines: polymer chemistry, surface science, electrochemistry and particle physics. The focus of this review is to highlight recent developments in the field of polymer brushes, specifically the application of photocatalytic lithography as a versatile patterning strategy, the study of grafted-from polymer brushes by electrochemical methods and, most importantly, the introduction of positron annihilation spectroscopy as a powerful technique for the investigation of the structure of polymer brushes and of their composites with nanoparticles.

Characterization of ZnO nanoparticles grown in presence of Folic acid template

PubMed Central

2012-01-01

Background ZnO nanoparticles (grown in the template of folic acid) are biologically useful, luminescent material. It can be used for multifunctional purposes, e.g., as biosensor, bioimaging, targeted drug delivery and as growth promoting medicine. Methods Sol–gel chemical method was used to develop the uniform ZnO nanoparticles, in a folic acid template at room temperature and pH ~ 7.5. Agglomeration of the particles was prevented due to surface charge density of folic acid in the medium. ZnO nanoparticle was further characterized by different physical methods. Results Nanocrystalline, wurtzite ZnO particles thus prepared show interesting structural as well as band gap properties due to capping with folic acid. Conclusions A rapid, easy and chemical preparative method for the growth of ZnO nanoparticles with important surface physical properties is discussed. Emphatically, after capping with folic acid, its photoluminescence properties are in the visible region. Therefore, the same can be used for monitoring local environmental properties of biosystems. PMID:22788841

The Human Genome Initiative of the Department of Energy

DOE R&D Accomplishments Database

1988-01-01

The structural characterization of genes and elucidation of their encoded functions have become a cornerstone of modern health research, biology and biotechnology. A genome program is an organized effort to locate and identify the functions of all the genes of an organism. Beginning with the DOE-sponsored, 1986 human genome workshop at Santa Fe, the value of broadly organized efforts supporting total genome characterization became a subject of intensive study. There is now national recognition that benefits will rapidly accrue from an effective scientific infrastructure for total genome research. In the US genome research is now receiving dedicated funds. Several other nations are implementing genome programs. Supportive infrastructure is being improved through both national and international cooperation. The Human Genome Initiative of the Department of Energy (DOE) is a focused program of Resource and Technology Development, with objectives of speeding and bringing economies to the national human genome effort. This report relates the origins and progress of the Initiative.

Online Hydrophobic Interaction Chromatography-Mass Spectrometry for the Analysis of Intact Monoclonal Antibodies.

PubMed

Chen, Bifan; Lin, Ziqing; Alpert, Andrew J; Fu, Cexiong; Zhang, Qunying; Pritts, Wayne A; Ge, Ying

2018-06-19

Therapeutic monoclonal antibodies (mAbs) are an important class of drugs for a wide spectrum of human diseases. Liquid chromatography (LC) coupled to mass spectrometry (MS) is one of the techniques in the forefront for comprehensive characterization of analytical attributes of mAbs. Among various protein chromatography modes, hydrophobic interaction chromatography (HIC) is a popular offline nondenaturing separation technique utilized to purify and analyze mAbs, typically with the use of non-MS-compatible mobile phases. Herein we demonstrate for the first time, the application of direct HIC-MS and HIC-tandem MS (MS/MS) with electron capture dissociation (ECD) for analyzing intact mAbs on quadrupole-time-of-flight (Q-TOF) and Fourier transform ion cyclotron resonance (FTICR) mass spectrometers, respectively. Our method allows for rapid determination of relative hydrophobicity, intact masses, and glycosylation profiles of mAbs as well as sequence and structural characterization of the complementarity-determining regions in an online configuration.

Cognitive subtypes of dyslexia are characterized by distinct patterns of grey matter volume.

PubMed

Jednoróg, Katarzyna; Gawron, Natalia; Marchewka, Artur; Heim, Stefan; Grabowska, Anna

2014-09-01

The variety of different causal theories together with inconsistencies about the anatomical brain markers emphasize the heterogeneity of developmental dyslexia. Attempts were made to test on a behavioral level the existence of subtypes of dyslexia showing distinguishable cognitive deficits. Importantly, no research was directly devoted to the investigation of structural brain correlates of these subtypes. Here, for the first time, we applied voxel-based morphometry (VBM) to study grey matter volume (GMV) differences in a relatively large sample (n = 46) of dyslexic children split into three subtypes based on the cognitive deficits: phonological, rapid naming, magnocellular/dorsal, and auditory attention shifting. VBM revealed GMV clusters specific for each studied group including areas of left inferior frontal gyrus, cerebellum, right putamen, and bilateral parietal cortex. In addition, using discriminant analysis on these clusters 79% of cross-validated cases were correctly re-classified into four groups (controls vs. three subtypes). Current results indicate that dyslexia may result from distinct cognitive impairments characterized by distinguishable anatomical markers.

Influence of drought conditions on brown trout biomass and size structure in the Black Hills, South Dakota

USGS Publications Warehouse

James, Daniel A.; Wilhite, Jerry W.; Chipps, Steven R.

2010-01-01

We evaluated the influence of drought conditions on the biomass of brown trout Salmo trutta in Spearfish Creek, upper Rapid Creek, and lower Rapid Creek in the Black Hills of western South Dakota. Stream discharge, mean summer water temperature, the biomass of juvenile and adult brown trout, and brown trout size structure were compared between two time periods: early (2000–2002) and late drought (2005–2007). Mean summer water temperatures were similar between the early- and late-drought periods in Spearfish Creek (12.4°C versus 11.5°C), lower Rapid Creek (19.2°C versus 19.3°C), and upper Rapid Creek (9.8°C in both periods). In contrast, mean annual discharge differed significantly between the two time periods in Spearfish Creek (1.95 versus 1.50 m3/s), lower Rapid Creek (2.01 versus 0.94 m3/s), and upper Rapid Creek (1.41 versus 0.84 m3/s). The mean biomass of adult brown trout in all three stream sections was significantly higher in the early-drought than in the late-drought period (238 versus 69 kg/ha in Spearfish Creek, 272 versus 91 kg/ha in lower Rapid Creek, and 159 versus 32 kg/ha in upper Rapid Creek). The biomass of juvenile brown trout was similar (43 versus 23 kg/ha) in Spearfish Creek in the two periods, declined from 136 to 45 kg/ha in lower Rapid Creek, and increased from 14 to 73 kg/ha in upper Rapid Creek. Size structure did not differ between the early- and late-drought periods in lower Rapid and Spearfish creeks, but it did in upper Rapid Creek. In addition to drought conditions, factors such as angler harvest, fish movements, and the nuisance algal species Didymosphenia geminata are discussed as possible contributors to the observed changes in brown trout biomass and size structure in Black Hills streams.

Effect of Initial Microstructure on Impact Toughness of 1200 MPa-Class High Strength Steel with Ultrafine Elongated Grain Structure

NASA Astrophysics Data System (ADS)

Jafari, Meysam; Garrison, Warren M.; Tsuzaki, Kaneaki

2014-02-01

A medium-carbon low-alloy steel was prepared with initial structures of either martensite or bainite. For both initial structures, warm caliber-rolling was conducted at 773 K (500 °C) to obtain ultrafine elongated grain (UFEG) structures with strong <110>//rolling direction (RD) fiber deformation textures. The UFEG structures consisted of spheroidal cementite particles distributed uniformly in a ferrite matrix of a transverse grain size of about 331 and 311 nm in samples with initial martensite and bainite structures, respectively. For both initial structures, the UFEG materials had similar tensile properties, upper shelf energy (145 J), and ductile-to-brittle transition temperatures 98 K (500 °C). Obtaining the martensitic structure requires more rapid cooling than is needed to obtain the bainitic structure and this more rapid cooling promote cracking. As the UFEG structures obtained from initial martensitic and bainitic structures have almost identical properties, but obtaining the bainitic structure does not require a rapid cooling which promotes cracking suggests the use of a bainitic structure in obtaining UFEG structures should be examined further.

Vanadium Geochemistry of Oil Sands Fluid Petroleum Coke.

PubMed

Nesbitt, Jake A; Lindsay, Matthew B J

2017-03-07

Vanadium has previously been linked to elevated toxicity of leachates derived from oil sands petroleum coke. However, geochemical controls on V mobility within coke deposits remain poorly constrained. Detailed examinations of porewater and solid-phase V geochemistry were therefore performed on oil sands fluid petroleum coke deposits in Alberta, Canada. Sample collection focused on both active and reclaimed deposits, which contained more than 3 × 10 7 m 3 of fluid petroleum coke. Dissolved V concentrations were highest (up to 3.0 mg L -1 ) immediately below the water table but decreased rapidly with increasing depth. This trend corresponded to a transition from mildly acidic (pH 6-7) and oxic conditions to mildly alkaline (pH 7-8.5) and anoxic conditions. Scanning electron microscopy (SEM), electron microprobe analysis (EMPA), and micro-X-ray fluorescence (μXRF) mapping revealed coke particles exhibited an internal structure characterized by successive concentric layers. The outer margins of these layers were characterized by elevated V, Fe, Si, and Al concentrations, indicating the presence of inorganic phases. Micro-X-ray absorption near-edge structure (μXANES) spectroscopy revealed that V speciation was dominated by V(IV) porphyrins except at outer margins of layers, where octahedrally coordinated V(III) was a major component. Minor to trace V(V) was also detected within fluid petroleum coke particles.

Sedimentation Velocity Analysis of Large Oligomeric Chromatin Complexes Using Interference Detection.

PubMed

Rogge, Ryan A; Hansen, Jeffrey C

2015-01-01

Sedimentation velocity experiments measure the transport of molecules in solution under centrifugal force. Here, we describe a method for monitoring the sedimentation of very large biological molecular assemblies using the interference optical systems of the analytical ultracentrifuge. The mass, partial-specific volume, and shape of macromolecules in solution affect their sedimentation rates as reflected in the sedimentation coefficient. The sedimentation coefficient is obtained by measuring the solute concentration as a function of radial distance during centrifugation. Monitoring the concentration can be accomplished using interference optics, absorbance optics, or the fluorescence detection system, each with inherent advantages. The interference optical system captures data much faster than these other optical systems, allowing for sedimentation velocity analysis of extremely large macromolecular complexes that sediment rapidly at very low rotor speeds. Supramolecular oligomeric complexes produced by self-association of 12-mer chromatin fibers are used to illustrate the advantages of the interference optics. Using interference optics, we show that chromatin fibers self-associate at physiological divalent salt concentrations to form structures that sediment between 10,000 and 350,000S. The method for characterizing chromatin oligomers described in this chapter will be generally useful for characterization of any biological structures that are too large to be studied by the absorbance optical system. © 2015 Elsevier Inc. All rights reserved.

Synthesis and Characterization of Silver-Doped Mesoporous Bioactive Glass and Its Applications in Conjunction with Electrospinning

PubMed Central

Ciraldo, Francesca E.; Goldmann, Wolfgang H.

2018-01-01

Since they were first developed in 2004, mesoporous bioactive glasses (MBGs) rapidly captured the interest of the scientific community thanks to their numerous beneficial properties. MBGs are synthesised by a combination of the sol–gel method with the chemistry of surfactants to obtain highly mesoporous (pore size from 5 to 20 nm) materials that, owing to their high surface area and ordered structure, are optimal candidates for controlled drug-delivery systems. In this work, we synthesised and characterised a silver-containing mesoporous bioactive glass (Ag-MBG). It was found that Ag-MBG is a suitable candidate for controlled drug delivery, showing a perfectly ordered mesoporous structure ideal for the loading of drugs together with optimal bioactivity, sustained release of silver from the matrix, and fast and strong bacterial inhibition against both Gram-positive and Gram-negative bacteria. Silver-doped mesoporous glass particles were used in three electrospinning-based techniques to produce PCL/Ag-MBG composite fibres, to coat bioactive glass scaffolds (via electrospraying), and for direct sol electrospinning. The results obtained in this study highlight the versatility and efficacy of Ag-substituted mesoporous bioactive glass and encourage further studies to characterize the biological response to Ag-MBG-based antibacterial controlled-delivery systems for tissue-engineering applications. PMID:29710768

Site-Specific Preparation of Intact Solid–Liquid Interfaces by Label-Free In Situ Localization and Cryo-Focused Ion Beam Lift-Out

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zachman, Michael J.; Asenath-Smith, Emily; Estroff, Lara A.

Abstract Scanning transmission electron microscopy (STEM) allows atomic scale characterization of solid–solid interfaces, but has seen limited applications to solid–liquid interfaces due to the volatility of liquids in the microscope vacuum. Although cryo-electron microscopy is routinely used to characterize hydrated samples stabilized by rapid freezing, sample thinning is required to access the internal interfaces of thicker specimens. Here, we adapt cryo-focused ion beam (FIB) “lift-out,” a technique recently developed for biological specimens, to prepare intact internal solid–liquid interfaces for high-resolution structural and chemical analysis by cryo-STEM. To guide the milling process we introduce a label-freein situmethod of localizing subsurface structuresmore » in suitable materials by energy dispersive X-ray spectroscopy (EDX). Monte Carlo simulations are performed to evaluate the depth-probing capability of the technique, and show good qualitative agreement with experiment. We also detail procedures to produce homogeneously thin lamellae, which enable nanoscale structural, elemental, and chemical analysis of intact solid–liquid interfaces by analytical cryo-STEM. This work demonstrates the potential of cryo-FIB lift-out and cryo-STEM for understanding physical and chemical processes at solid–liquid interfaces.« less

Ultrastructural and structural characterization of zygotes and embryos during development in Sargassum cymosum (Phaeophyceae, Fucales).

PubMed

Rover, Ticiane; Simioni, Carmen; Hable, Whitney; Bouzon, Zenilda L

2015-03-01

This study investigates the pattern and performance of cellular structures during the early development of zygotes and embryos of Sargassum cymosum. The early development S. cymosum germlings has already been characterized and compared with the pattern of development established for all fucoid algae, in which the zygote remains attached to the receptacle by mucilage during the establishment of polarity and early cell division. As in the algae Fucus and Silvetia, the first division is transverse across the longer axis of the zygote of S. cymosum. However, the cell that will give rise to the rhizoids is not determined in the first division; rather, the formation of this cell occurs with the second division, forming a small cell in the embryo shaded site. Stabilizing polarity during the process of forming a multicellular embryo occurs rapidly. During development, significant cytoplasmic alterations take place. Initially, the cytoplasm shows large clusters of phenolic compounds located in specific parts, but later, in the course of development, these compounds are dispersed in the cytoplasm, although a significant amount remains confined to the nucleus. Moreover, to produce more zygotes and higher growth rates for the germlings, the best conditions found for the species S. cymosum were 22 and 26 °C, respectively.

A cohort of new adhesive proteins identified from transcriptomic analysis of mussel foot glands.

PubMed

DeMartini, Daniel G; Errico, John M; Sjoestroem, Sebastian; Fenster, April; Waite, J Herbert

2017-06-01

The adaptive attachment of marine mussels to a wide range of substrates in a high-energy, saline environment has been explored for decades and is a significant driver of bioinspired wet adhesion research. Mussel attachment relies on a fibrous holdfast known as the byssus, which is made by a specialized appendage called the foot. Multiple adhesive and structural proteins are rapidly synthesized, secreted and moulded by the foot into holdfast threads. About 10 well-characterized proteins, namely the mussel foot proteins (Mfps), the preCols and the thread matrix proteins, are reported as representing the bulk of these structures. To explore how robust this proposition is, we sequenced the transcriptome of the glandular tissues that produce and secrete the various holdfast components using next-generation sequencing methods. Surprisingly, we found around 15 highly expressed genes that have not previously been characterized, but bear key similarities to the previously defined mussel foot proteins, suggesting additional contribution to byssal function. We verified the validity of these transcripts by polymerase chain reaction, cloning and Sanger sequencing as well as confirming their presence as proteins in the byssus. These newly identified proteins greatly expand the palette of mussel holdfast biochemistry and provide new targets for investigation into bioinspired wet adhesion. © 2017 The Author(s).

X-ray emission on hybird stars: ROSAT observations of alpha Trianguli Australis and iota Aurigae

NASA Technical Reports Server (NTRS)

Kashyap, V.; Rosner, R.; Harnden, F. R., Jr.; Maggio, A.; Micela, G.; Sciortino, S.

1994-01-01

We report on deep ROSAT observations of two Hybrid atmosphere stars, alpha TrA and iota Aur, and our analysis of these observations. We detect high-energy transient phenomena on alpha TrA and consider the implications of this discovery to the atmospheres of Hybrid stars. We detect iota Aur in the high-energy passband of ROSAT, implying the existence of multimillion degree plasma on the star. Our major results include the following: discovery of two large flare events, detected during pointed observations of alpha TrA; the demonstration that the flare emission most likely comes from the giant itself, rather than from a previously unseen low-mass companion star; the demonstration that the plasma characteristics associated with the flares and with the 'quiescent' component are essentially indistinguishable; and that the geometric dimensions of the emitting plasma are considerably smaller than the critical dimension characterizing stable 'hot' coronal loop structures. Our results suggest that alpha TrA does not have any steady X-ray emission consistent with theoretical expectations, and support the argument that Hybrid stars constitute a transitional type of object in which large-scale magnetic dynamo activity ceases, and the dominant spatial scales characterizing coronal structure rapidly decline as such stars evolve across the X-ray 'Dividing Line' in the H-R diagram.

Identification and characterization of a drug sensitive strain enables puromycin-based translational assays in Saccharomyces cerevisiae

PubMed Central

Cary, Gregory A.; Yoon, Sung Hwan; Torres, Cecilia Garmendia; Wang, Kathie; Hays, Michelle; Ludlow, Catherine; Goodlett, David R.; Dudley, Aimée M.

2014-01-01

Puromycin is an aminonucleoside antibiotic with structural similarity to aminoacyl tRNA. This structure allows the drug to bind the ribosomal A-site and incorporate into nascent polypeptides causing chain termination, ribosomal subunit dissociation, and widespread translational arrest at high concentrations. In contrast, at sufficiently low concentrations, puromycin incorporates primarily at the C-terminus of proteins. While a number of techniques utilize puromycin incorporation as a tool for probing translational activity in vivo, these methods cannot be applied in yeasts that are insensitive to puromycin. Here, we describe a mutant strain of the yeast Saccharomyces cerevisiae that is sensitive to puromycin and characterize the cellular response to the drug. Puromycin inhibits the growth of yeast cells mutant for erg6Δ, pdr1Δ, and pdr3Δ (EPP) on both solid and liquid media. Puromycin also induces the aggregation of the cytoplasmic processing body component Edc3 in the mutant strain. We establish that puromycin is rapidly incorporated into yeast proteins and test the effects of puromycin on translation in vivo. This work establishes the EPP strain as a valuable tool for implementing puromycin-based assays in yeast, which will enable new avenues of inquiry into protein production and maturation. PMID:24610064

Structural Genomics and Drug Discovery for Infectious Diseases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anderson, W.F.

The application of structural genomics methods and approaches to proteins from organisms causing infectious diseases is making available the three dimensional structures of many proteins that are potential drug targets and laying the groundwork for structure aided drug discovery efforts. There are a number of structural genomics projects with a focus on pathogens that have been initiated worldwide. The Center for Structural Genomics of Infectious Diseases (CSGID) was recently established to apply state-of-the-art high throughput structural biology technologies to the characterization of proteins from the National Institute for Allergy and Infectious Diseases (NIAID) category A-C pathogens and organisms causing emerging,more » or re-emerging infectious diseases. The target selection process emphasizes potential biomedical benefits. Selected proteins include known drug targets and their homologs, essential enzymes, virulence factors and vaccine candidates. The Center also provides a structure determination service for the infectious disease scientific community. The ultimate goal is to generate a library of structures that are available to the scientific community and can serve as a starting point for further research and structure aided drug discovery for infectious diseases. To achieve this goal, the CSGID will determine protein crystal structures of 400 proteins and protein-ligand complexes using proven, rapid, highly integrated, and cost-effective methods for such determination, primarily by X-ray crystallography. High throughput crystallographic structure determination is greatly aided by frequent, convenient access to high-performance beamlines at third-generation synchrotron X-ray sources.« less

Insights Into the Bifunctional Aphidicolan-16-ß-ol Synthase Through Rapid Biomolecular Modeling Approaches.

PubMed

Hirte, Max; Meese, Nicolas; Mertz, Michael; Fuchs, Monika; Brück, Thomas B

2018-01-01

Diterpene synthases catalyze complex, multi-step C-C coupling reactions thereby converting the universal, aliphatic precursor geranylgeranyl diphosphate into diverse olefinic macrocylces that form the basis for the structural diversity of the diterpene natural product family. Since catalytically relevant crystal structures of diterpene synthases are scarce, homology based biomolecular modeling techniques offer an alternative route to study the enzyme's reaction mechanism. However, precise identification of catalytically relevant amino acids is challenging since these models require careful preparation and refinement techniques prior to substrate docking studies. Targeted amino acid substitutions in this protein class can initiate premature quenching of the carbocation centered reaction cascade. The structural characterization of those alternative cyclization products allows for elucidation of the cyclization reaction cascade and provides a new source for complex macrocyclic synthons. In this study, new insights into structure and function of the fungal, bifunctional Aphidicolan-16-ß-ol synthase were achieved using a simplified biomolecular modeling strategy. The applied refinement methodologies could rapidly generate a reliable protein-ligand complex, which provides for an accurate in silico identification of catalytically relevant amino acids. Guided by our modeling data, ACS mutations lead to the identification of the catalytically relevant ACS amino acid network I626, T657, Y658, A786, F789, and Y923. Moreover, the ACS amino acid substitutions Y658L and D661A resulted in a premature termination of the cyclization reaction cascade en-route from syn-copalyl diphosphate to Aphidicolan-16-ß-ol. Both ACS mutants generated the diterpene macrocycle syn-copalol and a minor, non-hydroxylated labdane related diterpene, respectively. Our biomolecular modeling and mutational studies suggest that the ACS substrate cyclization occurs in a spatially restricted location of the enzyme's active site and that the geranylgeranyl diphosphate derived pyrophosphate moiety remains in the ACS active site thereby directing the cyclization process. Our cumulative data confirm that amino acids constituting the G-loop of diterpene synthases are involved in the open to the closed, catalytically active enzyme conformation. This study demonstrates that a simple and rapid biomolecular modeling procedure can predict catalytically relevant amino acids. The approach reduces computational and experimental screening efforts for diterpene synthase structure-function analyses.

Insights into the bifunctional Aphidicolan-16-ß-ol synthase through rapid biomolecular modelling approaches

NASA Astrophysics Data System (ADS)

Hirte, Max; Meese, Nicolas; Mertz, Michael; Fuchs, Monika; Brück, Thomas B.

2018-04-01

Diterpene synthases catalyze complex, multi-step C-C coupling reactions thereby converting the universal, aliphatic precursor geranylgeranyl diphosphate into diverse olefinic macrocylces that form the basis for the structural diversity of the diterpene natural product family. Since catalytically relevant crystal structures of diterpene synthases are scarce, homology based biomolecular modelling techniques offer an alternative route to study the enzyme’s reaction mechanism. However, precise identification of catalytically relevant amino acids is challenging since these models require careful preparation and refinement techniques prior to substrate docking studies. Targeted amino acid substitutions in this protein class can initiate premature quenching of the carbocation centered reaction cascade. The structural characterization of those alternative cyclization products allows for elucidation of the cyclization reaction cascade and provides a new source for complex macrocyclic synthons. In this study, new insights into structure and function of the fungal, bifunctional Aphidicolan-16-ß-ol synthase were achieved using a simplified biomolecular modelling strategy. The applied refinement methodologies could rapidly generate a reliable protein-ligand complex, which provides for an accurate in silico identification of catalytically relevant amino acids. Guided by our modelling data, ACS mutations lead to the identification of the catalytically relevant ACS amino acid network I626, T657, Y658, A786, F789 and Y923. Moreover, the ACS amino acid substitutions Y658L and D661A resulted in a premature termination of the cyclization reaction cascade en-route from syn-copalyl diphosphate to Aphidicolan-16-ß-ol. Both ACS mutants generated the diterpene macrocycle syn-copalol and a minor, non-hydroxylated labdane related diterpene, respectively. Our biomolecular modelling and mutational studies suggest that the ACS substrate cyclization occurs in a spatially restricted location of the enzyme’s active site and that the geranylgeranyl diphosphate derived pyrophosphate moiety remains in the ACS active site thereby directing the cyclization process. Our cumulative data confirm that amino acids constituting the G-loop of diterpene synthases are involved in the open to the closed, catalytically active enzyme conformation. This study demonstrates that a simple and rapid biomolecular modelling procedure can predict catalytically relevant amino acids. The approach reduces computational and experimental screening efforts for diterpene synthase structure-function analyses.

Rapid screening of 35 new psychoactive substances by ion mobility spectrometry (IMS) and direct analysis in real time (DART) coupled to quadrupole time-of-flight mass spectrometry (QTOF-MS).

PubMed

Gwak, Seongshin; Almirall, Jose R

2015-10-01

The recent propagation of new psychoactive substances (NPS) has led to the development of new techniques for the rapid characterization of controlled substances in this category. A commercial bench-top ion mobility spectrometer (IMS) with a (63) Ni ionization source and a direct analysis in real time (DART) coupled to quadrupole time-of-flight (QTOF) were used for the rapid characterization of 35 NPS. The advantages of these techniques are fast response, ease of operation, and minimal sample preparation. The characteristic reduced mobilities of each substance are reported as are the mass spectra of the 35 compounds. The acquired product ion scan mass spectra were also compared to a library database constructed by QTOF with a electrospray ionization (ESI) source and showed a consistent relative abundance for each peak over time. A total of four seized drug samples provided by the local forensic laboratory were analyzed in order to demonstrate the utility of this approach. The results of this study suggest that both IMS and DART-QTOF are promising alternatives for the rapid screening and characterization of these new psychoactive substances. Copyright © 2015 John Wiley & Sons, Ltd.

The Potential of Spaceborne Remote Sensing for Deriving Canopy Structure Metrics and Informing Biodiversity and Habitat Mapping

NASA Astrophysics Data System (ADS)

Goetz, S. J.; Dubayah, R.

2016-12-01

Research on characterization of canopy structure with remote sensing has exploded as airborne data sets have become more widely available to the biodiversity science and habitat management communities. While these advances are important in the context of increasing pressure on both habitat and wildlife, airborne data acquisitions are necessarily limited in geographic scope and thus in their general applicability to biome-scale biodiversity research initiatives, including international programs striving to implement the United Nations Convention on Biological Diversity (CBD) and the associated Aichi Biodiversity Targets. The lack of systematic metrics of canopy structure across large geographic domains also makes it difficult to implement the CBD Strategic Plan systematically across nations, as outlined in National Biodiversity Strategies and Action Plans. The Group on Earth Observations, Biodiversity Observation Network (GEO BON) has proposed a set of Essential Biodiversity Variables (EBVs) that could be used as a global-scale basis for biodiversity monitoring, but several of those EBVs are still limited by the availability of data on habitat 3D structure. Those limitations will be overcome in the near future with a suite of satellite missions that will provide an unprecedented level of active remote sensing measurements useful for deriving structure information, including Tandem-X, ICESat-2, BIOMASS and the Global Ecosystem Dynamics Investigation (GEDI). We will provide a brief overview of the rapid advance of measurements of canopy structure and the applications that have evolved in recent years in terms of 3D habitat characterization, species-specific habitat utilization, and the potential of these new space-based measurements. In this talk we will focus primarily on GEDI, a lidar mission to be installed on the International Space Station that is optimized for retrieving 3D canopy structure. GEDI and the other new missions will provide long-desired consistent and systematic information on EBVs from space, and thereby facilitate the implementation of international biodiversity policy objectives.

Genetic structure and demographic inference of the regular sea urchin Sterechinus neumayeri (Meissner, 1900) in the Southern Ocean: The role of the last glaciation.

PubMed

Díaz, Angie; Gérard, Karin; González-Wevar, Claudio; Maturana, Claudia; Féral, Jean-Pierre; David, Bruno; Saucède, Thomas; Poulin, Elie

2018-01-01

One of the most relevant characteristics of the extant Southern Ocean fauna is its resiliency to survive glacial processes of the Quaternary. These climatic events produced catastrophic habitat reductions and forced some marine benthic species to move, adapt or go extinct. The marine benthic species inhabiting the Antarctic upper continental shelf faced the Quaternary glaciations with different strategies that drastically modified population sizes and thus affected the amount and distribution of intraspecific genetic variation. Here we present new genetic information for the most conspicuous regular sea urchin of the Antarctic continental shelf, Sterechinus neumayeri. We studied the patterns of genetic diversity and structure in this broadcast-spawner across three Antarctic regions: Antarctic Peninsula, the Weddell Sea and Adélie Land in East Antarctica. Genetic analyses based on mitochondrial and nuclear markers suggested that S. neumayeri is a single genetic unit around the Antarctic continent. The species is characterized by low levels of genetic diversity and exhibits a typical star-like haplotype genealogy that supports the hypothesis of a single in situ refugium. Based on two mutation rates standardized for this genus, the Bayesian Skyline plot analyses detected a rapid demographic expansion after the Last Glacial Maximum. We propose a scenario of rapid postglacial expansion and recolonization of Antarctic shallow areas from a less ice-impacted refugium where the species survived the LGM. Considering the patterns of genetic diversity and structure recorded in the species, this refugium was probably located in East Antarctica.

Genetic structure and demographic inference of the regular sea urchin Sterechinus neumayeri (Meissner, 1900) in the Southern Ocean: The role of the last glaciation

PubMed Central

Gérard, Karin; González-Wevar, Claudio; Maturana, Claudia; Féral, Jean-Pierre; David, Bruno; Saucède, Thomas; Poulin, Elie

2018-01-01

One of the most relevant characteristics of the extant Southern Ocean fauna is its resiliency to survive glacial processes of the Quaternary. These climatic events produced catastrophic habitat reductions and forced some marine benthic species to move, adapt or go extinct. The marine benthic species inhabiting the Antarctic upper continental shelf faced the Quaternary glaciations with different strategies that drastically modified population sizes and thus affected the amount and distribution of intraspecific genetic variation. Here we present new genetic information for the most conspicuous regular sea urchin of the Antarctic continental shelf, Sterechinus neumayeri. We studied the patterns of genetic diversity and structure in this broadcast-spawner across three Antarctic regions: Antarctic Peninsula, the Weddell Sea and Adélie Land in East Antarctica. Genetic analyses based on mitochondrial and nuclear markers suggested that S. neumayeri is a single genetic unit around the Antarctic continent. The species is characterized by low levels of genetic diversity and exhibits a typical star-like haplotype genealogy that supports the hypothesis of a single in situ refugium. Based on two mutation rates standardized for this genus, the Bayesian Skyline plot analyses detected a rapid demographic expansion after the Last Glacial Maximum. We propose a scenario of rapid postglacial expansion and recolonization of Antarctic shallow areas from a less ice-impacted refugium where the species survived the LGM. Considering the patterns of genetic diversity and structure recorded in the species, this refugium was probably located in East Antarctica. PMID:29874287

Using UAS optical imagery and SfM photogrammetry to characterize the surface grain size of gravel bars in a braided river (Vénéon River, French Alps)

NASA Astrophysics Data System (ADS)

Vázquez-Tarrío, Daniel; Borgniet, Laurent; Liébault, Frédéric; Recking, Alain

2017-05-01

This paper explores the potential of unmanned aerial system (UAS) optical aerial imagery to characterize grain roughness and size distribution in a braided, gravel-bed river (Vénéon River, French Alps). With this aim in view, a Wolman field campaign (19 samples) and five UAS surveys were conducted over the Vénéon braided channel during summer 2015. The UAS consisted of a small quadcopter carrying a GoPro camera. Structure-from-Motion (SfM) photogrammetry was used to extract dense and accurate three-dimensional point clouds. Roughness descriptors (roughness heights, standard deviation of elevation) were computed from the SfM point clouds and were correlated with the median grain size of the Wolman samples. A strong relationship was found between UAS-SfM-derived grain roughness and Wolman grain size. The procedure employed has potential for the rapid and continuous characterization of grain size distribution in exposed bars of gravel-bed rivers. The workflow described in this paper has been successfully used to produce spatially continuous grain size information on exposed gravel bars and to explore textural changes following flow events.

Intrinsic disorder in scaffold proteins: Getting more from less

PubMed Central

Cortese, Marc S.; Uversky, Vladimir N.; Dunker, A. Keith

2008-01-01

Regulation, recognition and cell signaling involve the coordinated actions of many players. Signaling scaffolds, with their ability to bring together proteins belonging to common and/or interlinked pathways, play crucial roles in orchestrating numerous events by coordinating specific interactions among signaling proteins. This review examines the roles of intrinsic disorder (ID) in signaling scaffold protein function. Several well-characterized scaffold proteins with structurally and functionally characterized ID regions are used here to illustrate the importance of ID for scaffolding function. These examples include scaffolds that are mostly disordered, only partially disordered or those in which the ID resides in a scaffold partner. Specific scaffolds discussed include RNase, voltage-activated potassium channels, axin, BRCA1, GSK-3β, p53, Ste5, titin, Fus3, BRCA1, Titin, MAP2, D-AKAP2 and AKAP250. Among the mechanisms discussed are: molecular recognition features, fly-casting, ease of encounter complex formation, structural isolation of partners, modulation of interactions between bound partners, masking of intramolecular interaction sites, maximized interaction surface per residue, toleration of high evolutionary rates, binding site overlap, allosteric modification, palindromic binding, reduced constraints for alternative splicing, efficient regulation via posttranslational modification, efficient regulation via rapid degradation, protection of normally solvent-exposed sites, enhancing the plasticity of interaction and molecular crowding. We conclude that ID can enhance scaffold function by a diverse array of mechanisms. In other words, scaffold proteins utilize several ID-facilitated mechanisms to enhance function, and by doing so, get more functionality from less structure. PMID:18619997

In situ characterization of charge rate dependent stress and structure changes in V 2O 5 cathode prepared by atomic layer deposition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jung, Hyun; Gerasopoulos, Konstantinos; Talin, Albert Alec

Here, the insertion/extraction of lithium into/from various host materials is the basic process by which lithium-ion batteries reversible store charge. This process is generally accompanied by strain in the host material, inducing stress which can lead to capacity loss. Therefore, understanding of both the structural changes and the associated stress – investigated almost exclusively separate to date – is a critical factor for developing high-performance batteries. Here, we report an in situ method, which utilizes Raman spectroscopy in parallel with optical interferometry to study effects of varying charging rates (C-rates) on the structure and stress in a V 2O 5more » thin film cathode. Abrupt stress changes at specific crystal phase transitions in the Li—V—O system are observed and the magnitude of the stress changes with the amount of lithium inserted into the electrode are correlated. A linear increase in the stress as a function of x in Li xV 2O 5 is observed, indicating that C-rate does not directly contribute to larger intercalation stress. However, a more rapid increase in disorder within the Li xV 2O 5 layers is correlated with higher C-rate. Ultimately, these experiments demonstrate how the simultaneous stress/Raman in situ approach can be utilized as a characterization platform for investigating various critical factors affecting lithium-ion battery performance.« less

In situ characterization of charge rate dependent stress and structure changes in V 2O 5 cathode prepared by atomic layer deposition

DOE PAGES

Jung, Hyun; Gerasopoulos, Konstantinos; Talin, Albert Alec; ...

2016-11-22

Here, the insertion/extraction of lithium into/from various host materials is the basic process by which lithium-ion batteries reversible store charge. This process is generally accompanied by strain in the host material, inducing stress which can lead to capacity loss. Therefore, understanding of both the structural changes and the associated stress – investigated almost exclusively separate to date – is a critical factor for developing high-performance batteries. Here, we report an in situ method, which utilizes Raman spectroscopy in parallel with optical interferometry to study effects of varying charging rates (C-rates) on the structure and stress in a V 2O 5more » thin film cathode. Abrupt stress changes at specific crystal phase transitions in the Li—V—O system are observed and the magnitude of the stress changes with the amount of lithium inserted into the electrode are correlated. A linear increase in the stress as a function of x in Li xV 2O 5 is observed, indicating that C-rate does not directly contribute to larger intercalation stress. However, a more rapid increase in disorder within the Li xV 2O 5 layers is correlated with higher C-rate. Ultimately, these experiments demonstrate how the simultaneous stress/Raman in situ approach can be utilized as a characterization platform for investigating various critical factors affecting lithium-ion battery performance.« less

Urban population genetics of slum-dwelling rats (Rattus norvegicus) in Salvador, Brazil

PubMed Central

Kajdacsi, Brittney; Costa, Federico; Hyseni, Chaz; Porter, Fleur; Brown, Julia; Rodrigues, Gorete; Farias, Helena; Reis, Mitermeyer G.; Childs, James E.; Ko, Albert I.; Caccone, Adalgisa

2013-01-01

Throughout the developing world, urban centers with sprawling slum settlements are rapidly expanding and invading previously forested ecosystems. Slum communities are characterized by untended refuse, open sewers, and overgrown vegetation, which promote rodent infestation. Norway rats (Rattus norvegicus), are reservoirs for epidemic transmission of many zoonotic pathogens of public health importance. Understanding the population ecology of R. norvegicus is essential to formulate effective rodent control strategies, as this knowledge aids estimation of the temporal stability and spatial connectivity of populations. We screened for genetic variation, characterized the population genetic structure, and evaluated the extent and patterns of gene flow in the urban landscape using 17 microsatellite loci in 146 rats from 9 sites in the city of Salvador, Brazil. These sites were divided between three neighborhoods within the city spaced an average of 2.7 km apart. Surprisingly, we detected very little relatedness among animals trapped at the same site and found high levels of genetic diversity, as well as structuring across small geographic distances. Most FST comparisons among sites were statistically significant, including sites <400 m apart. Bayesian analyses grouped the samples in three genetic clusters, each associated with distinct sampling sites from different neighborhoods or valleys within neighborhoods. These data indicate the existence of complex genetic structure in R. norvegicus in Salvador, linked to the heterogeneous urban landscape. Future rodent control measures need to take into account the spatial and temporal linkage of rat populations in Salvador, as revealed by genetic data, to develop informed eradication strategies. PMID:24118116

Sequence characterization of heat shock protein gene of Cyclospora cayetanensis isolates from Nepal, Mexico, and Peru.

PubMed

Sulaiman, Irshad M; Torres, Patricia; Simpson, Steven; Kerdahi, Khalil; Ortega, Ynes

2013-04-01

We have described the development of a 2-step nested PCR protocol based on the characterization of the 70-kDa heat shock protein (HSP70) gene for rapid detection of the human-pathogenic Cyclospora cayetanensis parasite. We tested and validated these newly designed primer sets by PCR amplification followed by nucleotide sequencing of PCR-amplified HSP70 fragments belonging to 16 human C. cayetanensis isolates from 3 different endemic regions that include Nepal, Mexico, and Peru. No genetic polymorphism was observed among the isolates at the characterized regions of the HSP70 locus. This newly developed HSP70 gene-based nested PCR protocol provides another useful genetic marker for the rapid detection of C. cayetanensis in the future.

Non-T cell activation linker (NTAL): a transmembrane adaptor protein involved in immunoreceptor signaling.

PubMed

Brdicka, Tomás; Imrich, Martin; Angelisová, Pavla; Brdicková, Nadezda; Horváth, Ondrej; Spicka, Jirí; Hilgert, Ivan; Lusková, Petra; Dráber, Petr; Novák, Petr; Engels, Niklas; Wienands, Jürgen; Simeoni, Luca; Osterreicher, Jan; Aguado, Enrique; Malissen, Marie; Schraven, Burkhart; Horejsí, Václav

2002-12-16

A key molecule necessary for activation of T lymphocytes through their antigen-specific T cell receptor (TCR) is the transmembrane adaptor protein LAT (linker for activation of T cells). Upon TCR engagement, LAT becomes rapidly tyrosine phosphorylated and then serves as a scaffold organizing a multicomponent complex that is indispensable for induction of further downstream steps of the signaling cascade. Here we describe the identification and preliminary characterization of a novel transmembrane adaptor protein that is structurally and evolutionarily related to LAT and is expressed in B lymphocytes, natural killer (NK) cells, monocytes, and mast cells but not in resting T lymphocytes. This novel transmembrane adaptor protein, termed NTAL (non-T cell activation linker) is the product of a previously identified WBSCR5 gene of so far unknown function. NTAL becomes rapidly tyrosine-phosphorylated upon cross-linking of the B cell receptor (BCR) or of high-affinity Fcgamma- and Fc epsilon -receptors of myeloid cells and then associates with the cytoplasmic signaling molecules Grb2, Sos1, Gab1, and c-Cbl. NTAL expressed in the LAT-deficient T cell line J.CaM2.5 becomes tyrosine phosphorylated and rescues activation of Erk1/2 and minimal transient elevation of cytoplasmic calcium level upon TCR/CD3 cross-linking. Thus, NTAL appears to be a structural and possibly also functional homologue of LAT in non-T cells.

Repair of O6-methylguanine adducts in human telomeric G-quadruplex DNA by O6-alkylguanine-DNA alkyltransferase

PubMed Central

Hellman, Lance M.; Spear, Tyler J.; Koontz, Colton J.; Melikishvili, Manana; Fried, Michael G.

2014-01-01

O6-alkylguanine-DNA alkyltransferase (AGT) is a single-cycle DNA repair enzyme that removes pro-mutagenic O6-alkylguanine adducts from DNA. Its functions with short single-stranded and duplex substrates have been characterized, but its ability to act on other DNA structures remains poorly understood. Here, we examine the functions of this enzyme on O6-methylguanine (6mG) adducts in the four-stranded structure of the human telomeric G-quadruplex. On a folded 22-nt G-quadruplex substrate, binding saturated at 2 AGT:DNA, significantly less than the ∼5 AGT:DNA found with linear single-stranded DNAs of similar length, and less than the value found with the telomere sequence under conditions that inhibit quadruplex formation (4 AGT:DNA). Despite these differences, AGT repaired 6mG adducts located within folded G-quadruplexes, at rates that were comparable to those found for a duplex DNA substrate under analogous conditions. Repair was kinetically biphasic with the amplitudes of rapid and slow phases dependent on the position of the adduct within the G-quadruplex: in general, adducts located in the top or bottom tetrads of a quadruplex stack exhibited more rapid-phase repair than did adducts located in the inner tetrad. This distinction may reflect differences in the conformational dynamics of 6mG residues in G-quadruplex DNAs. PMID:25080506

Scaffolds with a standardized macro-architecture fabricated from several calcium phosphate ceramics using an indirect rapid prototyping technique

PubMed Central

Wilson, C. E.; van Blitterswijk, C. A.; Verbout, A. J.; de Bruijn, J. D.

2010-01-01

Calcium phosphate ceramics, commonly applied as bone graft substitutes, are a natural choice of scaffolding material for bone tissue engineering. Evidence shows that the chemical composition, macroporosity and microporosity of these ceramics influences their behavior as bone graft substitutes and bone tissue engineering scaffolds but little has been done to optimize these parameters. One method of optimization is to place focus on a particular parameter by normalizing the influence, as much as possible, of confounding parameters. This is difficult to accomplish with traditional fabrication techniques. In this study we describe a design based rapid prototyping method of manufacturing scaffolds with virtually identical macroporous architectures from different calcium phosphate ceramic compositions. Beta-tricalcium phosphate, hydroxyapatite (at two sintering temperatures) and biphasic calcium phosphate scaffolds were manufactured. The macro- and micro-architectures of the scaffolds were characterized as well as the influence of the manufacturing method on the chemistries of the calcium phosphate compositions. The structural characteristics of the resulting scaffolds were remarkably similar. The manufacturing process had little influence on the composition of the materials except for the consistent but small addition of, or increase in, a beta-tricalcium phosphate phase. Among other applications, scaffolds produced by the method described provide a means of examining the influence of different calcium phosphate compositions while confidently excluding the influence of the macroporous structure of the scaffolds. PMID:21069558

Characteristic Changes in Cell Surface Glycosylation Accompany Intestinal Epithelial Cell (IEC) Differentiation: High Mannose Structures Dominate the Cell Surface Glycome of Undifferentiated Enterocytes*

PubMed Central

Park, Dayoung; Brune, Kristin A.; Mitra, Anupam; Marusina, Alina I.; Maverakis, Emanual; Lebrilla, Carlito B.

2015-01-01

Changes in cell surface glycosylation occur during the development and differentiation of cells and have been widely correlated with the progression of several diseases. Because of their structural diversity and sensitivity to intra- and extracellular conditions, glycans are an indispensable tool for analyzing cellular transformations. Glycans present on the surface of intestinal epithelial cells (IEC) mediate interactions with billions of native microorganisms, which continuously populate the mammalian gut. A distinct feature of IECs is that they differentiate as they migrate upwards from the crypt base to the villus tip. In this study, nano-LC/ESI QTOF MS profiling was used to characterize the changes in glycosylation that correspond to Caco-2 cell differentiation. As Caco-2 cells differentiate to form a brush border membrane, a decrease in high mannose type glycans and a concurrent increase in fucosylated and sialylated complex/hybrid type glycans were observed. At day 21, when cells appear to be completely differentiated, remodeling of the cell surface glycome ceases. Differential expression of glycans during IEC maturation appears to play a key functional role in regulating the membrane-associated hydrolases and contributes to the mucosal surface innate defense mechanisms. Developing methodologies to rapidly identify changes in IEC surface glycans may lead to a rapid screening approach for a variety of disease states affecting the GI tract. PMID:26355101

URBAN/SUBURBAN WATERSHED CHARACTERIZATION

EPA Science Inventory

The ability to characterize the land surface and related pollutant source loadings is critical for reliable watershed modeling. Urban/suburban land uses are the most rapidly growing land use class, generating non-point source pollutant loadings likely to seriously impair streams...

Novel self-assembled gels and materials synthesis in unconventional environments

NASA Astrophysics Data System (ADS)

Irvin, Glen Clifford, Jr.

This thesis deals specifically with the fabrication of novel nanophase and polymer materials using novel microstructured mediums. Enzymatic polymerization in a new microemulsion system using dense carbon dioxide and fluorinated surfactants was carried out. The morphology, molecular weight, and chemical structure of the polymer are characterized through electron microscopy, HPLC, FTIR, and 1HNMR. Structural characteristics indicate similarity to polymers formed in AOT-inverse micelles. Spectroscopic information of the polymerization system on a molecular level has been performed. The results indicate strong hydrogen bonding interactions between the monomer, water, and perfluorinated surfactant implying the partitioning of the monomer to the surfactant headgroup region. An extension of the microemulsion environment is found with novel microemulsion based gels. The gels contain both lecithin and AOT surfactants where roughly equal volumes of hydrocarbon and water forms a three-dimensional gel network. This microemulsion system is unique from a fundamental scientific and practical interest. Analysis of the system microstructures using 1HNMR, 13CNMR 31PNNM, Rheology, SAXS, SANS, and conductivity is presented. Nanomaterial templated syntheses were conducted and are discussed. A new technique was developed for the rapid production of clathrate hydrates either in aqueous or water-in-microemulsion environments. The systems devised for this technology have significantly greater interfacial contact between water and gas molecules (clathrate hydrate constituents). The rapid clathrate hydrate technique was utilized for synthesis of nanoclusters in aqueous and reverse micelle based systems using the remarkable phenomenon of clathrate hydrate formation. Conversion of water to crystalline ice-like (clathrate hydrate) form is exploited to arrest particle growth, thereby restricting particle size to the nanometer range. The technique is used to generate high synthesis rates of nanoclusters (specifically ferrites) in aqueous solution. By controlling process conditions, ferrite particles with spherical or high aspect ratio acicular morphologies are obtained. Characterization of magnetic materials produced using this new technique was detailed with XRD, SQUID, and TEM. An extension of the rapid hydrate technique to AOT/water/Isooctane microemulsions found that for the same [water]/[AOT] ratio, nanoclusters of smaller size could be formed simply by subjecting the reversed micelles to hydrate forming conditions. Analysis of a model semiconductor (PbS) is presented using UV-VIS, XRD, EDAX, TEM, and Electron Diffraction.

Rapid Characterization of Shorelines using a Georeferenced Video Mapping System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anderson, Michael G.; Judd, Chaeli; Marcoe, K.

Increased understanding of shoreline conditions is needed, yet current approaches are limited in ability to characterize remote areas or document features at a finer resolution. Documentation using video mapping may provide a rapid and repeatable method for assessing the current state of the environment and determining changes to the shoreline over time. In this study, we compare two studies using boat-based, georeferenced video mapping in coastal Washington and the Columbia River Estuary to map and characterize coastal stressors and functional data. In both areas, mapping multiple features along the shoreline required approximation of the coastline. However, characterization of vertically orientedmore » features such as shoreline armoring and small features such as pilings and large woody debris was possible. In addition, end users noted that geovideo provides a permanent record to allow a user to examine recorded video anywhere along a transect or at discrete points.« less

High-speed separation and characterization of major constituents in Radix Paeoniae Rubra by fast high-performance liquid chromatography coupled with diode-array detection and time-of-flight mass spectrometry.

PubMed

Liu, E-Hu; Qi, Lian-Wen; Li, Bin; Peng, Yong-Bo; Li, Ping; Li, Chang-Yin; Cao, Jun

2009-01-01

A fast high-performance liquid chromatography (HPLC) method coupled with diode-array detection (DAD) and electrospray ionization time-of-flight mass spectrometry (ESI-TOFMS) has been developed for rapid separation and sensitive identification of major constituents in Radix Paeoniae Rubra (RPR). The total analysis time on a short column packed with 1.8-microm porous particles was about 20 min without a loss in resolution, six times faster than the performance of a conventional column analysis (115 min). The MS fragmentation behavior and structural characterization of major compounds in RPR were investigated here for the first time. The targets were rapidly screened from RPR matrix using a narrow mass window of 0.01 Da to restructure extracted ion chromatograms. Accurate mass measurements (less than 5 ppm error) for both the deprotonated molecule and characteristic fragment ions represent reliable identification criteria for these compounds in complex matrices with similar if not even better performance compared with tandem mass spectrometry. A total of 26 components were screened and identified in RPR including 11 monoterpene glycosides, 11 galloyl glucoses and 4 other phenolic compounds. From the point of time savings, resolving power, accurate mass measurement capability and full spectral sensitivity, the established fast HPLC/DAD/TOFMS method turns out to be a highly useful technique to identify constituents in complex herbal medicines. (c) 2008 John Wiley & Sons, Ltd.