Rapid measurement of 3J(H N-H alpha) and 3J(N-H beta) coupling constants in polypeptides.

PubMed

Barnwal, Ravi Pratap; Rout, Ashok K; Chary, Kandala V R; Atreya, Hanudatta S

2007-12-01

We present two NMR experiments, (3,2)D HNHA and (3,2)D HNHB, for rapid and accurate measurement of 3J(H N-H alpha) and 3J(N-H beta) coupling constants in polypeptides based on the principle of G-matrix Fourier transform NMR spectroscopy and quantitative J-correlation. These experiments, which facilitate fast acquisition of three-dimensional data with high spectral/digital resolution and chemical shift dispersion, will provide renewed opportunities to utilize them for sequence specific resonance assignments, estimation/characterization of secondary structure with/without prior knowledge of resonance assignments, stereospecific assignment of prochiral groups and 3D structure determination, refinement and validation. Taken together, these experiments have a wide range of applications from structural genomics projects to studying structure and folding in polypeptides.

Rapid on-site/in-situ detection of heavy metal ions in environmental water using a structure-switching DNA optical biosensor.

PubMed

Long, Feng; Zhu, Anna; Shi, Hanchang; Wang, Hongchen; Liu, Jingquan

2013-01-01

A structure-switching DNA optical biosensor for rapid on-site/in situ detection of heavy metal ions is reported. Mercury ions (Hg²⁺), highly toxic and ubiquitous pollutants, were selected as model target. In this system, fluorescence-labeled DNA containing T-T mismatch structure was introduced to bind with DNA probes immobilized onto the sensor surface. In the presence of Hg²⁺, some of the fluorescence-labeled DNAs bind with Hg²⁺ to form T-Hg²⁺-T complexes through the folding of themselves into a hairpin structure and dehybridization from the sensor surface, which leads to decrease in fluorescence signal. The total analysis time for a single sample was less than 10 min with detection limit of 1.2 nM. The rapid on-site/in situ determination of Hg²⁺ was readily performed in natural water. This sensing strategy can be extended in principle to other metal ions by substituting the T-Hg²⁺-T complexes with other specificity structures that selectively bind to other analytes.

Design and Control of Modular Spine-Like Tensegrity Structures

NASA Technical Reports Server (NTRS)

Mirletz, Brian T.; Park, In-Won; Flemons, Thomas E.; Agogino, Adrian K.; Quinn, Roger D.; SunSpiral, Vytas

2014-01-01

We present a methodology enabled by the NASA Tensegrity Robotics Toolkit (NTRT) for the rapid structural design of tensegrity robots in simulation and an approach for developing control systems using central pattern generators, local impedance controllers, and parameter optimization techniques to determine effective locomotion strategies for the robot. Biomimetic tensegrity structures provide advantageous properties to robotic locomotion and manipulation tasks, such as their adaptability and force distribution properties, flexibility, energy efficiency, and access to extreme terrains. While strides have been made in designing insightful static biotensegrity structures, gaining a clear understanding of how a particular structure can efficiently move has been an open problem. The tools in the NTRT enable the rapid exploration of the dynamics of a given morphology, and the links between structure, controllability, and resulting gait efficiency. To highlight the effectiveness of the NTRT at this exploration of morphology and control, we will provide examples from the designs and locomotion of four different modular spine-like tensegrity robots.

Rapid interferometric imaging of printed drug laden multilayer structures

NASA Astrophysics Data System (ADS)

Sandler, Niklas; Kassamakov, Ivan; Ehlers, Henrik; Genina, Natalja; Ylitalo, Tuomo; Haeggstrom, Edward

2014-02-01

The developments in printing technologies allow fabrication of micron-size nano-layered delivery systems to personal specifications. In this study we fabricated layered polymer structures for drug-delivery into a microfluidic channel and aimed to interferometrically assure their topography and adherence to each other. We present a scanning white light interferometer (SWLI) method for quantitative assurance of the topography of the embedded structure. We determined rapidly in non-destructive manner the thickness and roughness of the structures and whether the printed layers containing polymers or/and active pharmaceutical ingredients (API) adhere to each other. This is crucial in order to have predetermined drug release profiles. We also demonstrate non-invasive measurement of a polymer structure in a microfluidic channel. It shown that traceable interferometric 3D microscopy is a viable technique for detailed structural quality assurance of layered drug-delivery systems. The approach can have impact and find use in a much broader setting within and outside life sciences.

Microreactor Cells for High-Throughput X-ray Absorption Spectroscopy

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

Beesley, Angela; Tsapatsaris, Nikolaos; Weiher, Norbert

2007-01-19

High-throughput experimentation has been applied to X-ray Absorption spectroscopy as a novel route for increasing research productivity in the catalysis community. Suitable instrumentation has been developed for the rapid determination of the local structure in the metal component of precursors for supported catalysts. An automated analytical workflow was implemented that is much faster than traditional individual spectrum analysis. It allows the generation of structural data in quasi-real time. We describe initial results obtained from the automated high throughput (HT) data reduction and analysis of a sample library implemented through the 96 well-plate industrial standard. The results show that a fullymore » automated HT-XAS technology based on existing industry standards is feasible and useful for the rapid elucidation of geometric and electronic structure of materials.« less

Mechanical characteristics of heterogeneous structures obtained by high-temperature brazing of corrosion-resistant steels with rapidly quenched non-boron nickel-based alloys

NASA Astrophysics Data System (ADS)

Kalin, B.; Penyaz, M.; Ivannikov, A.; Sevryukov, O.; Bachurina, D.; Fedotov, I.; Voennov, A.; Abramov, E.

2018-01-01

Recently, the use rapidly quenched boron-containing nickel filler metals for high temperature brazing corrosion resistance steels different classes is perspective. The use of these alloys leads to the formation of a complex heterogeneous structure in the diffusion zone that contains separations of intermediate phases such as silicides and borides. This structure negatively affects the strength characteristics of the joint, especially under dynamic loads and in corrosive environment. The use of non-boron filler metals based on the Ni-Si-Be system is proposed to eliminate this structure in the brazed seam. Widely used austenitic 12Cr18Ni10Ti and ferrite-martensitic 16Cr12MoSiWNiVNb reactor steels were selected for research and brazing was carried out. The mechanical characteristics of brazed joints were determined using uniaxial tensile and impact toughness tests, and fractography was investigated by electron microscopy.

Rapid removal of acetimidoyl groups from proteins and peptides. Applications to primary structure determination.

PubMed Central

Dubois, G C; Robinson, E A; Inman, J K; Perham, R N; Appella, E

1981-01-01

Methylamine buffers can be used for the rapid quantitative removal of acetimidoyl groups from proteins and peptides modified by treatment with ethyl or methyl acetimidate. The half-life for displacement of acetimidoyl groups from fully amidinated proteins incubated in 3.44 M-methylamine/HCl buffer at pH 11.5 and 25 degrees C was approx. 26 min; this half life is 29 times less than that observed in ammonia/HCl buffer under the same conditions of pH and amine concentration. Incubation of acetimidated proteins with methylamine for 4 h resulted in greater than 95% removal of acetimidoyl groups. No deleterious effects on primary structure were detected by amino acid analysis or by automated Edman degradation. Reversible amidination of lysine residues, in conjunction with tryptic digestion, has been successfully applied to the determination of the amino acid sequence of an acetimidated mouse immunoglobulin heavy chain peptide. The regeneration of amino groups in amidinated proteins and peptides by methylaminolysis makes amidination a valuable alternative to citraconoylation and maleoylation in structural studies. PMID:6803762

Fold independent structural comparisons of protein-ligand binding sites for exploring functional relationships.

PubMed

Gold, Nicola D; Jackson, Richard M

2006-02-03

The rapid growth in protein structural data and the emergence of structural genomics projects have increased the need for automatic structure analysis and tools for function prediction. Small molecule recognition is critical to the function of many proteins; therefore, determination of ligand binding site similarity is important for understanding ligand interactions and may allow their functional classification. Here, we present a binding sites database (SitesBase) that given a known protein-ligand binding site allows rapid retrieval of other binding sites with similar structure independent of overall sequence or fold similarity. However, each match is also annotated with sequence similarity and fold information to aid interpretation of structure and functional similarity. Similarity in ligand binding sites can indicate common binding modes and recognition of similar molecules, allowing potential inference of function for an uncharacterised protein or providing additional evidence of common function where sequence or fold similarity is already known. Alternatively, the resource can provide valuable information for detailed studies of molecular recognition including structure-based ligand design and in understanding ligand cross-reactivity. Here, we show examples of atomic similarity between superfamily or more distant fold relatives as well as between seemingly unrelated proteins. Assignment of unclassified proteins to structural superfamiles is also undertaken and in most cases substantiates assignments made using sequence similarity. Correct assignment is also possible where sequence similarity fails to find significant matches, illustrating the potential use of binding site comparisons for newly determined proteins.

Text Mining for Protein Docking

PubMed Central

Badal, Varsha D.; Kundrotas, Petras J.; Vakser, Ilya A.

2015-01-01

The rapidly growing amount of publicly available information from biomedical research is readily accessible on the Internet, providing a powerful resource for predictive biomolecular modeling. The accumulated data on experimentally determined structures transformed structure prediction of proteins and protein complexes. Instead of exploring the enormous search space, predictive tools can simply proceed to the solution based on similarity to the existing, previously determined structures. A similar major paradigm shift is emerging due to the rapidly expanding amount of information, other than experimentally determined structures, which still can be used as constraints in biomolecular structure prediction. Automated text mining has been widely used in recreating protein interaction networks, as well as in detecting small ligand binding sites on protein structures. Combining and expanding these two well-developed areas of research, we applied the text mining to structural modeling of protein-protein complexes (protein docking). Protein docking can be significantly improved when constraints on the docking mode are available. We developed a procedure that retrieves published abstracts on a specific protein-protein interaction and extracts information relevant to docking. The procedure was assessed on protein complexes from Dockground (http://dockground.compbio.ku.edu). The results show that correct information on binding residues can be extracted for about half of the complexes. The amount of irrelevant information was reduced by conceptual analysis of a subset of the retrieved abstracts, based on the bag-of-words (features) approach. Support Vector Machine models were trained and validated on the subset. The remaining abstracts were filtered by the best-performing models, which decreased the irrelevant information for ~ 25% complexes in the dataset. The extracted constraints were incorporated in the docking protocol and tested on the Dockground unbound benchmark set, significantly increasing the docking success rate. PMID:26650466

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.

Quantitative Evaluation of Delamination in Composites Using Lamb Waves

NASA Astrophysics Data System (ADS)

Michalcová, L.; Hron, R.

2018-03-01

Ultrasonic guided wave monitoring has become very popular in the area of structural health monitoring (SHM) of aerospace structures. Any possible type of damage must be reliably assessed. The paper deals with delamination length determination in DCB specimens using Lamb waves. An analytical equation based on the velocity dependence on variable thickness is utilized. The group velocity of the fundamental antisymmetric A0 mode rapidly changes in a particular range of the frequency-thickness product. Using the same actuation frequency the propagation velocity is different for delaminated structure. Lamb wave based delamination lengths were compared to the visually determined lengths. The method of the wave velocity determination proved to be essential. More accurate results were achieved by tracking the maximum amplitude of A0 mode than the first signal arrival. These findings are considered as the basis for the damage evaluation of complex structures.

Fluid Mixing in the Eye Under Rapid Eye Movement

NASA Astrophysics Data System (ADS)

Huang, Jinglin; Gharib, Morteza

2017-11-01

Drug injection is an important technique in certain treatments of eye diseases. The efficacy of chemical mixing plays an important role in determining pharmacokinetics of injected drugs. In this study, we build a device to study the chemical mixing behavior in a spherical structure. The mixing process is visualized and analyzed qualitatively. We hope to understand the chemical convection and diffusion behaviors in correlation with controlled rapid mechanical movements. The results will have potential applications in treatment of eye diseases. Resnick Institute at Caltech.

Synaptic Neurotransmitter-Gated Receptors

PubMed Central

Smart, Trevor G.; Paoletti, Pierre

2012-01-01

Since the discovery of the major excitatory and inhibitory neurotransmitters and their receptors in the brain, many have deliberated over their likely structures and how these may relate to function. This was initially satisfied by the determination of the first amino acid sequences of the Cys-loop receptors that recognized acetylcholine, serotonin, GABA, and glycine, followed later by similar determinations for the glutamate receptors, comprising non-NMDA and NMDA subtypes. The last decade has seen a rapid advance resulting in the first structures of Cys-loop receptors, related bacterial and molluscan homologs, and glutamate receptors, determined down to atomic resolution. This now provides a basis for determining not just the complete structures of these important receptor classes, but also for understanding how various domains and residues interact during agonist binding, receptor activation, and channel opening, including allosteric modulation. This article reviews our current understanding of these mechanisms for the Cys-loop and glutamate receptor families. PMID:22233560

Prototyping of Dental Structures Using Laser Milling

NASA Astrophysics Data System (ADS)

Andreev, A. O.; Kosenko, M. S.; Petrovskiy, V. N.; Mironov, V. D.

2016-02-01

The results of experimental studies of the effect of an ytterbium fiber laser radiation parameters on processing efficiency and quality of ZrO2 ceramics widely used in stomatology are presented. Laser operating conditions with optimum characteristics for obtaining high quality final surfaces and rapid material removal of dental structures are determined. The ability of forming thin-walled ceramic structures by laser milling technology (a minimum wall thickness of 50 μm) is demonstrated. The examples of three-dimensional dental structures created in computer 3D-models of human teeth using laser milling are shown.

Protein structure determination by exhaustive search of Protein Data Bank derived databases.

PubMed

Stokes-Rees, Ian; Sliz, Piotr

2010-12-14

Parallel sequence and structure alignment tools have become ubiquitous and invaluable at all levels in the study of biological systems. We demonstrate the application and utility of this same parallel search paradigm to the process of protein structure determination, benefitting from the large and growing corpus of known structures. Such searches were previously computationally intractable. Through the method of Wide Search Molecular Replacement, developed here, they can be completed in a few hours with the aide of national-scale federated cyberinfrastructure. By dramatically expanding the range of models considered for structure determination, we show that small (less than 12% structural coverage) and low sequence identity (less than 20% identity) template structures can be identified through multidimensional template scoring metrics and used for structure determination. Many new macromolecular complexes can benefit significantly from such a technique due to the lack of known homologous protein folds or sequences. We demonstrate the effectiveness of the method by determining the structure of a full-length p97 homologue from Trichoplusia ni. Example cases with the MHC/T-cell receptor complex and the EmoB protein provide systematic estimates of minimum sequence identity, structure coverage, and structural similarity required for this method to succeed. We describe how this structure-search approach and other novel computationally intensive workflows are made tractable through integration with the US national computational cyberinfrastructure, allowing, for example, rapid processing of the entire Structural Classification of Proteins protein fragment database.

One-Shot Determination of Residual Dipolar Couplings: Application to the Structural Discrimination of Small Molecules Containing Multiple Stereocenters.

PubMed

Castañar, Laura; Garcia, Manuela; Hellemann, Erich; Nolis, Pau; Gil, Roberto R; Parella, Teodor

2016-11-18

A novel approach for the fast and efficient structural discrimination of molecules containing multiple stereochemical centers is described. A robust J-resolved HSQC experiment affording highly resolved 1 J CH / 1 T CH splittings along the indirect dimension and homodecoupled 1 H signals in the detected dimension is proposed. The experiment enables in situ distinction of both isotropic and anisotropic components of molecules dissolved in compressed PMMA gels, allowing a rapid and direct one-shot determination of accurate residual dipolar coupling constants from a single NMR spectrum.

Magnetic Properties of Rapid Cooled FeCoB Based Alloys Produced by Injection Molding

NASA Astrophysics Data System (ADS)

Nabialek, M.; Jeż, B.; Jeż, K.; Pietrusiewicz, P.; Gruszka, K.; Błoch, K.; Gondro, J.; Rzącki, J.; Abdullah, M. M. A. B.; Sandu, A. V.; Szota, M.

2018-06-01

The paper presents the results of investigations of the structure and magnetic properties of massive rapid cooled Fe50-xCo20+xB20Cu1Nb9 alloys (where x = 0, 5). Massive alloys were made using the method of injecting a liquid alloy into a copper mold. Samples were obtained in the form of 0.5 mm thick plates. The structure of the obtained samples was examined using an X-ray diffractometer equipped with a CuKα lamp. The phase composition of the alloys formed was determined using the Match program. By using Sherrer’s dependence the grain sizes of the identified crystalline phases were estimated. Using the Faraday magnetic balance, the magnetization of samples as a function of temperature in the range from room temperature to 850K was measured. Magnetization of saturation and value of the coercive field for the prepared alloys were determined on the basis of magnetic hysteresis loop measurement using the LakeShore vibration magnetometer.

Photogrammetric Modeling and Image-Based Rendering for Rapid Virtual Environment Creation

DTIC Science & Technology

2004-12-01

area and different methods have been proposed. Pertinent methods include: Camera Calibration , Structure from Motion, Stereo Correspondence, and Image...Based Rendering 1.1.1 Camera Calibration Determining the 3D structure of a model from multiple views becomes simpler if the intrinsic (or internal...can introduce significant nonlinearities into the image. We have found that camera calibration is a straightforward process which can simplify the

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

Multicycle rapid thermal annealing optimization of Mg-implanted GaN: Evolution of surface, optical, and structural properties

NASA Astrophysics Data System (ADS)

Greenlee, Jordan D.; Feigelson, Boris N.; Anderson, Travis J.; Tadjer, Marko J.; Hite, Jennifer K.; Mastro, Michael A.; Eddy, Charles R.; Hobart, Karl D.; Kub, Francis J.

2014-08-01

The first step of a multi-cycle rapid thermal annealing process was systematically studied. The surface, structure, and optical properties of Mg implanted GaN thin films annealed at temperatures ranging from 900 to 1200 °C were investigated by Raman spectroscopy, photoluminescence, UV-visible spectroscopy, atomic force microscopy, and Nomarski microscopy. The GaN thin films are capped with two layers of in-situ metal organic chemical vapor deposition -grown AlN and annealed in 24 bar of N2 overpressure to avoid GaN decomposition. The crystal quality of the GaN improves with increasing annealing temperature as confirmed by UV-visible spectroscopy and the full widths at half maximums of the E2 and A1 (LO) Raman modes. The crystal quality of films annealed above 1100 °C exceeds the quality of the as-grown films. At 1200 °C, Mg is optically activated, which is determined by photoluminescence measurements. However, at 1200 °C, the GaN begins to decompose as evidenced by pit formation on the surface of the samples. Therefore, it was determined that the optimal temperature for the first step in a multi-cycle rapid thermal anneal process should be conducted at 1150 °C due to crystal quality and surface morphology considerations.

RELATIONSHIP OF MICROBIAL COMMUNITY STRUCTURE AND CARBON DYNAMICS IN SOILS FROM BRAZILIAN SAVANNAS

EPA Science Inventory

Fertilization is a widespread management practice in savanna areas of central Brazil (Cerrado) that are undergoing rapid agricultural land use changes. We conducted field and laboratory studies in soils with added fertilizers to determine the effect that fertilization of native a...

20180318 - Rapid collection of experimental physicochemical property data to inform various models and testing methods (ACS Spring)

EPA Science Inventory

In order to determine the potential toxicological effects, toxicokinetics, and route(s) of exposure for chemicals, their structures and corresponding physicochemical properties are required. With this data, the risk for thousands of environmental chemicals can be prioritized. How...

Rapid Self-healing Nanocomposite Hydrogel with Tunable Dynamic Mechanics

NASA Astrophysics Data System (ADS)

Li, Qiaochu; Mishra, Sumeet; Chapman, Brian; Chen, Pangkuan; Tracy, Joseph; Holten-Andersen, Niels

The macroscopic healing rate and efficiency in self-repairing hydrogel materials are largely determined by the dissociation dynamics of their polymer network, which is hardly achieved in a controllable manner. Inspired by mussel's adhesion chemistry, we developed a novel approach to assemble inorganic nanoparticles and catechol-decorated PEG polymer into a hydrogel network. When utilized as reversible polymer-particle crosslinks, catechol-metal coordination bonds yield a unique gel network with dynamic mechanics controlled directly by interfacial crosslink structure. Taking advantage of this structure-property relationship at polymer-particle interfaces, we designed a hierarchically structured hybrid gel with two distinct relaxation timescales. By tuning the relative contribution of the two relaxation modes, we are able to finely control the gel's dynamic mechanical behavior from a viscoelastic fluid to a stiff solid, yet preserving its rapid self-healing property without the need for external stimuli.

Research of Energy Substitution Strategy of China

NASA Astrophysics Data System (ADS)

Zhang, Lifeng; kai, Chen

For a long time, China's energy endowment structure determines the production structure and consumption structure of energy are coal-based.This situation is difficult to change for quite a long time. With the rapid economic growth, industrialization and urbanization, the demand for energy, especially for oil, natural gas will continue to increase. But the oil and gas supply can not meet the needs of rapid growth. The most direct way is to import, and imports will be charged by the international energy situation, and will affect energy and economic security. In view of our country abundant coal resources, we can consider to use coal substituting oil and natural gas to reduce dependence on foreign energy, to strengthen energy and economic security. Therefore, using translog production function, the text forecasts substitution elasticity and the marginal substitution rate between the capital, coal, oil and natural gas, and puts forward substitution program.

A novel representation for planning 3-D collision-free paths

NASA Technical Reports Server (NTRS)

Bonner, Susan; Kelley, Robert B.

1990-01-01

A new scheme for the representation of objects, the successive spherical approximation (SSA), facilitates the rapid planning of collision-free paths in a dynamic three-dimensional environment. The hierarchical nature of the SSA allows collisions to be determined efficiently while still providing an exact representation of objects. The rapidity with which collisions can be detected, less than 1 sec per environment object per path, makes it possible to use a generate-and-test path-planning strategy driven by human conceptual knowledge to determine collision-free paths in a matter of seconds on a Sun 3/180 computer. A hierarchy of rules, based on the concept of a free space cell, is used to find heuristically satisfying collision-free paths in a structured environment.

Rapid analysis of protein backbone resonance assignments using cryogenic probes, a distributed Linux-based computing architecture, and an integrated set of spectral analysis tools.

PubMed

Monleón, Daniel; Colson, Kimberly; Moseley, Hunter N B; Anklin, Clemens; Oswald, Robert; Szyperski, Thomas; Montelione, Gaetano T

2002-01-01

Rapid data collection, spectral referencing, processing by time domain deconvolution, peak picking and editing, and assignment of NMR spectra are necessary components of any efficient integrated system for protein NMR structure analysis. We have developed a set of software tools designated AutoProc, AutoPeak, and AutoAssign, which function together with the data processing and peak-picking programs NMRPipe and Sparky, to provide an integrated software system for rapid analysis of protein backbone resonance assignments. In this paper we demonstrate that these tools, together with high-sensitivity triple resonance NMR cryoprobes for data collection and a Linux-based computer cluster architecture, can be combined to provide nearly complete backbone resonance assignments and secondary structures (based on chemical shift data) for a 59-residue protein in less than 30 hours of data collection and processing time. In this optimum case of a small protein providing excellent spectra, extensive backbone resonance assignments could also be obtained using less than 6 hours of data collection and processing time. These results demonstrate the feasibility of high throughput triple resonance NMR for determining resonance assignments and secondary structures of small proteins, and the potential for applying NMR in large scale structural proteomics projects.

Soil microbial succession along a chronosequence on a High Arctic glacier foreland, Ny-Ålesund, Svalbard: 10 years' change

NASA Astrophysics Data System (ADS)

Yoshitake, Shinpei; Uchida, Masaki; Iimura, Yasuo; Ohtsuka, Toshiyuki; Nakatsubo, Takayuki

2018-06-01

Rapid glacial retreat in the High Arctic causes the expansion of new habitats, but the successional trajectories of soil microbial communities are not fully understood. We examined microbial succession along a chronosequence twice with a 10-year interval in a High Arctic glacier foreland. Soil samples were collected from five study sites with different ages and phospholipid fatty acids analysis was conducted to investigate the microbial biomass and community structure. Microbial biomass did not differ significantly between the two sampling times but tended to increase with the chronosequence and showed a significant correlation with soil carbon (C) and nitrogen (N) content. Microbial community structure clearly differed along the chronosequence and was correlated with C and N content. The largest shift in community structure over 10 years was observed in the newly exposed sites after deglaciation. The accumulation of soil organic matter was regarded as an important determinant both of microbial biomass and community structure over the successional period. In contrast, the initial microbial community on the newly exposed soil changed rapidly even in the High Arctic, suggesting that some key soil processes such as C and N cycling can also shift within the relatively short period after rapid glacial retreat.

Shock loading and release behavior of silicon nitride

NASA Astrophysics Data System (ADS)

Kawai, N.; Tsuru, T.; Hidaka, N.; Liu, X.; Mashimo, T.

2017-01-01

Shock-reshock and shock-release experiments were performed on silicon nitride ceramics above and below its phase transition pressure. Experimental results clearly show the occurrence of elastic-plastic transition and phase transition during initial shock loading. The HEL and phase transition stress are determined as 11.6 and 34.5 GPa, respectively. Below the phase transition stress, the reshock profile consists of the single shock with short rise time, while the release profile shows the gradual release followed by rapid one. Above phase transition stress, reshock and release behavior varies with the initial shock stress. In the case of reshock and release from about 40 GPa, the reshock structure is considerably dispersed, while the release structure shows rapid release. In the reshock profile from about 50 GPa, the formation of the shock wave with the small ramped precursor is observed. And, the release response from same shocked condition shows initial gradual release and subsequent quite rapid one. These results would provide the information about how phase transformation kinetics effects on the reshock and release behavior.

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.

Development of Advanced Methods of Structural and Trajectory Analysis for Transport Aircraft

NASA Technical Reports Server (NTRS)

Ardema, Mark D.

1996-01-01

In this report the author describes: (1) development of advanced methods of structural weight estimation, and (2) development of advanced methods of flight path optimization. A method of estimating the load-bearing fuselage weight and wing weight of transport aircraft based on fundamental structural principles has been developed. This method of weight estimation represents a compromise between the rapid assessment of component weight using empirical methods based on actual weights of existing aircraft and detailed, but time-consuming, analysis using the finite element method. The method was applied to eight existing subsonic transports for validation and correlation. Integration of the resulting computer program, PDCYL, has been made into the weights-calculating module of the AirCraft SYNThesis (ACSYNT) computer program. ACSYNT bas traditionally used only empirical weight estimation methods; PDCYL adds to ACSYNT a rapid, accurate means of assessing the fuselage and wing weights of unconventional aircraft. PDCYL also allows flexibility in the choice of structural concept, as well as a direct means of determining the impact of advanced materials on structural weight.

Structure and Dissipation Characteristics of an Electron Diffusion Region Observed by MMS During a Rapid, Normal-Incidence Magnetopause Crossing

NASA Astrophysics Data System (ADS)

Torbert, R. B.; Burch, J. L.; Argall, M. R.; Alm, L.; Farrugia, C. J.; Forbes, T. G.; Giles, B. L.; Rager, A.; Dorelli, J.; Strangeway, R. J.; Ergun, R. E.; Wilder, F. D.; Ahmadi, N.; Lindqvist, P.-A.; Khotyaintsev, Y.

2017-12-01

On 22 October 2016, the Magnetospheric Multiscale (MMS) spacecraft encountered the electron diffusion region (EDR) when the magnetosheath field was southward, and there were signatures of fast reconnection, including flow jets, Hall fields, and large power dissipation. One rapid, normal-incidence crossing, during which the EDR structure was almost stationary in the boundary frame, provided an opportunity to observe the spatial structure for the zero guide field case of magnetic reconnection. The reconnection electric field was determined unambiguously to be 2-3 mV/m. There were clear signals of fluctuating parallel electric fields, up to 6 mV/m on the magnetosphere side of the diffusion region, associated with a Hall-like parallel current feature on the electron scale. The width of the main EDR structure was determined to be 2 km (1.8 de). Although the MMS spacecraft were in their closest tetrahedral separation of 8 km, the divergences and curls for these thin current structures could therefore not be computed in the usual manner. A method is developed to determine these quantities on a much smaller scale and applied to compute the normal component of terms in the generalized Ohm's law for the positions of each individual spacecraft (not a barocentric average). Although the gradient pressure term has a qualitative dependence that follows the observed variation of E + Ve × B, the quantitative magnitude of these terms differs by more than a factor of 2, which is shown to be greater than the respective errors. Thus, future research is required to find the manner in which Ohm's law is balanced.

SAIL--stereo-array isotope labeling.

PubMed

Kainosho, Masatsune; Güntert, Peter

2009-11-01

Optimal stereospecific and regiospecific labeling of proteins with stable isotopes enhances the nuclear magnetic resonance (NMR) method for the determination of the three-dimensional protein structures in solution. Stereo-array isotope labeling (SAIL) offers sharpened lines, spectral simplification without loss of information and the ability to rapidly collect and automatically evaluate the structural restraints required to solve a high-quality solution structure for proteins up to twice as large as before. This review gives an overview of stable isotope labeling methods for NMR spectroscopy with proteins and provides an in-depth treatment of the SAIL technology.

Helping safeguard Veterans Affairs' hospital buildings by advanced earthquake monitoring

USGS Publications Warehouse

Kalkan, Erol; Banga, Krishna; Ulusoy, Hasan S.; Fletcher, Jon Peter B.; Leith, William S.; Blair, James L.

2012-01-01

In collaboration with the U.S. Department of Veterans Affairs (VA), the National Strong Motion Project of the U.S. Geological Survey has recently installed sophisticated seismic systems that will monitor the structural integrity of hospital buildings during earthquake shaking. The new systems have been installed at more than 20 VA medical campuses across the country. These monitoring systems, which combine sensitive accelerometers and real-time computer calculations, are capable of determining the structural health of each structure rapidly after an event, helping to ensure the safety of patients and staff.

Rapid experimental SAD phasing and hot-spot identification with halogenated fragments

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

Bauman, Joseph D.; Harrison, Jerry Joe E. K.; Arnold, Eddy

2016-01-01

Through X-ray crystallographic fragment screening, 4-bromopyrazole was discovered to be a `magic bullet' that is capable of binding at many of the ligand `hot spots' found in HIV-1 reverse transcriptase (RT). The binding locations can be in pockets that are `hidden' in the unliganded crystal form, allowing rapid identification of these sites forin silicoscreening. In addition to hot-spot identification, this ubiquitous yet specific binding provides an avenue for X-ray crystallographic phase determination, which can be a significant bottleneck in the determination of the structures of novel proteins. The anomalous signal from 4-bromopyrazole or 4-iodopyrazole was sufficient to determine the structuresmore » of three proteins (HIV-1 RT, influenza A endonuclease and proteinase K) by single-wavelength anomalous dispersion (SAD) from single crystals. Both compounds are inexpensive, readily available, safe and very soluble in DMSO or water, allowing efficient soaking into crystals.« less

Cranial neural crest recycle surface integrins in a substratum-dependent manner to promote rapid motility.

PubMed

Strachan, Lauren R; Condic, Maureen L

2004-11-08

Cell migration is essential for proper development of numerous structures derived from embryonic neural crest cells (NCCs). Although the migratory pathways of NCCs have been determined, the molecular mechanisms regulating NCC motility remain unclear. NCC migration is integrin dependent, and recent work has shown that surface expression levels of particular integrin alpha subunits are important determinants of NCC motility in vitro. Here, we provide evidence that rapid cranial NCC motility on laminin requires integrin recycling. NCCs showed both ligand- and receptor-specific integrin regulation in vitro. On laminin, NCCs accumulated internalized laminin but not fibronectin receptors over 20 min, whereas on fibronectin neither type of receptor accumulated internally beyond 2 min. Internalized laminin receptors colocalized with receptor recycling vesicles and were subsequently recycled back to the cell surface. Blocking receptor recycling with bafilomycin A inhibited NCC motility on laminin, indicating that substratum-dependent integrin recycling is essential for rapid cranial neural crest migration.

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

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...

Skeletal and dental effects of rapid maxillary expansion assessed through three-dimensional imaging: A multicenter study.

PubMed

Luebbert, Joshua; Ghoneima, Ahmed; Lagravère, Manuel O

2016-03-01

The aim of this study was to determine the skeletal and dental changes in rapid maxillary expansion treatments in two different populations assessed through cone-beam computer tomography (CBCT). Twenty-one patients from Edmonton, Canada and 16 patients from Cairo, Egypt with maxillary transverse deficiency (11-17 years old) were treated with a tooth-borne maxillary expander (Hyrax). CBCTs were obtained from each patient at two time points (initial T1 and at removal of appliance at 3-6 months T2). CBCTs were analyzed using AVIZO software and landmarks were placed on skeletal and dental anatomical structures on the cranial base, maxilla and mandible. Descriptive statistics, intraclass correlation coefficients and one-way ANOVA analysis were used to determine if there were skeletal and dental changes and if these changes were statistically different between both populations. Descriptive statistics show that dental changes were larger than skeletal changes for both populations. Skeletal and dental changes between populations were not statistically different (P<0.05) from each other with the exception of the upper incisor proclination being larger in the Indiana group (P>0.05). Rapid maxillary expansion treatments in different populations demonstrate similar skeletal and dental changes. These changes are greater on the dental structures compared to the skeletal ones in a 4:1 ratio. Copyright © 2015 CEO. Published by Elsevier Masson SAS. All rights reserved.

Multicycle rapid thermal annealing optimization of Mg-implanted GaN: Evolution of surface, optical, and structural properties

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

Greenlee, Jordan D., E-mail: jordan.greenlee.ctr@nrl.navy.mil; Feigelson, Boris N.; Anderson, Travis J.

2014-08-14

The first step of a multi-cycle rapid thermal annealing process was systematically studied. The surface, structure, and optical properties of Mg implanted GaN thin films annealed at temperatures ranging from 900 to 1200 °C were investigated by Raman spectroscopy, photoluminescence, UV-visible spectroscopy, atomic force microscopy, and Nomarski microscopy. The GaN thin films are capped with two layers of in-situ metal organic chemical vapor deposition -grown AlN and annealed in 24 bar of N{sub 2} overpressure to avoid GaN decomposition. The crystal quality of the GaN improves with increasing annealing temperature as confirmed by UV-visible spectroscopy and the full widths at halfmore » maximums of the E{sub 2} and A{sub 1} (LO) Raman modes. The crystal quality of films annealed above 1100 °C exceeds the quality of the as-grown films. At 1200 °C, Mg is optically activated, which is determined by photoluminescence measurements. However, at 1200 °C, the GaN begins to decompose as evidenced by pit formation on the surface of the samples. Therefore, it was determined that the optimal temperature for the first step in a multi-cycle rapid thermal anneal process should be conducted at 1150 °C due to crystal quality and surface morphology considerations.« less

Automated structure determination of proteins with the SAIL-FLYA NMR method.

PubMed

Takeda, Mitsuhiro; Ikeya, Teppei; Güntert, Peter; Kainosho, Masatsune

2007-01-01

The labeling of proteins with stable isotopes enhances the NMR method for the determination of 3D protein structures in solution. Stereo-array isotope labeling (SAIL) provides an optimal stereospecific and regiospecific pattern of stable isotopes that yields sharpened lines, spectral simplification without loss of information, and the ability to collect rapidly and evaluate fully automatically the structural restraints required to solve a high-quality solution structure for proteins up to twice as large as those that can be analyzed using conventional methods. Here, we describe a protocol for the preparation of SAIL proteins by cell-free methods, including the preparation of S30 extract and their automated structure analysis using the FLYA algorithm and the program CYANA. Once efficient cell-free expression of the unlabeled or uniformly labeled target protein has been achieved, the NMR sample preparation of a SAIL protein can be accomplished in 3 d. A fully automated FLYA structure calculation can be completed in 1 d on a powerful computer system.

Perspective: Role of structure prediction in materials discovery and design

NASA Astrophysics Data System (ADS)

Needs, Richard J.; Pickard, Chris J.

2016-05-01

Materials informatics owes much to bioinformatics and the Materials Genome Initiative has been inspired by the Human Genome Project. But there is more to bioinformatics than genomes, and the same is true for materials informatics. Here we describe the rapidly expanding role of searching for structures of materials using first-principles electronic-structure methods. Structure searching has played an important part in unraveling structures of dense hydrogen and in identifying the record-high-temperature superconducting component in hydrogen sulfide at high pressures. We suggest that first-principles structure searching has already demonstrated its ability to determine structures of a wide range of materials and that it will play a central and increasing part in materials discovery and design.

Structural Insights into Bound Water in Crystalline Amino Acids: Experimental and Theoretical (17)O NMR.

PubMed

Michaelis, Vladimir K; Keeler, Eric G; Ong, Ta-Chung; Craigen, Kimberley N; Penzel, Susanne; Wren, John E C; Kroeker, Scott; Griffin, Robert G

2015-06-25

We demonstrate here that the (17)O NMR properties of bound water in a series of amino acids and dipeptides can be determined with a combination of nonspinning and magic-angle spinning experiments using a range of magnetic field strengths from 9.4 to 21.1 T. Furthermore, we propose a (17)O chemical shift fingerprint region for bound water molecules in biological solids that is well outside the previously determined ranges for carbonyl, carboxylic, and hydroxyl oxygens, thereby offering the ability to resolve multiple (17)O environments using rapid one-dimensional NMR techniques. Finally, we compare our experimental data against quantum chemical calculations using GIPAW and hybrid-DFT, finding intriguing discrepancies between the electric field gradients calculated from structures determined by X-ray and neutron diffraction.

An unusual type of polymorphism in a liquid crystal

DOE PAGES

Li, Lin; Salamonczyk, Miroslaw; Shadpour, Sasan; ...

2018-02-19

Polymorphism is a remarkable concept in chemistry, materials science, computer science, and biology. Whether it is the ability of a material to exist in two or more crystal structures, a single interface connecting to two different entities, or alternative phenotypes of an organism, polymorphism determines function and properties. In materials science, polymorphism can be found in an impressively wide range of materials, including crystalline materials, minerals, metals, alloys, and polymers. Here in this paper we report on polymorphism in a liquid crystal. A bent-core liquid crystal with a single chiral side chain forms two structurally and morphologically significantly different liquidmore » crystal phases solely depending on the cooling rate from the isotropic liquid state. On slow cooling, the thermodynamically more stable oblique columnar phase forms, and on rapid cooling, a not heretofore reported helical microfilament phase. Since structure determines function and properties, the structural color for these phases also differs.« less

An unusual type of polymorphism in a liquid crystal

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

Li, Lin; Salamonczyk, Miroslaw; Shadpour, Sasan

Polymorphism is a remarkable concept in chemistry, materials science, computer science, and biology. Whether it is the ability of a material to exist in two or more crystal structures, a single interface connecting to two different entities, or alternative phenotypes of an organism, polymorphism determines function and properties. In materials science, polymorphism can be found in an impressively wide range of materials, including crystalline materials, minerals, metals, alloys, and polymers. Here in this paper we report on polymorphism in a liquid crystal. A bent-core liquid crystal with a single chiral side chain forms two structurally and morphologically significantly different liquidmore » crystal phases solely depending on the cooling rate from the isotropic liquid state. On slow cooling, the thermodynamically more stable oblique columnar phase forms, and on rapid cooling, a not heretofore reported helical microfilament phase. Since structure determines function and properties, the structural color for these phases also differs.« less

Free-space laser communication system with rapid acquisition based on astronomical telescopes.

PubMed

Wang, Jianmin; Lv, Junyi; Zhao, Guang; Wang, Gang

2015-08-10

The general structure of a free-space optical (FSO) communication system based on astronomical telescopes is proposed. The light path for astronomical observation and for communication can be easily switched. A separate camera is used as a star sensor to determine the pointing direction of the optical terminal's antenna. The new system exhibits rapid acquisition and is widely applicable in various astronomical telescope systems and wavelengths. We present a detailed analysis of the acquisition time, which can be decreased by one order of magnitude compared with traditional optical communication systems. Furthermore, we verify software algorithms and tracking accuracy.

Identification and classification of cathinone unknowns by statistical analysis processing of direct analysis in real time-high resolution mass spectrometry-derived "neutral loss" spectra.

PubMed

Fowble, Kristen L; Shepard, Jason R E; Musah, Rabi A

2018-03-01

An approach to the rapid determination of the structures of novel synthetic cathinone designer drugs, also known as bath salts, is reported. While cathinones fragment so extensively by electron impact mass spectrometry that their mass spectra often cannot be used to identify the structure, collision-induced dissociation (CID) direct analysis in real time-high resolution mass spectrometry (DART-HRMS) experiments furnished spectra that provided diagnostic fragmentation patterns for the analyzed cathinones. From this data, neutral loss spectra, which reflect the presence of specific chemical moieties, could be acquired. These spectra showed striking similarities between cathinones sharing structural features such as pyrrolidine rings and methylenedioxy moieties. Principle component analysis (PCA) of the neutral loss spectra of nine synthetic cathinones of various types including ethcathinones, those containing a methylenedioxy moiety appended to the benzene ring, and pyrrolidine-containing structures, illustrated that cathinones falling within the same class clustered together and could be distinguished from those of other classes. Furthermore, hierarchical clustering analysis of the neutral loss data of a model set derived from 44 synthetic cathinones, furnished a dendrogram in which structurally similar cathinones clustered together. The ability of this model system to facilitate structure determination was tested using 4-fluoroethcathinone, 3,4-methylenedioxy-α-pyrrolidinohexanophenone (MDPHP), and ethylone, which fall into the ethcathinone, pyrrolidine-containing, and methylenedioxy-containing subclasses respectively. The results showed that their neutral loss spectra correctly fell within the ethcathinone, pyrrolidine-containing and methylenedioxy-containing cathinone clades of the dendrogram, and that the neutral loss information could be used to infer the structures of these compounds. The analysis and data processing steps are rapid and samples can be analyzed in their native form without any sample processing steps. The robustness of the dendrogram dataset can be readily increased by continued addition of newly discovered structures. The approach can be broadly applied to structure determination of unknowns, and would be particularly useful for analyses where sample amounts are limited. Copyright © 2017 Elsevier B.V. All rights reserved.

Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations

PubMed Central

Brodie, Nicholas I.; Popov, Konstantin I.; Petrotchenko, Evgeniy V.; Dokholyan, Nikolay V.; Borchers, Christoph H.

2017-01-01

We present an integrated experimental and computational approach for de novo protein structure determination in which short-distance cross-linking data are incorporated into rapid discrete molecular dynamics (DMD) simulations as constraints, reducing the conformational space and achieving the correct protein folding on practical time scales. We tested our approach on myoglobin and FK506 binding protein—models for α helix–rich and β sheet–rich proteins, respectively—and found that the lowest-energy structures obtained were in agreement with the crystal structure, hydrogen-deuterium exchange, surface modification, and long-distance cross-linking validation data. Our approach is readily applicable to other proteins with unknown structures. PMID:28695211

Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations.

PubMed

Brodie, Nicholas I; Popov, Konstantin I; Petrotchenko, Evgeniy V; Dokholyan, Nikolay V; Borchers, Christoph H

2017-07-01

We present an integrated experimental and computational approach for de novo protein structure determination in which short-distance cross-linking data are incorporated into rapid discrete molecular dynamics (DMD) simulations as constraints, reducing the conformational space and achieving the correct protein folding on practical time scales. We tested our approach on myoglobin and FK506 binding protein-models for α helix-rich and β sheet-rich proteins, respectively-and found that the lowest-energy structures obtained were in agreement with the crystal structure, hydrogen-deuterium exchange, surface modification, and long-distance cross-linking validation data. Our approach is readily applicable to other proteins with unknown structures.

Quantifying Hydrogen Bond Cooperativity in Water: VRT Spectroscopy of the Water Tetramer

NASA Astrophysics Data System (ADS)

Cruzan, J. D.; Braly, L. B.; Liu, Kun; Brown, M. G.; Loeser, J. G.; Saykally, R. J.

1996-01-01

Measurement of the far-infrared vibration-rotation tunneling spectrum of the perdeuterated water tetramer is described. Precisely determined rotational constants and relative intensity measurements indicate a cyclic quasi-planar minimum energy structure, which is in agreement with recent ab initio calculations. The O-O separation deduced from the data indicates a rapid exponential convergence to the ordered bulk value with increasing cluster size. Observed quantum tunneling splittings are interpreted in terms of hydrogen bond rearrangements connecting two degenerate structures.

Measurement of total acid number (TAN) and TAN boiling point distribution in petroleum products by electrospray ionization mass spectrometry.

PubMed

Qian, Kuangnan; Edwards, Kathleen E; Dechert, Gary J; Jaffe, Stephen B; Green, Larry A; Olmstead, William N

2008-02-01

We report a new method for rapid measurement of total acid number (TAN) and TAN boiling point (BP) distribution for petroleum crude and products. The technology is based on negative ion electrospray ionization mass spectrometry (ESI-MS) for selective ionization of petroleum acid and quantification of acid structures and molecular weight distributions. A chip-based nanoelectrospray system enables microscale (<200 mg) and higher throughput (20 samples/h) measurement. Naphthenic acid structures were assigned based on nominal masses of a set of predefined acid structures. Stearic acid is used as an internal standard to calibrate ESI-MS response factors for quantification purposes. With the use of structure-property correlations, boiling point distributions of TAN values can be calculated from the composition. The rapid measurement of TAN BP distributions by ESI is demonstrated for a series of high-TAN crudes and distillation cuts. TAN values determined by the technique agree well with those by the titration method. The distributed properties compare favorably with those measured by distillation and measurement of TAN of corresponding cuts.

To Keep or Not to Keep? The Question of Crystallographic Waters for Enzyme Simulations in Organic Solvent

PubMed Central

Dahanayake, Jayangika N.; Gautam, Devaki N.; Verma, Rajni; Mitchell-Koch, Katie R.

2016-01-01

The use of enzymes in non-aqueous solvents expands the use of biocatalysts to hydrophobic substrates, with the ability to tune selectivity of reactions through solvent selection. Non-aqueous enzymology also allows for fundamental studies on the role of water and other solvents in enzyme structure, dynamics, and function. Molecular dynamics simulations serve as a powerful tool in this area, providing detailed atomic information about the effect of solvents on enzyme properties. However, a common protocol for non-aqueous enzyme simulations does not exist. If you want to simulate enzymes in non-aqueous solutions, how many and which crystallographic waters do you keep? In the present work, this question is addressed by determining which crystallographic water molecules lead most quickly to an equilibrated protein structure. Five different methods of selecting and keeping crystallographic waters are used in order to discover which crystallographic waters lead the protein structure to reach an equilibrated structure more rapidly in organic solutions. It is found that buried waters contribute most to rapid equilibration in organic solvent, with slow-diffusing waters giving similar results. PMID:27403032

Novel micronisation β-carotene using rapid expansion supercritical solution with co-solvent

NASA Astrophysics Data System (ADS)

Kien, Le Anh

2017-09-01

Rapid expansion of supercritical solution (RESS) is the most common approach of pharmaceutical pacticle forming methods using supercritical fluids. The RESS method is a technology producing a small solid product with a very narrow particle size distribution, organic solvent-free particles. This process is also simple and easy to control the operating parameters in comparision with other ways based on supercritical techniques. In this study, β-carotene, a strongly colored red-orange pigment abundant in plants and fruits, has been forming by RESS. In addition, the size and morphology effect of four different RESS parameters including co-solvent, extraction temperature, and extraction pressure and expansion nozzle temperature has surveyed. The particle size distribution has been determined by using laser diffraction experiment. SEM has conducted to analyze the surface structure, DSC and FTIR for thermal and chemical structure analysis.

Quantitative Restoration of the Evolution of Mantle Structures Using Data Assimilation

NASA Astrophysics Data System (ADS)

Ismail-Zadeh, A.; Schubert, G.; Tsepelev, I.

2008-12-01

Rapid progress in imaging deep Earth structures and in studies of physical and chemical properties of mantle rocks facilitates research in assimilation of data related to mantle dynamics. We present a quantitative approach to assimilation of geophysical and geodetic data, which allows for incorporating observations and unknown initial conditions for mantle temperature and flow into a three-dimensional dynamic model in order to determine the initial conditions in the geological past. Once the conditions are determined the evolution of mantle structures can be restore backward in time. We apply data assimilation techniques to model the evolution of mantle plumes and lithospheric slabs. We show that the geometry of the mantle structures changes with time diminishing the degree of surface curvature of the structures, because the heat conduction smoothes the complex thermal surfaces of mantle bodies with time. Present seismic tomography images of mantle structures do not allow definition of the sharp shapes of these structures. Assimilation of mantle temperature and flow to the geological past instead provides a quantitative tool to restore thermal shapes of prominent structures in the past from their diffusive shapes at present.

Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)

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

Hura, Greg L.; Menon, Angeli L.; Hammel, Michal

2009-07-20

We present an efficient pipeline enabling high-throughput analysis of protein structure in solution with small angle X-ray scattering (SAXS). Our SAXS pipeline combines automated sample handling of microliter volumes, temperature and anaerobic control, rapid data collection and data analysis, and couples structural analysis with automated archiving. We subjected 50 representative proteins, mostly from Pyrococcus furiosus, to this pipeline and found that 30 were multimeric structures in solution. SAXS analysis allowed us to distinguish aggregated and unfolded proteins, define global structural parameters and oligomeric states for most samples, identify shapes and similar structures for 25 unknown structures, and determine envelopes formore » 41 proteins. We believe that high-throughput SAXS is an enabling technology that may change the way that structural genomics research is done.« less

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.

Shock loading and release behavior of silicon nitride

NASA Astrophysics Data System (ADS)

Kawai, Nobuaki; Tsuru, Taiki; Hidaka, Naoto; Liu, Xun; Mashimo, Tsutomu

2015-06-01

Shock-reshock and shock-release experiments were performed on silicon nitride ceramics above and below its phase transition pressure. Experimental results clearly show the occurrence of elastic-plastic transition and phase transition during initial shock loading. The HEL and phase transition stress are determined as 11.6 GPa and 34.5 GPa, respectively. Below the phase transition point, the reshock profile consists of the single shock with short rise time, while the release profile shows the gradual release followed by more rapid one. Above the phase transition point, reshock and release behavior varies with the initial shock stress. In the case of reshock and release from about 40 GPa, the reshock structure is considerably dispersed, while the release structure shows rapid release. In the reshock profile from about 50 GPa, the formation of the shock wave with the small ramped precursor is observed. And, the release response from same condition shows initial gradual release and subsequent quite rapid one. These results would provide the information about how phase transformation kinetics effects on the reshock and release behavior.

The development of structure in the expanding universe

NASA Technical Reports Server (NTRS)

Silk, J.; White, S. D.

1978-01-01

A model for clustering in an expanding universe is developed based on an application of the coagulation equation to the collision and aggregation of bound condensations. While the growth rate of clustering is determined by the rate at which density fluctuations reach the nonlinear regime and therefore depends on the initial fluctuation spectrum, the mass spectrum rapidly approaches a self-similar limiting form. This form is determined by the tidal processes which lead to the merging of condensations, and is not dependent on initial conditions.

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.

SIMS: A Hybrid Method for Rapid Conformational Analysis

PubMed Central

Gipson, Bryant; Moll, Mark; Kavraki, Lydia E.

2013-01-01

Proteins are at the root of many biological functions, often performing complex tasks as the result of large changes in their structure. Describing the exact details of these conformational changes, however, remains a central challenge for computational biology due the enormous computational requirements of the problem. This has engendered the development of a rich variety of useful methods designed to answer specific questions at different levels of spatial, temporal, and energetic resolution. These methods fall largely into two classes: physically accurate, but computationally demanding methods and fast, approximate methods. We introduce here a new hybrid modeling tool, the Structured Intuitive Move Selector (sims), designed to bridge the divide between these two classes, while allowing the benefits of both to be seamlessly integrated into a single framework. This is achieved by applying a modern motion planning algorithm, borrowed from the field of robotics, in tandem with a well-established protein modeling library. sims can combine precise energy calculations with approximate or specialized conformational sampling routines to produce rapid, yet accurate, analysis of the large-scale conformational variability of protein systems. Several key advancements are shown, including the abstract use of generically defined moves (conformational sampling methods) and an expansive probabilistic conformational exploration. We present three example problems that sims is applied to and demonstrate a rapid solution for each. These include the automatic determination of “active” residues for the hinge-based system Cyanovirin-N, exploring conformational changes involving long-range coordinated motion between non-sequential residues in Ribose-Binding Protein, and the rapid discovery of a transient conformational state of Maltose-Binding Protein, previously only determined by Molecular Dynamics. For all cases we provide energetic validations using well-established energy fields, demonstrating this framework as a fast and accurate tool for the analysis of a wide range of protein flexibility problems. PMID:23935893

Transcript Lifetime Is Balanced between Stabilizing Stem-Loop Structures and Degradation-Promoting Polyadenylation in Plant Mitochondria

PubMed Central

Kuhn, Josef; Tengler, Ulrike; Binder, Stefan

2001-01-01

To determine the influence of posttranscriptional modifications on 3′ end processing and RNA stability in plant mitochondria, pea atp9 and Oenothera atp1 transcripts were investigated for the presence and function of 3′ nonencoded nucleotides. A 3′ rapid amplification of cDNA ends approach initiated at oligo(dT)-adapter primers finds the expected poly(A) tails predominantly attached within the second stem or downstream of the double stem-loop structures at sites of previously mapped 3′ ends. Functional studies in a pea mitochondrial in vitro processing system reveal a rapid removal of the poly(A) tails up to termini at the stem-loop structure but little if any influence on further degradation of the RNA. In contrast 3′ poly(A) tracts at RNAs without such stem-loop structures significantly promote total degradation in vitro. To determine the in vivo identity of 3′ nonencoded nucleotides more accurately, pea atp9 transcripts were analyzed by a direct anchor primer ligation-reverse transcriptase PCR approach. This analysis identified maximally 3-nucleotide-long nonencoded extensions most frequently of adenosines combined with cytidines. Processing assays with substrates containing homopolymer stretches of different lengths showed that 10 or more adenosines accelerate RNA processivity, while 3 adenosines have no impact on RNA life span. Thus polyadenylation can generally stimulate the decay of RNAs, but processivity of degradation is almost annihilated by the stabilizing effect of the stem-loop structures. These antagonistic actions thus result in the efficient formation of 3′ processed and stable transcripts. PMID:11154261

Mapping the universe in three dimensions

PubMed Central

Haynes, Martha P.

1996-01-01

The determination of the three-dimensional layout of galaxies is critical to our understanding of the evolution of galaxies and the structures in which they lie, to our determination of the fundamental parameters of cosmology, and to our understanding of both the past and future histories of the universe at large. The mapping of the large scale structure in the universe via the determination of galaxy red shifts (Doppler shifts) is a rapidly growing industry thanks to technological developments in detectors and spectrometers at radio and optical wavelengths. First-order application of the red shift-distance relation (Hubble’s law) allows the analysis of the large-scale distribution of galaxies on scales of hundreds of megaparsecs. Locally, the large-scale structure is very complex but the overall topology is not yet clear. Comparison of the observed red shifts with ones expected on the basis of other distance estimates allows mapping of the gravitational field and the underlying total density distribution. The next decade holds great promise for our understanding of the character of large-scale structure and its origin. PMID:11607714

Mapping the universe in three dimensions.

PubMed

Haynes, M P

1996-12-10

The determination of the three-dimensional layout of galaxies is critical to our understanding of the evolution of galaxies and the structures in which they lie, to our determination of the fundamental parameters of cosmology, and to our understanding of both the past and future histories of the universe at large. The mapping of the large scale structure in the universe via the determination of galaxy red shifts (Doppler shifts) is a rapidly growing industry thanks to technological developments in detectors and spectrometers at radio and optical wavelengths. First-order application of the red shift-distance relation (Hubble's law) allows the analysis of the large-scale distribution of galaxies on scales of hundreds of megaparsecs. Locally, the large-scale structure is very complex but the overall topology is not yet clear. Comparison of the observed red shifts with ones expected on the basis of other distance estimates allows mapping of the gravitational field and the underlying total density distribution. The next decade holds great promise for our understanding of the character of large-scale structure and its origin.

Three-dimensional imaging of nanoscale materials by using coherent x-rays

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

Miao, Jianwei

X-ray crystallography is currently the primary methodology used to determine the 3D structure of materials and macromolecules. However, many nanostructures, disordered materials, biomaterials, hybrid materials and biological specimens are noncrystalline and, hence, their structures are not accessible by X-ray crystallography. Probing these structures therefore requires the employment of different approaches. A very promising technique currently under rapid development is X-ray diffraction microscopy (or lensless imaging), in which the coherent X-ray diffraction pattern of a noncrystalline specimen is measured and then directly phased to obtain a high-resolution image. Through the DOE support over the past three years, we have applied X-raymore » diffraction microscopy to quantitative imaging of GaN quantum dot particles, and revealed the internal GaN-Ga2O3 core shell structure in three dimensions. By exploiting the abrupt change in the scattering cross-section near electronic resonances, we carried out the first experimental demonstration of resonant X-ray diffraction microscopy for element specific imaging. We performed nondestructive and quantitative imaging of buried Bi structures inside a Si crystal by directly phasing coherent X-ray diffraction patterns acquired below and above the Bi M5 edge. We have also applied X-ray diffraction microscopy to nondestructive imaging of mineral crystals inside biological composite materials - intramuscular fish bone - at the nanometer scale resolution. We identified mineral crystals in collagen fibrils at different stages of mineralization and proposed a dynamic mechanism to account for the nucleation and growth of mineral crystals in the collagen matrix. In addition, we have also discovered a novel 3D imaging modality, denoted ankylography, which allows for complete 3D structure determination without the necessity of sample titling or scanning. We showed that when the diffraction pattern of a finite object is sampled at a sufficiently fine scale on the Ewald sphere, the 3D structure of the object is determined by the 2D spherical pattern. We confirmed the theoretical analysis by performing 3D numerical reconstructions of a sodium silicate glass structure at 2 A resolution from a 2D spherical diffraction pattern alone. As X-ray free electron lasers are under rapid development worldwide, ankylography may open up a new horizon to obtain the 3D structure of a non-crystalline specimen from a single pulse and allow time-resolved 3D structure determination of disordered materials.« less

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

Rapid optical determination of β-lactamase and antibiotic activity

PubMed Central

2014-01-01

Background The absence of rapid tests evaluating antibiotic susceptibility results in the empirical prescription of antibiotics. This can lead to treatment failures due to escalating antibiotic resistance, and also furthers the emergence of drug-resistant bacteria. This study reports a rapid optical method to detect β-lactamase and thereby assess activity of β-lactam antibiotics, which could provide an approach for targeted prescription of antibiotics. The methodology is centred on a fluorescence quenching based probe (β-LEAF – β-Lactamase Enzyme Activated Fluorophore) that mimics the structure of β-lactam antibiotics. Results The β-LEAF assay was performed for rapid determination of β-lactamase production and activity of β-lactam antibiotic (cefazolin) on a panel of Staphylococcus aureus ATCC strains and clinical isolates. Four of the clinical isolates were determined to be lactamase producers, with the capacity to inactivate cefazolin, out of the twenty-five isolates tested. These results were compared against gold standard methods, nitrocefin disk test for β-lactamase detection and disk diffusion for antibiotic susceptibility, showing results to be largely consistent. Furthermore, in the sub-set of β-lactamase producers, it was demonstrated and validated that multiple antibiotics (cefazolin, cefoxitin, cefepime) could be assessed simultaneously to predict the antibiotic that would be most active for a given bacterial isolate. Conclusions The study establishes the rapid β-LEAF assay for β-lactamase detection and prediction of antibiotic activity using S. aureus clinical isolates. Although the focus in the current study is β-lactamase-based resistance, the overall approach represents a broad diagnostic platform. In the long-term, these studies form the basis for the development of assays utilizing a broader variety of targets, pathogens and drugs. PMID:24708478

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

Wasielewski, M.R.; Gast, P.; Norris, J.R.

Photoexcitation of the reaction center protein from purple photosynthetic bacteria results in rapid (< 5 ps) formation of a radical pair, P/sup F/ composed of an oxidized bacteriochlorophyll a dimer, P/sup +/ and a reduced bacteriopheophytin a, I/sup -/. The recent crystallization of the reaction center protein from R. viridis enables us to use magnetic resonance to obtain structural information about the reaction center relatively rapidly. We have grown large numbers of R. viridis reaction center crystals and have determined the orientation of the triplet axis system of the primary donor to within + 1 degree as well as amore » number of magnetically non-equivalent donor sites in the crystal.« less

Determining landscape-scale changes in forest structure and possible management responses to Phytophthora ramorum in the Mt. Tamalpais watershed, Marin County, California

Treesearch

Janet Klein; Andrea Williams; John Menke

2013-01-01

The Marin Municipal Water District's (MMWD) 7487 ha Mt. Tamalpais watershed in Marin County, California has the dubious distinction of being one of the earliest and most extensive areas impacted by Phytophthora ramorum in California. Rapid die off of tanoaks (Notholithocarpus densiflorus (Hook. & Arn.) Manos, Cannon...

Mechanical and physical properties of composite panels manufactured from Chinese tallow tree furnish

Treesearch

Todd F. Shupe; Leslie H. Groom; Thomas L. Eberhardt; Timothy G. Rials; Chung Y. Hse; Thomas Pesacreta

2006-01-01

Chinese tallow tree is a noxious, invasive plant in the southeastern United States. It is generally considered a nuisance and has no current commercial use. The objective of this research was to determine the technical feasibility of using the stem wood of this species for particleboard, fiberboard, and structural flakeboard. Due to its rapid growth, Chinese tallow...

DapF stabilizes the substrate-favoring conformation of RppH to stimulate its RNA-pyrophosphohydrolase activity in Escherichia coli.

PubMed

Wang, Qiang; Zhang, Delin; Guan, Zeyuan; Li, Dongqin; Pei, Kai; Liu, Jian; Zou, Tingting; Yin, Ping

2018-06-21

mRNA decay is an important strategy by which bacteria can rapidly adapt to their ever-changing surroundings. The 5'-terminus state of mRNA determines the velocity of decay of many types of RNA. In Escherichia coli, RNA pyrophosphohydrolase (RppH) is responsible for the removal of the 5'-terminal triphosphate from hundreds of mRNAs and triggers its rapid degradation by ribonucleases. A diaminopimelate epimerase, DapF, can directly interact with RppH and stimulate its hydrolysis activity in vivo and in vitro. However, the molecular mechanism remains to be elucidated. Here, we determined the complex structure of DapF-RppH as a heterotetramer in a 2:2 molar ratio. DapF-bound RppH exhibits an RNA-favorable conformation similar to the RNA-bound state, suggesting that association with DapF promotes and stabilizes RppH in a conformation that facilitates substrate RNA binding and thus stimulates the activity of RppH. To our knowledge, this is the first published structure of an RNA-pyrophosphohydrolysis complex in bacteria. Our study provides a framework for further investigation of the potential regulators involved in the RNA-pyrophosphohydrolysis process in prokaryotes.

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

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

[Assessment of a rapid diagnostic test and portable fluorescent microscopy for malaria diagnosis in Cotonou (Bénin)].

PubMed

Ogouyèmi-Hounto, A; Kinde-Gazard, D; Keke, C; Gonçalves, E; Alapini, N; Adjovi, F; Adisso, L; Bossou, C; Denon, Y V; Massougbodji, A

2013-02-01

The aim of the study was to determine the accuracy of a rapid diagnostic test (SD Bioline Malaria Ag P.f/ Pan®) and fluorescent microscopy (CyScope®) in confirming presumptive malaria diagnosis in Cotonou. Thick blood smear was used as the reference technique for comparison. Testing was conducted on persons between the ages of 6 months and 70 years at two hospitals from June to October 2010. If malaria was suspected in the sample by the nurse based on clinical findings and sent to laboratory for confirmation, one thick smear, one rapid diagnostic test and one slide for the fluorescent microscopy were performed. All tests were read in hospital laboratories involved with the quality control of thick blood smear in the parasitology laboratory of National University Hospital of Cotonou. A total of 354 patients with clinical diagnosis of malaria were included. Malaria prevalence determined by thick smear, rapid diagnostic test and fluorescent microscopy was 22.8%, 25.4%, and 25.1% respectively. The sensitivity, specificity, positive and negative predictive values compared to the thick smears were 96.3, 95.6, 86.7, and 98.9% for rapid diagnostic test; and 97.5, 96.7, 89.8, and 99.27% for fluorescent microscopy. With these performances, these tests meet acceptability standards recommended by WHO for rapid tests (sensitivity > 95%). These two methods have advantages for the confirmation of malaria diagnosis in peripheral health structures that lack the resources to conduct diagnosis confirmation by the thick blood smear.

Rapid Solidification and Phase Transformations in Additive Manufactured Materials

DOE PAGES

Asle Zaeem, Mohsen; Clarke, Amy Jean

2016-01-14

Within the past few years, additive manufacturing (AM) has emerged as a promising manufacturing technique to enable the production of complex engineering structures with high efficiency and accuracy. Among the important factors establishing AM as a sustainable manufacturing process is the ability to control the microstructures and properties of AM products. In most AM processes, such as laser sintering (LS), laser melting (LM), and laser metal deposition (LMD), rapid solidification and high-temperature phase transformations play primary roles in determining nano- and microstructures, and consequently the mechanical and other properties of AM products. This topic of JOM is dedicated to summarizingmore » the current research efforts in the area of rapid solidification and phase transformations in additively manufactured materials. Finally, a brief summary follows below of 10 journal articles in this topic.« less

The effect of erosion on the fatigue limit of metallic materials for aerospace applications

NASA Astrophysics Data System (ADS)

Kordatos, E. Z.; Exarchos, D. A.; Matikas, T. E.

2018-03-01

This work deals with the study of the fatigue behavior of metallic materials for aerospace applications which have undergone erosion. Particularly, an innovative non-destructive methodology based on infrared lock-in thermography was applied on aluminum samples for the rapid determination of their fatigue limit. The effect of erosion on the structural integrity of materials can lead to a catastrophic failure and therefore an efficient assessment of the fatigue behavior is of high importance. Infrared thermography (IRT) as a non-destructive, non-contact, real time and full field method can be employed in order the fatigue limit to be rapidly determined. The basic principle of this method is the detection and monitoring of the intrinsically dissipated energy due to the cyclic fatigue loading. This methodology was successfully applied on both eroded and non-eroded aluminum specimens in order the severity of erosion to be evaluated.

Dynamics of sleep/wake determination--Normal and abnormal

NASA Astrophysics Data System (ADS)

Mahowald, Mark W.; Schenck, Carlos H.; O'Connor, Kevin A.

1991-10-01

Virtually all members of the animal kingdom experience a relentless and powerful cycling of states of being: wakefulness, rapid eye movement sleep, and nonrapid eye movement sleep. Each of these states is composed of a number of physiologic variables generated in a variety of neural structures. The predictable oscillations of these states are driven by presumed neural pacemakers which are entrained to the 24 h geophysical environment by the light/dark cycle. Experiments in nature have indicated that wake/sleep rhythm perturbations may occur either involving desynchronization of the basic 24 h wake/sleep cycle within the geophysical 24 h cycle (circadian rhythm disturbances) or involving the rapid oscillation or incomplete declaration of state (such as narcolepsy). The use of phase spaces to describe states of being may be of interest in the description of state determination in both illness and health. Some fascinating clinical and experimental phenomena may represent bifurcations in the sleep/wake control system.

2.2 Å resolution cryo-EM structure of β-galactosidase in complex with a cell-permeant inhibitor.

PubMed

Bartesaghi, Alberto; Merk, Alan; Banerjee, Soojay; Matthies, Doreen; Wu, Xiongwu; Milne, Jacqueline L S; Subramaniam, Sriram

2015-06-05

Cryo-electron microscopy (cryo-EM) is rapidly emerging as a powerful tool for protein structure determination at high resolution. Here we report the structure of a complex between Escherichia coli β-galactosidase and the cell-permeant inhibitor phenylethyl β-D-thiogalactopyranoside (PETG), determined by cryo-EM at an average resolution of ~2.2 angstroms (Å). Besides the PETG ligand, we identified densities in the map for ~800 water molecules and for magnesium and sodium ions. Although it is likely that continued advances in detector technology may further enhance resolution, our findings demonstrate that preparation of specimens of adequate quality and intrinsic protein flexibility, rather than imaging or image-processing technologies, now represent the major bottlenecks to routinely achieving resolutions close to 2 Å using single-particle cryo-EM. Copyright © 2015, American Association for the Advancement of Science.

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.

Simulation of the β-voltaic effect in silicon pin structures irradiated with electrons from a nickel-63 β source

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

Nagornov, Yu. S., E-mail: Nagornov.Yuri@gmail.com; Murashev, V. N.

2016-01-15

The prospects of β voltaics as electric-power sources for semiconductor circuits are considered. Experimental studies show that charging of the surface and a decrease in the electrovoltaic power are important. Simulation of the β-voltaic effect induced by electrons from a nickel-63 source on silicon pin structures is performed; it is shown that the coefficient of the collection of generated charge carriers can be as high as 13%. The dose dependences of the performance efficiency of silicon β-voltaic structures are determined for the case of irradiation with α particles and γ-ray photons; it is shown that 1.3 × 10{sup 14} andmore » 10{sup 20} cm{sup –2}, respectively, are the threshold doses, above which a rapid decrease in efficiency occurs. The optimal parameters of microchannel structures in β-voltaic electronics, in which the width of the channels and the distance between them correspond to 3 and 10 μm, are determined.« less

Laser-Induced Breakdown Spectroscopy (LIBS) for the Measurement of Spatial Structures and Fuel Distribution in Flames.

PubMed

Kotzagianni, Maria; Kakkava, Eirini; Couris, Stelios

2016-04-01

Laser-induced breakdown spectroscopy (LIBS) is used for the mapping of local structures (i.e., reactants and products zones) and for the determination of fuel distribution by means of the local equivalence ratio ϕ in laminar, premixed air-hydrocarbon flames. The determination of laser threshold energy to induce breakdown in the different zones of flames is employed for the identification and demarcation of the local structures of a premixed laminar flame, while complementary results about fuel concentration were obtained from measurements of the cyanogen (CN) band Β(2)Σ(+)--Χ(2)Σ(+), (Δυ = 0) at 388.3 nm and the ratio of the atomic lines of hydrogen (Hα) and oxygen (O(I)), Hα/O. The combination of these LIBS-based methods provides a relatively simple to use, rapid, and accurate tool for online and in situ combustion diagnostics, providing valuable information about the fuel distribution and the spatial variations of the local structures of a flame. © The Author(s) 2016.

Analysis of Glycosaminoglycans Using Mass Spectrometry

PubMed Central

Staples, Gregory O.; Zaia, Joseph

2015-01-01

The glycosaminoglycans (GAGs) are linear polysaccharides expressed on animal cell surfaces and in extracellular matrices. Their biosynthesis is under complex control and confers a domain structure that is essential to their ability to bind to protein partners. Key to understanding the functions of GAGs are methods to determine accurately and rapidly patterns of sulfation, acetylation and uronic acid epimerization that correlate with protein binding or other biological activities. Mass spectrometry (MS) is particularly suitable for the analysis of GAGs for biomedical purposes. Using modern ionization techniques it is possible to accurately determine molecular weights of GAG oligosaccharides and their distributions within a mixture. Methods for direct interfacing with liquid chromatography have been developed to permit online mass spectrometric analysis of GAGs. New tandem mass spectrometric methods for fine structure determination of GAGs are emerging. This review summarizes MS-based approaches for analysis of GAGs, including tissue extraction and chromatographic methods compatible with LC/MS and tandem MS. PMID:25705143

A deep look into the spray coating process in real-time—the crucial role of x-rays

NASA Astrophysics Data System (ADS)

Roth, Stephan V.

2016-10-01

Tailoring functional thin films and coating by rapid solvent-based processes is the basis for the fabrication of large scale high-end applications in nanotechnology. Due to solvent loss of the solution or dispersion inherent in the installation of functional thin films and multilayers the spraying and drying processes are strongly governed by non-equilibrium kinetics, often passing through transient states, until the final structure is installed. Therefore, the challenge is to observe the structural build-up during these coating processes in a spatially and time-resolved manner on multiple time and length scales, from the nanostructure to macroscopic length scales. During installation, the interaction of solid-fluid interfaces and between the different layers, the flow and evaporation themselves determine the structure of the coating. Advanced x-ray scattering methods open a powerful pathway for observing the involved processes in situ, from the spray to the coating, and allow for gaining deep insight in the nanostructuring processes. This review first provides an overview over these rapidly evolving methods, with main focus on functional coatings, organic photovoltaics and organic electronics. Secondly the role and decisive advantage of x-rays is outlined. Thirdly, focusing on spray deposition as a rapidly emerging method, recent advances in investigations of spray deposition of functional materials and devices via advanced x-ray scattering methods are presented.

Magnetic assembly of nonmagnetic particles into photonic crystal structures.

PubMed

He, Le; Hu, Yongxing; Kim, Hyoki; Ge, Jianping; Kwon, Sunghoon; Yin, Yadong

2010-11-10

We report the rapid formation of photonic crystal structures by assembly of uniform nonmagnetic colloidal particles in ferrofluids using external magnetic fields. Magnetic manipulation of nonmagnetic particles with size down to a few hundred nanometers, suitable building blocks for producing photonic crystals with band gaps located in the visible regime, has been difficult due to their weak magnetic dipole moment. Increasing the dipole moment of magnetic holes has been limited by the instability of ferrofluids toward aggregation at high concentration or under strong magnetic field. By taking advantage of the superior stability of highly surface-charged magnetite nanocrystal-based ferrofluids, in this paper we have been able to successfully assemble 185 nm nonmagnetic polymer beads into photonic crystal structures, from 1D chains to 3D assemblies as determined by the interplay of magnetic dipole force and packing force. In a strong magnetic field with large field gradient, 3D photonic crystals with high reflectance (83%) in the visible range can be rapidly produced within several minutes, making this general strategy promising for fast creation of large-area photonic crystals using nonmagnetic particles as building blocks.

Impacts of forest harvest on active carbon and microbial properties of a volcanic ash cap soil in northern Idaho

Treesearch

Deborah S. Page-Dumroese; Matt D. Busse; Steven T. Overby; Brian D. Gardner; Joanne M. Tirocke

2015-01-01

Soil quality assessments are essential for determining impacts on belowground microbial community structure and function. We evaluated the suitability of active carbon (C), a rapid field test, as an indicator of soil biological quality in five paired forest stands (clear cut harvested 40 years prior and unharvested) growing on volcanic ash-cap soils in northern Idaho....

Structure-based assessment of disease-related mutations in human voltage-gated sodium channels.

PubMed

Huang, Weiyun; Liu, Minhao; Yan, S Frank; Yan, Nieng

2017-06-01

Voltage-gated sodium (Na v ) channels are essential for the rapid upstroke of action potentials and the propagation of electrical signals in nerves and muscles. Defects of Na v channels are associated with a variety of channelopathies. More than 1000 disease-related mutations have been identified in Na v channels, with Na v 1.1 and Na v 1.5 each harboring more than 400 mutations. Na v channels represent major targets for a wide array of neurotoxins and drugs. Atomic structures of Na v channels are required to understand their function and disease mechanisms. The recently determined atomic structure of the rabbit voltage-gated calcium (Ca v ) channel Ca v 1.1 provides a template for homology-based structural modeling of the evolutionarily related Na v channels. In this Resource article, we summarized all the reported disease-related mutations in human Na v channels, generated a homologous model of human Na v 1.7, and structurally mapped disease-associated mutations. Before the determination of structures of human Na v channels, the analysis presented here serves as the base framework for mechanistic investigation of Na v channelopathies and for potential structure-based drug discovery.

Co-extinction in a host-parasite network: identifying key hosts for network stability.

PubMed

Dallas, Tad; Cornelius, Emily

2015-08-17

Parasites comprise a substantial portion of total biodiversity. Ultimately, this means that host extinction could result in many secondary extinctions of obligate parasites and potentially alter host-parasite network structure. Here, we examined a highly resolved fish-parasite network to determine key hosts responsible for maintaining parasite diversity and network structure (quantified here as nestedness and modularity). We evaluated four possible host extinction orders and compared the resulting co-extinction dynamics to random extinction simulations; including host removal based on estimated extinction risk, parasite species richness and host level contributions to nestedness and modularity. We found that all extinction orders, except the one based on realistic extinction risk, resulted in faster declines in parasite diversity and network structure relative to random biodiversity loss. Further, we determined species-level contributions to network structure were best predicted by parasite species richness and host family. Taken together, we demonstrate that a small proportion of hosts contribute substantially to network structure and that removal of these hosts results in rapid declines in parasite diversity and network structure. As network stability can potentially be inferred through measures of network structure, our findings may provide insight into species traits that confer stability.

Targeting of a Nicotiana plumbaginifolia H+ -ATPase to the plasma membrane is not by default and requires cytosolic structural determinants.

PubMed

Lefebvre, Benoit; Batoko, Henri; Duby, Geoffrey; Boutry, Marc

2004-07-01

The structural determinants involved in the targeting of multitransmembrane-span proteins to the plasma membrane (PM) remain poorly understood. The plasma membrane H+ -ATPase (PMA) from Nicotiana plumbaginifolia, a well-characterized 10 transmembrane-span enzyme, was used as a model to identify structural elements essential for targeting to the PM. When PMA2 and PMA4, representatives of the two main PMA subfamilies, were fused to green fluorescent protein (GFP), the chimeras were shown to be still functional and to be correctly and rapidly targeted to the PM in transgenic tobacco. By contrast, chimeric proteins containing various combinations of PMA transmembrane spanning domains accumulated in the Golgi apparatus and not in the PM and displayed slow traffic properties through the secretory pathway. Individual deletion of three of the four cytosolic domains did not prevent PM targeting, but deletion of the large loop or of its nucleotide binding domain resulted in GFP fluorescence accumulating exclusively in the endoplasmic reticulum. The results show that, at least for this polytopic protein, the PM is not the default pathway and that, in contrast with single-pass membrane proteins, cytosolic structural determinants are required for correct targeting.

Targeting of a Nicotiana plumbaginifolia H+-ATPase to the Plasma Membrane Is Not by Default and Requires Cytosolic Structural Determinants

PubMed Central

Lefebvre, Benoit; Batoko, Henri; Duby, Geoffrey; Boutry, Marc

2004-01-01

The structural determinants involved in the targeting of multitransmembrane-span proteins to the plasma membrane (PM) remain poorly understood. The plasma membrane H+-ATPase (PMA) from Nicotiana plumbaginifolia, a well-characterized 10 transmembrane–span enzyme, was used as a model to identify structural elements essential for targeting to the PM. When PMA2 and PMA4, representatives of the two main PMA subfamilies, were fused to green fluorescent protein (GFP), the chimeras were shown to be still functional and to be correctly and rapidly targeted to the PM in transgenic tobacco. By contrast, chimeric proteins containing various combinations of PMA transmembrane spanning domains accumulated in the Golgi apparatus and not in the PM and displayed slow traffic properties through the secretory pathway. Individual deletion of three of the four cytosolic domains did not prevent PM targeting, but deletion of the large loop or of its nucleotide binding domain resulted in GFP fluorescence accumulating exclusively in the endoplasmic reticulum. The results show that, at least for this polytopic protein, the PM is not the default pathway and that, in contrast with single-pass membrane proteins, cytosolic structural determinants are required for correct targeting. PMID:15208389

Measurement of the inclusive jet cross section at D0 Run II (in French)

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

Agram, Jean-Laurent

2004-12-17

This work describes the measurement of inclusive jets cross section in the DØ experiment. This cross section is computed as a function of jet transverse momentum, in several rapidity intervals. This quantity is sensitive to the proton structure and is crucial for the determination of parton distribution functions (PDF), essentially for the gluon at high proton momentum fraction. The measurement presented here gives the first values obtained for Tevatron Run II for the cross section in several rapidity intervals, for an integrated luminosity of 143 pb -1. The results are in agreement, within the uncertainties, with theoretical Standard Model predictions,more » showing no evidence for new physics.« less

Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution

NASA Astrophysics Data System (ADS)

Greenwood, Jeremy R.; Calkins, David; Sullivan, Arron P.; Shelley, John C.

2010-06-01

Generating the appropriate protonation states of drug-like molecules in solution is important for success in both ligand- and structure-based virtual screening. Screening collections of millions of compounds requires a method for determining tautomers and their energies that is sufficiently rapid, accurate, and comprehensive. To maximise enrichment, the lowest energy tautomers must be determined from heterogeneous input, without over-enumerating unfavourable states. While computationally expensive, the density functional theory (DFT) method M06-2X/aug-cc-pVTZ(-f) [PB-SCRF] provides accurate energies for enumerated model tautomeric systems. The empirical Hammett-Taft methodology can very rapidly extrapolate substituent effects from model systems to drug-like molecules via the relationship between pKT and pKa. Combining the two complementary approaches transforms the tautomer problem from a scientific challenge to one of engineering scale-up, and avoids issues that arise due to the very limited number of measured pKT values, especially for the complicated heterocycles often favoured by medicinal chemists for their novelty and versatility. Several hundreds of pre-calculated tautomer energies and substituent pKa effects are tabulated in databases for use in structural adjustment by the program Epik, which treats tautomers as a subset of the larger problem of the protonation states in aqueous ensembles and their energy penalties. Accuracy and coverage is continually improved and expanded by parameterizing new systems of interest using DFT and experimental data. Recommendations are made for how to best incorporate tautomers in molecular design and virtual screening workflows.

Cancer Associated E17K Mutation Causes Rapid Conformational Drift in AKT1 Pleckstrin Homology (PH) Domain

PubMed Central

Kumar, Ambuj; Purohit, Rituraj

2013-01-01

Background AKT1 (v-akt murine thymoma viral oncogene homologue 1) kinase is one of the most frequently activated proliferated and survival pathway of cancer. Recently it has been shown that E17K mutation in the Pleckstrin Homology (PH) domain of AKT1 protein leads to cancer by amplifying the phosphorylation and membrane localization of protein. The mutant has shown resistance to AKT1/2 inhibitor VIII drug molecule. In this study we have demonstrated the detailed structural and molecular consequences associated with the activity regulation of mutant protein. Methods The docking score exhibited significant loss in the interaction affinity to AKT1/2 inhibitor VIII drug molecule. Furthermore, the molecular dynamics simulation studies presented an evidence of rapid conformational drift observed in mutant structure. Results There was no stability loss in mutant as compared to native structure and the major cation–π interactions were also shown to be retained. Moreover, the active residues involved in membrane localization of protein exhibited significant rise in NHbonds formation in mutant. The rise in NHbond formation in active residues accounts for the 4-fold increase in the membrane localization potential of protein. Conclusion The overall result suggested that, although the mutation did not induce any stability loss in structure, the associated pathological consequences might have occurred due to the rapid conformational drifts observed in the mutant AKT1 PH domain. General Significance The methodology implemented and the results obtained in this work will facilitate in determining the core molecular mechanisms of cancer-associated mutations and in designing their potential drug inhibitors. PMID:23741320

Rapid determination of enantiomeric excess: a focus on optical approaches.

PubMed

Leung, Diana; Kang, Sung Ok; Anslyn, Eric V

2012-01-07

High-throughput screening (HTS) methods are becoming increasingly essential in discovering chiral catalysts or auxiliaries for asymmetric transformations due to the advent of parallel synthesis and combinatorial chemistry. Both parallel synthesis and combinatorial chemistry can lead to the exploration of a range of structural candidates and reaction conditions as a means to obtain the highest enantiomeric excess (ee) of a desired transformation. One current bottleneck in these approaches to asymmetric reactions is the determination of ee, which has led researchers to explore a wide range of HTS techniques. To be truly high-throughput, it has been proposed that a technique that can analyse a thousand or more samples per day is needed. Many of the current approaches to this goal are based on optical methods because they allow for a rapid determination of ee due to quick data collection and their parallel analysis capabilities. In this critical review these techniques are reviewed with a discussion of their respective advantages and drawbacks, and with a contrast to chromatographic methods (180 references). This journal is © The Royal Society of Chemistry 2012

The impact of hospital structure and restructuring on the nursing workforce.

PubMed

Duffield, Christine; Kearin, Mark; Johnston, Judy; Leonard, Joanna

2007-01-01

Health systems throughout much of the world have been subject to 'reform' in recent years as countries have attempted to contain the rapidly rising costs of health care. Changes to hospital structures (restructuring) have been an important part of these reforms. A significant impact of current approaches to restructuring is the loss of, or changes to, nursing management roles and functions. Australian hospitals Little evaluation has been undertaken to determine the impact of hospital structure and organisational restructuring on the nursing workforce. There is some indication that nurses have experienced a loss of key management positions, which may impact on their capacity to ensure that adequate and safe care is provided at the ward level.

Energy Approach-Based Simulation of Structural Materials High-Cycle Fatigue

NASA Astrophysics Data System (ADS)

Balayev, A. F.; Korolev, A. V.; Kochetkov, A. V.; Sklyarova, A. I.; Zakharov, O. V.

2016-02-01

The paper describes the mechanism of micro-cracks development in solid structural materials based on the theory of brittle fracture. A probability function of material cracks energy distribution is obtained using a probabilistic approach. The paper states energy conditions for cracks growth at material high-cycle loading. A formula allowing to calculate the amount of energy absorbed during the cracks growth is given. The paper proposes a high- cycle fatigue evaluation criterion allowing to determine the maximum permissible number of solid body loading cycles, at which micro-cracks start growing rapidly up to destruction.

A laboratory-scale pretreatment and hydrolysis assay for determination of reactivity in cellulosic biomass feedstocks.

PubMed

Wolfrum, Edward J; Ness, Ryan M; Nagle, Nicholas J; Peterson, Darren J; Scarlata, Christopher J

2013-11-14

The rapid determination of the release of structural sugars from biomass feedstocks is an important enabling technology for the development of cellulosic biofuels. An assay that is used to determine sugar release for large numbers of samples must be robust, rapid, and easy to perform, and must use modest amounts of the samples to be tested.In this work we present a laboratory-scale combined pretreatment and saccharification assay that can be used as a biomass feedstock screening tool. The assay uses a commercially available automated solvent extraction system for pretreatment followed by a small-scale enzymatic hydrolysis step. The assay allows multiple samples to be screened simultaneously, and uses only ~3 g of biomass per sample. If the composition of the biomass sample is known, the results of the assay can be expressed as reactivity (fraction of structural carbohydrate present in the biomass sample released as monomeric sugars). We first present pretreatment and enzymatic hydrolysis experiments on a set of representative biomass feedstock samples (corn stover, poplar, sorghum, switchgrass) in order to put the assay in context, and then show the results of the assay applied to approximately 150 different feedstock samples covering 5 different materials. From the compositional analysis data we identify a positive correlation between lignin and structural carbohydrates, and from the reactivity data we identify a negative correlation between both carbohydrate and lignin content and total reactivity. The negative correlation between lignin content and total reactivity suggests that lignin may interfere with sugar release, or that more mature samples (with higher structural sugars) may have more recalcitrant lignin. The assay presented in this work provides a robust and straightforward method to measure the sugar release after pretreatment and saccharification that can be used as a biomass feedstock screening tool. We demonstrated the utility of the assay by identifying correlations between feedstock composition and reactivity in a population of 150 samples.

Pattern changes in determinants of Chinese emissions

NASA Astrophysics Data System (ADS)

Mi, Zhifu; Meng, Jing; Guan, Dabo; Shan, Yuli; Liu, Zhu; Wang, Yutao; Feng, Kuishuang; Wei, Yi-Ming

2017-07-01

The Chinese economy has been recovering slowly from the global financial crisis, but it cannot achieve the same rapid development of the pre-recession period. Instead, the country has entered a new phase of economic development—a ‘new normal’. We use a structural decomposition analysis and environmental input-output analysis to estimate the determinants of China’s carbon emission changes during 2005-2012. China’s imports are linked to a global multi-regional input-output model based on the Global Trade and Analysis Project database to calculate the embodied CO2 emissions in imports. We find that the global financial crisis has affected the drivers of China’s carbon emission growth. From 2007 to 2010, the CO2 emissions induced by China’s exports dropped, whereas emissions induced by capital formation grew rapidly. In the ‘new normal’, the strongest factors that offset CO2 emissions have shifted from efficiency gains to structural upgrading. Efficiency was the strongest factor offsetting China’s CO2 emissions before 2010 but drove a 1.4% increase in emissions in the period 2010-2012. By contrast, production structure and consumption patterns caused a 2.6% and 1.3% decrease, respectively, in China’s carbon emissions from 2010 to 2012. In addition, China tends to shift gradually from an investment to a consumption-driven economy. The proportion of CO2 emissions induced by consumption had a declining trend before 2010 but grew from 28.6%-29.1% during 2010-2012.

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.

Computer-Aided Design Of Turbine Blades And Vanes

NASA Technical Reports Server (NTRS)

Hsu, Wayne Q.

1988-01-01

Quasi-three-dimensional method for determining aerothermodynamic configuration of turbine uses computer-interactive analysis and design and computer-interactive graphics. Design procedure executed rapidly so designer easily repeats it to arrive at best performance, size, structural integrity, and engine life. Sequence of events in aerothermodynamic analysis and design starts with engine-balance equations and ends with boundary-layer analysis and viscous-flow calculations. Analysis-and-design procedure interactive and iterative throughout.

Analytical-HZETRN Model for Rapid Assessment of Active Magnetic Radiation Shielding

NASA Technical Reports Server (NTRS)

Washburn, S. A.; Blattnig, S. R.; Singleterry, R. C.; Westover, S. C.

2014-01-01

The use of active radiation shielding designs has the potential to reduce the radiation exposure received by astronauts on deep-space missions at a significantly lower mass penalty than designs utilizing only passive shielding. Unfortunately, the determination of the radiation exposure inside these shielded environments often involves lengthy and computationally intensive Monte Carlo analysis. In order to evaluate the large trade space of design parameters associated with a magnetic radiation shield design, an analytical model was developed for the determination of flux inside a solenoid magnetic field due to the Galactic Cosmic Radiation (GCR) radiation environment. This analytical model was then coupled with NASA's radiation transport code, HZETRN, to account for the effects of passive/structural shielding mass. The resulting model can rapidly obtain results for a given configuration and can therefore be used to analyze an entire trade space of potential variables in less time than is required for even a single Monte Carlo run. Analyzing this trade space for a solenoid magnetic shield design indicates that active shield bending powers greater than 15 Tm and passive/structural shielding thicknesses greater than 40 g/cm2 have a limited impact on reducing dose equivalent values. Also, it is shown that higher magnetic field strengths are more effective than thicker magnetic fields at reducing dose equivalent.

[Rapid identification of two new isomers in bear bile powder by LC-Q-TOF-MS combined with PCC oxidation].

PubMed

Jian, Long-Hai; Hu, Chun; Yu, Hong; Wang, Ke; Ji, Shen

2013-07-01

A rapid method of Liquid chromatography-quadrupole time-of-flight mass spectrometry (LC-Q-TOF-MS) combined with pyridinium chlorochromate (PCC) oxidation has been developed to determine chemical structures of two novel isomers in bear bile powder. Derivatives of ursodeoxycholic acid (UDCA) and chenodeoxycholic acid (CDCA) were semi-synthesized by PCC oxidation, then were analyzed by LC-Q-TOF-MS. Separation was carried out on a reverse column with the mobile phase of acetonitrile-0.1% formic acid (45:55). The data of Q-TOF-MS was acquired by MS, MS/MS, positive and negative modes. Since UDCA and CDCA were stereochemical isomeric at an alcohol position, two oxidation products were same and have been confirmed by LC-Q-TOF-MS. Other two products were also determined based on the PCC oxidation theory. Samples of bear bile powder were dissolved by methanol and measured by LC-Q-TOF-MS. Two unknown peaks were found and identified by matching their retention times and accurate mass spectra ions with PCC oxidation productS. Finally, the structures of two new bile acids in bear bile powder were confirmed as 3alpha-hydroxy-7-oxo-5beta-cholanic acid, 7alpha-hydroxy-3-oxo-5beta-cholanic acid, respectively.

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.

NASA Advanced Concepts Office, Earth-To-Orbit Team Design Process and Tools

NASA Technical Reports Server (NTRS)

Waters, Eric D.; Garcia, Jessica; Beers, Benjamin; Philips, Alan; Holt, James B.; Threet, Grady E., Jr.

2013-01-01

The Earth to Orbit (ETO) Team of the Advanced Concepts Office (ACO) at NASA Marshal Space Flight Center (MSFC) is considered the preeminent group to go to for prephase A and phase A concept definition. The ACO team has been at the forefront of a multitude of launch vehicle studies determining the future direction of the Agency as a whole due, in part, to their rapid turnaround time in analyzing concepts and their ability to cover broad trade spaces of vehicles in that limited timeframe. Each completed vehicle concept includes a full mass breakdown of each vehicle to tertiary subsystem components, along with a vehicle trajectory analysis to determine optimized payload delivery to specified orbital parameters, flight environments, and delta v capability. Additionally, a structural analysis of the vehicle based on material properties and geometries is performed as well as an analysis to determine the flight loads based on the trajectory outputs. As mentioned, the ACO Earth to Orbit Team prides themselves on their rapid turnaround time and often need to fulfill customer requests within limited schedule or little advanced notice. Due to working in this fast paced environment, the ETO team has developed some finely honed skills and methods to maximize the delivery capability to meet their customer needs. This paper will describe the interfaces between the 3 primary disciplines used in the design process; weights and sizing, trajectory, and structural analysis, as well as the approach each discipline employs to streamline their particular piece of the design process.

The Role of Mesopontine NGF in Sleep and Wakefulness

PubMed Central

Ramos, Oscar V.; Torterolo, Pablo; Lim, Vincent; Chase, Michael H.; Sampogna, Sharon; Yamuy, Jack

2011-01-01

The microinjection of nerve growth factor (NGF) into the cat pontine tegmentum rapidly induces rapid eye movement (REM) sleep. To determine if NGF is involved in naturally-occurring REM sleep, we examined whether it is present in mesopontine cholinergic structures that promote the initiation of REM sleep, and whether the blockade of NGF production in these structures suppresses REM sleep. We found that cholinergic neurons in the cat dorsolateral mesopontine tegmentum exhibited NGF-like immunoreactivity. In addition, the microinjection of an oligodeoxyribonucleotide (OD) directed against cat NGF mRNA into this region resulted in a reduction in the time spent in REM sleep in conjunction with an increase in the time spent in wakefulness. Sleep and wakefulness returned to baseline conditions 2 to 5 days after antisense OD administration. The preceding antisense OD-induced effects occurred in conjunction with the suppression of NGF-like immunoreactivity within the site of antisense OD injection. These data support the hypothesis that NGF is involved in the modulation of naturally-occurring sleep and wakefulness. PMID:21840513

Evaluating the efficacy of a structure-derived amino acid substitution matrix in detecting protein homologs by BLAST and PSI-BLAST.

PubMed

Goonesekere, Nalin Cw

2009-01-01

The large numbers of protein sequences generated by whole genome sequencing projects require rapid and accurate methods of annotation. The detection of homology through computational sequence analysis is a powerful tool in determining the complex evolutionary and functional relationships that exist between proteins. Homology search algorithms employ amino acid substitution matrices to detect similarity between proteins sequences. The substitution matrices in common use today are constructed using sequences aligned without reference to protein structure. Here we present amino acid substitution matrices constructed from the alignment of a large number of protein domain structures from the structural classification of proteins (SCOP) database. We show that when incorporated into the homology search algorithms BLAST and PSI-blast, the structure-based substitution matrices enhance the efficacy of detecting remote homologs.

Spectrofluorometric determination of DNA and RNA with berberine

NASA Astrophysics Data System (ADS)

Gong, Guo-Quan; Zong, Zhi-Xin; Song, Yu-Min

1999-08-01

On binding to nucleic acids, the dye berberine increases its fluorescence quantum efficiency by a factor of 25-30. Based on this, an easy, rapid and accurate method for the determination of nucleic acids was developed. Berberine is very like ethidium bromide (EB), but it is non-poisonous. Determination can be made at any pH between 4 and 10, where the native structure of DNA and RNA is not disrupted. The maximum emission is near 520 nm for excitation at 355 or 450 nm. This method has good sensitivity (0.01 μg ml -1 of ctDNA), high selectivity and a wide linear range (0.05-14.0 μg ml -1 of ctDNA).

The Effects of Reducing the Structural Mass of the Transit Habitat on the Cryogenic Propellant Required for a Human Phobos Mission

NASA Technical Reports Server (NTRS)

Zipay, John Joseph

2016-01-01

A technique for rapidly determining the relationship between the pressurized volume, structural mass and the cryogenic propellant required to be delivered to Earth orbit for a Mars Transit Habitat is provided. This technique is based on assumptions for the required delta-V's, the Exploration Upper Stage performance and the historical structural masses for human spacecraft from Mercury Program through the International Space Station. If the Mars Transit Habitat is constructed from aluminum, structural mass estimates based on the habitat pressurized volume are accurate to within 15%. Other structural material options for the Mars Transit Habitat are also evaluated. The results show that small, achievable reductions in the structural mass of the Transit Habitat can save tens of thousands of pounds of cryogenic propellant that need to be delivered to Earth orbit for a human Phobos Mission.

The Effects of Reducing the Structural Mass of the Transit Habitat on the Cryogenic Propellant Required for a Human Phobos Mission

NASA Technical Reports Server (NTRS)

Zipay, John J.

2016-01-01

A technique for rapidly determining the relationship between the pressurized volume, structural mass and the cryogenic propellant required to be delivered to Earth orbit for a Mars Transit Habitat is provided. This technique is based on assumptions for the required delta-V's, the Exploration Upper Stage performance and the historical structural masses for human spacecraft from Mercury Program through the International Space Station. If the Mars Transit Habitat is constructed from aluminum, structural mass estimates based on the habitat pressurized volume are accurate to within 15 percent. Other structural material options for the Mars Transit Habitat are also evaluated. The results show that small, achievable reductions in the structural mass of the Transit Habitat can save tens of thousands of pounds of cryogenic propellant that need to be delivered to Earth orbit for a human Phobos Mission.

PONDEROSA-C/S: client-server based software package for automated protein 3D structure determination.

PubMed

Lee, Woonghee; Stark, Jaime L; Markley, John L

2014-11-01

Peak-picking Of Noe Data Enabled by Restriction Of Shift Assignments-Client Server (PONDEROSA-C/S) builds on the original PONDEROSA software (Lee et al. in Bioinformatics 27:1727-1728. doi: 10.1093/bioinformatics/btr200, 2011) and includes improved features for structure calculation and refinement. PONDEROSA-C/S consists of three programs: Ponderosa Server, Ponderosa Client, and Ponderosa Analyzer. PONDEROSA-C/S takes as input the protein sequence, a list of assigned chemical shifts, and nuclear Overhauser data sets ((13)C- and/or (15)N-NOESY). The output is a set of assigned NOEs and 3D structural models for the protein. Ponderosa Analyzer supports the visualization, validation, and refinement of the results from Ponderosa Server. These tools enable semi-automated NMR-based structure determination of proteins in a rapid and robust fashion. We present examples showing the use of PONDEROSA-C/S in solving structures of four proteins: two that enable comparison with the original PONDEROSA package, and two from the Critical Assessment of automated Structure Determination by NMR (Rosato et al. in Nat Methods 6:625-626. doi: 10.1038/nmeth0909-625 , 2009) competition. The software package can be downloaded freely in binary format from http://pine.nmrfam.wisc.edu/download_packages.html. Registered users of the National Magnetic Resonance Facility at Madison can submit jobs to the PONDEROSA-C/S server at http://ponderosa.nmrfam.wisc.edu, where instructions, tutorials, and instructions can be found. Structures are normally returned within 1-2 days.

Communication at pediatric rapid response events: a survey of health care providers.

PubMed

McCrory, Michael C; Aboumatar, Hanan A; Hunt, Elizabeth A

2015-06-01

The objective of this study was to explore perceptions of communication quality at pediatric rapid response events and to determine whether these perceptions differed between rapid response team (RRT) members (RRTm) and floor providers (FP). This survey study was conducted of clinical providers involved in RRT events at a tertiary care children's hospital. Perceptions of RRT communication were assessed by using a 5-point Likert scale, and qualitative comments were collected. Responses were compared between RRTm (responder nurses and intensive care fellows) and FP (floor nurses and resident physicians). Survey response was 64% (18 of 28) for RRTm and 70% (194 of 278) for FP. RRTm gave lower ratings than FP for communication of: (1) the purpose of the call; (2) airway and breathing; (3) circulation; (4) background information; and (5) possible diagnosis and treatment. RRTm were more likely than FP to indicate that description of background information delayed communication of critical management problems ("often": RRTm, 7 of 17 [41%]; FP, 23 of 175 [13%]; "always": RRTm, 2 of 18 [12%]; FP, 19 of 175 [11%]; P=.001 for overall comparison). A structured approach for communication was generally supported, although less strongly among floor nurses. Themes from qualitative responses included role confusion, fractured room entry, and a dismissive attitude by RRTm. A disconnect in perceived quality of communication was observed between RRTm and FP at pediatric rapid response events. A structured approach with well-defined roles may improve communication quality. Copyright © 2015 by the American Academy of Pediatrics.

Brain Hyperglycemia Induced by Heroin: Association with Metabolic Neural Activation.

PubMed

Solis, Ernesto; Bola, R Aaron; Fasulo, Bradley J; Kiyatkin, Eugene A

2017-02-15

Glucose enters the brain extracellular space from arterial blood, and its proper delivery is essential for metabolic activity of brain cells. By using enzyme-based biosensors coupled with high-speed amperometry in freely moving rats, we previously showed that glucose levels in the nucleus accumbens (NAc) display high variability, increasing rapidly following exposure to various arousing stimuli. In this study, the same technology was used to assess NAc glucose fluctuations induced by intravenous heroin. Heroin passively injected at a low dose optimal for maintaining self-administration behavior (100 μg/kg) induces a rapid but moderate glucose rise (∼150-200 μM or ∼15-25% over resting baseline). When the heroin dose was doubled and tripled, the increase became progressively larger in magnitude and longer in duration. Heroin-induced glucose increases also occurred in other brain structures (medial thalamus, lateral striatum, hippocampus), suggesting that brain hyperglycemia is a whole-brain phenomenon but changes were notably distinct in each structure. While local vasodilation appears to be the possible mechanism underlying the rapid rise in extracellular glucose levels, the driving factor for this vasodilation (central vs peripheral) remains to be clarified. The heroin-induced NAc glucose increases positively correlated with increases in intracerebral heat production determined in separate experiments using multisite temperature recordings (NAc, temporal muscle and skin). However, glucose levels rise very rapidly, preceding much slower increases in brain heat production, a measure of metabolic activation associated with glucose consumption.

Rapid black hole growth under anisotropic radiation feedback

NASA Astrophysics Data System (ADS)

Sugimura, Kazuyuki; Hosokawa, Takashi; Yajima, Hidenobu; Omukai, Kazuyuki

2017-07-01

Discovery of high-redshift (z > 6) supermassive black holes (BHs) may indicate that the rapid (or super-Eddington) gas accretion has aided their quick growth. Here, we study such rapid accretion of the primordial gas on to intermediate-mass (102-105 M⊙) BHs under anisotropic radiation feedback. We perform two-dimensional radiation hydrodynamics simulations that solve the flow structure across the Bondi radius, from far outside of the Bondi radius down to a central part that is larger than a circum-BH accretion disc. The radiation from the unresolved circum-BH disc is analytically modelled considering self-shadowing effect. We show that the flow settles into a steady state, where the flow structure consists of two distinct parts: (1) bipolar ionized outflowing regions, where the gas is pushed outward by thermal gas pressure and super-Eddington radiation pressure, and (2) an equatorial neutral inflowing region, where the gas falls towards the central BH without affected by radiation feedback. The resulting accretion rate is much higher than that in the case of isotropic radiation, far exceeding the Eddington-limited rate to reach a value slightly lower than the Bondi one. The opening angle of the equatorial inflowing region is determined by the luminosity and directional dependence of the central radiation. We find that photoevaporation from its surfaces set the critical opening angle of about 10° below which the accretion to the BH is quenched. We suggest that the shadowing effect allows even stellar-remnant BHs to grow rapidly enough to become high-redshift supermassive BHs.

Black liquor and the hangover effect: fish assemblage recovery dynamics following a pulse disturbance

PubMed Central

Piller, Kyle R; Geheber, Aaron D

2015-01-01

Anthropogenic perturbations impact aquatic systems causing wide-ranging responses, from assemblage restructuring to assemblage recovery. Previous studies indicate the duration and intensity of disturbances play a role in the dynamics of assemblage recovery. In August 2011, the Pearl River, United States, was subjected to a weak black liquor spill from a paper mill which resulted in substantial loss of fish in a large stretch of the main channel. We quantified resilience and recovery of fish assemblage structure in the impacted area following the event. We compared downstream (impacted) assemblages to upstream (unimpacted) assemblages to determine initial impacts on structure. Additionally, we incorporated historic fish collections (1988–2011) to examine impacts on assemblage structure across broad temporal scales. Based on NMDS, upstream and downstream sites generally showed similar assemblage structure across sample periods with the exception of the 2 months postdischarge, where upstream and downstream sites visually differed. Multivariate analysis of variance (PERMANOVA) indicated significant seasonal variation among samples, but found no significant interaction between impacted and unimpacted assemblages following the discharge event. However, multivariate dispersion (MVDISP) showed greater variance among assemblage structure following the discharge event. These results suggest that 2 months following the disturbance represent a time period of stochasticity in regard to assemblage structure dynamics, and this was followed by rapid recovery. We term this dynamic the “hangover effect” as it represents the time frame from the cessation of the perturbation to the assemblage's return to predisturbance conditions. The availability and proximity of tributaries and upstream refugia, which were not affected by the disturbance, as well as the rapid recovery of abiotic parameters likely played a substantial role in assemblage recovery. This study not only demonstrates rapid recovery in an aquatic system, but further demonstrates the value of continuous, long-term, data collections which enhance our understanding of assemblage dynamics. PMID:26120432

Spectral Properties of Dirac Billiards at the van Hove Singularities.

PubMed

Dietz, B; Klaus, T; Miski-Oglu, M; Richter, A; Wunderle, M; Bouazza, C

2016-01-15

We study distributions of the ratios of level spacings of rectangular and Africa-shaped superconducting microwave resonators containing circular scatterers on a triangular grid, so-called Dirac billiards (DBs). The high-precision measurements allowed the determination of, respectively, all 1651 and 1823 eigenfrequencies in the first two bands. The resonance densities are similar to that of graphene. They exhibit two sharp peaks at the van Hove singularities which separate the band structure into regions with a linear and a quadratic dispersion relation, respectively. In the vicinity of the van Hove singularities we observe rapid changes in, e.g., the wave function structure. Accordingly, we question whether the spectral properties are there still determined by the shapes of the DBs. The commonly used statistical measures are no longer applicable; however, we demonstrate in this Letter that the ratio distributions provide suitable measures.

Measuring Moisture Levels in Graphite Epoxy Composite Sandwich Structures

NASA Technical Reports Server (NTRS)

Nurge, Mark; Youngquist, Robert; Starr, Stanley

2011-01-01

Graphite epoxy composite (GEC) materials are used in the construction of rocket fairings, nose cones, interstage adapters, and heat shields due to their high strength and light weight. However, they absorb moisture depending on the environmental conditions they are exposed to prior to launch. Too much moisture absorption can become a problem when temperature and pressure changes experienced during launch cause the water to vaporize. The rapid state change of the water can result in structural failure of the material. In addition, heat and moisture combine to weaken GEC structures. Diffusion models that predict the total accumulated moisture content based on the environmental conditions are one accepted method of determining if the material strength has been reduced to an unacceptable level. However, there currently doesn t exist any field measurement technique to estimate the actual moisture content of a composite structure. A multi-layer diffusion model was constructed with Mathematica to predict moisture absorption and desorption from the GEC sandwich structure. This model is used in conjunction with relative humidity/temperature sensors both on the inside and outside of the material to determine the moisture levels in the structure. Because the core materials have much higher diffusivity than the face sheets, a single relative humidity measurement will accurately reflect the moisture levels in the core. When combined with an external relative humidity measurement, the model can be used to determine the moisture levels in the face sheets. Since diffusion is temperaturedependent, the temperature measurements are used to determine the diffusivity of the face sheets for the model computations.

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.

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

Large Magneto-ionic Variations toward the Galactic Center Magnetar, PSR J1745-2900

NASA Astrophysics Data System (ADS)

Desvignes, G.; Eatough, R. P.; Pen, U. L.; Lee, K. J.; Mao, S. A.; Karuppusamy, R.; Schnitzeler, D. H. F. M.; Falcke, H.; Kramer, M.; Wucknitz, O.; Spitler, L. G.; Torne, P.; Liu, K.; Bower, G. C.; Cognard, I.; Lyne, A. G.; Stappers, B. W.

2018-01-01

Polarized radio emission from PSR J1745‑2900 has already been used to investigate the strength of the magnetic field in the Galactic center (GC), close to Sagittarius A*. Here we report how persistent radio emission from this magnetar, for over four years since its discovery, has revealed large changes in the observed Faraday rotation measure (RM), by up to 3500 rad m‑2 (a 5% fractional change). From simultaneous analysis of the dispersion measure, we determine that these fluctuations are dominated by variations in either the projected magnetic field or the free electron content within the GC, along the changing line of sight to the rapidly moving magnetar. From a structure function analysis of RM variations, and a recent epoch of rapid change of RM, we determine a minimum scale of magneto-ionic fluctuations of size ∼2 au at the GC distance, inferring PSR J1745‑2900 is just ∼0.1 pc behind an additional scattering screen.

Application of Raman spectroscopy to identification and sorting of post-consumer plastics for recycling

DOEpatents

Sommer, Edward J.; Rich, John T.

2001-01-01

A high accuracy rapid system for sorting a plurality of waste products by polymer type. The invention involves the application of Raman spectroscopy and complex identification techniques to identify and sort post-consumer plastics for recycling. The invention reads information unique to the molecular structure of the materials to be sorted to identify their chemical compositions and uses rapid high volume sorting techniques to sort them into product streams at commercially viable throughput rates. The system employs a laser diode (20) for irradiating the material sample (10), a spectrograph (50) is used to determine the Raman spectrum of the material sample (10) and a microprocessor based controller (70) is employed to identify the polymer type of the material sample (10).

A Participatory Action Research Pilot Study of Urban Health Disparities Using Rapid Assessment Response and Evaluation

PubMed Central

Brown, David Richard; Hernández, Agueda; Saint-Jean, Gilbert; Evans, Siân; Tafari, Ida; Brewster, Luther G.; Celestin, Michel J.; Gómez-Estefan, Carlos; Regalado, Fernando; Akal, Siri; Nierenberg, Barry; Kauschinger, Elaine D.; Schwartz, Robert; Page, J. Bryan

2008-01-01

Healthy People 2010 made it a priority to eliminate health disparities. We used a rapid assessment response and evaluation (RARE) to launch a program of participatory action research focused on health disparities in an urban, disadvantaged Black community serviced by a major south Florida health center. We formed partnerships with community members, identified local health disparities, and guided interventions targeting health disparities. We describe the RARE structure used to triangulate data sources and guide intervention plans as well as findings and conclusions drawn from scientific literature and epidemiological, historic, planning, clinical, and ethnographic data. Disenfranchisement and socioeconomic deprivation emerged as the principal determinants of local health disparities and the most appropriate targets for intervention. PMID:18048802

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.

Investigations of rapid thermal annealing induced structural evolution of ZnO: Ge nanocomposite thin films via GISAXS

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

Ceylan, Abdullah, E-mail: aceylanabd@yahoo.com; Ozcan, Yusuf; Orujalipoor, Ilghar

2016-06-07

In this work, we present in depth structural investigations of nanocomposite ZnO: Ge thin films by utilizing a state of the art grazing incidence small angle x-ray spectroscopy (GISAXS) technique. The samples have been deposited by sequential r.f. and d.c. sputtering of ZnO and Ge thin film layers, respectively, on single crystal Si(100) substrates. Transformation of Ge layers into Ge nanoparticles (Ge-np) has been initiated by ex-situ rapid thermal annealing of asprepared thin film samples at 600 °C for 30, 60, and 90 s under forming gas atmosphere. A special attention has been paid on the effects of reactive and nonreactivemore » growth of ZnO layers on the structural evolution of Ge-np. GISAXS analyses have been performed via cylindrical and spherical form factor calculations for different nanostructure types. Variations of the size, shape, and distributions of both ZnO and Ge nanostructures have been determined. It has been realized that GISAXS results are not only remarkably consistent with the electron microscopy observations but also provide additional information on the large scale size and shape distribution of the nanostructured components.« less

Computer program for determining mass properties of a rigid structure

NASA Technical Reports Server (NTRS)

Hull, R. A.; Gilbert, J. L.; Klich, P. J.

1978-01-01

A computer program was developed for the rapid computation of the mass properties of complex structural systems. The program uses rigid body analyses and permits differences in structural material throughout the total system. It is based on the premise that complex systems can be adequately described by a combination of basic elemental shapes. Simple geometric data describing size and location of each element and the respective material density or weight of each element were the only required input data. From this minimum input, the program yields system weight, center of gravity, moments of inertia and products of inertia with respect to mutually perpendicular axes through the system center of gravity. The program also yields mass properties of the individual shapes relative to component axes.

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...

Determination of the mechanical properties of solid and cellular polymeric dosage forms by diametral compression.

PubMed

Blaesi, Aron H; Saka, Nannaji

2016-07-25

At present, the immediate-release solid dosage forms, such as the oral tablets and capsules, are granular solids. They release drug rapidly and have adequate mechanical properties, but their manufacture is fraught with difficulties inherent in processing particulate matter. Such difficulties, however, could be overcome by liquid-based processing. Therefore, we have recently introduced polymeric cellular (i.e., highly porous) dosage forms prepared from a melt process. Experiments have shown that upon immersion in a dissolution medium, the cellular dosage forms with polyethylene glycol (PEG) as excipient and with predominantly open-cell topology disintegrate by exfoliation, thus enabling rapid drug release. If the volume fraction of voids of the open-cell structures is too large, however, their mechanical strength is adversely affected. At present, the common method for determining the tensile strength of brittle, solid dosage forms (such as select granular forms) is the diametral compression test. In this study, the theory of diametral compression is first refined to demonstrate that the relevant mechanical properties of ductile and cellular solids (i.e., the elastic modulus and the yield strength) can also be extracted from this test. Diametral compression experiments are then conducted on PEG-based solid and cellular dosage forms. It is found that the elastic modulus and yield strength of the open-cell structures are about an order of magnitude smaller than those of the non-porous solids, but still are substantially greater than the stiffness and strength requirements for handling the dosage forms manually. This work thus demonstrates that melt-processed polymeric cellular dosage forms that release drug rapidly can be designed and manufactured to have adequate mechanical properties. Copyright © 2016. Published by Elsevier B.V.

The influence of condensed tannin structure on rate of microbial mineralization and reactivity to chemical assays.

PubMed

Norris, Charlotte E; Preston, Caroline M; Hogg, Karen E; Titus, Brian D

2011-03-01

We examined how tannin structure influences reactivity in tannin assays and carbon and nitrogen mineralization. Condensed tannins from the foliage of ten tree and shrub species and from pecan shells (Carya illinoensis) had different proportions of: (a) epicatechin (cis) and catechin (trans) isomers, (b) procyanidin (PC) and prodelphinidin (PD) monomers, and (c) different chain lengths. The response of each tannin to several widely used tannin assays was determined. Although there was some variation in response to proanthocyanidin (butanol/HCl) and Folin Ciocalteu assays, we did not deduce any predictable relationship between tannin structure and response to either assay. There was little variation in protein precipitation among the different tannins. To assess biological activity, six of the tannins were incubated with forest humus for 22 days. We determined that, while PC-based tannins remained at least partly extractable for the duration of the incubation, tannins with a high proportion of PD subunits rapidly became unextractable from soil. There was a positive correlation between net nitrogen mineralization and cis chemical structure. Carbon mineralization was enhanced initially by the addition of tannins to humus, but after 22 days, a negative correlation between the proportion of cis subunits and respiration was determined. Overall, we were not able to demonstrate consistent effects of structure on either microbial mineralization or reactivity to chemical assays; such relationships remain elusive.

Cellulose esters synthesized using a tetrabutylammonium acetate and dimethylsulfoxide solvent system

NASA Astrophysics Data System (ADS)

Yu, Yongqi; Miao, Jiaojiao; Jiang, Zeming; Sun, Haibo; Zhang, Liping

2016-07-01

Cellulose acetate (CA) and cellulose acetate propionate (CAP) were homogeneously synthesized in a novel tetrabutylammonium acetate/dimethyl sulfoxide (DMSO) solvent system, without any catalyst, at temperatures below 70 °C. The molecular structures of the cellulose esters (CEs) and distributions of the substituents in the anhydroglucose repeating units were determined using 13C cross-polarization magic angle spinning nuclear magnetic resonance spectroscopy, and the degree of substitution (DS) values were determined using 1H nuclear magnetic resonance spectroscopy. The structures of the CEs, regenerated cellulose (RC), and pulp were determined using Fourier transform infrared spectroscopy. The thermal properties of the products were determined using thermogravimetric analysis. The temperatures of initial decomposition of the CEs were up to 40 °C higher than those of the RC and pulp. All the CEs were highly soluble in DMSO, but were insoluble in acetone. CAs with DS values less than 2.6 swelled or were poorly dissolved in CHCl3, but those with DS values above 2.9 dissolved rapidly. CAPs with DS values above 2.6 had good solubilities in ethyl acetate.

Label-free determination of lipid composition and secondary protein structure of human salivary noncancerous and cancerous tissues by Raman microspectroscopy.

PubMed

Brozek-Pluska, Beata; Kopec, Monika; Niedzwiecka, Izabela; Morawiec-Sztandera, Alina

2015-04-07

The applications of optical spectroscopic methods in cancer detection open new possibilities in oncological diagnostics. Raman spectroscopy and Raman imaging represent noninvasive, label-free, and rapidly developing tools in cancer diagnosis. In the study described in this paper Raman microspectroscopy has been employed to examine noncancerous and cancerous human salivary gland tissues of the same patient. The most significant differences between noncancerous and cancerous tissues were found in regions typical for the vibrations of lipids and proteins. The detailed analysis of secondary structures of proteins contained in the cancerous and the noncancerous tissues is also presented.

RAPID COMMUNICATION: Study of superstructure II in multiferroic BiMnO3

NASA Astrophysics Data System (ADS)

Ge, Bing-Hui; Li, Fang-Hua; Li, Xue-Ming; Wang, Yu-Mei; Chi, Zhen-Hua; Jin, Chang-Qing

2008-09-01

The crystal structure of the minor phase, named superstructure II, existing in multiferroic compound BiMnO3 has been studied by electron diffraction and high-resolution transmission electron microscopy. Domains of major and minor phases coexisting in BiMnO3 were observed in high-resolution electron microscope images. The unit cell of minor phase was determined to be triclinic with the size 4×4×4 times as large as the distorted perovskite subcell. The [111] and [10bar 1] projected structure maps of the minor phase have been derived from the corresponding images by means of the image processing. A possible rough three-dimensional (3D) structure model was proposed based on the 3D structural information extracted from the two projected structure maps. Since there is no inversion centre in the proposed model, the minor phase may contribute to the ferroelectric property of BiMnO3.

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.

Structure and function of echinoderm telomerase RNA

PubMed Central

Podlevsky, Joshua D.; Li, Yang; Chen, Julian J.-L.

2016-01-01

Telomerase is a ribonucleoprotein (RNP) enzyme that requires an integral telomerase RNA (TR) subunit, in addition to the catalytic telomerase reverse transcriptase (TERT), for enzymatic function. The secondary structures of TRs from the three major groups of species, ciliates, fungi, and vertebrates, have been studied extensively and demonstrate dramatic diversity. Herein, we report the first comprehensive secondary structure of TR from echinoderms—marine invertebrates closely related to vertebrates—determined by phylogenetic comparative analysis of 16 TR sequences from three separate echinoderm classes. Similar to vertebrate TR, echinoderm TR contains the highly conserved template/pseudoknot and H/ACA domains. However, echinoderm TR lacks the ancestral CR4/5 structural domain found throughout vertebrate and fungal TRs. Instead, echinoderm TR contains a distinct simple helical region, termed eCR4/5, that is functionally equivalent to the CR4/5 domain. The urchin and brittle star eCR4/5 domains bind specifically to their respective TERT proteins and stimulate telomerase activity. Distinct from vertebrate telomerase, the echinoderm TR template/pseudoknot domain with the TERT protein is sufficient to reconstitute significant telomerase activity. This gain-of-function of the echinoderm template/pseudoknot domain for conferring telomerase activity presumably facilitated the rapid structural evolution of the eCR4/5 domain throughout the echinoderm lineage. Additionally, echinoderm TR utilizes the template-adjacent P1.1 helix as a physical template boundary element to prevent nontelomeric DNA synthesis, a mechanism used by ciliate and fungal TRs. Thus, the chimeric and eccentric structural features of echinoderm TR provide unparalleled insights into the rapid evolution of telomerase RNP structure and function. PMID:26598712

Geometric structure of thin SiO xN y films on Si(100)

NASA Astrophysics Data System (ADS)

Behrens, K.-M.; Klinkenberg, E.-D.; Finster, J.; Meiwes-Broer, K.-H.

1998-05-01

Thin films of amorphous stoichometric SiO xN y are deposited on radiation-heated Si(100) by rapid thermal low-pressure chemical vapour deposition. We studied the whole range of possible compositions. In order to determine the geometric structure, we used EXAFS and photoelectron spectroscopy. Tetrahedrons constitute the short-range units with a central Si atom connected to N and O. The distribution of the possible tetrahedrons can be described by a mixture of the Random Bonding Model and the Random Mixture Model. For low oxygen contents x/( x+ y)≤0.3, the geometric structure of the film is almost the structure of a-Si 3N 4, with the oxygen preferably on top of Si-N 3 triangles. Higher oxygen contents induce changes in the bond lengths, bond angles and coordination numbers.

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.

An Exponential Regulator for Rapidity Divergences

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

Li, Ye; Neill, Duff; Zhu, Hua Xing

2016-04-01

Finding an efficient and compelling regularization of soft and collinear degrees of freedom at the same invariant mass scale, but separated in rapidity is a persistent problem in high-energy factorization. In the course of a calculation, one encounters divergences unregulated by dimensional regularization, often called rapidity divergences. Once regulated, a general framework exists for their renormalization, the rapidity renormalization group (RRG), leading to fully resummed calculations of transverse momentum (to the jet axis) sensitive quantities. We examine how this regularization can be implemented via a multi-differential factorization of the soft-collinear phase-space, leading to an (in principle) alternative non-perturbative regularization ofmore » rapidity divergences. As an example, we examine the fully-differential factorization of a color singlet's momentum spectrum in a hadron-hadron collision at threshold. We show how this factorization acts as a mother theory to both traditional threshold and transverse momentum resummation, recovering the classical results for both resummations. Examining the refactorization of the transverse momentum beam functions in the threshold region, we show that one can directly calculate the rapidity renormalized function, while shedding light on the structure of joint resummation. Finally, we show how using modern bootstrap techniques, the transverse momentum spectrum is determined by an expansion about the threshold factorization, leading to a viable higher loop scheme for calculating the relevant anomalous dimensions for the transverse momentum spectrum.« less

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.

Oral Motor Abilities Are Task Dependent: A Factor Analytic Approach to Performance Rate.

PubMed

Staiger, Anja; Schölderle, Theresa; Brendel, Bettina; Bötzel, Kai; Ziegler, Wolfram

2017-01-01

Measures of performance rates in speech-like or volitional nonspeech oral motor tasks are frequently used to draw inferences about articulation rate abnormalities in patients with neurologic movement disorders. The study objective was to investigate the structural relationship between rate measures of speech and of oral motor behaviors different from speech. A total of 130 patients with neurologic movement disorders and 130 healthy subjects participated in the study. Rate data was collected for oral reading (speech), rapid syllable repetition (speech-like), and rapid single articulator movements (nonspeech). The authors used factor analysis to determine whether the different rate variables reflect the same or distinct constructs. The behavioral data were most appropriately captured by a measurement model in which the different task types loaded onto separate latent variables. The data on oral motor performance rates show that speech tasks and oral motor tasks such as rapid syllable repetition or repetitive single articulator movements measure separate traits.

Sustainable Odds

NASA Astrophysics Data System (ADS)

Smith, L. A.

2016-12-01

While probability forecasting has many philosophical and mathematical attractions, it is something of a dishonest nonsense if acting on such forecasts is expected to lead to rapid ruin. Model-based probabilities, when interpreted as actionable, are shown to lead to the rapid ruin of a cooperative entity offering odds interpreting the probability forecasts at face value. Arguably, these odds would not be considered "fair", but inasmuch as some definitions of "fair odds" include this case, this presentation will focus on "sustainable odds": Odds which are not expected to lead to the rapid ruin of the cooperative under the assumption that those placing bets have no information beyond that available to the forecast system. It is argued that sustainable odds will not correspond to probabilities outside the Perfect Model Scenario, that the "implied probabilities" determined from sustainable odds will always sum to more than one, and that the excess of this sum over one reflects the skill of the forecast system, being a quantitative measure of structural model error.

Thalassosamide, a Siderophore Discovered from the Marine-Derived Bacterium Thalassospira profundimaris.

PubMed

Zhang, Fan; Barns, Kenneth; Hoffmann, F Michael; Braun, Doug R; Andes, David R; Bugni, Tim S

2017-09-22

Here we describe the rapid identification and prioritization of novel active marine natural products using an improved dereplication strategy. During the course of our screening of marine natural product libraries, a new cyclic trihydroxamate compound, thalassosamide, was discovered from the α-proteobacterium Thalassospira profundimaris. Its structure was determined by 2D NMR and MS/MS experiments, and the absolute configuration of the lysine-derived units was established by Marfey's analysis, whereas that of C-9, 9', and 9″ was determined via the circular dichroism data of the [Rh 2 (OCOCF 3 ) 4 ] complex and DFT NMR calculations. Thalassosamide showed moderate in vivo efficacy against Pseudomonas aeruginosa.

The use of Ni-Cr-Si-Be filler metals for brazing of stainless steels

NASA Astrophysics Data System (ADS)

Ivannikov, A.; Fedotov, V.; Suchkov, A.; Penyaz, M.; Fedotov, I.; Tarasov, B.

2016-04-01

Nanocrystalline ribbon filler metal-alloys of system Ni-Cr-Si-Be are produced by the rapidly quenching of the melt method. By these filler metals carried out hight temperature vacuum brazing of austenitic steels (12Kh18N10T and Kh18N8G2) and austenitic-ferritic class EI-811 (12Kh21N5T). The basic laws of structure-phase state foundation of brazed joints are determined, features of the interaction of the molten filler metal to the brazed materials are identified, the optimal temperature and time parameters of the brazing process are determined.

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

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.

Carbon Fiber TOW Angle Determination Using Microwave Reflectometry

NASA Technical Reports Server (NTRS)

Wilson, William C.; Moore, Jason P.; Juarez, Peter D.

2016-01-01

NASA's Advanced Composites Project is investigating technologies that increase automated remote inspection of aircraft composite structures. Therefore, microwave Frequency Domain Reflectometry (FDR) is being investigated as a method of enabling rapid remote inspection of angular orientation of the tow using microwave radiation. This work will present preliminary data demonstrating that frequency shifts in the reflection spectrum of a carbon fiber tow sample are indicative of the angle of the tow with respect to an interrogating antenna's linear polarized output.

Customizing model membranes and samples for NMR spectroscopic studies of complex membrane proteins.

PubMed

Sanders, C R; Oxenoid, K

2000-11-23

Both solution and solid state nuclear magnetic resonance (NMR) techniques for structural determination are advancing rapidly such that it is possible to contemplate bringing these techniques to bear upon integral membrane proteins having multiple transmembrane segments. This review outlines existing and emerging options for model membrane media for use in such studies and surveys the special considerations which must be taken into account when preparing larger membrane proteins for NMR spectroscopic studies.

Rovers minimize human disturbance in research on wild animals.

PubMed

Le Maho, Yvon; Whittington, Jason D; Hanuise, Nicolas; Pereira, Louise; Boureau, Matthieu; Brucker, Mathieu; Chatelain, Nicolas; Courtecuisse, Julien; Crenner, Francis; Friess, Benjamin; Grosbellet, Edith; Kernaléguen, Laëtitia; Olivier, Frédérique; Saraux, Claire; Vetter, Nathanaël; Viblanc, Vincent A; Thierry, Bernard; Tremblay, Pascale; Groscolas, René; Le Bohec, Céline

2014-12-01

Investigating wild animals while minimizing human disturbance remains an important methodological challenge. When approached by a remote-operated vehicle (rover) which can be equipped to make radio-frequency identifications, wild penguins had significantly lower and shorter stress responses (determined by heart rate and behavior) than when approached by humans. Upon immobilization, the rover-unlike humans-did not disorganize colony structure, and stress rapidly ceased. Thus, rovers can reduce human disturbance of wild animals and the resulting scientific bias.

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.

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

Klesmith, Justin R.; Bacik, John -Paul; Michalczyk, Ryszard

Synthetic metabolic pathways often suffer from low specific productivity, and new methods that quickly assess pathway functionality for many thousands of variants are urgently needed. Here we present an approach that enables the rapid and parallel determination of sequence effects on flux for complete gene-encoding sequences. We show that this method can be used to determine the effects of over 8000 single point mutants of a pyrolysis oil catabolic pathway implanted in Escherichia coli. Experimental sequence-function data sets predicted whether fitness-enhancing mutations to the enzyme levoglucosan kinase resulted from enhanced catalytic efficiency or enzyme stability. A structure of one designmore » incorporating 38 mutations elucidated the structural basis of high fitness mutations. One design incorporating 15 beneficial mutations supported a 15-fold improvement in growth rate and greater than 24-fold improvement in enzyme activity relative to the starting pathway. Lastly, this technique can be extended to improve a wide variety of designed pathways.« less

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.

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…

Toward superconducting critical current by design

DOE PAGES

Sadovskyy, Ivan A.; Jia, Ying; Leroux, Maxime; ...

2016-03-31

The interaction of vortex matter with defects in applied superconductors directly determines their current carrying capacity. Defects range from chemically grown nanostructures and crystalline imperfections to the layered structure of the material itself. The vortex-defect interactions are non-additive in general, leading to complex dynamic behavior that has proven difficult to capture in analytical models. With recent rapid progress in computational powers, a new paradigm has emerged that aims at simulation assisted design of defect structures with predictable ‘critical-current-by-design’: analogous to the materials genome concept of predicting stable materials structures of interest. We demonstrate the feasibility of this paradigm by combiningmore » large-scale time-dependent Ginzburg-Landau numerical simulations with experiments on commercial high temperature superconductor (HTS) containing well-controlled correlated defects.« less

Robust feature extraction for rapid classification of damage in composites

NASA Astrophysics Data System (ADS)

Coelho, Clyde K.; Reynolds, Whitney; Chattopadhyay, Aditi

2009-03-01

The ability to detect anomalies in signals from sensors is imperative for structural health monitoring (SHM) applications. Many of the candidate algorithms for these applications either require a lot of training examples or are very computationally inefficient for large sample sizes. The damage detection framework presented in this paper uses a combination of Linear Discriminant Analysis (LDA) along with Support Vector Machines (SVM) to obtain a computationally efficient classification scheme for rapid damage state determination. LDA was used for feature extraction of damage signals from piezoelectric sensors on a composite plate and these features were used to train the SVM algorithm in parts, reducing the computational intensity associated with the quadratic optimization problem that needs to be solved during training. SVM classifiers were organized into a binary tree structure to speed up classification, which also reduces the total training time required. This framework was validated on composite plates that were impacted at various locations. The results show that the algorithm was able to correctly predict the different impact damage cases in composite laminates using less than 21 percent of the total available training data after data reduction.

Pressure relaxation and diffusion of vacancies in rapidly grown helium crystals

NASA Astrophysics Data System (ADS)

Birchenko, A. P.; Mikhin, N. P.; Rudavskii, E. Ya.; Smirnov, S. N.; Fysun, Ya. Yu.

2018-04-01

An experimental study of the features of pressure relaxation in rapidly grown crystals of a diluted solid solution 3He-4He, at temperatures above 1.3 K, was performed. A cylindrical cell with capacitive pressure sensors at the ends was used for measurements. It was found that, when the helium crystals were grown at cooling rates ≳4 mK/s, the difference in pressure ΔP registered by the sensors at 1.3 K reached 2.4 bars. The ΔP value decreased with subsequent stepwise increase in temperature, but reached zero only after thorough annealing at the premelting temperatures. The kinetics of pressure changes at the sample ends at different temperatures was recorded. The results obtained were interpreted within the framework of the structural relaxation model based on the monovacancy diffusion mechanism. The proposed model made it possible to explain the dependence of ΔP on the time and temperature recorded in the experiment, as well as to determine the activation energy of the structural relaxation process and the diffusion coefficient of vacancies. The details of the vacancy model are described in the Appendix.

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 analysis of controlled substances using desorption electrospray ionization mass spectrometry.

PubMed

Rodriguez-Cruz, Sandra E

2006-01-01

The recently developed technique of desorption electrospray ionization (DESI) has been applied to the rapid analysis of controlled substances. Experiments have been performed using a commercial ThermoFinnigan LCQ Advantage MAX ion-trap mass spectrometer with limited modifications. Results from the ambient sampling of licit and illicit tablets demonstrate the ability of the DESI technique to detect the main active ingredient(s) or controlled substance(s), even in the presence of other higher-concentration components. Full-scan mass spectrometry data provide preliminary identification by molecular weight determination, while rapid analysis using the tandem mass spectrometry (MS/MS) mode provides fragmentation data which, when compared to the laboratory-generated ESI-MS/MS spectral library, provide structural information and final identification of the active ingredient(s). The consecutive analysis of tablets containing different active components indicates there is no cross-contamination or interference from tablet to tablet, demonstrating the reliability of the DESI technique for rapid sampling (one tablet/min or better). Active ingredients have been detected for tablets in which the active component represents less than 1% of the total tablet weight, demonstrating the sensitivity of the technique. The real-time sampling of cannabis plant material is also presented.

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.

Structure and evolution of the large scale solar and heliospheric magnetic fields. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Hoeksema, J. T.

1984-01-01

Structure and evolution of large scale photospheric and coronal magnetic fields in the interval 1976-1983 were studied using observations from the Stanford Solar Observatory and a potential field model. The solar wind in the heliosphere is organized into large regions in which the magnetic field has a componenet either toward or away from the sun. The model predicts the location of the current sheet separating these regions. Near solar minimum, in 1976, the current sheet lay within a few degrees of the solar equator having two extensions north and south of the equator. Soon after minimum the latitudinal extent began to increase. The sheet reached to at least 50 deg from 1978 through 1983. The complex structure near maximum occasionally included multiple current sheets. Large scale structures persist for up to two years during the entire interval. To minimize errors in determining the structure of the heliospheric field particular attention was paid to decreasing the distorting effects of rapid field evolution, finding the optimum source surface radius, determining the correction to the sun's polar field, and handling missing data. The predicted structure agrees with direct interplanetary field measurements taken near the ecliptic and with coronameter and interplanetary scintillation measurements which infer the three dimensional interplanetary magnetic structure. During most of the solar cycle the heliospheric field cannot be adequately described as a dipole.

Algal and water-quality data for Rapid Creek and Canyon Lake near Rapid City, South Dakota, 2007

USGS Publications Warehouse

Hoogestraat, Galen K.; Putnam, Larry D.; Graham, Jennifer L.

2008-01-01

This report summarizes the results of algae and water-quality sampling on Rapid Creek and Canyon Lake during May and September 2007. The overall purpose of the study was to determine the algal community composition of Rapid Creek and Canyon Lake in relation to organisms that are known producers of unwanted tastes and odors in drinking-water supplies. Algal assemblage structure (phytoplankton and periphyton) was examined at 16 sites on Rapid Creek and Canyon Lake during May and September 2007, and actinomycetes bacteria were sampled at the Rapid City water treatment plant intake in May 2007, to determine if taste-and-odor producing organisms were present. During the May 2007 sampling, 3 Rapid Creek sites and 4 Canyon Lake sites were quantitatively sampled for phytoplankton in the water column, 7 Rapid Creek sites were quantitatively sampled for attached periphyton, and 4 lake and retention pond sites were qualitatively sampled for periphyton. Five Rapid Creek sites were sampled for geosmin and 2-methylisoborneol, two common taste-and-odor causing compounds known to affect water supplies. During the September 2007 sampling, 4 Rapid Creek sites were quantitatively sampled for attached periphyton, and 3 Canyon Lake sites were qualitatively sampled for periphyton. Water temperature, dissolved oxygen, pH, and specific conductance were measured during each sampling event. Methods of collection and sample analysis are presented for the various types of biological and chemical constituent samples. Diatoms comprised 91-100 percent of the total algal biovolume in periphyton samples collected during May and September. Cyanobacteria (also called blue-green algae) were detected in 7 of the 11 quantitative periphyton samples and ranged from 0.01 to 2.0 percent of the total biovolume. Cyanobacteria were present in 3 of the 7 phytoplankton samples collected in May, but the relative biovolumes were small (0.01-0.2 percent). Six of seven qualitative samples collected from Canyon Lake and retention ponds during May and September also contained cyanobacteria. Geosmin and 2-methylisoborneol concentrations were less than detection limits (0.005 ug/L) in all five of the Rapid Creek samples collected in May. Actinomycetes bacteria were present at the water treatment plant intake in May 2007, at a concentration of 6 colonies per milliliter. During this study, no taste-and-odor problems with the drinking water within the study area were reported. However, the presence of cyanobacterial taxa known to contain taste-and-odor producing strains (such as Leptolyngbya, Phormidium, and Anabaena) indicates the potential for taste-and-odor problems under certain physical and chemical conditions.

Exploring Molecular Mechanisms of Paradoxical Activation in the BRAF Kinase Dimers: Atomistic Simulations of Conformational Dynamics and Modeling of Allosteric Communication Networks and Signaling Pathways

PubMed Central

Tse, Amanda; Verkhivker, Gennady M.

2016-01-01

The recent studies have revealed that most BRAF inhibitors can paradoxically induce kinase activation by promoting dimerization and enzyme transactivation. Despite rapidly growing number of structural and functional studies about the BRAF dimer complexes, the molecular basis of paradoxical activation phenomenon is poorly understood and remains largely hypothetical. In this work, we have explored the relationships between inhibitor binding, protein dynamics and allosteric signaling in the BRAF dimers using a network-centric approach. Using this theoretical framework, we have combined molecular dynamics simulations with coevolutionary analysis and modeling of the residue interaction networks to determine molecular determinants of paradoxical activation. We have investigated functional effects produced by paradox inducer inhibitors PLX4720, Dabrafenib, Vemurafenib and a paradox breaker inhibitor PLX7904. Functional dynamics and binding free energy analyses of the BRAF dimer complexes have suggested that negative cooperativity effect and dimer-promoting potential of the inhibitors could be important drivers of paradoxical activation. We have introduced a protein structure network model in which coevolutionary residue dependencies and dynamic maps of residue correlations are integrated in the construction and analysis of the residue interaction networks. The results have shown that coevolutionary residues in the BRAF structures could assemble into independent structural modules and form a global interaction network that may promote dimerization. We have also found that BRAF inhibitors could modulate centrality and communication propensities of global mediating centers in the residue interaction networks. By simulating allosteric communication pathways in the BRAF structures, we have determined that paradox inducer and breaker inhibitors may activate specific signaling routes that correlate with the extent of paradoxical activation. While paradox inducer inhibitors may facilitate a rapid and efficient communication via an optimal single pathway, the paradox breaker may induce a broader ensemble of suboptimal and less efficient communication routes. The central finding of our study is that paradox breaker PLX7904 could mimic structural, dynamic and network features of the inactive BRAF-WT monomer that may be required for evading paradoxical activation. The results of this study rationalize the existing structure-functional experiments by offering a network-centric rationale of the paradoxical activation phenomenon. We argue that BRAF inhibitors that amplify dynamic features of the inactive BRAF-WT monomer and intervene with the allosteric interaction networks may serve as effective paradox breakers in cellular environment. PMID:27861609

Rapid Inspection of Aerospace Structures - Is It Autonomous Yet?

NASA Technical Reports Server (NTRS)

Bar-Cohen, Yoseph; Backes, Paul; Joffe, Benjamin

1996-01-01

The trend to increase the usage of aging aircraft added a great deal of urgency to the ongoing need for low-cost, rapid, simple-to-operate, reliable and efficient NDE methods for detection and characterization of flaws in aircraft structures. In many cases, the problem of inspection is complex due to the limitation of current technology and the need to disassemble aircraft structures and testing them in lab conditions. To overcome these limitations, reliable field inspection tools are being developed for rapid NDE of large and complex-shape structures, that can operate at harsh, hostal and remote conditions with minimum human interface. In recent years, to address the need for rapid inspection in field conditions, numerous portable scanners were developed using NDE methods, including ultrasonics, shearography, thermography. This paper is written with emphasis on ultrasonic NDE scanners, their evolution and the expected direction of growth.

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.

Regeneration and health: a structured, rapid literature review.

PubMed

McCartney, G; Hearty, W; Taulbut, M; Mitchell, R; Dryden, R; Collins, C

2017-07-01

To identify and synthesise what is known about the impacts of regeneration on health, health inequalities and their socio-economic determinants. Rapid, structured literature review. A rapid, structured approach was undertaken to identifying relevant studies involving a search of peer-reviewed literature databases, an Internet search to identify relevant grey literature, and a review of articles citing two key systematic reviews. The identified citations were screened, critically appraised according to the research design and narratively synthesised. Of the 1382 identified citations, 46 were screened as relevant to the review and included in the synthesis. Fifteen citations were reviews but most of the evidence identified or included within the reviews was of medium or low quality due to a lack of longitudinal follow-up, low response rates or attrition. The evidence base on the impacts of regeneration is generally not of high quality and is prone to bias. However, it is theorised as being an important means of addressing the socio-economic determinants of health. Housing refurbishment (generally, and for specific improvements) seems likely to lead to small improvements in health, whereas rehousing and mixed-tenure approaches have less clear impacts on health and carry risks of disruption to social networks and higher rents. Changes in the social composition of communities (gentrification) is a common outcome of regeneration and some 'partnership' approaches to regeneration have been shown to have caused difficulties within communities. The evidence base for regeneration activities is limited but they have substantial potential to contribute to improving population health. Better quality evidence is available for there being positive health impacts from housing-led regeneration programmes involving refurbishment and specific housing improvements. There is also some evidence of the potential harms of regeneration activities, including social stratification (gentrification and residualisation) and the destabilisation of existing community organisations. Broader labour market and housing policy approaches are also likely to be important as a context for understanding impacts. Regeneration programmes require careful design, implementation and evaluation if they are to contribute to improved health and reduced health inequalities. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Structural insights into Rhino-Deadlock complex for germline piRNA cluster specification.

PubMed

Yu, Bowen; Lin, Yu An; Parhad, Swapnil S; Jin, Zhaohui; Ma, Jinbiao; Theurkauf, William E; Zhang, Zz Zhao; Huang, Ying

2018-06-01

PIWI-interacting RNAs (piRNAs) silence transposons in germ cells to maintain genome stability and animal fertility. Rhino, a rapidly evolving heterochromatin protein 1 (HP1) family protein, binds Deadlock in a species-specific manner and so defines the piRNA-producing loci in the Drosophila genome. Here, we determine the crystal structures of Rhino-Deadlock complex in Drosophila melanogaster and simulans In both species, one Rhino binds the N-terminal helix-hairpin-helix motif of one Deadlock protein through a novel interface formed by the beta-sheet in the Rhino chromoshadow domain. Disrupting the interface leads to infertility and transposon hyperactivation in flies. Our structural and functional experiments indicate that electrostatic repulsion at the interaction interface causes cross-species incompatibility between the sibling species. By determining the molecular architecture of this piRNA-producing machinery, we discover a novel HP1-partner interacting mode that is crucial to piRNA biogenesis and transposon silencing. We thus explain the cross-species incompatibility of two sibling species at the molecular level. © 2018 The Authors.

Marsh canopy structure changes and the Deepwater Horizon oil spill

USGS Publications Warehouse

Ramsey, Elijah W.; Rangoonwala, Amina; Jones, Cathleen E.

2016-01-01

Marsh canopy structure was mapped yearly from 2009 to 2012 in the Barataria Bay, Louisiana coastal region that was impacted by the 2010 Deepwater Horizon (DWH) oil spill. Based on the previously demonstrated capability of NASA's UAVSAR polarimetric synthetic aperture radar (PolSAR) image data to map Spartina alterniflora marsh canopy structure, structure maps combining the leaf area index (LAI) and leaf angle distribution (LAD, orientation) were constructed for yearly intervals that were directly relatable to the 2010 LAI-LAD classification. The yearly LAI-LAD and LAI difference maps were used to investigate causes for the previously revealed dramatic change in marsh structure from prespill (2009) to postspill (2010, spill cessation), and the occurrence of structure features that exhibited abnormal spatial and temporal patterns. Water level and salinity records showed that freshwater releases used to keep the oil offshore did not cause the rapid growth from 2009 to 2010 in marsh surrounding the inner Bay. Photointerpretation of optical image data determined that interior marsh patches exhibiting rapid change were caused by burns and burn recovery, and that the pattern of 2010 to 2011 LAI decreases in backshore marsh and extending along some tidal channels into the interior marsh were not associated with burns. Instead, the majority of 2010 to 2011 shoreline features aligned with vectors displaying the severity of 2010 shoreline oiling from the DWH spill. Although the association is not conclusive of a causal oil impact, the coexistent pattern is a significant discovery. PolSAR marsh structure mapping provided a unique perspective of marsh biophysical status that enhanced detection of change and monitoring of trends important to management effectiveness.

Simple, rapid, and environmentally friendly method for the separation of isoflavones using ultra-high performance supercritical fluid chromatography.

PubMed

Wu, Wenjie; Zhang, Yuan; Wu, Hanqiu; Zhou, Weie; Cheng, Yan; Li, Hongna; Zhang, Chuanbin; Li, Lulu; Huang, Ying; Zhang, Feng

2017-07-01

Isoflavones are natural substances that exhibit hormone-like pharmacological activities. The separation of isoflavones remains an analytical challenge because of their similar structures. We show that ultra-high performance supercritical fluid chromatography can be an appropriate tool to achieve the fast separation of 12 common dietary isoflavones. Among the five tested columns the Torus DEA column was found to be the most effective column for the separation of these isoflavones. The impact of individual parameters on the retention time and separation factor was evaluated. These parameters were optimized to develop a simple, rapid, and green method for the separation of the 12 target analytes. It only took 12.91 min using gradient elution with methanol as an organic modifier and formic acid as an additive. These isoflavones were determined with limit of quantitation ranging from 0.10 to 0.50 μg/mL, which was sufficient for reliable determination of various matrixes. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

[Rapid analysis of the radionuclides plutonium and americium-241 in soils].

PubMed

Egorov, A V; Klochkova, N V

2009-01-01

The paper shows it possible to perform a rapid analysis of the isotopes of plutomium and americium-241. The basis of the developed rapid analysis is X-spectrometric determination of the amount of plutonium isotopes and gamma-spectrometric determination of the radionuclide 241AM.

Determination of psilocybin in Psilocybe semilanceata by capillary zone electrophoresis.

PubMed

Pedersen-Bjergaard, S; Sannes, E; Rasmussen, K E; Tønnesen, F

1997-07-04

A capillary zone electrophoretic (CZE) method was developed for the rapid determination of psilocybin in Psilocybe semilanceata. Following a simple two step extraction with 3.0+2.0 ml methanol, the hallucinogenic compound was effectively separated from matrix components by CZE utilizing a 10 mM borate-phosphate running buffer adjusted to pH 11.5. The identity of psilocybin was confirmed by migration time information and by UV spectra, while quantitation was accomplished utilizing barbital as internal standard. The calibration curve for psilocybin was linear within 0.01-1 mg/ml, while intra-day and inter-day variations of quantitative data were 0.5 and 2.5% R.S.D., respectively. In addition to psilocybin, the method was also suitable for the determination of the structurally related compound baeocystin.

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.

Structural requirements for the cytoprotective actions of mono-unsaturated fatty acids in the pancreatic β-cell line, BRIN-BD11

PubMed Central

Dhayal, S; Welters, H J; Morgan, N G

2008-01-01

Background and purpose: Exposure of pancreatic β-cells to long-chain free fatty acids leads to differential responses according to the chain length and degree of unsaturation. In particular, long-chain saturated molecules such as palmitate (C16:0) cause apoptosis, whereas equivalent mono-unsaturated species (for example, palmitoleate (C16:1)) are not overtly toxic. Moreover, mono-unsaturates exert a powerful cytoprotective response against a range of proapoptotic stimuli. However, the structural requirements that determine cytoprotection have not been determined and form the basis of the present study. Experimental approach: BRIN-BD11 and INS-1 β-cells were exposed either to the saturated fatty acid palmitate, or to serum withdrawal, to mediate cytotoxicity. The protective effects of a wide range of mono-unsaturated fatty acid derivatives were tested in cytotoxicity assays. Effector caspase activity was also measured and correlated with viability. Key results: The cytotoxic actions of palmitate were inhibited dose-dependently by long-chain mono-unsaturated fatty acids with a defined potency order C18:1>C16:1≫C14:1. The configuration of the double bond was also important with cis forms being more potent than trans forms. Alkylated mono-unsaturated fatty-acid derivates were also cytoprotective, although their efficacy declined as the alkyl chain length increased. Cytoprotection was achieved rapidly on addition of mono-unsaturates and correlated with a rapid and dramatic inhibition of caspase-3/7 activity in palmitate-treated cells. Conclusions and implications: The data reveal the structural requirements that dictate the cytoprotective actions of mono-unsaturated fatty acids in pancreatic β-cells. Metabolic activation is not required and the data point at the potential involvement of a fatty acid receptor in mediating cytoprotection. PMID:18297101

Rapid Discrimination of Gram-Positive and Gram-Negative Bacteria in Liquid Samples by Using NaOH-Sodium Dodecyl Sulfate Solution and Flow Cytometry

PubMed Central

Wada, Atsushi; Kono, Mari; Kawauchi, Sawako; Takagi, Yuri; Morikawa, Takashi; Funakoshi, Kunihiro

2012-01-01

Background For precise diagnosis of urinary tract infections (UTI), and selection of the appropriate prescriptions for their treatment, we explored a simple and rapid method of discriminating gram-positive and gram-negative bacteria in liquid samples. Methodology/Principal Findings We employed the NaOH-sodium dodecyl sulfate (SDS) solution conventionally used for plasmid extraction from Escherichia coli and the automated urine particle analyzer UF-1000i (Sysmex Corporation) for our novel method. The NaOH-SDS solution was used to determine differences in the cell wall structures between gram-positive and gram-negative bacteria, since the tolerance to such chemicals reflects the thickness and structural differences of bacterial cell walls. The UF-1000i instrument was used as a quantitative bacterial counter. We found that gram-negative bacteria, including E. coli, in liquid culture could easily be lysed by direct addition of equal volumes of NaOH-SDS solution. In contrast, Enterococcus faecalis, which is a gram-positive bacterium, could not be completely lysed by the solution. We then optimized the reaction time of the NaOH-SDS treatment at room temperature by using 3 gram-positive and 4 gram-negative bacterial strains and determined that the optimum reaction time was 5 min. Finally, in order to evaluate the generalizability of this method, we treated 8 gram-positive strains and 8 gram-negative strains, or 4 gram-positive and 4 gram-negative strains incubated in voluntary urine from healthy volunteers in the same way and demonstrated that all the gram-positive bacteria were discriminated quantitatively from gram negative bacteria using this method. Conclusions/Significance Using our new method, we could easily discriminate gram-positive and gram-negative bacteria in liquid culture media within 10 min. This simple and rapid method may be useful for determining the treatment course of patients with UTIs, especially for those without a prior history of UTIs. The method may be easily applied in order to obtain additional information for clinical prescriptions from bacteriuria. PMID:23077549

Rapid Determination of Mercury in Seafood in an Introductory Environmental Science Class

ERIC Educational Resources Information Center

Rice, Jeanette K.; Jenkins, J. David; Manley, A. Citabria; Sorel, Eric; Smith, C. Jimmy

2005-01-01

An experiment is described which allows easy, rapid determination of mercury levels in commercially seafood samples from a contaminated area. Students gain experience in the preparation of a calibration curve, the determination of unknown concentrations, and risk assessment based on experimentally determined data.

Social determinants of disability-based disadvantage in Solomon islands.

PubMed

Gartrell, Alexandra; Jennaway, Megan; Manderson, Lenore; Fangalasuu, Judy; Dolaiano, Simon

2018-04-01

Development discourse widely recognises that disability is the result of economic and social processes and structures that fail to accommodate persons with disabilities. Empirical work on the relationship between disability and poverty however, conceptualize poverty through an economic resource lens in high-income countries. To address this conceptual gap this article uses a social determinants of health perspective to examine how socio-cultural, economic and political contexts shape disability-based disadvantage. This article draws upon ethnographic research and supplementary data collected using rapid assessment techniques in Solomon Islands. Findings suggest that the disability-poverty nexus and inequalities in health, wellbeing and quality of life must be understood within broader patterns of social vulnerability that are institutionalised in landownership and patterns of descent, gendered power relations and disability specific stigmas that preclude social and productive engagement . This article demonstrates how a social determinant of health perspective that closely examines lived experiences of disability provides critical analytical insights into the structural mechanisms that constitute disability-based disadvantage. This article provides foundation knowledge on which policies and further research to promote disability-inclusion and equity can be based.

Anchor of Ni2+ on the Agmatine Sulfate-Modified Electrodes for the Determination of H2O2 in Food

NASA Astrophysics Data System (ADS)

Yan, Yuhua; Zhang, Zhonghui; Xiao, Mingshu; Zhou, Hualan

2017-07-01

A method was developed to conveniently and rapidly determine hydrogen peroxide (H2O2) in food. The glassy carbon electrode (GCE) modified with agmatine sulfate (AS) easily anchoring nickel ion was attached to AS with polyamine structure. As a result, more Ni2+ was obtained and transformed to Ni(OH)2/NiOOH on the AS-GCE, which caused the electrode to own much better electrocatalytic performance on H2O2. Based on these, the content of H2O2 in thin sheet of bean curd sample was detected with standard addition method, by which good results were obtained.

Explaining gender differences in ill-health in South Korea: the roles of socio-structural, psychosocial, and behavioral factors.

PubMed

Chun, Heeran; Khang, Young-Ho; Kim, Il-Ho; Cho, Sung-Il

2008-09-01

This study examines and explains the gender disparity in health despite rapid modernization in South Korea where the social structure is still based on traditional gender relations. A nationally representative sample of 2897 men and 3286 women aged 25-64 from the 2001 Korean National Health and Nutrition Examination Survey was analyzed. Health indicators included self rated health and chronic disease. Age-adjusted prevalence was computed according to a gender and odds ratios (OR) derived from logistic regression. Percentage changes in OR by inclusion of determinant variables (socio-structural, psychosocial, and behavioral) into the base logistic regression model were used to estimate the contributions to the gender gap in two morbidity measures. Results showed a substantial female excess in ill-health in both measures, revealing an increasing disparity in the older age group. Group-specific age-adjusted prevalence of ill-health showed an inverse relationship to socioeconomic position. When adjusting for each determinant, employment status, education, and depression contributed the greatest to the gender gap. After adjusting for all suggested determinants, 78% for self rated health and 86% for chronic disease in excess OR could be explained. After stratifying for age, the full model provided a complete explanation for the female excess in chronic illness, but for self rated health a female excess was still evident for the younger age group. Socio-structural factors played a crucial role in accounting for female excess in ill-health. This result calls for greater attention to gender-based health inequality stemming from socio-structural determinants in South Korea. Cross-cultural validation studies are suggested for further discussion of the link between changing gender relations and the gender health gap in morbidity in diverse settings.

The speed of metacognition: taking time to get to know one's structural knowledge.

PubMed

Mealor, Andy D; Dienes, Zoltan

2013-03-01

The time course of different metacognitive experiences of knowledge was investigated using artificial grammar learning. Experiment 1 revealed that when participants are aware of the basis of their judgments (conscious structural knowledge) decisions are made most rapidly, followed by decisions made with conscious judgment but without conscious knowledge of underlying structure (unconscious structural knowledge), and guess responses (unconscious judgment knowledge) were made most slowly, even when controlling for differences in confidence and accuracy. In experiment 2, short response deadlines decreased the accuracy of unconscious but not conscious structural knowledge. Conversely, the deadline decreased the proportion of conscious structural knowledge in favour of guessing. Unconscious structural knowledge can be applied rapidly but becomes more reliable with additional metacognitive processing time whereas conscious structural knowledge is an all-or-nothing response that cannot always be applied rapidly. These dissociations corroborate quite separate theories of recognition (dual-process) and metacognition (higher order thought and cross-order integration). Copyright © 2012 Elsevier Inc. All rights reserved.

Monoclonal Antibody Interactions with Micro- and Nanoparticles: Adsorption, Aggregation and Accelerated Stress Studies

PubMed Central

Bee, Jared S.; Chiu, David; Sawicki, Suzanne; Stevenson, Jennifer L.; Chatterjee, Koustuv; Freund, Erwin; Carpenter, John F.; Randolph, Theodore W.

2009-01-01

Therapeutic proteins are exposed to various wetted surfaces that could shed sub-visible particles. In this work we measured the adsorption of a monoclonal antibody (mAb) to various microparticles, characterized the adsorbed mAb secondary structure, and determined the reversibility of adsorption. We also developed and used a front-face fluorescence quenching method to determine that the mAb tertiary structure was near-native when adsorbed to glass, cellulose and silica. Initial adsorption to each of the materials tested was rapid. During incubation studies, exposure to the air-water interface was a significant cause of aggregation but acted independently of the effects of microparticles. Incubations with glass, cellulose, stainless steel or Fe2O3 microparticles gave very different results. Cellulose preferentially adsorbed aggregates from solution. Glass and Fe2O3 adsorbed the mAb but did not cause aggregation. Adsorption to stainless steel microparticles was irreversible, and caused appearance of soluble aggregates upon incubation. The secondary structure of mAb adsorbed to glass and cellulose was near-native. We suggest that the protocol described in this work could be a useful preformulation stress screening tool to determine the sensitivity of a therapeutic protein to exposure to common surfaces encountered during processing and storage. PMID:19492408

Micro-Mirrors for Nanoscale Three-Dimensional Microscopy

PubMed Central

Seale, Kevin; Janetopoulos, Chris; Wikswo, John

2013-01-01

A research-grade optical microscope is capable of resolving fine structures in two-dimensional images. However, three-dimensional resolution, or the ability of the microscope to distinguish between objects lying above or below the focal plane from in-focus objects, is not nearly as good as in-plane resolution. In this issue of ACS Nano, McMahon et al. report the use of mirrored pyramidal wells with a conventional microscope for rapid, 3D localization and tracking of nanoparticles. Mirrors have been used in microscopy before, but recent work with MPWs is unique because it enables the rapid determination of the x-, y-, and z-position of freely diffusing nanoparticles and cellular nanostructures with unprecedented speed and spatial accuracy. As inexpensive tools for 3D visualization, mirrored pyramidal wells may prove to be invaluable aids in nanotechnology and engineering of nanomaterials. PMID:19309167

Application of Rapid Prototyping Pelvic Model for Patients with DDH to Facilitate Arthroplasty Planning: A Pilot Study.

PubMed

Xu, Jie; Li, Deng; Ma, Ruo-fan; Barden, Bertram; Ding, Yue

2015-11-01

Total hip arthroplasty (THA) is challenging in cases of osteoarthritis secondary to developmental dysplasia of the hip (DDH). Acetabular deficiency makes the positioning of the acetabular component difficult. Computer tomography based, patient-individual three dimensional (3-D) rapid prototype technology (RPT)-models were used to plan the placement of acetabular cup so that a surgeon was able to identify pelvic structures, assess the ideal extent of reaming and determine the size of cup after a reconstructive procedure. Intraclass correlation coefficients (ICCs) were used to analyze the agreement between the sizes of chosen components on the basis of preoperative planning and the actual sizes used in the operation. The use of the 3-D RPT-model facilitates the surgical procedures due to better planning and improved orientation. Copyright © 2015 Elsevier Inc. All rights reserved.

Rapid Evaporation in Fuel Injection

NASA Astrophysics Data System (ADS)

McCahan, S.; Kessler, C.

1997-11-01

Preheating fuel prior to injection through a nozzle can induce a superheated state during expansion. The resulting rapid evaporation improves atomization of the fluid and, therefore, may improve combustion efficiency. A sufficient degree of superheat im posed on a fuel with a high specific heat (retrograde fluid) can theoretically result in complete evaporation. In the work done by Sloss and McCahan (APS/DFD meeting 1996), dodecane, fuel oil, kerosene, and diesel oil were studied. In this continuation of the same study, decane and tetradecane are preheated to temperatures ranging from 20^oC to 330^oC at a p ressure of 10 bar and injected into a chamber at 1 bar. A simple converging nozzle is used. Photographs taken of the resulting sprays are used to determine cone angles and make qualitative observations of droplet size and spray structure.

Searches for New Physics Using High Mass Dimuons at the CDF II Experiment

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

Karagoz Unel, Muge

2004-12-01

This work describes the measurement of inclusive jets cross section in the D0 experiment. This cross section is computed as a function of jet transverse momentum, in several rapidity intervals. This quantity is sensitive to the proton structure and is crucial for the determination of parton distribution functions (PDF), essentially for the gluon at high proton momentum fraction. The measurement presented here gives the first values obtained for Tevatron Run II for the cross section in several rapidity intervals, for an integrated luminosity of 143 pb -1. The results are in agreement, within the uncertainties, with theoretical Standard Model predictions,more » showing no evidence for new physics. This work points out the aspects of the detector which need better understanding to reach Run I precision and to constrain the PDFs.« less

RAPID and DDS

NASA Technical Reports Server (NTRS)

Utz, Hans Heinrich

2011-01-01

This talk gives an overview of the the Robot Applications Programmers Interface Delegate (RAPID) as well as the distributed systems middleware Data Distribution Service (DDS). DDS is an open software standard, RAPID is cleared for open-source release under NOSA. RAPID specifies data-structures and semantics for high-level telemetry published by NASA robotic software. These data-structures are supported by multiple robotic platforms at Johnson Space Center (JSC), Jet Propulsion Laboratory (JPL) and Ames Research Center (ARC), providing high-level interoperability between those platforms. DDS is used as the middleware for data transfer. The feature set of the middleware heavily influences the design decision made in the RAPID specification. So it is appropriate to discuss both in this introductory talk.

Accurate Rapid Lifetime Determination on Time-Gated FLIM Microscopy with Optical Sectioning

PubMed Central

Silva, Susana F.; Domingues, José Paulo

2018-01-01

Time-gated fluorescence lifetime imaging microscopy (FLIM) is a powerful technique to assess the biochemistry of cells and tissues. When applied to living thick samples, it is hampered by the lack of optical sectioning and the need of acquiring many images for an accurate measurement of fluorescence lifetimes. Here, we report on the use of processing techniques to overcome these limitations, minimizing the acquisition time, while providing optical sectioning. We evaluated the application of the HiLo and the rapid lifetime determination (RLD) techniques for accurate measurement of fluorescence lifetimes with optical sectioning. HiLo provides optical sectioning by combining the high-frequency content from a standard image, obtained with uniform illumination, with the low-frequency content of a second image, acquired using structured illumination. Our results show that HiLo produces optical sectioning on thick samples without degrading the accuracy of the measured lifetimes. We also show that instrument response function (IRF) deconvolution can be applied with the RLD technique on HiLo images, improving greatly the accuracy of the measured lifetimes. These results open the possibility of using the RLD technique with pulsed diode laser sources to determine accurately fluorescence lifetimes in the subnanosecond range on thick multilayer samples, providing that offline processing is allowed. PMID:29599938

Accurate Rapid Lifetime Determination on Time-Gated FLIM Microscopy with Optical Sectioning.

PubMed

Silva, Susana F; Domingues, José Paulo; Morgado, António Miguel

2018-01-01

Time-gated fluorescence lifetime imaging microscopy (FLIM) is a powerful technique to assess the biochemistry of cells and tissues. When applied to living thick samples, it is hampered by the lack of optical sectioning and the need of acquiring many images for an accurate measurement of fluorescence lifetimes. Here, we report on the use of processing techniques to overcome these limitations, minimizing the acquisition time, while providing optical sectioning. We evaluated the application of the HiLo and the rapid lifetime determination (RLD) techniques for accurate measurement of fluorescence lifetimes with optical sectioning. HiLo provides optical sectioning by combining the high-frequency content from a standard image, obtained with uniform illumination, with the low-frequency content of a second image, acquired using structured illumination. Our results show that HiLo produces optical sectioning on thick samples without degrading the accuracy of the measured lifetimes. We also show that instrument response function (IRF) deconvolution can be applied with the RLD technique on HiLo images, improving greatly the accuracy of the measured lifetimes. These results open the possibility of using the RLD technique with pulsed diode laser sources to determine accurately fluorescence lifetimes in the subnanosecond range on thick multilayer samples, providing that offline processing is allowed.

The electric field structure of auroral arcs as determined from barium plasma injection experiments

NASA Technical Reports Server (NTRS)

Wescott, E. M.

1981-01-01

Barium plasma injection experiments have revealed a number of features of electric fields in and near auroral forms extending from a few hundred to many thousands of km in altitude. There is evidence for V-type potential structures over some auroras, but not in others. For some auroral arcs, large E fields are found at ionospheric altitudes outside the arc but the E field inside the arc is near zero. In a few other auroras, most recently one investigated in an experiment conducted from Poker Flat on March 22, 1980, large, rapidly fluctuating E fields were detected by barium plasma near 600 km altitude. These E fields suggest that the motion of auroral rays can be an effect of low-altitude electric fields, or that V-type potential structures may be found at low altitudes.

A MEMS-based Air Flow Sensor with a Free-standing Micro-cantilever Structure.

PubMed

Wang, Yu-Hsiang; Lee, Chia-Yen; Chiang, Che-Ming

2007-10-17

This paper presents a micro-scale air flow sensor based on a free-standingcantilever structure. In the fabrication process, MEMS techniques are used to deposit asilicon nitride layer on a silicon wafer. A platinum layer is deposited on the silicon nitridelayer to form a piezoresistor, and the resulting structure is then etched to create afreestanding micro-cantilever. When an air flow passes over the surface of the cantileverbeam, the beam deflects in the downward direction, resulting in a small variation in theresistance of the piezoelectric layer. The air flow velocity is determined by measuring thechange in resistance using an external LCR meter. The experimental results indicate that theflow sensor has a high sensitivity (0.0284 ω/ms -1 ), a high velocity measurement limit (45ms -1 ) and a rapid response time (0.53 s).

Development of flexural vibration inspection techniques to rapidly assess the structural health of rural bridge systems

Treesearch

Brian K. Brashaw; Robert Vatalaro; Xiping Wang; Kevin Sarvela; James P. Wacker

2008-01-01

Approximately 4,000 vehicle bridges in the State of Minnesota contain structural timber members. Recent research at the University of Minnesota Duluth Natural Resources Research Institute (UMD NRRI) has been conducted on vibration testing of timber bridges as a means of developing rapid in-place testing techniques for assessing the structural health of bridges. The...

Assessment of RapidEye vegetation indices for estimation of leaf area index and biomass in corn and soybean crops

NASA Astrophysics Data System (ADS)

Kross, Angela; McNairn, Heather; Lapen, David; Sunohara, Mark; Champagne, Catherine

2015-02-01

Leaf area index (LAI) and biomass are important indicators of crop development and the availability of this information during the growing season can support farmer decision making processes. This study demonstrates the applicability of RapidEye multi-spectral data for estimation of LAI and biomass of two crop types (corn and soybean) with different canopy structure, leaf structure and photosynthetic pathways. The advantages of Rapid Eye in terms of increased temporal resolution (∼daily), high spatial resolution (∼5 m) and enhanced spectral information (includes red-edge band) are explored as an individual sensor and as part of a multi-sensor constellation. Seven vegetation indices based on combinations of reflectance in green, red, red-edge and near infrared bands were derived from RapidEye imagery between 2011 and 2013. LAI and biomass data were collected during the same period for calibration and validation of the relationships between vegetation indices and LAI and dry above-ground biomass. Most indices showed sensitivity to LAI from emergence to 8 m2/m2. The normalized difference vegetation index (NDVI), the red-edge NDVI and the green NDVI were insensitive to crop type and had coefficients of variations (CV) ranging between 19 and 27%; and coefficients of determination ranging between 86 and 88%. The NDVI performed best for the estimation of dry leaf biomass (CV = 27% and r2 = 090) and was also insensitive to crop type. The red-edge indices did not show any significant improvement in LAI and biomass estimation over traditional multispectral indices. Cumulative vegetation indices showed strong performance for estimation of total dry above-ground biomass, especially for corn (CV ≤ 20%). This study demonstrated that continuous crop LAI monitoring over time and space at the field level can be achieved using a combination of RapidEye, Landsat and SPOT data and sensor-dependant best-fit functions. This approach eliminates/reduces the need for reflectance resampling, VIs inter-calibration and spatial resampling.

Forest Landscape Assessment Tool (FLAT): rapid assessment for land management

Treesearch

Lisa Ciecko; David Kimmett; Jesse Saunders; Rachael Katz; Kathleen L. Wolf; Oliver Bazinet; Jeffrey Richardson; Weston Brinkley; Dale J. Blahna

2016-01-01

The Forest Landscape Assessment Tool (FLAT) is a set of procedures and tools used to rapidly determine forest ecological conditions and potential threats. FLAT enables planners and managers to understand baseline conditions, determine and prioritize restoration needs across a landscape system, and conduct ongoing monitoring to achieve land management goals. The rapid...

Development of high resolution NMR spectroscopy as a structural tool

NASA Astrophysics Data System (ADS)

Feeney, James

1992-06-01

The discovery of the nuclear magnetic resonance (NMR) phenomenon and its development and exploitation as a scientific tool provide an excellent basis for a case-study for examining the factors which control the evolution of scientific techniques. Since the detection of the NMR phenomenon and the subsequent rapid discovery of all the important NMR spectral parameters in the late 1940s, the method has emerged as one of the most powerful techniques for determining structures of molecules in solution and for analysis of complex mixtures. The method has made a dramatic impact on the development of structural chemistry over the last 30 years and is now one of the key techniques in this area. Support for NMR instrumentation attracts a dominant slice of public funding in most scientifically developed countries. The technique is an excellent example of how instrumentation and technology have revolutionised structural chemistry and it is worth exploring how it has been developed so successfully. Clearly its wide range of application and the relatively direct connection between the NMR data and molecular structure has created a major market for the instrumentation. This has provided several competing manufacturers with the incentive to develop better and better instruments. Understanding the complexity of the basics of NMR spectroscopy has been an ongoing challenge attracting the attention of physicists. The well-organised specialist NMR literature and regular scientific meetings have ensured rapid exploitation of any theoretical advances that have a practical relevance. In parallel, the commercial development of the technology has allowed the fruits of such theoretical advances to be enjoyed by the wider scientific community.

A Particle Representation Model for the Deformation of Homogeneous Turbulence

NASA Technical Reports Server (NTRS)

Kassinos, S. C.; Reynolds, W. C.

1996-01-01

In simple flows, where the mean deformation rates are mild and the turbulence has time to come to equilibrium with the mean flow, the Reynolds stresses are determined by the applied strain rate. Hence in these flows, it is often adequate to use an eddy-viscosity representation. The modern family of kappa-epsilon models has been very useful in predicting near equilibrium turbulent flows, where the rms deformation rate S is small compared to the reciprocal time scale of the turbulence (epsilon/kappa). In modern engineering applications, turbulence models are quite often required to predict flows with very rapid deformations (large S kappa/epsilon). In these flows, the structure takes some time to respond and eddy viscosity models are inadequate. The response of turbulence to rapid deformations is given by rapid distortion theory (RDT). Under RDT the nonlinear effects due to turbulence-turbulence interactions are neglected in the governing equations, but even when linearized in this fashion, the governing equations are unclosed at the one-point level due to the non-locality of the pressure fluctuations.

Rapid structural analysis of nanomaterials in aqueous solutions

NASA Astrophysics Data System (ADS)

Ryuzaki, Sou; Tsutsui, Makusu; He, Yuhui; Yokota, Kazumichi; Arima, Akihide; Morikawa, Takanori; Taniguchi, Masateru; Kawai, Tomoji

2017-04-01

Rapid structural analysis of nanoscale matter in a liquid environment represents innovative technologies that reveal the identities and functions of biologically important molecules. However, there is currently no method with high spatio-temporal resolution that can scan individual particles in solutions to gain structural information. Here we report the development of a nanopore platform realizing quantitative structural analysis for suspended nanomaterials in solutions with a high z-axis and xy-plane spatial resolution of 35.8 ± 1.1 and 12 nm, respectively. We used a low thickness-to-diameter aspect ratio pore architecture for achieving cross sectional areas of analyte (i.e. tomograms). Combining this with multiphysics simulation methods to translate ionic current data into tomograms, we demonstrated rapid structural analysis of single polystyrene (Pst) beads and single dumbbell-like Pst beads in aqueous solutions.

Structure-Function Modeling of Optical Coherence Tomography and Standard Automated Perimetry in the Retina of Patients with Autosomal Dominant Retinitis Pigmentosa

PubMed Central

Smith, Travis B.; Parker, Maria; Steinkamp, Peter N.; Weleber, Richard G.; Smith, Ning; Wilson, David J.

2016-01-01

Purpose To assess relationships between structural and functional biomarkers, including new topographic measures of visual field sensitivity, in patients with autosomal dominant retinitis pigmentosa. Methods Spectral domain optical coherence tomography line scans and hill of vision (HOV) sensitivity surfaces from full-field standard automated perimetry were semi-automatically aligned for 60 eyes of 35 patients. Structural biomarkers were extracted from outer retina b-scans along horizontal and vertical midlines. Functional biomarkers were extracted from local sensitivity profiles along the b-scans and from the full visual field. These included topographic measures of functional transition such as the contour of most rapid sensitivity decline around the HOV, herein called HOV slope for convenience. Biomarker relationships were assessed pairwise by coefficients of determination (R2) from mixed-effects analysis with automatic model selection. Results Structure-function relationships were accurately modeled (conditional R2>0.8 in most cases). The best-fit relationship models and correlation patterns for horizontally oriented biomarkers were different than vertically oriented ones. The structural biomarker with the largest number of significant functional correlates was the ellipsoid zone (EZ) width, followed by the total photoreceptor layer thickness. The strongest correlation observed was between EZ width and HOV slope distance (marginal R2 = 0.85, p<10−10). The mean sensitivity defect at the EZ edge was 7.6 dB. Among all functional biomarkers, the HOV slope mean value, HOV slope mean distance, and maximum sensitivity along the b-scan had the largest number of significant structural correlates. Conclusions Topographic slope metrics show promise as functional biomarkers relevant to the transition zone. EZ width is strongly associated with the location of most rapid HOV decline. PMID:26845445

Structure-Function Modeling of Optical Coherence Tomography and Standard Automated Perimetry in the Retina of Patients with Autosomal Dominant Retinitis Pigmentosa.

PubMed

Smith, Travis B; Parker, Maria; Steinkamp, Peter N; Weleber, Richard G; Smith, Ning; Wilson, David J

2016-01-01

To assess relationships between structural and functional biomarkers, including new topographic measures of visual field sensitivity, in patients with autosomal dominant retinitis pigmentosa. Spectral domain optical coherence tomography line scans and hill of vision (HOV) sensitivity surfaces from full-field standard automated perimetry were semi-automatically aligned for 60 eyes of 35 patients. Structural biomarkers were extracted from outer retina b-scans along horizontal and vertical midlines. Functional biomarkers were extracted from local sensitivity profiles along the b-scans and from the full visual field. These included topographic measures of functional transition such as the contour of most rapid sensitivity decline around the HOV, herein called HOV slope for convenience. Biomarker relationships were assessed pairwise by coefficients of determination (R2) from mixed-effects analysis with automatic model selection. Structure-function relationships were accurately modeled (conditional R(2)>0.8 in most cases). The best-fit relationship models and correlation patterns for horizontally oriented biomarkers were different than vertically oriented ones. The structural biomarker with the largest number of significant functional correlates was the ellipsoid zone (EZ) width, followed by the total photoreceptor layer thickness. The strongest correlation observed was between EZ width and HOV slope distance (marginal R(2) = 0.85, p<10(-10)). The mean sensitivity defect at the EZ edge was 7.6 dB. Among all functional biomarkers, the HOV slope mean value, HOV slope mean distance, and maximum sensitivity along the b-scan had the largest number of significant structural correlates. Topographic slope metrics show promise as functional biomarkers relevant to the transition zone. EZ width is strongly associated with the location of most rapid HOV decline.

Solving the nanostructure problem: exemplified on metallic alloy nanoparticles

NASA Astrophysics Data System (ADS)

Petkov, Valeri; Prasai, Binay; Ren, Yang; Shan, Shiyao; Luo, Jin; Joseph, Pharrah; Zhong, Chuan-Jian

2014-08-01

With current technology moving rapidly toward smaller scales nanometer-size materials, hereafter called nanometer-size particles (NPs), are being produced in increasing numbers and explored for various useful applications ranging from photonics and catalysis to detoxification of wastewater and cancer therapy. Nature also is a prolific producer of useful NPs. Evidence can be found in ores on the ocean floor, minerals and soils on land and in the human body that, when water is excluded, is mostly made of proteins that are 6-10 nm in size and globular in shape. Precise knowledge of the 3D atomic-scale structure, that is how atoms are arranged in space, is a crucial prerequisite for understanding and so gaining more control over the properties of any material, including NPs. In the case of bulk materials such knowledge is fairly easy to obtain by Bragg diffraction experiments. Determining the 3D atomic-scale structure of NPs is, however, still problematic spelling trouble for science and technology at the nanoscale. Here we explore this so-called ``nanostructure problem'' from a practical point of view arguing that it can be solved when its technical, that is the inapplicability of Bragg diffraction to NPs, and fundamental, that is the incompatibility of traditional crystallography with NPs, aspects are both addressed properly. As evidence we present a successful and broadly applicable, 6-step approach to determining the 3D atomic-scale structure of NPs based on a suitable combination of a few experimental and computational techniques. This approach is exemplified on 5 nm sized PdxNi100-x particles (x = 26, 56 and 88) explored for catalytic applications. Furthermore, we show how once an NP atomic structure is determined precisely, a strategy for improving NP structure-dependent properties of particular interest to science and technology can be designed rationally and not subjectively as frequently done now.With current technology moving rapidly toward smaller scales nanometer-size materials, hereafter called nanometer-size particles (NPs), are being produced in increasing numbers and explored for various useful applications ranging from photonics and catalysis to detoxification of wastewater and cancer therapy. Nature also is a prolific producer of useful NPs. Evidence can be found in ores on the ocean floor, minerals and soils on land and in the human body that, when water is excluded, is mostly made of proteins that are 6-10 nm in size and globular in shape. Precise knowledge of the 3D atomic-scale structure, that is how atoms are arranged in space, is a crucial prerequisite for understanding and so gaining more control over the properties of any material, including NPs. In the case of bulk materials such knowledge is fairly easy to obtain by Bragg diffraction experiments. Determining the 3D atomic-scale structure of NPs is, however, still problematic spelling trouble for science and technology at the nanoscale. Here we explore this so-called ``nanostructure problem'' from a practical point of view arguing that it can be solved when its technical, that is the inapplicability of Bragg diffraction to NPs, and fundamental, that is the incompatibility of traditional crystallography with NPs, aspects are both addressed properly. As evidence we present a successful and broadly applicable, 6-step approach to determining the 3D atomic-scale structure of NPs based on a suitable combination of a few experimental and computational techniques. This approach is exemplified on 5 nm sized PdxNi100-x particles (x = 26, 56 and 88) explored for catalytic applications. Furthermore, we show how once an NP atomic structure is determined precisely, a strategy for improving NP structure-dependent properties of particular interest to science and technology can be designed rationally and not subjectively as frequently done now. Electronic supplementary information (ESI) available: XRD patterns, TEM and 3D structure modeling results. See DOI: 10.1039/c4nr01633e

PhyreStorm: A Web Server for Fast Structural Searches Against the PDB.

PubMed

Mezulis, Stefans; Sternberg, Michael J E; Kelley, Lawrence A

2016-02-22

The identification of structurally similar proteins can provide a range of biological insights, and accordingly, the alignment of a query protein to a database of experimentally determined protein structures is a technique commonly used in the fields of structural and evolutionary biology. The PhyreStorm Web server has been designed to provide comprehensive, up-to-date and rapid structural comparisons against the Protein Data Bank (PDB) combined with a rich and intuitive user interface. It is intended that this facility will enable biologists inexpert in bioinformatics access to a powerful tool for exploring protein structure relationships beyond what can be achieved by sequence analysis alone. By partitioning the PDB into similar structures, PhyreStorm is able to quickly discard the majority of structures that cannot possibly align well to a query protein, reducing the number of alignments required by an order of magnitude. PhyreStorm is capable of finding 93±2% of all highly similar (TM-score>0.7) structures in the PDB for each query structure, usually in less than 60s. PhyreStorm is available at http://www.sbg.bio.ic.ac.uk/phyrestorm/. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

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

Determination of boiling point of petrochemicals by gas chromatography-mass spectrometry and multivariate regression analysis of structural activity relationship.

PubMed

Fakayode, Sayo O; Mitchell, Breanna S; Pollard, David A

2014-08-01

Accurate understanding of analyte boiling points (BP) is of critical importance in gas chromatographic (GC) separation and crude oil refinery operation in petrochemical industries. This study reported the first combined use of GC separation and partial-least-square (PLS1) multivariate regression analysis of petrochemical structural activity relationship (SAR) for accurate BP determination of two commercially available (D3710 and MA VHP) calibration gas mix samples. The results of the BP determination using PLS1 multivariate regression were further compared with the results of traditional simulated distillation method of BP determination. The developed PLS1 regression was able to correctly predict analytes BP in D3710 and MA VHP calibration gas mix samples, with a root-mean-square-%-relative-error (RMS%RE) of 6.4%, and 10.8% respectively. In contrast, the overall RMS%RE of 32.9% and 40.4%, respectively obtained for BP determination in D3710 and MA VHP using a traditional simulated distillation method were approximately four times larger than the corresponding RMS%RE of BP prediction using MRA, demonstrating the better predictive ability of MRA. The reported method is rapid, robust, and promising, and can be potentially used routinely for fast analysis, pattern recognition, and analyte BP determination in petrochemical industries. Copyright © 2014 Elsevier B.V. All rights reserved.

Orbital thermal analysis of lattice structured spacecraft using color video display techniques

NASA Technical Reports Server (NTRS)

Wright, R. L.; Deryder, D. D.; Palmer, M. T.

1983-01-01

A color video display technique is demonstrated as a tool for rapid determination of thermal problems during the preliminary design of complex space systems. A thermal analysis is presented for the lattice-structured Earth Observation Satellite (EOS) spacecraft at 32 points in a baseline non Sun-synchronous (60 deg inclination) orbit. Large temperature variations (on the order of 150 K) were observed on the majority of the members. A gradual decrease in temperature was observed as the spacecraft traversed the Earth's shadow, followed by a sudden rise in temperature (100 K) as the spacecraft exited the shadow. Heating rate and temperature histories of selected members and color graphic displays of temperatures on the spacecraft are presented.

Features of Crystallization of Rapidly Quenched Ni45Ti32Hf18Cu5 and Ni25Ti32Hf18Cu25 Alloys from Melt with High-Temperature Shape Memory Effect

NASA Astrophysics Data System (ADS)

Pushin, A. V.; Pushin, V. G.; Kuntsevich, T. E.; Kuranova, N. N.; Makarov, V. V.; Uksusnikov, A. N.; Kourov, N. I.

2017-12-01

A comparative study of the structure and the chemical and phase composition of Ni45Ti32Hf18Cu5 and Ni25Ti32Hf18Cu25 amorphous alloys obtained by fast-quenching of melt stream by spinning has been carried out by transmission and scanning electron microscopy and X-ray diffraction. The critical temperatures of their devitrification were determined by the data of temperatures measurements of electrical resistance. The features of the formation of ultrafine structure and the phase transformation at the vitrification depending on the regimes of heat treatment and chemical composition of alloy have been established.

Comprehensive sequence-flux mapping of a levoglucosan utilization pathway in E. coli

DOE PAGES

Klesmith, Justin R.; Bacik, John -Paul; Michalczyk, Ryszard; ...

2015-09-14

Synthetic metabolic pathways often suffer from low specific productivity, and new methods that quickly assess pathway functionality for many thousands of variants are urgently needed. Here we present an approach that enables the rapid and parallel determination of sequence effects on flux for complete gene-encoding sequences. We show that this method can be used to determine the effects of over 8000 single point mutants of a pyrolysis oil catabolic pathway implanted in Escherichia coli. Experimental sequence-function data sets predicted whether fitness-enhancing mutations to the enzyme levoglucosan kinase resulted from enhanced catalytic efficiency or enzyme stability. A structure of one designmore » incorporating 38 mutations elucidated the structural basis of high fitness mutations. One design incorporating 15 beneficial mutations supported a 15-fold improvement in growth rate and greater than 24-fold improvement in enzyme activity relative to the starting pathway. Lastly, this technique can be extended to improve a wide variety of designed pathways.« less

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

Amaya, Andrew J.; Pathak, Harshad; Modak, Viraj P.

Using an X-ray laser, we investigated the crystal structure of ice formed by homogeneous ice nucleation in deeply supercooled water nanodrops (r ≈ 10 nm) at ~225 K. The nanodrops were formed by condensation of vapor in a supersonic nozzle, and the ice was probed within 100 μs of freezing using femtosecond wide-angle X-ray scattering at the Linac Coherent Light Source free-electron X-ray laser. The X-ray diffraction spectra indicate that this ice has a metastable, predominantly cubic structure; the shape of the first ice diffraction peak suggests stacking-disordered ice with a cubicity value, χ, in the range of 0.78 ±more » 0.05. The cubicity value determined here is higher than those determined in experiments with micron-sized drops but comparable to those found in molecular dynamics simulations. Lastly, the high cubicity is most likely caused by the extremely low freezing temperatures and by the rapid freezing, which occurs on a ~1 μs time scale in single nanodroplets.« less

Protein crystal growth in microgravity: Temperature induced large scale crystallization of insulin

NASA Technical Reports Server (NTRS)

Long, Marianna M.; Delucas, Larry J.; Smith, C.; Carson, M.; Moore, K.; Harrington, Michael D.; Pillion, D. J.; Bishop, S. P.; Rosenblum, W. M.; Naumann, R. J.

1994-01-01

One of the major stumbling blocks that prevents rapid structure determination using x-ray crystallography is macro-molecular crystal growth. There are many examples where crystallization takes longer than structure determination. In some cases, it is impossible to grow useful crystals on earth. Recent experiments conducted in conjuction with NASA on various Space Shuttle missions have demonstrated that protein crystals often grow larger and display better internal molecular order than their earth-grown counterparts. This paper reports results from three Shuttle flights using the Protein Crystallization Facility (PCF). The PCF hardware produced large, high-quality insulin crystals by using a temperature change as the sole means to affect protein solubility and thus, crystallization. The facility consists of cylinders/containers with volumes of 500, 200, 100, and 50 ml. Data from the three Shuttle flights demonstrated that larger, higher resolution crystals (as evidenced by x-ray diffraction data) were obtained from the microgravity experiments when compared to earth-grown crystals.

How Cubic Can Ice Be?

DOE PAGES

Amaya, Andrew J.; Pathak, Harshad; Modak, Viraj P.; ...

2017-06-28

Using an X-ray laser, we investigated the crystal structure of ice formed by homogeneous ice nucleation in deeply supercooled water nanodrops (r ≈ 10 nm) at ~225 K. The nanodrops were formed by condensation of vapor in a supersonic nozzle, and the ice was probed within 100 μs of freezing using femtosecond wide-angle X-ray scattering at the Linac Coherent Light Source free-electron X-ray laser. The X-ray diffraction spectra indicate that this ice has a metastable, predominantly cubic structure; the shape of the first ice diffraction peak suggests stacking-disordered ice with a cubicity value, χ, in the range of 0.78 ±more » 0.05. The cubicity value determined here is higher than those determined in experiments with micron-sized drops but comparable to those found in molecular dynamics simulations. Lastly, the high cubicity is most likely caused by the extremely low freezing temperatures and by the rapid freezing, which occurs on a ~1 μs time scale in single nanodroplets.« less

Annotation and structural elucidation of bovine milk oligosaccharides and determination of novel fucosylated structures

PubMed Central

Aldredge, Danielle L; Geronimo, Maria R; Hua, Serenus; Nwosu, Charles C; Lebrilla, Carlito B; Barile, Daniela

2013-01-01

Bovine milk oligosaccharides (BMOs) are recognized by the dairy and food industries, as well as by infant formula manufacturers, as novel, high-potential bioactive food ingredients. Recent studies revealed that bovine milk contains complex oligosaccharides structurally related to those previously thought to be present in only human milk. These BMOs are microbiotic modulators involved in important biological activities, including preventing pathogen binding to the intestinal epithelium and serving as nutrients for a selected class of beneficial bacteria. Only a small number of BMO structures are fully elucidated. To better understand the potential of BMOs as a class of biotherapeutics, their detailed structure analysis is needed. This study initiated the development of a structure library of BMOs and a comprehensive evaluation of structure-related specificity. The bovine milk glycome was profiled by high-performance mass spectrometry and advanced separation techniques to obtain a comprehensive catalog of BMOs, including several novel, lower abundant neutral and fucosylated oligosaccharides that are often overlooked during analysis. Structures were identified using isomer-specific tandem mass spectroscopy and targeted exoglycosidase digestions to produce a BMO library detailing retention time, accurate mass and structure to allow their rapid identification in future studies. PMID:23436288

Structural architecture of the human long non-coding RNA, steroid receptor RNA activator

PubMed Central

Novikova, Irina V.; Hennelly, Scott P.; Sanbonmatsu, Karissa Y.

2012-01-01

While functional roles of several long non-coding RNAs (lncRNAs) have been determined, the molecular mechanisms are not well understood. Here, we report the first experimentally derived secondary structure of a human lncRNA, the steroid receptor RNA activator (SRA), 0.87 kB in size. The SRA RNA is a non-coding RNA that coactivates several human sex hormone receptors and is strongly associated with breast cancer. Coding isoforms of SRA are also expressed to produce proteins, making the SRA gene a unique bifunctional system. Our experimental findings (SHAPE, in-line, DMS and RNase V1 probing) reveal that this lncRNA has a complex structural organization, consisting of four domains, with a variety of secondary structure elements. We examine the coevolution of the SRA gene at the RNA structure and protein structure levels using comparative sequence analysis across vertebrates. Rapid evolutionary stabilization of RNA structure, combined with frame-disrupting mutations in conserved regions, suggests that evolutionary pressure preserves the RNA structural core rather than its translational product. We perform similar experiments on alternatively spliced SRA isoforms to assess their structural features. PMID:22362738

Discovering rules for protein-ligand specificity using support vector inductive logic programming.

PubMed

Kelley, Lawrence A; Shrimpton, Paul J; Muggleton, Stephen H; Sternberg, Michael J E

2009-09-01

Structural genomics initiatives are rapidly generating vast numbers of protein structures. Comparative modelling is also capable of producing accurate structural models for many protein sequences. However, for many of the known structures, functions are not yet determined, and in many modelling tasks, an accurate structural model does not necessarily tell us about function. Thus, there is a pressing need for high-throughput methods for determining function from structure. The spatial arrangement of key amino acids in a folded protein, on the surface or buried in clefts, is often the determinants of its biological function. A central aim of molecular biology is to understand the relationship between such substructures or surfaces and biological function, leading both to function prediction and to function design. We present a new general method for discovering the features of binding pockets that confer specificity for particular ligands. Using a recently developed machine-learning technique which couples the rule-discovery approach of inductive logic programming with the statistical learning power of support vector machines, we are able to discriminate, with high precision (90%) and recall (86%) between pockets that bind FAD and those that bind NAD on a large benchmark set given only the geometry and composition of the backbone of the binding pocket without the use of docking. In addition, we learn rules governing this specificity which can feed into protein functional design protocols. An analysis of the rules found suggests that key features of the binding pocket may be tied to conformational freedom in the ligand. The representation is sufficiently general to be applicable to any discriminatory binding problem. All programs and data sets are freely available to non-commercial users at http://www.sbg.bio.ic.ac.uk/svilp_ligand/.

Determination of the Structure and Catalytic Mechanism of Sorghum bicolor Caffeic Acid O-Methyltransferase and the Structural Impact of Three brown midrib12 Mutations1[W

PubMed Central

Green, Abigail R.; Lewis, Kevin M.; Barr, John T.; Jones, Jeffrey P.; Lu, Fachuang; Ralph, John; Vermerris, Wilfred; Sattler, Scott E.; Kang, ChulHee

2014-01-01

Using S-adenosyl-methionine as the methyl donor, caffeic acid O-methyltransferase from sorghum (Sorghum bicolor; SbCOMT) methylates the 5-hydroxyl group of its preferred substrate, 5-hydroxyconiferaldehyde. In order to determine the mechanism of SbCOMT and understand the observed reduction in the lignin syringyl-to-guaiacyl ratio of three brown midrib12 mutants that carry COMT gene missense mutations, we determined the apo-form and S-adenosyl-methionine binary complex SbCOMT crystal structures and established the ternary complex structure with 5-hydroxyconiferaldehyde by molecular modeling. These structures revealed many features shared with monocot ryegrass (Lolium perenne) and dicot alfalfa (Medicago sativa) COMTs. SbCOMT steady-state kinetic and calorimetric data suggest a random bi-bi mechanism. Based on our structural, kinetic, and thermodynamic results, we propose that the observed reactivity hierarchy among 4,5-dihydroxy-3-methoxycinnamyl (and 3,4-dihydroxycinnamyl) aldehyde, alcohol, and acid substrates arises from the ability of the aldehyde to stabilize the anionic intermediate that results from deprotonation of the 5-hydroxyl group by histidine-267. Additionally, despite the presence of other phenylpropanoid substrates in vivo, sinapaldehyde is the preferential product, as demonstrated by its low Km for 5-hydroxyconiferaldehyde. Unlike its acid and alcohol substrates, the aldehydes exhibit product inhibition, and we propose that this is due to nonproductive binding of the S-cis-form of the aldehydes inhibiting productive binding of the S-trans-form. The S-cis-aldehydes most likely act only as inhibitors, because the high rotational energy barrier around the 2-propenyl bond prevents S-trans-conversion, unlike alcohol substrates, whose low 2-propenyl bond rotational energy barrier enables rapid S-cis/S-trans-interconversion. PMID:24948836

Automatic Aircraft Structural Topology Generation for Multidisciplinary Optimization and Weight Estimation

NASA Technical Reports Server (NTRS)

Sensmeier, Mark D.; Samareh, Jamshid A.

2005-01-01

An approach is proposed for the application of 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. This 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. A demonstration of this process is shown for two sample aircraft wing designs.

Breeding-assisted genomics.

PubMed

Poland, Jesse

2015-04-01

The revolution of inexpensive sequencing has ushered in an unprecedented age of genomics. The promise of using this technology to accelerate plant breeding is being realized with a vision of genomics-assisted breeding that will lead to rapid genetic gain for expensive and difficult traits. The reality is now that robust phenotypic data is an increasing limiting resource to complement the current wealth of genomic information. While genomics has been hailed as the discipline to fundamentally change the scope of plant breeding, a more symbiotic relationship is likely to emerge. In the context of developing and evaluating large populations needed for functional genomics, none excel in this area more than plant breeders. While genetic studies have long relied on dedicated, well-structured populations, the resources dedicated to these populations in the context of readily available, inexpensive genotyping is making this philosophy less tractable relative to directly focusing functional genomics on material in breeding programs. Through shifting effort for basic genomic studies from dedicated structured populations, to capturing the entire scope of genetic determinants in breeding lines, we can move towards not only furthering our understanding of functional genomics in plants, but also rapidly improving crops for increased food security, availability and nutrition. Copyright © 2015 Elsevier Ltd. All rights reserved.

Human LINE-1 retrotransposition requires a metastable coiled coil and a positively charged N-terminus in L1ORF1p

PubMed Central

Khazina, Elena

2018-01-01

LINE-1 (L1) is an autonomous retrotransposon, which acted throughout mammalian evolution and keeps contributing to human genotypic diversity, genetic disease and cancer. L1 encodes two essential proteins: L1ORF1p, a unique RNA-binding protein, and L1ORF2p, an endonuclease and reverse transcriptase. L1ORF1p contains an essential, but rapidly evolving N-terminal portion, homo-trimerizes via a coiled coil and packages L1RNA into large assemblies. Here, we determined crystal structures of the entire coiled coil domain of human L1ORF1p. We show that retrotransposition requires a non-ideal and metastable coiled coil structure, and a strongly basic L1ORF1p amino terminus. Human L1ORF1p therefore emerges as a highly calibrated molecular machine, sensitive to mutation but functional in different hosts. Our analysis rationalizes the locally rapid L1ORF1p sequence evolution and reveals striking mechanistic parallels to coiled coil-containing membrane fusion proteins. It also suggests how trimeric L1ORF1p could form larger meshworks and indicates critical novel steps in L1 retrotransposition. PMID:29565245

If I had a magic wand....Wish list of a dermatologist (Conference Presentation)

NASA Astrophysics Data System (ADS)

Kelly, Kristen M.

2016-02-01

Challenges in dermatology that can be addressed by photonics research will be explored. Non-invasive, real-time diagnosis of skin lesions would eliminate biopsy risks, minimize patient anxiety by providing more rapid answers and allow diagnosis and treatment in a single visit. Multiple approaches have been tried, but significant limitations of current technologies make them impractical for routine clinic implementation. Photonics can also be used for treatment assessment to determine if intervention is adequate or if further treatment is needed. Ideal feedback should be non-invasive, rapid and accurate. Monitoring for potential adverse effects can greatly improve treatment safety, allowing clinicians to push the limits of therapy while preventing serious complications. Light based therapies can also be improved by increasing photon penetration and selectivity for targeted cells or skin structures. Current light based treatments are in many cases limited by photon penetration. In addition, we often seek to damage a specific chromophore but are not able to distinguish between targeted disease and non-targeted normal structures such as the cells of a melanoma and normal melanocytes and port wine stain versus normal vasculature. Scientist and clinician collaboration can address these and other issues and greatly improve patient care.

Comparative hazard analysis and toxicological modeling of diverse nanomaterials using the embryonic zebrafish (EZ) metric of toxicity

NASA Astrophysics Data System (ADS)

Harper, Bryan; Thomas, Dennis; Chikkagoudar, Satish; Baker, Nathan; Tang, Kaizhi; Heredia-Langner, Alejandro; Lins, Roberto; Harper, Stacey

2015-06-01

The integration of rapid assays, large datasets, informatics, and modeling can overcome current barriers in understanding nanomaterial structure-toxicity relationships by providing a weight-of-the-evidence mechanism to generate hazard rankings for nanomaterials. Here, we present the use of a rapid, low-cost assay to perform screening-level toxicity evaluations of nanomaterials in vivo. Calculated EZ Metric scores, a combined measure of morbidity and mortality in developing embryonic zebrafish, were established at realistic exposure levels and used to develop a hazard ranking of diverse nanomaterial toxicity. Hazard ranking and clustering analysis of 68 diverse nanomaterials revealed distinct patterns of toxicity related to both the core composition and outermost surface chemistry of nanomaterials. The resulting clusters guided the development of a surface chemistry-based model of gold nanoparticle toxicity. Our findings suggest that risk assessments based on the size and core composition of nanomaterials alone may be wholly inappropriate, especially when considering complex engineered nanomaterials. Research should continue to focus on methodologies for determining nanomaterial hazard based on multiple sub-lethal responses following realistic, low-dose exposures, thus increasing the availability of quantitative measures of nanomaterial hazard to support the development of nanoparticle structure-activity relationships.

Solution structure and function of the "tandem inactivation domain" of the neuronal A-type potassium channel Kv1.4.

PubMed

Wissmann, Ralph; Bildl, Wolfgang; Oliver, Dominik; Beyermann, Michael; Kalbitzer, Hans-Robert; Bentrop, Detlef; Fakler, Bernd

2003-05-02

Cumulative inactivation of voltage-gated (Kv) K(+) channels shapes the presynaptic action potential and determines timing and strength of synaptic transmission. Kv1.4 channels exhibit rapid "ball-and-chain"-type inactivation gating. Different from all other Kvalpha subunits, Kv1.4 harbors two inactivation domains at its N terminus. Here we report the solution structure and function of this "tandem inactivation domain" using NMR spectroscopy and patch clamp recordings. Inactivation domain 1 (ID1, residues 1-38) consists of a flexible N terminus anchored at a 5-turn helix, whereas ID2 (residues 40-50) is a 2.5-turn helix made up of small hydrophobic amino acids. Functional analysis suggests that only ID1 may work as a pore-occluding ball domain, whereas ID2 most likely acts as a "docking domain" that attaches ID1 to the cytoplasmic face of the channel. Deletion of ID2 slows inactivation considerably and largely impairs cumulative inactivation. Together, the concerted action of ID1 and ID2 may promote rapid inactivation of Kv1.4 that is crucial for the channel function in short term plasticity.

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

Wholeness and primary and secondary food structure effects on in vitro digestion patterns determine nutritionally distinct carbohydrate fractions in cereal foods.

PubMed

Mishra, Suman; Monro, John

2012-12-01

Starchy foods of differing structure, including bakery products, breakfast cereals, pastas, and pulses were digested in vitro. Bakery products and processed breakfast cereals with little resilient structure yielded large amounts of rapidly available carbohydrate (RAC), less slowly digested starch (SDS) and little inaccessible digestible starch (IDS) (70:22:8%). Partially processed grains, such as rolled oats contained an increased proportion of SDS (55:38:7%). Pastas, being dense starch structures digested more gradually to completion by superficial erosion, yielding approximately equal proportions of RAC and SDS but little IDS (43:52:4%). Pulses, which retained their cellular morphology, digested more linearly yielding a lower proportion of RAC, a larger proportion of SDS and more IDS (9:69:22%). Preservation of native "primary" structure, and use of processing to create "secondary" structure, are both means by which wholeness, in the sense of intactness, can be used to influence carbohydrate digestion to make foods of lower glycaemic impact. Copyright © 2012 Elsevier Ltd. All rights reserved.

Hydrometeor Trajectories and Distributions in a Simulation of TC Rapid Intensification (RI)

NASA Astrophysics Data System (ADS)

Zhu, Z.; Zhu, P.

2010-12-01

It has long been recognized that the microphysics scheme used in a numerical simulation of tropical cyclones (TC) can greatly affect the precipitation distribution, intensity and thermodynamic structure of the simulated TC. This suggests that the mixing ratios, concentrations and size distributions of hydrometeor(snow, graupel,rain,cloud ice) are important factors in the evolution of TC . The transport of hydrometeor may have a strong influence on these factors through its interactions with the growth and the latent heat forcing of hydrometeor and the wind filed, hence is a key to understanding TC microphysics. Schematic hydrometeor trajectories were first constructed using 3-D wind field and particle fallspeeds derived from airborne radar observations in a steady-state mature hurricane,Alicia(1983). Since then, little effort has been put in understanding hydrometeor transport in TC, especially the potential link between its evolution and the intensity and structure changes in a non-steady-state TC. This study is focused on investigating such a link by means of numerical simulations of TC Rapid Intensification(RI) using WRF model. We use the tracer utility in WRF to construct hydrometeor trajectories. Most of the popular microphysics schemes are tested, and the most reasonable test( which is determined by comparing the simulated TC intensity and structure with airborne radar observations) and the ensemble mean of all the tests are picked for detailed examinations.

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.

Fine structure of striations observed in barium plasma injections in the magnetospheric cleft

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

Simons, D.J.; Eastman, T.E.; Pongratz, M.B.

1976-01-01

In January and November of 1975, the Los Alamos Scientific Laboratory sponsored four high altitude shaped charge barium plasma injections in the magnetospheric cleft region. These experiments were TORDO UNO (January 6), TORDO DOS (January 11), PERIQUITO UNO (November 25), and PERIQUITO DOS (November 28). All four injections took place near 500 km altitude, and optical data were taken from two aircraft and a ground station. The TORDO DOS and the PERIQUITO experiments showed rapid formation of striations (within one minute after injection), and fast horizontal spreading in contrast with TORDO UNO. In PERIQUITO DOS, the debris cloud spread magneticallymore » east-west with a small net northerly motion. TORDO UNO shows very rapid poleward motion, and the remaining two events resulted in magnetically east-west horizontal spreading, with no noticeable poleward motion. Striations observed in the PERIQUITO DOS experiment separate in opposite directions with relative velocities of up to 3 km/sec. These field-aligned structures appear to form in sheets of approximately constant magnetic latitude. Significant spatial variations occur on a scale of less than 200 meters. Spatial frequency power spectra across these striations have been determined at various times. Observations of the debris cloud and the fast barium streak show strong field-aligned coherency of striation fine structure, indicating a field line mapping of transverse electric fields and gradients.« less

The Dubai Community Psychiatric Survey: II. Development of the Socio-cultural Change Questionnaire.

PubMed

Bebbington, P; Ghubash, R; Hamdi, E

1993-04-01

The Dubai Community Psychiatric Survey was carried out to assess the effect of very rapid social change on the mental health of women in Dubai, one of the United Arab Emirates. In order to measure social change at an individual level, we developed a questionnaire covering behaviour and attitudes in a wide range of situations, the Socio-cultural Change Questionnaire (ScCQ). In this paper we give an account of the considerations that determined the form of the ScCQ, its structural characteristics, and its validity.

A Study of the Dependence of Microsegregation on Critical Solidification Parameters in Rapidly-Quenched Structures.

DTIC Science & Technology

1980-12-01

a formulation given in many sources (Refs. 1-3). The laser is assumed to penetrate completely through the material (making a " keyhole ") and the heat...absorbed laser power as determined from calor- imetric measurements. The analytical predictions were brought to close agree- ment with the experimental...kW power setting would be about 45 kW/cm 2. This value is close to the 50 kW/cm2 line predicted by the model. As in Fig. 13, the laser dwell time is

Noise Impact Inventory of Elevated Structures in U.S. Urban Rail Rapid Transit Systems

DOT National Transportation Integrated Search

1980-09-01

This report presents the results of the third task of a five-task program dealing with the reduction of noise from elevated structures in use in U.S. rail rapid transit systems. This report is an inventory and impact assessment of the noise radiated ...

Large-Scale Noniridescent Structural Color Printing Enabled by Infiltration-Driven Nonequilibrium Colloidal Assembly.

PubMed

Bai, Ling; Mai, Van Cuong; Lim, Yun; Hou, Shuai; Möhwald, Helmuth; Duan, Hongwei

2018-03-01

Structural colors originating from interaction of light with intricately arranged micro-/nanostructures have stimulated considerable interest because of their inherent photostability and energy efficiency. In particular, noniridescent structural color with wide viewing angle has been receiving increasing attention recently. However, no method is yet available for rapid and large-scale fabrication of full-spectrum structural color patterns with wide viewing angles. Here, infiltration-driven nonequilibrium assembly of colloidal particles on liquid-permeable and particle-excluding substrates is demonstrated to direct the particles to form amorphous colloidal arrays (ACAs) within milliseconds. The infiltration-assisted (IFAST) colloidal assembly opens new possibilities for rapid manufacture of noniridescent structural colors of ACAs and straightforward structural color mixing. Full-spectrum noniridescent structural colors are successfully produced by mixing primary structural colors of red, blue, and yellow using a commercial office inkjet printer. Rapid fabrication of large-scale structural color patterns with sophisticated color combination/layout by IFAST printing is realized. The IFAST technology is versatile for developing structural color patterns with wide viewing angles, as colloidal particles, inks, and substrates are flexibly designable for diverse applications. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A simple and sensitive method for determining plasma cell isotype and monoclonality in bone marrow using flowcytometry.

PubMed

van Zaanen, H C; Vet, R J; de Jong, C M; von dem Borne, A E; van Oers, M H

1995-09-01

In this paper we describe a new, rapid and sensitive method to determine plasma cell isotype and clonality in bone marrow using flowcytometry. With the use of a new fixation and permeabilization reagent (Permeafix), which preserves cell structure and morphology, and a monoclonal antibody (Mab) specific for plasma cells (B-B4), it has become possible to specifically select plasma cells and to determine the cytoplasmatic immunoglobulins by flowcytometry. Thirty successive bone marrow aspirates from multiple myeloma patients and patients with MGUS were studied as well as 10 bone marrow samples from patients with reactive plasmacytosis. Each sample was analysed both by immunofluorescence on cytospin smears and FACS analysis. There were no discrepancies between plasma cell isotype as determined by FACS and cytospin. Moreover, FACS analysis was shown to allow detection of very low numbers of plasma cells and to determine whether these plasma cells are mono- or polyclonal. Possible applications are discussed.

Life in the fast lane for protein crystallization and X-ray crystallography

NASA Technical Reports Server (NTRS)

Pusey, Marc L.; Liu, Zhi-Jie; Tempel, Wolfram; Praissman, Jeremy; Lin, Dawei; Wang, Bi-Cheng; Gavira, Jose A.; Ng, Joseph D.

2005-01-01

The common goal for structural genomic centers and consortiums is to decipher as quickly as possible the three-dimensional structures for a multitude of recombinant proteins derived from known genomic sequences. Since X-ray crystallography is the foremost method to acquire atomic resolution for macromolecules, the limiting step is obtaining protein crystals that can be useful of structure determination. High-throughput methods have been developed in recent years to clone, express, purify, crystallize and determine the three-dimensional structure of a protein gene product rapidly using automated devices, commercialized kits and consolidated protocols. However, the average number of protein structures obtained for most structural genomic groups has been very low compared to the total number of proteins purified. As more entire genomic sequences are obtained for different organisms from the three kingdoms of life, only the proteins that can be crystallized and whose structures can be obtained easily are studied. Consequently, an astonishing number of genomic proteins remain unexamined. In the era of high-throughput processes, traditional methods in molecular biology, protein chemistry and crystallization are eclipsed by automation and pipeline practices. The necessity for high-rate production of protein crystals and structures has prevented the usage of more intellectual strategies and creative approaches in experimental executions. Fundamental principles and personal experiences in protein chemistry and crystallization are minimally exploited only to obtain "low-hanging fruit" protein structures. We review the practical aspects of today's high-throughput manipulations and discuss the challenges in fast pace protein crystallization and tools for crystallography. Structural genomic pipelines can be improved with information gained from low-throughput tactics that may help us reach the higher-bearing fruits. Examples of recent developments in this area are reported from the efforts of the Southeast Collaboratory for Structural Genomics (SECSG).

Life in the Fast Lane for Protein Crystallization and X-Ray Crystallography

NASA Technical Reports Server (NTRS)

Pusey, Marc L.; Liu, Zhi-Jie; Tempel, Wolfram; Praissman, Jeremy; Lin, Dawei; Wang, Bi-Cheng; Gavira, Jose A.; Ng, Joseph D.

2004-01-01

The common goal for structural genomic centers and consortiums is to decipher as quickly as possible the three-dimensional structures for a multitude of recombinant proteins derived from known genomic sequences. Since X-ray crystallography is the foremost method to acquire atomic resolution for macromolecules, the limiting step is obtaining protein crystals that can be useful of structure determination. High-throughput methods have been developed in recent years to clone, express, purify, crystallize and determine the three-dimensional structure of a protein gene product rapidly using automated devices, commercialized kits and consolidated protocols. However, the average number of protein structures obtained for most structural genomic groups has been very low compared to the total number of proteins purified. As more entire genomic sequences are obtained for different organisms from the three kingdoms of life, only the proteins that can be crystallized and whose structures can be obtained easily are studied. Consequently, an astonishing number of genomic proteins remain unexamined. In the era of high-throughput processes, traditional methods in molecular biology, protein chemistry and crystallization are eclipsed by automation and pipeline practices. The necessity for high rate production of protein crystals and structures has prevented the usage of more intellectual strategies and creative approaches in experimental executions. Fundamental principles and personal experiences in protein chemistry and crystallization are minimally exploited only to obtain "low-hanging fruit" protein structures. We review the practical aspects of today s high-throughput manipulations and discuss the challenges in fast pace protein crystallization and tools for crystallography. Structural genomic pipelines can be improved with information gained from low-throughput tactics that may help us reach the higher-bearing fruits. Examples of recent developments in this area are reported from the efforts of the Southeast Collaboratory for Structural Genomics (SECSG).

Embedded spacecraft thermal control using ultrasonic consolidation

NASA Astrophysics Data System (ADS)

Clements, Jared W.

Research has been completed in order to rapidly manufacture spacecraft thermal control technologies embedded in spacecraft structural panels using ultrasonic consolidation. This rapid manufacturing process enables custom thermal control designs in the time frame necessary for responsive space. Successfully embedded components include temperature sensors, heaters, wire harnessing, pre-manufactured heat pipes, and custom integral heat pipes. High conductivity inserts and custom integral pulsating heat pipes were unsuccessfully attempted. This research shows the viability of rapid manufacturing of spacecraft structures with embedded thermal control using ultrasonic consolidation.

REPETITA: detection and discrimination of the periodicity of protein solenoid repeats by discrete Fourier transform

PubMed Central

Marsella, Luca; Sirocco, Francesco; Trovato, Antonio; Seno, Flavio; Tosatto, Silvio C.E.

2009-01-01

Motivation: Proteins with solenoid repeats evolve more quickly than non-repetitive ones and their periodicity may be rapidly hidden at sequence level, while still evident in structure. In order to identify these repeats, we propose here a novel method based on a metric characterizing amino-acid properties (polarity, secondary structure, molecular volume, codon diversity, electric charge) using five previously derived numerical functions. Results: The five spectra of the candidate sequences coding for structural repeats, obtained by Discrete Fourier Transform (DFT), show common features allowing determination of repeat periodicity with excellent results. Moreover it is possible to introduce a phase space parameterized by two quantities related to the Fourier spectra which allow for a clear distinction between a non-homologous set of globular proteins and proteins with solenoid repeats. The DFT method is shown to be competitive with other state of the art methods in the detection of solenoid structures, while improving its performance especially in the identification of periodicities, since it is able to recognize the actual repeat length in most cases. Moreover it highlights the relevance of local structural propensities in determining solenoid repeats. Availability: A web tool implementing the algorithm presented in the article (REPETITA) is available with additional details on the data sets at the URL: http://protein.bio.unipd.it/repetita/. Contact: silvio.tosatto@unipd.it PMID:19478001

Tapping and listening: a new approach to bolt looseness monitoring

NASA Astrophysics Data System (ADS)

Kong, Qingzhao; Zhu, Junxiao; Ho, Siu Chun Michael; Song, Gangbing

2018-07-01

Bolted joints are among the most common building blocks used across different types of structures, and are often the key components that sew all other structural parts together. Monitoring and assessment of looseness in bolted structures is one of the most attractive topics in mechanical, aerospace, and civil engineering. This paper presents a new percussion-based non-destructive approach to determine the health condition of bolted joints with the help of machine learning. The proposed method is very similar to the percussive diagnostic techniques used in clinical examinations to diagnose the health of patients. Due to the different interfacial properties among the bolts, nuts and the host structure, bolted joints can generate unique sounds when it is excited by impacts, such as from tapping. Power spectrum density, as a signal feature, was used to recognize and classify recorded tapping data. A machine learning model using the decision tree method was employed to identify the bolt looseness level. Experiments demonstrated that the newly proposed method for bolt looseness detection is very easy to implement by ‘listening to tapping’ and the monitoring accuracy is very high. With the rapid in robotics, the proposed approach has great potential to be implemented with intimately weaving robotics and machine learning to produce a cyber-physical system that can automatically inspect and determine the health of a structure.

Triggering HIV polyprotein processing by light using rapid photodegradation of a tight-binding protease inhibitor.

PubMed

Schimer, Jiří; Pávová, Marcela; Anders, Maria; Pachl, Petr; Šácha, Pavel; Cígler, Petr; Weber, Jan; Majer, Pavel; Řezáčová, Pavlína; Kräusslich, Hans-Georg; Müller, Barbara; Konvalinka, Jan

2015-03-09

HIV protease (PR) is required for proteolytic maturation in the late phase of HIV replication and represents a prime therapeutic target. The regulation and kinetics of viral polyprotein processing and maturation are currently not understood in detail. Here we design, synthesize, validate and apply a potent, photodegradable HIV PR inhibitor to achieve synchronized induction of proteolysis. The compound exhibits subnanomolar inhibition in vitro. Its photolabile moiety is released on light irradiation, reducing the inhibitory potential by 4 orders of magnitude. We determine the structure of the PR-inhibitor complex, analyze its photolytic products, and show that the enzymatic activity of inhibited PR can be fully restored on inhibitor photolysis. We also demonstrate that proteolysis of immature HIV particles produced in the presence of the inhibitor can be rapidly triggered by light enabling thus to analyze the timing, regulation and spatial requirements of viral processing in real time.

Effect of Chemical Treatments on Flax Fibre Reinforced Polypropylene Composites on Tensile and Dome Forming Behaviour

PubMed Central

Wang, Wentian; Lowe, Adrian; Kalyanasundaram, Shankar

2015-01-01

Tensile tests were performed on two different natural fibre composites (same constituent material, similar fibre fraction and thickness but different weave structure) to determine changes in mechanical properties caused by various aqueous chemical treatments and whether any permanent changes remain on drying. Scanning electronic microscopic examinations suggested that flax fibres and the flax/polypropylene interface were affected by the treatments resulting in tensile property variations. The ductility of natural fibre composites was improved significantly under wet condition and mechanical properties (elongation-to-failure, stiffness and strength) can almost retain back to pre-treated levels when dried from wet condition. Preheating is usually required to improve the formability of material in rapid forming, and the chemical treatments performed in this study were far more effective than preheating. The major breakthrough in improving the formability of natural fibre composites can aid in rapid forming of this class of material system. PMID:25789505

Rapid assessment of the antigenic integrity of tetrameric HLA complexes by human monoclonal HLA antibodies.

PubMed

Eijsink, Chantal; Kester, Michel G D; Franke, Marry E I; Franken, Kees L M C; Heemskerk, Mirjam H M; Claas, Frans H J; Mulder, Arend

2006-08-31

The ability of tetrameric major histocompatibility complex (MHC) class I-peptide complexes (tetramers) to detect antigen-specific T lymphocyte responses has yielded significant information about the generation of in vivo immunity in numerous antigenic systems. Here we present a novel method for rapid validation of tetrameric HLA molecules based on the presence of allodeterminants. Human monoclonal antibodies (mAbs) recognizing polymorphic determinants on HLA class I were immobilized on polystyrene microparticles and used to probe the structural integrity of tetrameric HLA class I molecules by flow cytometry. A total of 22 tetramers, based on HLA-A1, A2, A3, A24, B7 and B8 were reactive with their counterpart mAbs, thus confirming their antigenic integrity. A positive outcome of this mAb test ensures that tetrameric HLA class I can be used with greater confidence in subsequent functional assays.

Modelling proteins' hidden conformations to predict antibiotic resistance

NASA Astrophysics Data System (ADS)

Hart, Kathryn M.; Ho, Chris M. W.; Dutta, Supratik; Gross, Michael L.; Bowman, Gregory R.

2016-10-01

TEM β-lactamase confers bacteria with resistance to many antibiotics and rapidly evolves activity against new drugs. However, functional changes are not easily explained by differences in crystal structures. We employ Markov state models to identify hidden conformations and explore their role in determining TEM's specificity. We integrate these models with existing drug-design tools to create a new technique, called Boltzmann docking, which better predicts TEM specificity by accounting for conformational heterogeneity. Using our MSMs, we identify hidden states whose populations correlate with activity against cefotaxime. To experimentally detect our predicted hidden states, we use rapid mass spectrometric footprinting and confirm our models' prediction that increased cefotaxime activity correlates with reduced Ω-loop flexibility. Finally, we design novel variants to stabilize the hidden cefotaximase states, and find their populations predict activity against cefotaxime in vitro and in vivo. Therefore, we expect this framework to have numerous applications in drug and protein design.

Triggering HIV polyprotein processing by light using rapid photodegradation of a tight-binding protease inhibitor

PubMed Central

Schimer, Jiří; Pávová, Marcela; Anders, Maria; Pachl, Petr; Šácha, Pavel; Cígler, Petr; Weber, Jan; Majer, Pavel; Řezáčová, Pavlína; Kräusslich, Hans-Georg; Müller, Barbara; Konvalinka, Jan

2015-01-01

HIV protease (PR) is required for proteolytic maturation in the late phase of HIV replication and represents a prime therapeutic target. The regulation and kinetics of viral polyprotein processing and maturation are currently not understood in detail. Here we design, synthesize, validate and apply a potent, photodegradable HIV PR inhibitor to achieve synchronized induction of proteolysis. The compound exhibits subnanomolar inhibition in vitro. Its photolabile moiety is released on light irradiation, reducing the inhibitory potential by 4 orders of magnitude. We determine the structure of the PR-inhibitor complex, analyze its photolytic products, and show that the enzymatic activity of inhibited PR can be fully restored on inhibitor photolysis. We also demonstrate that proteolysis of immature HIV particles produced in the presence of the inhibitor can be rapidly triggered by light enabling thus to analyze the timing, regulation and spatial requirements of viral processing in real time. PMID:25751579

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.

Engineered Antibodies for Monitoring of Polynuclear Aromatic Hydrocarbons

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

Alexander E. Karu Ph.D; Victoria A. Roberts Ph.D.; Qing X. Li, Ph.D.

2002-01-17

This project was undertaken to fill needs in ODE's human and ecosystem health effects research, site remediation, rapid emergency response, and regulatory compliance monitoring programs. Doe has greatly stimulated development and validation of antibody-based, rapid, field-portable detection systems for small hazardous compounds. These range from simple dipsticks, microplate enzyme-linked immunosorbent assays (ELISAs), and hand-held colorimeters, to ultrasensitive microfluidic reactors, fiber-optic sensors and microarrays that can identify multiple analytes from patterns of cross-reactivity. Unfortunately, the technology to produce antibodies with the most desirable properties did not keep pace. Lack of antibodies remains a limiting factor in production and practical use ofmore » such devices. The goals of our project were to determine the chemical and structural bases for the antibody-analyte binding interactions using advanced computational chemistry, and to use this information to create useful new binding properties through in vitro genetic engineering and combinatorial library methods.« less

Modelling proteins’ hidden conformations to predict antibiotic resistance

PubMed Central

Hart, Kathryn M.; Ho, Chris M. W.; Dutta, Supratik; Gross, Michael L.; Bowman, Gregory R.

2016-01-01

TEM β-lactamase confers bacteria with resistance to many antibiotics and rapidly evolves activity against new drugs. However, functional changes are not easily explained by differences in crystal structures. We employ Markov state models to identify hidden conformations and explore their role in determining TEM’s specificity. We integrate these models with existing drug-design tools to create a new technique, called Boltzmann docking, which better predicts TEM specificity by accounting for conformational heterogeneity. Using our MSMs, we identify hidden states whose populations correlate with activity against cefotaxime. To experimentally detect our predicted hidden states, we use rapid mass spectrometric footprinting and confirm our models’ prediction that increased cefotaxime activity correlates with reduced Ω-loop flexibility. Finally, we design novel variants to stabilize the hidden cefotaximase states, and find their populations predict activity against cefotaxime in vitro and in vivo. Therefore, we expect this framework to have numerous applications in drug and protein design. PMID:27708258

A novel data-mining approach leveraging social media to monitor consumer opinion of sitagliptin.

PubMed

Akay, Altug; Dragomir, Andrei; Erlandsson, Björn-Erik

2015-01-01

A novel data mining method was developed to gauge the experience of the drug Sitagliptin (trade name Januvia) by patients with diabetes mellitus type 2. To this goal, we devised a two-step analysis framework. Initial exploratory analysis using self-organizing maps was performed to determine structures based on user opinions among the forum posts. The results were a compilation of user's clusters and their correlated (positive or negative) opinion of the drug. Subsequent modeling using network analysis methods was used to determine influential users among the forum members. These findings can open new avenues of research into rapid data collection, feedback, and analysis that can enable improved outcomes and solutions for public health and important feedback for the manufacturer.

A Statistical Study of Rapid Sunspot Structure Change Associated with Flares

NASA Astrophysics Data System (ADS)

Chen, Wei-Zhong; Liu, Chang; Song, Hui; Deng, Na; Tan, Chang-Yi; Wang, Hai-Min

2007-10-01

We reported recently some rapid changes of sunspot structure in white-light (WL) associated with major flares. We extend the study to smaller events and present here results of a statistical study of this phenomenon. In total, we investigate 403 events from 1998 May 9 to 2004 July 17, including 40 X-class, 174 M-class, and 189 C-class flares. By monitoring the structure of the flaring active regions using the WL observations from the Transition Region and Coronal Explorer (TRACE), we find that segments in the outer sunspot structure decayed rapidly right after many flares; and that, on the other hand, the central part of sunspots near the flare-associated magnetic neutral line became darkened. These rapid and permanent changes are evidenced in the time profiles of WL mean intensity and are not likely resulted from the flare emissions. Our study further shows that the outer sunspot structure decay as well as the central structure darkening are more likely to be detected in larger solar flares. For X-class flares, over 40% events show distinct sunspot structure change. For M- and C-class flares, this percentage drops to 17% and 10%, respectively. The results of this statistical study support our previously proposed reconnection picture, i.e., the flare-related magnetic fields evolve from a highly inclined to a more vertical configuration.

Marine Chemical Ecology: Chemical Signals and Cues Structure Marine Populations, Communities, and Ecosystems

PubMed Central

Hay, Mark E.

2012-01-01

Chemical cues constitute much of the language of life in the sea. Our understanding of biotic interactions and their effects on marine ecosystems will advance more rapidly if this language is studied and understood. Here, I review how chemical cues regulate critical aspects of the behavior of marine organisms from bacteria to phytoplankton to benthic invertebrates and water column fishes. These chemically mediated interactions strongly affect population structure, community organization, and ecosystem function. Chemical cues determine foraging strategies, feeding choices, commensal associations, selection of mates and habitats, competitive interactions, and transfer of energy and nutrients within and among ecosystems. In numerous cases, the indirect effects of chemical signals on behavior have as much or more effect on community structure and function as the direct effects of consumers and pathogens. Chemical cues are critical for understanding marine systems, but their omnipresence and impact are inadequately recognized. PMID:21141035

Structural complexities in the active layers of organic electronics.

PubMed

Lee, Stephanie S; Loo, Yueh-Lin

2010-01-01

The field of organic electronics has progressed rapidly in recent years. However, understanding the direct structure-function relationships between the morphology in electrically active layers and the performance of devices composed of these materials has proven difficult. The morphology of active layers in organic electronics is inherently complex, with heterogeneities existing across multiple length scales, from subnanometer to micron and millimeter range. A major challenge still facing the organic electronics community is understanding how the morphology across all of the length scales in active layers collectively determines the device performance of organic electronics. In this review we highlight experiments that have contributed to the elucidation of structure-function relationships in organic electronics and also point to areas in which knowledge of such relationships is still lacking. Such knowledge will lead to the ability to select active materials on the basis of their inherent properties for the fabrication of devices with prespecified characteristics.

Information generation and processing systems that regulate periodontal structure and function.

PubMed

Bartold, P Mark; McCulloch, Christopher A

2013-10-01

The periodontium is a very dynamic organ that responds rapidly to mechanical and chemical stimuli. It is very complex in that it is composed of two hard tissues (cementum and bone) and two soft connective tissues (periodontal ligament and gingiva). Together these tissues are defined by the molecules expressed by the resident periodontal cells in each compartment and this determines not only the structure and function of the periodontium but also how it responds to infection and inflammation. The biological activity of these molecules is tightly regulated in time and space to preserve tissue homeostasis, influence inflammatory responses and participate in tissue regeneration. In this issue of Periodontology 2000 we explore new experimental approaches and data sets which help to understand the molecules and cells that regulate tissue form and structure in health, disease and regeneration. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Condom social marketing, Pentecostalism, and structural adjustment in Mozambique: a clash of AIDS prevention messages.

PubMed

Pfeiffer, James

2004-03-01

Despite significant debate about the efficacy, ideology, and ethics of the method, condom social marketing (CSM) has become the dominant approach to AIDS education in many sub-Saharan African countries. However, critics have charged that social marketing (SM) distracts from the structural determinants of health-related behavior and excludes genuine community participation. This article argues that the diffusion of SM techniques in Africa is not driven by demonstrated efficacy but is attributable to the promotion of privatization and free markets in the structural adjustment era across the region. The CSM experience in a central Mozambican community reveals the dangers of using the method at the expense of community dialogue and participation to confront the AIDS epidemic. The advertising campaign developed to sell condoms has clashed with Pentecostal and Independent Churches, now a majority of the population, that have expanded rapidly across the region spreading a contrasting message about sexuality and risky behavior.

A MEMS-based Air Flow Sensor with a Free-standing Micro-cantilever Structure

PubMed Central

Wang, Yu-Hsiang; Lee, Chia-Yen; Chiang, Che-Ming

2007-01-01

This paper presents a micro-scale air flow sensor based on a free-standing cantilever structure. In the fabrication process, MEMS techniques are used to deposit a silicon nitride layer on a silicon wafer. A platinum layer is deposited on the silicon nitride layer to form a piezoresistor, and the resulting structure is then etched to create a freestanding micro-cantilever. When an air flow passes over the surface of the cantilever beam, the beam deflects in the downward direction, resulting in a small variation in the resistance of the piezoelectric layer. The air flow velocity is determined by measuring the change in resistance using an external LCR meter. The experimental results indicate that the flow sensor has a high sensitivity (0.0284 Ω/ms-1), a high velocity measurement limit (45 ms-1) and a rapid response time (0.53 s). PMID:28903233

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

Eigenmodes of Multilayer Slit Structures

NASA Astrophysics Data System (ADS)

Kovalenko, A. N.

2017-12-01

We generalize the high-efficiency numerical-analytical method of calculating the eigenmodes of a microstrip line, which was proposed in [1], to multilayer slit structures. The obtained relationships make it possible to allow for the multilayer nature of the medium on the basis of solving the electrodynamic problem for a two-layer structure. The algebraic models of a single line and coupled slit lines in a multilayer dielectric medium are constructed. The matrix elements of the system of linear algebraic equations, which is used to determine the expansion coefficients of the electric field inside the slits in a Chebyshev basis, are converted to rapidly convergent series. The constructed models allow one to use computer simulation to obtain numerical results with high speed and accuracy, regardless of the number of dielectric layers. The presented results of a numerical study of the method convergence confirm high efficiency of the method.

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

Hushur, Anwar; Manghnani, Murli H.; Werheit, Helmut

Single-crystal B4.3C boron carbide is investigated concerning the pressure-dependence of optical properties and of Raman-active phonons up to ~70 GPa. The high concentration of structural defects determining the electronic properties of boron carbide at ambient conditions initially decrease and finally vanish with pressure increasing. We obtain this immediately from transparency photos, allowing to estimate the pressure-dependent variation of the absorption edge rapidly increasing around 55 GPa. Glass-like transparency at pressures exceeding 60 GPa indicate that the width of the band exceeds ~3.1 eV thus making boron carbide a wide-gap semiconductor. Furthermore, the spectra of Raman–active phonons indicate a pressure-dependent phasemore » transition in single-crystal natB4.3C boron carbide near 35 GPa., particularly related to structural changes in connection with the C-B-C chains, while the basic icosahedral structure remains largely unaffected.« less

Es structure using an HF radar

NASA Astrophysics Data System (ADS)

From, W. R.; Whitehead, J. D.

1986-05-01

By using an HF radar which produces a steerable beam about 4° wide and measures angle of arrival and Doppler shift of radio echoes, the structure of various types of mid-latitude sporadic E (Es) has been determined. Totally reflecting Es is a very smooth layer, tilted less than 1° from the horizontal. Partially reflecting Es consists of clouds of ionization. These clouds vary in size from a few kilometers to 25 km in the direction of movement and larger in the transverse direction. Echoes often disappear rapidly: the clouds either disappear quickly or have sharp edges. Spread Es has a curious structure of small clouds, each of which reflects only for a few seconds, but each cloud moves with the same velocity, typically 100 m/s, even though the heights of the clouds vary up to 10 km. It is difficult to reconcile this finding with the presence of wind shears.

Es structure using an HF radar

NASA Astrophysics Data System (ADS)

From, W. R.; Whitehead, J. D.

Using an HF radar which produces a steerable beam about 4 deg wide and measures angle of arrival and Doppler shift of radio echoes, the structure of various types of midlatitude sporadic E (Es) has been determined. Totally reflecting Es is a very smooth layer, tilted less than 1 deg from the horizontal. Partially reflecting Es consists of clouds of ionization. These clouds vary in size from a few kilometers to 25 km in the direction of movement and larger in the transverse direction. Echoes often disappear rapidly: the clouds either disappear quickly or have sharp edges. Spread Es has a curious structure of small clouds each of which reflects only for a few seconds, but each cloud moves with the same velocity, typically 100 m/s, even though the heights of the clouds vary up to 10 km. It is difficult to reconcile this finding with the presence of wind shears.

Exploring the Early Structure of a Rapidly Decompressed Particle Bed

NASA Astrophysics Data System (ADS)

Zunino, Heather; Adrian, R. J.; Clarke, Amanda; Johnson, Blair; Arizona State University Collaboration

2017-11-01

Rapid expansion of dense, pressurized beds of fine particles subjected to rapid reduction of the external pressure is studied in a vertical shock tube. A near-sonic expansion wave impinges on the particle bed-gas interface and rapidly unloads the particle bed. A high-speed video camera captures events occurring during bed expansion. The particle bed does not expand homogeneously, but breaks down into horizontal slabs and then transforms into a cellular-type structure. There are several key parameters that affect the particle bed evolution, including particle size and initial bed height. Analyses of this bed structure evolution from experiments with varying particle sizes and initial bed heights is presented. This work is supported by the U.S. Department of Energy, National Nuclear Security Administration, Advanced Simulation and Computing Program, as a Cooperative Agreement under the Predictive Science and Academic Alliance Program, under Contract No. DE-NA0002378.

Sex reversal triggers the rapid transition from genetic to temperature-dependent sex.

PubMed

Holleley, Clare E; O'Meally, Denis; Sarre, Stephen D; Marshall Graves, Jennifer A; Ezaz, Tariq; Matsubara, Kazumi; Azad, Bhumika; Zhang, Xiuwen; Georges, Arthur

2015-07-02

Sex determination in animals is amazingly plastic. Vertebrates display contrasting strategies ranging from complete genetic control of sex (genotypic sex determination) to environmentally determined sex (for example, temperature-dependent sex determination). Phylogenetic analyses suggest frequent evolutionary transitions between genotypic and temperature-dependent sex determination in environmentally sensitive lineages, including reptiles. These transitions are thought to involve a genotypic system becoming sensitive to temperature, with sex determined by gene-environment interactions. Most mechanistic models of transitions invoke a role for sex reversal. Sex reversal has not yet been demonstrated in nature for any amniote, although it occurs in fish and rarely in amphibians. Here we make the first report of reptile sex reversal in the wild, in the Australian bearded dragon (Pogona vitticeps), and use sex-reversed animals to experimentally induce a rapid transition from genotypic to temperature-dependent sex determination. Controlled mating of normal males to sex-reversed females produces viable and fertile offspring whose phenotypic sex is determined solely by temperature (temperature-dependent sex determination). The W sex chromosome is eliminated from this lineage in the first generation. The instantaneous creation of a lineage of ZZ temperature-sensitive animals reveals a novel, climate-induced pathway for the rapid transition between genetic and temperature-dependent sex determination, and adds to concern about adaptation to rapid global climate change.

Inter-spin distance determination using L-band (1-2 GHz) non-adiabatic rapid sweep electron paramagnetic resonance (NARS EPR)

PubMed Central

Kittell, Aaron W.; Hustedt, Eric J.; Hyde, James S.

2014-01-01

Site-directed spin-labeling electron paramagnetic resonance (SDSL EPR) provides insight into the local structure and motion of a spin probe strategically attached to a molecule. When a second spin is introduced to the system, macromolecular information can be obtained through measurement of inter-spin distances either by continuous wave (CW) or pulsed electron double resonance (ELDOR) techniques. If both methodologies are considered, inter-spin distances of 8 to 80 Å can be experimentally determined. However, there exists a region at the upper limit of the conventional X-band (9.5 GHz) CW technique and the lower limit of the four-pulse double electron-electron resonance (DEER) experiment where neither method is particularly reliable. The work presented here utilizes L-band (1.9 GHz) in combination with non-adiabatic rapid sweep (NARS) EPR to address this opportunity by increasing the upper limit of the CW technique. Because L-band linewidths are three to seven times narrower than those at X-band, dipolar broadenings that are small relative to the X-band inhomogeneous linewidth become observable, but the signal loss due to the frequency dependence of the Boltzmann factor, has made L-band especially challenging. NARS has been shown to increase sensitivity by a factor of five, and overcomes much of this loss, making L-band distance determination more feasible [1]. Two different systems are presented and distances of 18–30 Å have been experimentally determined at physiologically relevant temperatures. Measurements are in excellent agreement with a helical model and values determined by DEER. PMID:22750251

Conformational changes accompany activation of reovirus RNA-dependent RNA transcription

PubMed Central

Mendez, Israel I.; Weiner, Scott G.; She, Yi-Min; Yeager, Mark; Coombs, Kevin M.

2009-01-01

Many critical biologic processes involve dynamic interactions between proteins and nucleic acids. Such dynamic processes are often difficult to delineate by conventional static methods. For example, while a variety of nucleic acid polymerase structures have been determined at atomic resolution, the details of how some multi-protein transcriptase complexes actively produce mRNA, as well as conformational changes associated with activation of such complexes, remain poorly understood. The mammalian reovirus innermost capsid (core) manifests all enzymatic activities necessary to produce mRNA from each of the 10 encased double-stranded RNA genes. We used rapid freezing and electron cryo-microscopy to trap and visualize transcriptionally active reovirus core particles and compared them to inactive core images. Rod-like density centered within actively transcribing core spike channels was attributed to exiting nascent mRNA. Comparative radial density plots of active and inactive core particles identified several structural changes in both internal and external regions of the icosahedral core capsid. Inactive and transcriptionally active cores were partially digested with trypsin and identities of initial tryptic peptides determined by mass spectrometry. Differentially-digested peptides, which also suggest transcription-associated conformational changes, were placed within the known 3-dimensional structures of major core proteins. PMID:18321727

Averaged kick maps: less noise, more signal…and probably less bias

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

Pražnikar, Jure; Afonine, Pavel V.; Gunčar, Gregor

2009-09-01

Averaged kick maps are the sum of a series of individual kick maps, where each map is calculated from atomic coordinates modified by random shifts. These maps offer the possibility of an improved and less model-biased map interpretation. Use of reliable density maps is crucial for rapid and successful crystal structure determination. Here, the averaged kick (AK) map approach is investigated, its application is generalized and it is compared with other map-calculation methods. AK maps are the sum of a series of kick maps, where each kick map is calculated from atomic coordinates modified by random shifts. As such, theymore » are a numerical analogue of maximum-likelihood maps. AK maps can be unweighted or maximum-likelihood (σ{sub A}) weighted. Analysis shows that they are comparable and correspond better to the final model than σ{sub A} and simulated-annealing maps. The AK maps were challenged by a difficult structure-validation case, in which they were able to clarify the problematic region in the density without the need for model rebuilding. The conclusion is that AK maps can be useful throughout the entire progress of crystal structure determination, offering the possibility of improved map interpretation.« less

A modified PATH algorithm rapidly generates transition states comparable to those found by other well established algorithms

PubMed Central

Chandrasekaran, Srinivas Niranj; Das, Jhuma; Dokholyan, Nikolay V.; Carter, Charles W.

2016-01-01

PATH rapidly computes a path and a transition state between crystal structures by minimizing the Onsager-Machlup action. It requires input parameters whose range of values can generate different transition-state structures that cannot be uniquely compared with those generated by other methods. We outline modifications to estimate these input parameters to circumvent these difficulties and validate the PATH transition states by showing consistency between transition-states derived by different algorithms for unrelated protein systems. Although functional protein conformational change trajectories are to a degree stochastic, they nonetheless pass through a well-defined transition state whose detailed structural properties can rapidly be identified using PATH. PMID:26958584

Temporal Structure and Complexity Affect Audio-Visual Correspondence Detection

PubMed Central

Denison, Rachel N.; Driver, Jon; Ruff, Christian C.

2013-01-01

Synchrony between events in different senses has long been considered the critical temporal cue for multisensory integration. Here, using rapid streams of auditory and visual events, we demonstrate how humans can use temporal structure (rather than mere temporal coincidence) to detect multisensory relatedness. We find psychophysically that participants can detect matching auditory and visual streams via shared temporal structure for crossmodal lags of up to 200 ms. Performance on this task reproduced features of past findings based on explicit timing judgments but did not show any special advantage for perfectly synchronous streams. Importantly, the complexity of temporal patterns influences sensitivity to correspondence. Stochastic, irregular streams – with richer temporal pattern information – led to higher audio-visual matching sensitivity than predictable, rhythmic streams. Our results reveal that temporal structure and its complexity are key determinants for human detection of audio-visual correspondence. The distinctive emphasis of our new paradigms on temporal patterning could be useful for studying special populations with suspected abnormalities in audio-visual temporal perception and multisensory integration. PMID:23346067

Structural, Functional, and Genetic Analysis of Sorangicin Inhibition of Bacterial RNA Polymerase

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

Campbell,E.; Pavlova, O.; Zenkin, N.

2005-01-01

A combined structural, functional, and genetic approach was used to investigate inhibition of bacterial RNA polymerase (RNAP) by sorangicin (Sor), a macrolide polyether antibiotic. Sor lacks chemical and structural similarity to the ansamycin rifampicin (Rif), an RNAP inhibitor widely used to treat tuberculosis. Nevertheless, structural analysis revealed Sor binds in the same RNAP {beta} subunit pocket as Rif, with almost complete overlap of RNAP binding determinants, and functional analysis revealed that both antibiotics inhibit transcription by directly blocking the path of the elongating transcript at a length of 2-3 nucleotides. Genetic analysis indicates that Rif binding is extremely sensitive tomore » mutations expected to change the shape of the antibiotic binding pocket, while Sor is not. We suggest that conformational flexibility of Sor, in contrast to the rigid conformation of Rif, allows Sor to adapt to changes in the binding pocket. This has important implications for drug design against rapidly mutating targets.« less

Crystal structure of full-length Zika virus NS5 protein reveals a conformation similar to Japanese encephalitis virus NS5

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

Upadhyay, Anup K.; Cyr, Matthew; Longenecker, Kenton

The rapid spread of the recentZika virus(ZIKV) epidemic across various countries in the American continent poses a major health hazard for the unborn fetuses of pregnant women. To date, there is no effective medical intervention. The nonstructural protein 5 ofZika virus(ZIKV-NS5) is critical for ZIKV replication through the 5'-RNA capping and RNA polymerase activities present in its N-terminal methyltransferase (MTase) and C-terminal RNA-dependent RNA polymerase (RdRp) domains, respectively. The crystal structure of the full-length ZIKV-NS5 protein has been determined at 3.05 Å resolution from a crystal belonging to space groupP2 12 12 and containing two protein molecules in the asymmetricmore » unit. The structure is similar to that reported for the NS5 protein fromJapanese encephalitis virusand suggests opportunities for structure-based drug design targeting either its MTase or RdRp domain.« less

Advanced earthquake monitoring system for U.S. Department of Veterans Affairs medical buildings--instrumentation

USGS Publications Warehouse

Kalkan, Erol; Banga, Krishna; Ulusoy, Hasan S.; Fletcher, Jon Peter B.; Leith, William S.; Reza, Shahneam; Cheng, Timothy

2012-01-01

In collaboration with the U.S. Department of Veterans Affairs (VA), the National Strong Motion Project (NSMP; http://nsmp.wr.usgs.gov/) of the U.S. Geological Survey has been installing sophisticated seismic systems that will monitor the structural integrity of 28 VA hospital buildings located in seismically active regions of the conterminous United States, Alaska, and Puerto Rico during earthquake shaking. These advanced monitoring systems, which combine the use of sensitive accelerometers and real-time computer calculations, are designed to determine the structural health of each hospital building rapidly after an event, helping the VA to ensure the safety of patients and staff. This report presents the instrumentation component of this project by providing details of each hospital building, including a summary of its structural, geotechnical, and seismic hazard information, as well as instrumentation objectives and design. The structural-health monitoring component of the project, including data retrieval and processing, damage detection and localization, automated alerting system, and finally data dissemination, will be presented in a separate report.

Bouncing dynamics of liquid drops impact on ridge structure: an effective approach to reduce the contact time.

PubMed

Li, Tao; Zhang, Lishu; Wang, Zhichao; Duan, Yunrui; Li, Jie; Wang, Junjun; Li, Hui

2018-06-20

Surfaces designed so that liquid metals do not stick to them but instead rebound as soon as possible have received considerable attention due to their significant importance in many practical technologies. We herein design a ridge structure that can induce the drop to rapidly rebound through the combination effect of centre-drawing recoil and the resulting faster retraction velocity. The suitable sharp-angle of the ridge for minimizing the contact time is determined as 20-30°. Further analysis reveals that multi-ridge structure or two-ridge structure with gaps can reduce more contact time. We also highlight the role the impact velocity played in minimizing the contact time, which has been a neglected parameter previously. Our studies would open up a new way to reduce the contact time and control the bouncing dynamics of metal drops, which provides guidance for some potential applications, such as preventing splashing molten drops from depositing on clean surface.

Propagule pressure determines recruitment from a commercial shipping pier.

PubMed

Hedge, Luke H; Johnston, Emma L

2012-01-01

Artificial structures associated with shipping and boating activities provide habitats for a diverse suite of non-indigenous marine species. Little is known about the proportion of invader success in nearby waters that is attributable to these structures. Areas close to piles, wharves and piers are likely to be exposed to increasing levels of propagule pressure, enhancing the recruitment of non-indigenous species. Recruitment of non-indigenous and native marine biofouling taxa were evaluated at different distances from a large commercial shipping pier. Since artificial structures also represent a desirable habitat for fish, how predation on marine invertebrates influences the establishment of non-indigenous and native species was also evaluated. The colonisation of several non-indigenous marine species declined rapidly with distance from the structure. Little evidence was found to suggest that predators have much influence on the colonisation success of marine sessile invertebrate species, non-indigenous or otherwise. It is suggested that propagule pressure, not predation, more strongly predicts establishment success in these biofouling assemblages.

SIMBAD : a sequence-independent molecular-replacement pipeline

DOE PAGES

Simpkin, Adam J.; Simkovic, Felix; Thomas, Jens M. H.; ...

2018-06-08

The conventional approach to finding structurally similar search models for use in molecular replacement (MR) is to use the sequence of the target to search against those of a set of known structures. Sequence similarity often correlates with structure similarity. Given sufficient similarity, a known structure correctly positioned in the target cell by the MR process can provide an approximation to the unknown phases of the target. An alternative approach to identifying homologous structures suitable for MR is to exploit the measured data directly, comparing the lattice parameters or the experimentally derived structure-factor amplitudes with those of known structures. Here,more » SIMBAD , a new sequence-independent MR pipeline which implements these approaches, is presented. SIMBAD can identify cases of contaminant crystallization and other mishaps such as mistaken identity (swapped crystallization trays), as well as solving unsequenced targets and providing a brute-force approach where sequence-dependent search-model identification may be nontrivial, for example because of conformational diversity among identifiable homologues. The program implements a three-step pipeline to efficiently identify a suitable search model in a database of known structures. The first step performs a lattice-parameter search against the entire Protein Data Bank (PDB), rapidly determining whether or not a homologue exists in the same crystal form. The second step is designed to screen the target data for the presence of a crystallized contaminant, a not uncommon occurrence in macromolecular crystallography. Solving structures with MR in such cases can remain problematic for many years, since the search models, which are assumed to be similar to the structure of interest, are not necessarily related to the structures that have actually crystallized. To cater for this eventuality, SIMBAD rapidly screens the data against a database of known contaminant structures. Where the first two steps fail to yield a solution, a final step in SIMBAD can be invoked to perform a brute-force search of a nonredundant PDB database provided by the MoRDa MR software. Through early-access usage of SIMBAD , this approach has solved novel cases that have otherwise proved difficult to solve.« less

SIMBAD : a sequence-independent molecular-replacement pipeline

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

Simpkin, Adam J.; Simkovic, Felix; Thomas, Jens M. H.

The conventional approach to finding structurally similar search models for use in molecular replacement (MR) is to use the sequence of the target to search against those of a set of known structures. Sequence similarity often correlates with structure similarity. Given sufficient similarity, a known structure correctly positioned in the target cell by the MR process can provide an approximation to the unknown phases of the target. An alternative approach to identifying homologous structures suitable for MR is to exploit the measured data directly, comparing the lattice parameters or the experimentally derived structure-factor amplitudes with those of known structures. Here,more » SIMBAD , a new sequence-independent MR pipeline which implements these approaches, is presented. SIMBAD can identify cases of contaminant crystallization and other mishaps such as mistaken identity (swapped crystallization trays), as well as solving unsequenced targets and providing a brute-force approach where sequence-dependent search-model identification may be nontrivial, for example because of conformational diversity among identifiable homologues. The program implements a three-step pipeline to efficiently identify a suitable search model in a database of known structures. The first step performs a lattice-parameter search against the entire Protein Data Bank (PDB), rapidly determining whether or not a homologue exists in the same crystal form. The second step is designed to screen the target data for the presence of a crystallized contaminant, a not uncommon occurrence in macromolecular crystallography. Solving structures with MR in such cases can remain problematic for many years, since the search models, which are assumed to be similar to the structure of interest, are not necessarily related to the structures that have actually crystallized. To cater for this eventuality, SIMBAD rapidly screens the data against a database of known contaminant structures. Where the first two steps fail to yield a solution, a final step in SIMBAD can be invoked to perform a brute-force search of a nonredundant PDB database provided by the MoRDa MR software. Through early-access usage of SIMBAD , this approach has solved novel cases that have otherwise proved difficult to solve.« less

Phase transformations in SrAl2Si2O8 glass

NASA Technical Reports Server (NTRS)

Drummond, Charles H., III; Bansal, Narottam P.

1992-01-01

Bulk glass of SrAl2Si2O8 composition crystallized at temperatures below 1000 C into hexacelsian, a hexagonal phase which undergoes a reversible, rapid transformation to an orthorhombic phase at 758 C, and at higher temperatures crystallized as celsian, a monoclinic phase. The glass transition temperature and crystallization onset temperature were determined to be 883 C and 1086 C, respectively, from DSC at a heating rate of 20 C/min. Thermal expansion of the various phases and density and bend strengths of cold isostatically pressed glass powder bars, sintered at various temperatures, were measured. The kinetics of the hexacelsian-to-celsian transformation for SrAl2Si2O8 were studied. Hexacelsian flakes were isothermally heat treated at temperatures from 1025-1200 C for various times. Avrami plots were determined by quantitatively measuring the amount of monoclinic celsian formed at various times using x ray diffraction. The Avrami constant was determined to be 1.1, suggesting a diffusionless, one dimensional transformation mechanism. The activation energy was determined from an Arrhenius plot of 1n k vs. 1/T to be 125 kilocal/mole. This value is consistent with a mechanism which transforms the layered hexacelsian structure to a three dimensional framework celsian structure and involves the breaking of Si-O bonds.

Centrality dependence of charged jet production in p-Pb collisions at √{s_NN} = 5.02 TeV

NASA Astrophysics Data System (ADS)

Adam, J.; Adamová, D.; Aggarwal, M. M.; Aglieri Rinella, G.; Agnello, M.; Agrawal, N.; Ahammed, Z.; Ahmad, S.; Ahn, S. U.; Aiola, S.; Akindinov, A.; Alam, S. N.; Albuquerque, D. S. D.; Aleksandrov, D.; Alessandro, B.; Alexandre, D.; Alfaro Molina, R.; Alici, A.; Alkin, A.; Almaraz, J. R. M.; Alme, J.; Alt, T.; Altinpinar, S.; Altsybeev, I.; Alves Garcia Prado, C.; Andrei, C.; Andronic, A.; Anguelov, V.; Antičić, T.; Antinori, F.; Antonioli, P.; Aphecetche, L.; Appelshäuser, H.; Arcelli, S.; Arnaldi, R.; Arnold, O. W.; Arsene, I. C.; Arslandok, M.; Audurier, B.; Augustinus, A.; Averbeck, R.; Azmi, M. D.; Badalà, A.; Baek, Y. W.; Bagnasco, S.; Bailhache, R.; Bala, R.; Balasubramanian, S.; Baldisseri, A.; Baral, R. C.; Barbano, A. M.; Barbera, R.; Barile, F.; Barnaföldi, G. G.; Barnby, L. S.; Barret, V.; Bartalini, P.; Barth, K.; Bartke, J.; Bartsch, E.; Basile, M.; Bastid, N.; Basu, S.; Bathen, B.; Batigne, G.; Batista Camejo, A.; Batyunya, B.; Batzing, P. C.; Bearden, I. G.; Beck, H.; Bedda, C.; Behera, N. K.; Belikov, I.; Bellini, F.; Bello Martinez, H.; Bellwied, R.; Belmont, R.; Belmont-Moreno, E.; Belyaev, V.; Bencedi, G.; Beole, S.; Berceanu, I.; Bercuci, A.; Berdnikov, Y.; Berenyi, D.; Bertens, R. A.; Berzano, D.; Betev, L.; Bhasin, A.; Bhat, I. R.; Bhati, A. K.; Bhattacharjee, B.; Bhom, J.; Bianchi, L.; Bianchi, N.; Bianchin, C.; Bielčík, J.; Bielčíková, J.; Bilandzic, A.; Biro, G.; Biswas, R.; Biswas, S.; Bjelogrlic, S.; Blair, J. T.; Blau, D.; Blume, C.; Bock, F.; Bogdanov, A.; Bøggild, H.; Boldizsár, L.; Bombara, M.; Book, J.; Borel, H.; Borissov, A.; Borri, M.; Bossú, F.; Botta, E.; Bourjau, C.; Braun-Munzinger, P.; Bregant, M.; Breitner, T.; Broker, T. A.; Browning, T. A.; Broz, M.; Brucken, E. J.; Bruna, E.; Bruno, G. E.; Budnikov, D.; Buesching, H.; Bufalino, S.; Buncic, P.; Busch, O.; Buthelezi, Z.; Butt, J. B.; Buxton, J. T.; Cabala, J.; Caffarri, D.; Cai, X.; Caines, H.; Calero Diaz, L.; Caliva, A.; Calvo Villar, E.; Camerini, P.; Carena, F.; Carena, W.; Carnesecchi, F.; Castillo Castellanos, J.; Castro, A. J.; Casula, E. A. R.; Ceballos Sanchez, C.; Cepila, J.; Cerello, P.; Cerkala, J.; Chang, B.; Chapeland, S.; Chartier, M.; Charvet, J. L.; Chattopadhyay, S.; Chattopadhyay, S.; Chauvin, A.; Chelnokov, V.; Cherney, M.; Cheshkov, C.; Cheynis, B.; Chibante Barroso, V.; Chinellato, D. D.; Cho, S.; Chochula, P.; Choi, K.; Chojnacki, M.; Choudhury, S.; Christakoglou, P.; Christensen, C. H.; Christiansen, P.; Chujo, T.; Chung, S. U.; Cicalo, C.; Cifarelli, L.; Cindolo, F.; Cleymans, J.; Colamaria, F.; Colella, D.; Collu, A.; Colocci, M.; Conesa Balbastre, G.; Conesa del Valle, Z.; Connors, M. E.; Contreras, J. G.; Cormier, T. M.; Corrales Morales, Y.; Cortés Maldonado, I.; Cortese, P.; Cosentino, M. R.; Costa, F.; Crochet, P.; Cruz Albino, R.; Cuautle, E.; Cunqueiro, L.; Dahms, T.; Dainese, A.; Danisch, M. C.; Danu, A.; Das, D.; Das, I.; Das, S.; Dash, A.; Dash, S.; De, S.; De Caro, A.; de Cataldo, G.; de Conti, C.; de Cuveland, J.; De Falco, A.; De Gruttola, D.; De Marco, N.; De Pasquale, S.; Deisting, A.; Deloff, A.; Dénes, E.; Deplano, C.; Dhankher, P.; Di Bari, D.; Di Mauro, A.; Di Nezza, P.; Diaz Corchero, M. A.; Dietel, T.; Dillenseger, P.; Divià, R.; Djuvsland, Ø.; Dobrin, A.; Domenicis Gimenez, D.; Dönigus, B.; Dordic, O.; Drozhzhova, T.; Dubey, A. K.; Dubla, A.; Ducroux, L.; Dupieux, P.; Ehlers, R. J.; Elia, D.; Endress, E.; Engel, H.; Epple, E.; Erazmus, B.; Erdemir, I.; Erhardt, F.; Espagnon, B.; Estienne, M.; Esumi, S.; Eum, J.; Evans, D.; Evdokimov, S.; Eyyubova, G.; Fabbietti, L.; Fabris, D.; Faivre, J.; Fantoni, A.; Fasel, M.; Feldkamp, L.; Feliciello, A.; Feofilov, G.; Ferencei, J.; Fernández Téllez, A.; Ferreiro, E. G.; Ferretti, A.; Festanti, A.; Feuillard, V. J. G.; Figiel, J.; Figueredo, M. A. S.; Filchagin, S.; Finogeev, D.; Fionda, F. M.; Fiore, E. M.; Fleck, M. G.; Floris, M.; Foertsch, S.; Foka, P.; Fokin, S.; Fragiacomo, E.; Francescon, A.; Frankenfeld, U.; Fronze, G. G.; Fuchs, U.; Furget, C.; Furs, A.; Fusco Girard, M.; Gaardhøje, J. J.; Gagliardi, M.; Gago, A. M.; Gallio, M.; Gangadharan, D. R.; Ganoti, P.; Gao, C.; Garabatos, C.; Garcia-Solis, E.; Gargiulo, C.; Gasik, P.; Gauger, E. F.; Germain, M.; Gheata, M.; Ghosh, P.; Ghosh, S. K.; Gianotti, P.; Giubellino, P.; Giubilato, P.; Gladysz-Dziadus, E.; Glässel, P.; Goméz Coral, D. M.; Gomez Ramirez, A.; Gonzalez, A. S.; Gonzalez, V.; González-Zamora, P.; Gorbunov, S.; Görlich, L.; Gotovac, S.; Grabski, V.; Grachov, O. A.; Graczykowski, L. K.; Graham, K. L.; Grelli, A.; Grigoras, A.; Grigoras, C.; Grigoriev, V.; Grigoryan, A.; Grigoryan, S.; Grinyov, B.; Grion, N.; Gronefeld, J. M.; Grosse-Oetringhaus, J. F.; Grosso, R.; Guber, F.; Guernane, R.; Guerzoni, B.; Gulbrandsen, K.; Gunji, T.; Gupta, A.; Gupta, R.; Haake, R.; Haaland, Ø.; Hadjidakis, C.; Haiduc, M.; Hamagaki, H.; Hamar, G.; Hamon, J. C.; Harris, J. W.; Harton, A.; Hatzifotiadou, D.; Hayashi, S.; Heckel, S. T.; Hellbär, E.; Helstrup, H.; Herghelegiu, A.; Herrera Corral, G.; Hess, B. A.; Hetland, K. F.; Hillemanns, H.; Hippolyte, B.; Horak, D.; Hosokawa, R.; Hristov, P.; Humanic, T. J.; Hussain, N.; Hussain, T.; Hutter, D.; Hwang, D. S.; Ilkaev, R.; Inaba, M.; Incani, E.; Ippolitov, M.; Irfan, M.; Ivanov, M.; Ivanov, V.; Izucheev, V.; Jacazio, N.; Jacobs, P. M.; Jadhav, M. B.; Jadlovska, S.; Jadlovsky, J.; Jahnke, C.; Jakubowska, M. J.; Jang, H. J.; Janik, M. A.; Jayarathna, P. H. S. Y.; Jena, C.; Jena, S.; Jimenez Bustamante, R. T.; Jones, P. G.; Jusko, A.; Kalinak, P.; Kalweit, A.; Kamin, J.; Kang, J. H.; Kaplin, V.; Kar, S.; Karasu Uysal, A.; Karavichev, O.; Karavicheva, T.; Karayan, L.; Karpechev, E.; Kebschull, U.; Keidel, R.; Keijdener, D. L. D.; Keil, M.; Mohisin Khan, M.; Khan, P.; Khan, S. A.; Khanzadeev, A.; Kharlov, Y.; Kileng, B.; Kim, D. W.; Kim, D. J.; Kim, D.; Kim, H.; Kim, J. S.; Kim, M.; Kim, S.; Kim, T.; Kirsch, S.; Kisel, I.; Kiselev, S.; Kisiel, A.; Kiss, G.; Klay, J. L.; Klein, C.; Klein, J.; Klein-Bösing, C.; Klewin, S.; Kluge, A.; Knichel, M. L.; Knospe, A. G.; Kobdaj, C.; Kofarago, M.; Kollegger, T.; Kolojvari, A.; Kondratiev, V.; Kondratyeva, N.; Kondratyuk, E.; Konevskikh, A.; Kopcik, M.; Kostarakis, P.; Kour, M.; Kouzinopoulos, C.; Kovalenko, O.; Kovalenko, V.; Kowalski, M.; Koyithatta Meethaleveedu, G.; Králik, I.; Kravčáková, A.; Krivda, M.; Krizek, F.; Kryshen, E.; Krzewicki, M.; Kubera, A. M.; Kučera, V.; Kuhn, C.; Kuijer, P. G.; Kumar, A.; Kumar, J.; Kumar, L.; Kumar, S.; Kurashvili, P.; Kurepin, A.; Kurepin, A. B.; Kuryakin, A.; Kweon, M. J.; Kwon, Y.; La Pointe, S. L.; La Rocca, P.; Ladron de Guevara, P.; Lagana Fernandes, C.; Lakomov, I.; Langoy, R.; Lapidus, K.; Lara, C.; Lardeux, A.; Lattuca, A.; Laudi, E.; Lea, R.; Leardini, L.; Lee, G. R.; Lee, S.; Lehas, F.; Lehner, S.; Lemmon, R. C.; Lenti, V.; Leogrande, E.; León Monzón, I.; León Vargas, H.; Leoncino, M.; Lévai, P.; Li, S.; Li, X.; Lien, J.; Lietava, R.; Lindal, S.; Lindenstruth, V.; Lippmann, C.; Lisa, M. A.; Ljunggren, H. M.; Lodato, D. F.; Loenne, P. I.; Loginov, V.; Loizides, C.; Lopez, X.; López Torres, E.; Lowe, A.; Luettig, P.; Lunardon, M.; Luparello, G.; Lutz, T. H.; Maevskaya, A.; Mager, M.; Mahajan, S.; Mahmood, S. M.; Maire, A.; Majka, R. D.; Malaev, M.; Maldonado Cervantes, I.; Malinina, L.; Mal'Kevich, D.; Malzacher, P.; Mamonov, A.; Manko, V.; Manso, F.; Manzari, V.; Marchisone, M.; Mareš, J.; Margagliotti, G. V.; Margotti, A.; Margutti, J.; Marín, A.; Markert, C.; Marquard, M.; Martin, N. A.; Martin Blanco, J.; Martinengo, P.; Martínez, M. I.; Martínez García, G.; Martinez Pedreira, M.; Mas, A.; Masciocchi, S.; Masera, M.; Masoni, A.; Mastroserio, A.; Matyja, A.; Mayer, C.; Mazer, J.; Mazzoni, M. A.; Mcdonald, D.; Meddi, F.; Melikyan, Y.; Menchaca-Rocha, A.; Meninno, E.; Mercado Pérez, J.; Meres, M.; Miake, Y.; Mieskolainen, M. M.; Mikhaylov, K.; Milano, L.; Milosevic, J.; Mischke, A.; Mishra, A. N.; Miśkowiec, D.; Mitra, J.; Mitu, C. M.; Mohammadi, N.; Mohanty, B.; Molnar, L.; Montaño Zetina, L.; Montes, E.; Moreira De Godoy, D. A.; Moreno, L. A. P.; Moretto, S.; Morreale, A.; Morsch, A.; Muccifora, V.; Mudnic, E.; Mühlheim, D.; Muhuri, S.; Mukherjee, M.; Mulligan, J. D.; Munhoz, M. G.; Munzer, R. H.; Murakami, H.; Murray, S.; Musa, L.; Musinsky, J.; Naik, B.; Nair, R.; Nandi, B. K.; Nania, R.; Nappi, E.; Naru, M. U.; Natal da Luz, H.; Nattrass, C.; Navarro, S. R.; Nayak, K.; Nayak, R.; Nayak, T. K.; Nazarenko, S.; Nedosekin, A.; Nellen, L.; Ng, F.; Nicassio, M.; Niculescu, M.; Niedziela, J.; Nielsen, B. S.; Nikolaev, S.; Nikulin, S.; Nikulin, V.; Noferini, F.; Nomokonov, P.; Nooren, G.; Noris, J. C. C.; Norman, J.; Nyanin, A.; Nystrand, J.; Oeschler, H.; Oh, S.; Oh, S. K.; Ohlson, A.; Okatan, A.; Okubo, T.; Olah, L.; Oleniacz, J.; Oliveira Da Silva, A. C.; Oliver, M. H.; Onderwaater, J.; Oppedisano, C.; Orava, R.; Oravec, M.; Ortiz Velasquez, A.; Oskarsson, A.; Otwinowski, J.; Oyama, K.; Ozdemir, M.; Pachmayer, Y.; Pagano, D.; Pagano, P.; Paić, G.; Pal, S. K.; Pan, J.; Pandey, A. K.; Papikyan, V.; Pappalardo, G. S.; Pareek, P.; Park, W. J.; Parmar, S.; Passfeld, A.; Paticchio, V.; Patra, R. N.; Paul, B.; Pei, H.; Peitzmann, T.; Pereira Da Costa, H.; Peresunko, D.; Perez Lezama, E.; Peskov, V.; Pestov, Y.; Petráček, V.; Petrov, V.; Petrovici, M.; Petta, C.; Piano, S.; Pikna, M.; Pillot, P.; Pimentel, L. O. D. L.; Pinazza, O.; Pinsky, L.; Piyarathna, D. B.; Płoskoń, M.; Planinic, M.; Pluta, J.; Pochybova, S.; Podesta-Lerma, P. L. M.; Poghosyan, M. G.; Polichtchouk, B.; Poljak, N.; Poonsawat, W.; Pop, A.; Porteboeuf-Houssais, S.; Porter, J.; Pospisil, J.; Prasad, S. K.; Preghenella, R.; Prino, F.; Pruneau, C. A.; Pshenichnov, I.; Puccio, M.; Puddu, G.; Pujahari, P.; Punin, V.; Putschke, J.; Qvigstad, H.; Rachevski, A.; Raha, S.; Rajput, S.; Rak, J.; Rakotozafindrabe, A.; Ramello, L.; Rami, F.; Raniwala, R.; Raniwala, S.; Räsänen, S. S.; Rascanu, B. T.; Rathee, D.; Read, K. F.; Redlich, K.; Reed, R. J.; Rehman, A.; Reichelt, P.; Reidt, F.; Ren, X.; Renfordt, R.; Reolon, A. R.; Reshetin, A.; Reygers, K.; Riabov, V.; Ricci, R. A.; Richert, T.; Richter, M.; Riedler, P.; Riegler, W.; Riggi, F.; Ristea, C.; Rocco, E.; Rodríguez Cahuantzi, M.; Rodriguez Manso, A.; Røed, K.; Rogochaya, E.; Rohr, D.; Röhrich, D.; Ronchetti, F.; Ronflette, L.; Rosnet, P.; Rossi, A.; Roukoutakis, F.; Roy, A.; Roy, C.; Roy, P.; Rubio Montero, A. J.; Rui, R.; Russo, R.; Ruzza, B. D.; Ryabinkin, E.; Ryabov, Y.; Rybicki, A.; Saarinen, S.; Sadhu, S.; Sadovsky, S.; Šafařík, K.; Sahlmuller, B.; Sahoo, P.; Sahoo, R.; Sahoo, S.; Sahu, P. K.; Saini, J.; Sakai, S.; Saleh, M. A.; Salzwedel, J.; Sambyal, S.; Samsonov, V.; Šándor, L.; Sandoval, A.; Sano, M.; Sarkar, D.; Sarkar, N.; Sarma, P.; Scapparone, E.; Scarlassara, F.; Schiaua, C.; Schicker, R.; Schmidt, C.; Schmidt, H. R.; Schmidt, M.; Schuchmann, S.; Schukraft, J.; Schulc, M.; Schutz, Y.; Schwarz, K.; Schweda, K.; Scioli, G.; Scomparin, E.; Scott, R.; Šefčík, M.; Seger, J. E.; Sekiguchi, Y.; Sekihata, D.; Selyuzhenkov, I.; Senosi, K.; Senyukov, S.; Serradilla, E.; Sevcenco, A.; Shabanov, A.; Shabetai, A.; Shadura, O.; Shahoyan, R.; Shahzad, M. I.; Shangaraev, A.; Sharma, A.; Sharma, M.; Sharma, M.; Sharma, N.; Sheikh, A. I.; Shigaki, K.; Shou, Q.; Shtejer, K.; Sibiriak, Y.; Siddhanta, S.; Sielewicz, K. M.; Siemiarczuk, T.; Silvermyr, D.; Silvestre, C.; Simatovic, G.; Simonetti, G.; Singaraju, R.; Singh, R.; Singha, S.; Singhal, V.; Sinha, B. C.; Sinha, T.; Sitar, B.; Sitta, M.; Skaali, T. B.; Slupecki, M.; Smirnov, N.; Snellings, R. J. M.; Snellman, T. W.; Song, J.; Song, M.; Song, Z.; Soramel, F.; Sorensen, S.; Souza, R. D. de; Sozzi, F.; Spacek, M.; Spiriti, E.; Sputowska, I.; Spyropoulou-Stassinaki, M.; Stachel, J.; Stan, I.; Stankus, P.; Stenlund, E.; Steyn, G.; Stiller, J. H.; Stocco, D.; Strmen, P.; Suaide, A. A. P.; Sugitate, T.; Suire, C.; Suleymanov, M.; Suljic, M.; Sultanov, R.; Šumbera, M.; Sumowidagdo, S.; Szabo, A.; Szarka, I.; Szczepankiewicz, A.; Szymanski, M.; Tabassam, U.; Takahashi, J.; Tambave, G. J.; Tanaka, N.; Tarhini, M.; Tariq, M.; Tarzila, M. G.; Tauro, A.; Tejeda Muñoz, G.; Telesca, A.; Terasaki, K.; Terrevoli, C.; Teyssier, B.; Thäder, J.; Thakur, D.; Thomas, D.; Tieulent, R.; Tikhonov, A.; Timmins, A. R.; Toia, A.; Trogolo, S.; Trombetta, G.; Trubnikov, V.; Trzaska, W. H.; Tsuji, T.; Tumkin, A.; Turrisi, R.; Tveter, T. S.; Ullaland, K.; Uras, A.; Usai, G. L.; Utrobicic, A.; Vala, M.; Valencia Palomo, L.; Vallero, S.; Van Der Maarel, J.; Van Hoorne, J. W.; van Leeuwen, M.; Vanat, T.; Vande Vyvre, P.; Varga, D.; Vargas, A.; Vargyas, M.; Varma, R.; Vasileiou, M.; Vasiliev, A.; Vauthier, A.; Vázquez Doce, O.; Vechernin, V.; Veen, A. M.; Veldhoen, M.; Velure, A.; Vercellin, E.; Vergara Limón, S.; Vernet, R.; Verweij, M.; Vickovic, L.; Viinikainen, J.; Vilakazi, Z.; Villalobos Baillie, O.; Villatoro Tello, A.; Vinogradov, A.; Vinogradov, L.; Vinogradov, Y.; Virgili, T.; Vislavicius, V.; Viyogi, Y. P.; Vodopyanov, A.; Völkl, M. A.; Voloshin, K.; Voloshin, S. A.; Volpe, G.; Haller, B. von; Vorobyev, I.; Vranic, D.; Vrláková, J.; Vulpescu, B.; Wagner, B.; Wagner, J.; Wang, H.; Wang, M.; Watanabe, D.; Watanabe, Y.; Weber, M.; Weber, S. G.; Weiser, D. F.; Wessels, J. P.; Westerhoff, U.; Whitehead, A. M.; Wiechula, J.; Wikne, J.; Wilk, G.; Wilkinson, J.; Williams, M. C. S.; Windelband, B.; Winn, M.; Yang, P.; Yano, S.; Yasin, Z.; Yin, Z.; Yokoyama, H.; Yoo, I.-K.; Yoon, J. H.; Yurchenko, V.; Zaborowska, A.; Zaccolo, V.; Zaman, A.; Zampolli, C.; Zanoli, H. J. C.; Zaporozhets, S.; Zardoshti, N.; Zarochentsev, A.; Závada, P.; Zaviyalov, N.; Zbroszczyk, H.; Zgura, I. S.; Zhalov, M.; Zhang, H.; Zhang, X.; Zhang, Y.; Zhang, C.; Zhang, Z.; Zhao, C.; Zhigareva, N.; Zhou, D.; Zhou, Y.; Zhou, Z.; Zhu, H.; Zhu, J.; Zichichi, A.; Zimmermann, A.; Zimmermann, M. B.; Zinovjev, G.; Zyzak, M.

2016-05-01

Measurements of charged jet production as a function of centrality are presented for p-Pb collisions recorded at √{s_{NN}}= 5.02 TeV with the ALICE detector. Centrality classes are determined via the energy deposit in neutron calorimeters at zero degree, close to the beam direction, to minimise dynamical biases of the selection. The corresponding number of participants or binary nucleon-nucleon collisions is determined based on the particle production in the Pb-going rapidity region. Jets have been reconstructed in the central rapidity region from charged particles with the anti-k_{T} algorithm for resolution parameters R = 0.2 and R = 0.4 in the transverse momentum range 20 to 120 GeV/ c. The reconstructed jet momentum and yields have been corrected for detector effects and underlying-event background. In the five centrality bins considered, the charged jet production in p-Pb collisions is consistent with the production expected from binary scaling from pp collisions. The ratio of jet yields reconstructed with the two different resolution parameters is also independent of the centrality selection, demonstrating the absence of major modifications of the radial jet structure in the reported centrality classes.

Understanding the formation mechanism of graphene frameworks synthesized by solvothermal and rapid pyrolytic processes based on an alcohol-sodium hydroxide system.

PubMed

Cui, Huijuan; Zheng, Jianfeng; Yang, Pengju; Zhu, Yanyan; Wang, Zhijian; Zhu, Zhenping

2015-06-03

The determination of ways to facilitate the 2D-oriented assembly of carbons into graphene instead of other carbon structures while restraining the π-π stacking interaction is a challenge for the controllable bulk synthesis of graphene, which is vital both scientifically and technically. In this study, graphene frameworks (GFs) are synthesized by solvothermal and rapid pyrolytic processes based on an alcohol-sodium hydroxide system. The evolution mechanism of GFs is investigated systematically. Under sodium catalysis, the abundant carbon atoms produced by the fast decomposition of solvothermal intermediate self-assembled to graphene. The existence of abundant ether bonds may be favorable for 3D graphene formation. More importantly, GFs were successfully obtained using acetic acid as the carbon source in the synthetic process, suggesting the reasonability of analyzing the formation mechanism. It is quite possible to determine more favorable routes to synthesize graphene under this cognition. The electrochemical energy storage capacity of GFs was also studied, which revealed a high supercapacitor performance with a specific capacitance of 310.7 F/g at the current density of 0.2 A/g.

Rapid Screening Method for New Psychoactive Substances of Forensic Interest: Electrochemistry and Analytical Determination of Phenethylamines Derivatives (NBOMe) via Cyclic and Differential Pulse Voltammetry.

PubMed

Andrade, Ana Flávia B; Mamo, Samuel Kasahun; Gonzalez-Rodriguez, Jose

2017-02-07

The NBOMe derivatives are phenethylamines derived from the 2C class of hallucinogens. Only a few human pharmacologic studies have been conducted on these drugs, and several cases of intoxication and deaths have been reported. Presently, NBOMe are not a part of the routine drugs-of-abuse screening procedure for many police forces, and there are no rapid immunoassay screening tests that can detect the presence of those compounds. In this Article, the voltammetric behavior of 25B NBOMe and 25I NBOMe were investigated and their electroanalytical characteristics determined for the first time. A novel, fast, and sensitive screening method for the identification of the two most common NBOMes (25B-NBOMe and 25I-NBOMe) in real samples is reported. The method uses the electrochemical oxidation of these molecules to produce an analytical signal that can be related to the NBOMe concentration with an average lower limit of quantitation of 0.01 mg/mL for both of them. The method is selective enough to identify the two compounds individually, even given the great similarity in their structure.

Aerodynamic and structural studies of joined-wing aircraft

NASA Technical Reports Server (NTRS)

Kroo, Ilan; Smith, Stephen; Gallman, John

1991-01-01

A method for rapidly evaluating the structural and aerodynamic characteristics of joined-wing aircraft was developed and used to study the fundamental advantages attributed to this concept. The technique involves a rapid turnaround aerodynamic analysis method for computing minimum trimmed drag combined with a simple structural optimization. A variety of joined-wing designs are compared on the basis of trimmed drag, structural weight, and, finally, trimmed drag with fixed structural weight. The range of joined-wing design parameters resulting in best cruise performance is identified. Structural weight savings and net drag reductions are predicted for certain joined-wing configurations compared with conventional cantilever-wing configurations.

Refinement of NMR structures using implicit solvent and advanced sampling techniques.

PubMed

Chen, Jianhan; Im, Wonpil; Brooks, Charles L

2004-12-15

NMR biomolecular structure calculations exploit simulated annealing methods for conformational sampling and require a relatively high level of redundancy in the experimental restraints to determine quality three-dimensional structures. Recent advances in generalized Born (GB) implicit solvent models should make it possible to combine information from both experimental measurements and accurate empirical force fields to improve the quality of NMR-derived structures. In this paper, we study the influence of implicit solvent on the refinement of protein NMR structures and identify an optimal protocol of utilizing these improved force fields. To do so, we carry out structure refinement experiments for model proteins with published NMR structures using full NMR restraints and subsets of them. We also investigate the application of advanced sampling techniques to NMR structure refinement. Similar to the observations of Xia et al. (J.Biomol. NMR 2002, 22, 317-331), we find that the impact of implicit solvent is rather small when there is a sufficient number of experimental restraints (such as in the final stage of NMR structure determination), whether implicit solvent is used throughout the calculation or only in the final refinement step. The application of advanced sampling techniques also seems to have minimal impact in this case. However, when the experimental data are limited, we demonstrate that refinement with implicit solvent can substantially improve the quality of the structures. In particular, when combined with an advanced sampling technique, the replica exchange (REX) method, near-native structures can be rapidly moved toward the native basin. The REX method provides both enhanced sampling and automatic selection of the most native-like (lowest energy) structures. An optimal protocol based on our studies first generates an ensemble of initial structures that maximally satisfy the available experimental data with conventional NMR software using a simplified force field and then refines these structures with implicit solvent using the REX method. We systematically examine the reliability and efficacy of this protocol using four proteins of various sizes ranging from the 56-residue B1 domain of Streptococcal protein G to the 370-residue Maltose-binding protein. Significant improvement in the structures was observed in all cases when refinement was based on low-redundancy restraint data. The proposed protocol is anticipated to be particularly useful in early stages of NMR structure determination where a reliable estimate of the native fold from limited data can significantly expedite the overall process. This refinement procedure is also expected to be useful when redundant experimental data are not readily available, such as for large multidomain biomolecules and in solid-state NMR structure determination.

The microdopant effects of surfactant elements on structure-phase transitions during the rapid quenched crystallization of Fe-C-based melts

NASA Astrophysics Data System (ADS)

Polukhin, V. A.; Belyakova, R. M.; Rigmant, L. K.

2008-02-01

The nature of microdopant effects of surfactant Te and H2 reagents on structure-phase transitions in rapidly quenched and crystallized eutectic Fe-C-based melts were studied by experimental and computer methods. On the base of results of statistic-geometrical analysis the new information about the structure changes in multi-scaling systems -from meso- to nano-ones were obtained.

Mechanochemical formation of heterogeneous diamond structures during rapid uniaxial compression in graphite

NASA Astrophysics Data System (ADS)

Kroonblawd, Matthew P.; Goldman, Nir

2018-05-01

We predict mechanochemical formation of heterogeneous diamond structures from rapid uniaxial compression in graphite using quantum molecular dynamics simulations. Ensembles of simulations reveal the formation of different diamondlike products starting from thermal graphite crystal configurations. We identify distinct classes of final products with characteristic probabilities of formation, stress states, and electrical properties and show through simulations of rapid quenching that these products are nominally stable and can be recovered at room temperature and pressure. Some of the diamond products exhibit significant disorder and partial closure of the energy gap between the highest-occupied and lowest-unoccupied molecular orbitals (i.e., the HOMO-LUMO gap). Seeding atomic vacancies in graphite significantly biases toward forming products with small HOMO-LUMO gap. We show that a strong correlation between the HOMO-LUMO gap and disorder in tetrahedral bonding configurations informs which kinds of structural defects are associated with gap closure. The rapid diffusionless transformation of graphite is found to lock vacancy defects into the final diamond structure, resulting in configurations that prevent s p3 bonding and lead to localized HOMO and LUMO states with a small gap.

The application of compressive sampling in rapid ultrasonic computerized tomography (UCT) technique of steel tube slab (STS).

PubMed

Jiang, Baofeng; Jia, Pengjiao; Zhao, Wen; Wang, Wentao

2018-01-01

This paper explores a new method for rapid structural damage inspection of steel tube slab (STS) structures along randomly measured paths based on a combination of compressive sampling (CS) and ultrasonic computerized tomography (UCT). In the measurement stage, using fewer randomly selected paths rather than the whole measurement net is proposed to detect the underlying damage of a concrete-filled steel tube. In the imaging stage, the ℓ1-minimization algorithm is employed to recover the information of the microstructures based on the measurement data related to the internal situation of the STS structure. A numerical concrete tube model, with the various level of damage, was studied to demonstrate the performance of the rapid UCT technique. Real-world concrete-filled steel tubes in the Shenyang Metro stations were detected using the proposed UCT technique in a CS framework. Both the numerical and experimental results show the rapid UCT technique has the capability of damage detection in an STS structure with a high level of accuracy and with fewer required measurements, which is more convenient and efficient than the traditional UCT technique.

EzMol: A Web Server Wizard for the Rapid Visualization and Image Production of Protein and Nucleic Acid Structures.

PubMed

Reynolds, Christopher R; Islam, Suhail A; Sternberg, Michael J E

2018-01-31

EzMol is a molecular visualization Web server in the form of a software wizard, located at http://www.sbg.bio.ic.ac.uk/ezmol/. It is designed for easy and rapid image manipulation and display of protein molecules, and is intended for users who need to quickly produce high-resolution images of protein molecules but do not have the time or inclination to use a software molecular visualization system. EzMol allows the upload of molecular structure files in PDB format to generate a Web page including a representation of the structure that the user can manipulate. EzMol provides intuitive options for chain display, adjusting the color/transparency of residues, side chains and protein surfaces, and for adding labels to residues. The final adjusted protein image can then be downloaded as a high-resolution image. There are a range of applications for rapid protein display, including the illustration of specific areas of a protein structure and the rapid prototyping of images. Copyright © 2018. Published by Elsevier Ltd.

Utility of the Determine Syphilis TP rapid test in commercial sex venues in Peru.

PubMed

Campos, P E; Buffardi, A L; Chiappe, M; Buendía, C; Garcia, P J; Carcamo, C P; Garnett, G; White, P; Holmes, K K

2006-12-01

This study sought to evaluate the utility of the Determine Syphilis TP test performed in Peruvian commercial sex venues for the detection of active syphilis; and determine the feasibility of integrating rapid syphilis testing for female sex workers (FSW) into existing health outreach services. We tested 3586 female sex workers for syphilis by Determine in the field using whole blood fingerstick, and by rapid plasma reagin (RPR) and Treponema pallidum haemagglutination assay (TPHA) in a central laboratory in Lima using sera. 97.4% of the FSW offered rapid syphilis testing participated; and among those who tested positive, 87% visited the local health centre for treatment. More than twice as many specimens were RPR reactive using serum in Lima (5.7%) than tested positive by whole blood Determine in the field (2.8%), and although most were confirmed by TPHA, only a small proportion (0.7%) were RPR reactive at >or=1:8 dilutions, and likely indicating active syphilis. Sensitivity, specificity and positive predictive value of the Determine Syphilis TP test in whole blood when compared to serum RPR reactivity at any dilution confirmed by TPHA as the gold standard were 39.3%, 99.2% and 71.4%, respectively. Sensitivity improved to 64.0% when using serum RPR >or=1:8 confirmed by TPHA. Invalid tests were rare (0.3%). Rapid syphilis testing in sex work venues proved feasible, but Determine using whole blood obtained by fingerstick was substantially less sensitive than reported in previous laboratory-based studies using serum. Although easy to perform in outreach venues, the utility of this rapid syphilis test was relatively low in settings where a large proportion of the targeted population has been previously tested and treated.

Utility of the Determine Syphilis TP rapid test in commercial sex venues in Peru

PubMed Central

Campos, P E; Buffardi, A L; Chiappe, M; Buendía, C; Garcia, P J; Carcamo, C P; Garnett, G; White, P

2006-01-01

Objectives This study sought to evaluate the utility of the Determine Syphilis TP test performed in Peruvian commercial sex venues for the detection of active syphilis; and determine the feasibility of integrating rapid syphilis testing for female sex workers (FSW) into existing health outreach services. Methods We tested 3586 female sex workers for syphilis by Determine in the field using whole blood fingerstick, and by rapid plasma reagin (RPR) and Treponema pallidum haemagglutination assay (TPHA) in a central laboratory in Lima using sera. Results 97.4% of the FSW offered rapid syphilis testing participated; and among those who tested positive, 87% visited the local health centre for treatment. More than twice as many specimens were RPR reactive using serum in Lima (5.7%) than tested positive by whole blood Determine in the field (2.8%), and although most were confirmed by TPHA, only a small proportion (0.7%) were RPR reactive at ⩾1:8 dilutions, and likely indicating active syphilis. Sensitivity, specificity and positive predictive value of the Determine Syphilis TP test in whole blood when compared to serum RPR reactivity at any dilution confirmed by TPHA as the gold standard were 39.3%, 99.2% and 71.4%, respectively. Sensitivity improved to 64.0% when using serum RPR ⩾1:8 confirmed by TPHA. Invalid tests were rare (0.3%). Conclusions Rapid syphilis testing in sex work venues proved feasible, but Determine using whole blood obtained by fingerstick was substantially less sensitive than reported in previous laboratory‐based studies using serum. Although easy to perform in outreach venues, the utility of this rapid syphilis test was relatively low in settings where a large proportion of the targeted population has been previously tested and treated. PMID:17116642

Molecularly Imprinted Nanomicrospheres as Matrix Solid-Phase Dispersant Combined with Gas Chromatography for Determination of Four Phosphorothioate Pesticides in Carrot and Yacon

PubMed Central

Zhou, Mengchun; Hu, Nana; Shu, Shaohua; Wang, Mo

2015-01-01

An efficient, rapid, and selective method for sample pretreatment, namely, molecularly imprinted matrix solid-phase dispersion (MI-MSPD) coupled with gas chromatography (GC), was developed for the rapid isolation of four phosphorothioate organophosphorus pesticides (tolclofos-methyl, phoxim, chlorpyrifos, and parathion-methyl) from carrot and yacon samples. New molecularly imprinted polymer nanomicrospheres were synthesized by using typical structural analogue tolclofos-methyl as a dummy template via surface grafting polymerization on nanosilica. Then, these four pesticides in carrot and yacon were extracted and adsorbed using the imprinted nanomicrospheres and further determined by gas chromatography. Under the optimized conditions, a good linearity of four pesticides was obtained in a range of 0.05–17.0 ng·g−1 with R varying from 0.9971 to 0.9996, and the detection limit of the method was 0.012~0.026 ng·g−1 in carrot and yacon samples. The recovery rates at two spiked levels were in the range of 85.4–105.6% with RSD ≤9.6%. The presented MI-MSPD method combined the advantages of MSPD for allowing the extraction, dispersion, and homogenization in two steps and the advantages of MIPs for high affinity and selectivity towards four phosphorothioate pesticides, which could be applied to the determination of pesticide residues in complicated vegetal samples. PMID:25954569

Molecularly imprinted nanomicrospheres as matrix solid-phase dispersant combined with gas chromatography for determination of four phosphorothioate pesticides in carrot and yacon.

PubMed

Zhou, Mengchun; Hu, Nana; Shu, Shaohua; Wang, Mo

2015-01-01

An efficient, rapid, and selective method for sample pretreatment, namely, molecularly imprinted matrix solid-phase dispersion (MI-MSPD) coupled with gas chromatography (GC), was developed for the rapid isolation of four phosphorothioate organophosphorus pesticides (tolclofos-methyl, phoxim, chlorpyrifos, and parathion-methyl) from carrot and yacon samples. New molecularly imprinted polymer nanomicrospheres were synthesized by using typical structural analogue tolclofos-methyl as a dummy template via surface grafting polymerization on nanosilica. Then, these four pesticides in carrot and yacon were extracted and adsorbed using the imprinted nanomicrospheres and further determined by gas chromatography. Under the optimized conditions, a good linearity of four pesticides was obtained in a range of 0.05-17.0 ng·g(-1) with R varying from 0.9971 to 0.9996, and the detection limit of the method was 0.012~0.026 ng·g(-1) in carrot and yacon samples. The recovery rates at two spiked levels were in the range of 85.4-105.6% with RSD ≤9.6%. The presented MI-MSPD method combined the advantages of MSPD for allowing the extraction, dispersion, and homogenization in two steps and the advantages of MIPs for high affinity and selectivity towards four phosphorothioate pesticides, which could be applied to the determination of pesticide residues in complicated vegetal samples.

Micro- and nano-CT textural analysis of an experimental volcanic fulgurite.

NASA Astrophysics Data System (ADS)

Cimarelli, Corrado; Yilmaz, Tim; Colombier, Mathieu; Villanova, Julie; Höfer, Lucas; Hess, Kai-Uwe; Ruthensteiner, Bernhard; Dingwell, Donald

2017-04-01

Fulgurites are natural glasses formed by cloud to ground lightning discharges causing rapid heating into rocks or unconsolidated sediments. Volcanic lightning can determine the re-melting and even ablation of newly formed or just deposited volcanic tephra during explosive eruptions. In this case the pristine material is already constituted by glass that can be further modified by the discharge. Although volcanic lightning discharges are generally less energetic than those produced by thunderclouds, the high temperatures reached by the lightning channel are well in excess of the low melting temperature of glass material. Here we have experimentally reproduced a fulgurite by single impulse voltage discharges (134 kV, 331 A, 10.5 J) on a target glass material. We have chosen borosilicate glass fibers (180 microns nominal length) as starting material to better account for the structural and chemical modification of the single particles after discharge-melting. The structure of the small fulgurite is best resolved through X-ray micro- and nano-computed tomography. Micro-CT analysis was carried out on a phoenix nanotom m with a voxelsize of 1 µm3. Additionally a 3D reconstruction with a voxel size of 150 nm3 has been analyzed at the new nano-analysis beamline ID16B at the ESRF. 3D analysis was carried out using Avizo 9.2 software, which allows non-destructive analysis of the fragile structure of the sample. The sample shows the channel-like structure typical for natural fulgurites with an inner void channel and internal wall constituted by the melted fibers. About 33% of the total solid volume of the fulgurite is melted to form the inner wall. The inner wall is characterized by nano- to micro-metric vesicles determined by volatile exsolution (mainly H2O) during the instantaneous heating and trapped in the low viscosity melt by the subsequent rapid quenching. Progressively outward the fulgurite shows the intricate delicate structure of the pristine glass fibers. Our results demonstrate that structural and chemical alteration of low viscosity glass material is possible by small impulse discharges with relatively low currents, thus reproducing a plausible scenario for electrical discharges during volcanic eruptions. Our experiment opens the opportunity for systematic constrained experimental investigation of the modification induced by volcanic lightning on tephra.

Revealing the hidden networks of interaction in mobile animal groups allows prediction of complex behavioral contagion.

PubMed

Rosenthal, Sara Brin; Twomey, Colin R; Hartnett, Andrew T; Wu, Hai Shan; Couzin, Iain D

2015-04-14

Coordination among social animals requires rapid and efficient transfer of information among individuals, which may depend crucially on the underlying structure of the communication network. Establishing the decision-making circuits and networks that give rise to individual behavior has been a central goal of neuroscience. However, the analogous problem of determining the structure of the communication network among organisms that gives rise to coordinated collective behavior, such as is exhibited by schooling fish and flocking birds, has remained almost entirely neglected. Here, we study collective evasion maneuvers, manifested through rapid waves, or cascades, of behavioral change (a ubiquitous behavior among taxa) in schooling fish (Notemigonus crysoleucas). We automatically track the positions and body postures, calculate visual fields of all individuals in schools of ∼150 fish, and determine the functional mapping between socially generated sensory input and motor response during collective evasion. We find that individuals use simple, robust measures to assess behavioral changes in neighbors, and that the resulting networks by which behavior propagates throughout groups are complex, being weighted, directed, and heterogeneous. By studying these interaction networks, we reveal the (complex, fractional) nature of social contagion and establish that individuals with relatively few, but strongly connected, neighbors are both most socially influential and most susceptible to social influence. Furthermore, we demonstrate that we can predict complex cascades of behavioral change at their moment of initiation, before they actually occur. Consequently, despite the intrinsic stochasticity of individual behavior, establishing the hidden communication networks in large self-organized groups facilitates a quantitative understanding of behavioral contagion.

NSLS-II biomedical beamlines for micro-crystallography, FMX, and for highly automated crystallography, AMX: New opportunities for advanced data collection

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

Fuchs, Martin R., E-mail: mfuchs@bnl.gov; Bhogadi, Dileep K.; Jakoncic, Jean

We present the final design of the x-ray optics and experimental stations of two macromolecular crystallography (MX) beamlines at the National Synchrotron Light Source-II. The microfocusing FMX beamline will deliver a flux of ∼5×10{sup 12} ph/s at 1 Å into a 1 – 20 µm spot, its flux density surpassing current MX beamlines by up to two orders of magnitude. It covers an energy range from 5 – 30 keV. The highly automated AMX beamline is optimized for high throughput, with beam sizes from 4 – 100 µm, an energy range of 5 – 18 keV and a flux atmore » 1 Å of ∼10{sup 13} ph/s. A focus in designing the beamlines lay on achieving high beam stability, for example by implementing a horizontal bounce double crystal monochromator at FMX. A combination of compound refractive lenses and bimorph mirror optics at FMX supports rapid beam size changes. Central components of the in-house developed experimental stations are horizontal axis goniometers with a target sphere of confusion of 100 nm, piezo-slits for dynamic beam size changes during diffraction experiments, dedicated secondary goniometers for data collection from specimen in crystallization plates, and next generation pixel array detectors. FMX and AMX will support a broad range of biomedical structure determination methods from serial crystallography on micron-sized crystals, to structure determination of complexes in large unit cells, to rapid sample screening and room temperature data collection of crystals in trays.« less

Revealing the hidden networks of interaction in mobile animal groups allows prediction of complex behavioral contagion

PubMed Central

Rosenthal, Sara Brin; Twomey, Colin R.; Hartnett, Andrew T.; Wu, Hai Shan; Couzin, Iain D.

2015-01-01

Coordination among social animals requires rapid and efficient transfer of information among individuals, which may depend crucially on the underlying structure of the communication network. Establishing the decision-making circuits and networks that give rise to individual behavior has been a central goal of neuroscience. However, the analogous problem of determining the structure of the communication network among organisms that gives rise to coordinated collective behavior, such as is exhibited by schooling fish and flocking birds, has remained almost entirely neglected. Here, we study collective evasion maneuvers, manifested through rapid waves, or cascades, of behavioral change (a ubiquitous behavior among taxa) in schooling fish (Notemigonus crysoleucas). We automatically track the positions and body postures, calculate visual fields of all individuals in schools of ∼150 fish, and determine the functional mapping between socially generated sensory input and motor response during collective evasion. We find that individuals use simple, robust measures to assess behavioral changes in neighbors, and that the resulting networks by which behavior propagates throughout groups are complex, being weighted, directed, and heterogeneous. By studying these interaction networks, we reveal the (complex, fractional) nature of social contagion and establish that individuals with relatively few, but strongly connected, neighbors are both most socially influential and most susceptible to social influence. Furthermore, we demonstrate that we can predict complex cascades of behavioral change at their moment of initiation, before they actually occur. Consequently, despite the intrinsic stochasticity of individual behavior, establishing the hidden communication networks in large self-organized groups facilitates a quantitative understanding of behavioral contagion. PMID:25825752

Investigating Differences in Gas-Phase Conformations of 25-Hydroxyvitamin D3 Sodiated Epimers using Ion Mobility-Mass Spectrometry and Theoretical Modeling

NASA Astrophysics Data System (ADS)

Chouinard, Christopher D.; Cruzeiro, Vinícius Wilian D.; Beekman, Christopher R.; Roitberg, Adrian E.; Yost, Richard A.

2017-08-01

Drift tube ion mobility coupled with mass spectrometry was used to investigate the gas-phase structure of 25-hydroxyvitamin D3 (25OHD3) and D2 (25OHD2) epimers, and to evaluate its potential in rapid separation of these compounds. Experimental results revealed two distinct drift species for the 25OHD3 sodiated monomer, whereas only one of these conformations was observed for its epimer (epi25OHD3). The unique species allowed 25OHD3 to be readily distinguished, and the same pattern was observed for 25OHD2 epimers. Theoretical modeling of 25OHD3 epimers identified energetically stable gas-phase structures, indicating that both compounds may adopt a compact "closed" conformation, but that 25OHD3 may also adopt a slightly less energetically favorable "open" conformation that is not accessible to its epimer. Calculated theoretical collision cross-sections for these structures agreed with experimental results to <2%. Experimentation indicated that additional energy in the ESI source (i.e., increased temperature, spray voltage) affected the ratio of 25OHD3 conformations, with the less energetically favorable "open" conformation increasing in relative intensity. Finally, LC-IM-MS results yielded linear quantitation of 25OHD3, in the presence of the epimer interference, at biologically relevant concentrations. This study demonstrates that ion mobility can be used in tandem with theoretical modeling to determine structural differences that contribute to drift separation. These separation capabilities provide potential for rapid (<60 ms) identification of 25OHD3 and 25OHD2 in mixtures with their epimers.

Herbarium specimens reveal a historical shift in phylogeographic structure of common ragweed during native range disturbance.

PubMed

Martin, Michael D; Zimmer, Elizabeth A; Olsen, Morten T; Foote, Andrew D; Gilbert, M Thomas P; Brush, Grace S

2014-04-01

Invasive plants provide ample opportunity to study evolutionary shifts that occur after introduction to novel environments. However, although genetic characters pre-dating introduction can be important determinants of later success, large-scale investigations of historical genetic structure have not been feasible. Common ragweed (Ambrosia artemisiifolia L.) is an invasive weed native to North America that is known for its allergenic pollen. Palynological records from sediment cores indicate that this species was uncommon before European colonization of North America, and ragweed populations expanded rapidly as settlers deforested the landscape on a massive scale, later becoming an aggressive invasive with populations established globally. Towards a direct comparison of genetic structure now and during intense anthropogenic disturbance of the late 19th century, we sampled 45 natural populations of common ragweed across its native range as well as historical herbarium specimens collected up to 140 years ago. Bayesian clustering analyses of 453 modern and 473 historical samples genotyped at three chloroplast spacer regions and six nuclear microsatellite loci reveal that historical ragweed's spatial genetic structure mirrors both the palaeo-record of Ambrosia pollen deposition and the historical pattern of agricultural density across the landscape. Furthermore, for unknown reasons, this spatial genetic pattern has changed substantially in the intervening years. Following on previous work relating morphology and genetic expression between plants collected from eastern North America and Western Europe, we speculate that the cluster associated with humans' rapid transformation of the landscape is a likely source of these aggressive invasive populations. © 2014 John Wiley & Sons Ltd.

Structure Design and Realization of Rapid Medicine Dispensing System

NASA Astrophysics Data System (ADS)

Liu, Xiangquan

In this paper, the main components and function of rapid medicine dispensing system is analyzed, structure design of automatic feeding device, sloping storeroom, automatic dispensing device and automatic sorting device is completed. The system adopts medicine conveyer working in with manipulator to realize automatic batch supply of the boxed medicine, adopts sloping storeroom as warehouse of medicine to realize dense depositing, adopts dispensing mechanism which includes elevator, turning panel and electric magnet to realize rapid medicine dispensing, adopts sorting conveyor belt and sorting device to send medicine to designated outlet.

The ins and outs of lncRNA structure: How, why and what comes next?

PubMed

Blythe, Amanda J; Fox, Archa H; Bond, Charles S

2016-01-01

The field of structural biology has the unique advantage of being able to provide a comprehensive picture of biological mechanisms at the molecular and atomic level. Long noncoding RNAs (lncRNAs) represent the new frontier in the molecular biology of complex organisms yet remain the least characterised of all the classes of RNA. Thousands of new lncRNAs are being reported each year yet very little structural data exists for this rapidly expanding field. The length of lncRNAs ranges from 200 nt to over 100 kb in length and they generally exhibit low cellular abundance. Therefore, obtaining sufficient quantities of lncRNA to use for structural analysis is challenging. However, as technologies develop structures of lncRNAs are starting to emerge providing important information regarding their mechanism of action. Here we review the current methods used to determine the structure of lncRNA and lncRNA:protein complexes and describe the significant contribution structural biology has and will make to the field of lncRNA research. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa. Copyright © 2015 Elsevier B.V. All rights reserved.

Configuration selection for a 450-passenger ultraefficient 2020 aircraft

NASA Astrophysics Data System (ADS)

Paulus, D.; Salmon, T.; Mohr, B.; Roessler, C.; Petersson, Ӧ.; Stroscher, F.; Baier, H.; Hornung, M.

2013-12-01

This paper describes the configuration selection process in the FP7 project ACFA (Active Control for Flexible Aircraft) 2020 in view of the Advisory Council for Aeronautics Research in Europe (ACARE) aims. The design process challenges and the comparison of a blended wing body (BWB) aircraft with a wide body carry-through wing box (CWB) configuration are described in detail. Furthermore, the interactions between the conceptual design and structural design using multidisciplinary design optimization (MDO) to rapidly generate and adapt structural models to design changes and provide early feedback of mass and center of gravity values for these nontraditional configurations are discussed. Comparison of the two concepts determined that the developed all-lifting BWB airframe has the potential for a significant reduced fuel consumption compared to the CWB.

Placenta and Placental Derivatives in Regenerative Therapies: Experimental Studies, History, and Prospects

PubMed Central

Prokopyuk, Volodymyr; Pogozhykh, Denys

2018-01-01

Placental structures, capable to persist in a genetically foreign organism, are a natural model of allogeneic engraftment carrying a number of distinctive properties. In this review, the main features of the placenta and its derivatives such as structure, cellular composition, immunological and endocrine aspects, and the ability to invasion and deportation are discussed. These features are considered from a perspective that determines the placental material as a unique source for regenerative cell therapies and a lesson for immunological tolerance. A historical overview of clinical applications of placental extracts, cells, and tissue components is described. Empirically accumulated data are summarized and compared with modern research. Furthermore, we define scopes and outlooks of application of placental cells and tissues in the rapidly progressing field of regenerative medicine. PMID:29535770

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.

Structural Basis for Nucleotide Exchange in Heterotrimeric G Proteins

PubMed Central

Dror, Ron O.; Mildorf, Thomas J.; Hilger, Daniel; Manglik, Aashish; Borhani, David W.; Arlow, Daniel H.; Philippsen, Ansgar; Villanueva, Nicolas; Yang, Zhongyu; Lerch, Michael T.; Hubbell, Wayne L.; Kobilka, Brian K.; Sunahara, Roger K.; Shaw, David E.

2016-01-01

G protein–coupled receptors (GPCRs) relay diverse extracellular signals into cells by catalyzing nucleotide release from heterotrimeric G proteins, but the mechanism underlying this quintessential molecular signaling event has remained unclear. Here we use atomic-level simulations to elucidate the nucleotide-release mechanism. We find that the G protein α subunit Ras and helical domains—previously observed to separate widely upon receptor binding to expose the nucleotide-binding site—separate spontaneously and frequently even in the absence of a receptor. Domain separation is necessary but not sufficient for rapid nucleotide release. Rather, receptors catalyze nucleotide release by favoring an internal structural rearrangement of the Ras domain that weakens its nucleotide affinity. We use double electron-electron resonance spectroscopy and protein engineering to confirm predictions of our computationally determined mechanism. PMID:26089515

Automated fine structure image analysis method for discrimination of diabetic retinopathy stage using conjunctival microvasculature images

PubMed Central

Khansari, Maziyar M; O’Neill, William; Penn, Richard; Chau, Felix; Blair, Norman P; Shahidi, Mahnaz

2016-01-01

The conjunctiva is a densely vascularized mucus membrane covering the sclera of the eye with a unique advantage of accessibility for direct visualization and non-invasive imaging. The purpose of this study is to apply an automated quantitative method for discrimination of different stages of diabetic retinopathy (DR) using conjunctival microvasculature images. Fine structural analysis of conjunctival microvasculature images was performed by ordinary least square regression and Fisher linear discriminant analysis. Conjunctival images between groups of non-diabetic and diabetic subjects at different stages of DR were discriminated. The automated method’s discriminate rates were higher than those determined by human observers. The method allowed sensitive and rapid discrimination by assessment of conjunctival microvasculature images and can be potentially useful for DR screening and monitoring. PMID:27446692

Antibody Epitope Analysis to Investigate Folded Structure, Allosteric Conformation, and Evolutionary Lineage of Proteins.

PubMed

Wong, Sienna; Jin, J-P

2017-01-01

Study of folded structure of proteins provides insights into their biological functions, conformational dynamics and molecular evolution. Current methods of elucidating folded structure of proteins are laborious, low-throughput, and constrained by various limitations. Arising from these methods is the need for a sensitive, quantitative, rapid and high-throughput method not only analysing the folded structure of proteins, but also to monitor dynamic changes under physiological or experimental conditions. In this focused review, we outline the foundation and limitations of current protein structure-determination methods prior to discussing the advantages of an emerging antibody epitope analysis for applications in structural, conformational and evolutionary studies of proteins. We discuss the application of this method using representative examples in monitoring allosteric conformation of regulatory proteins and the determination of the evolutionary lineage of related proteins and protein isoforms. The versatility of the method described herein is validated by the ability to modulate a variety of assay parameters to meet the needs of the user in order to monitor protein conformation. Furthermore, the assay has been used to clarify the lineage of troponin isoforms beyond what has been depicted by sequence homology alone, demonstrating the nonlinear evolutionary relationship between primary structure and tertiary structure of proteins. The antibody epitope analysis method is a highly adaptable technique of protein conformation elucidation, which can be easily applied without the need for specialized equipment or technical expertise. When applied in a systematic and strategic manner, this method has the potential to reveal novel and biomedically meaningful information for structure-function relationship and evolutionary lineage of proteins. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Structural Significance of Lipid Diversity as Studied by Small Angle Neutron and X-ray Scattering

DOE PAGES

Kučerka, Norbert; Heberle, Frederick A.; Pan, Jianjun; ...

2015-09-21

In this paper, we review recent developments in the rapidly growing field of membrane biophysics, with a focus on the structural properties of single lipid bilayers determined by different scattering techniques, namely neutron and X-ray scattering. The need for accurate lipid structural properties is emphasized by the sometimes conflicting results found in the literature, even in the case of the most studied lipid bilayers. Increasingly, accurate and detailed structural models require more experimental data, such as those from contrast varied neutron scattering and X-ray scattering experiments that are jointly refined with molecular dynamics simulations. This experimental and computational approach producesmore » robust bilayer structural parameters that enable insights, for example, into the interplay between collective membrane properties and its components (e.g., hydrocarbon chain length and unsaturation, and lipid headgroup composition). Finally, from model studies such as these, one is better able to appreciate how a real biological membrane can be tuned by balancing the contributions from the lipid’s different moieties (e.g., acyl chains, headgroups, backbones, etc.).« less

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

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.

Prostate specific antigen velocity as a measure of the natural history of prostate cancer: defining a 'rapid riser' subset.

PubMed

Nam, R K; Klotz, L H; Jewett, M A; Danjoux, C; Trachtenberg, J

1998-01-01

To study the rate of change in prostate specific antigen (PSA velocity) in patients with prostate cancer initially managed by 'watchful waiting'. Serial PSA levels were determined in 141 patients with prostate cancer confirmed by biopsy, who were initially managed expectantly and enrolled between May 1990 and December 1995. Sixty-seven patients eventually underwent surgery (mean age 59 years) because they chose it (the decision for surgery was not based on PSA velocity). A cohort of 74 patients remained on 'watchful waiting' (mean age 69 years). Linear regression and logarithmic transformations were used to segregate those patients who showed a rapid rise, defined as a > 50% rise in PSA per year (or a doubling time of < 2 years) and designated 'rapid risers'. An initial analysis based on a minimum of two PSA values showed that 31% were rapid risers. Only 15% of patients with more than three serial PSA determinations over > or = 6 months showed a rapid rise in PSA level. There was no advantage of log-linear analysis over linear regression models. Three serial PSA determinations over > or = 6 months in patients with clinically localized prostate cancer identifies a subset (15%) of patients with a rapidly rising PSA level. Shorter PSA surveillance with fewer PSA values may falsely identify patients with rapid rises in PSA level. However, further follow-up is required to determine if a rapid rise in PSA level identifies a subset of patients with an aggressive biological phenotype who are either still curable or who have already progressed to incurability through metastatic disease.

Is there a common motor dysregulation in sleepwalking and REM sleep behaviour disorder?

PubMed

Haridi, Mehdi; Weyn Banningh, Sebastian; Clé, Marion; Leu-Semenescu, Smaranda; Vidailhet, Marie; Arnulf, Isabelle

2017-10-01

This study sought to determine if there is any overlap between the two major non-rapid eye movement and rapid eye movement parasomnias, i.e. sleepwalking/sleep terrors and rapid eye movement sleep behaviour disorder. We assessed adult patients with sleepwalking/sleep terrors using rapid eye movement sleep behaviour disorder screening questionnaires and determined if they had enhanced muscle tone during rapid eye movement sleep. Conversely, we assessed rapid eye movement sleep behaviour disorder patients using the Paris Arousal Disorders Severity Scale and determined if they had more N3 awakenings. The 251 participants included 64 patients with rapid eye movement sleep behaviour disorder (29 with idiopathic rapid eye movement sleep behaviour disorder and 35 with rapid eye movement sleep behaviour disorder associated with Parkinson's disease), 62 patients with sleepwalking/sleep terrors, 66 old healthy controls (age-matched with the rapid eye movement sleep behaviour disorder group) and 59 young healthy controls (age-matched with the sleepwalking/sleep terrors group). They completed the rapid eye movement sleep behaviour disorder screening questionnaire, rapid eye movement sleep behaviour disorder single question and Paris Arousal Disorders Severity Scale. In addition, all the participants underwent a video-polysomnography. The sleepwalking/sleep terrors patients scored positive on rapid eye movement sleep behaviour disorder scales and had a higher percentage of 'any' phasic rapid eye movement sleep without atonia when compared with controls; however, these patients did not have higher tonic rapid eye movement sleep without atonia or complex behaviours during rapid eye movement sleep. Patients with rapid eye movement sleep behaviour disorder had moderately elevated scores on the Paris Arousal Disorders Severity Scale but did not exhibit more N3 arousals (suggestive of non-rapid eye movement parasomnia) than the control group. These results indicate that dream-enacting behaviours (assessed by rapid eye movement sleep behaviour disorder screening questionnaires) are commonly reported by sleepwalking/sleep terrors patients, thus decreasing the questionnaire's specificity. Furthermore, sleepwalking/sleep terrors patients have excessive twitching during rapid eye movement sleep, which may result either from a higher dreaming activity in rapid eye movement sleep or from a more generalised non-rapid eye movement/rapid eye movement motor dyscontrol during sleep. © 2017 European Sleep Research Society.

[Rapid ecological assessment of tropical fish communities in a gold mine area of Costa Rica].

PubMed

Espinoza Mendiola, Mario

2008-12-01

Gold mining impacts have generated a great concern regarding aquatic systems and habitat fragmentation. Anthropogenic disturbances on the structure and heterogeneity of a system can have an important effect on aquatic community stability. Ecological rapid assessments (1996, 2002, and 2007) were employed to determine the structure, composition and distribution of tropical fish communities in several rivers and smaller creeks from a gold mining area in Cerro Crucitas, Costa Rica. In addition, species composition and relative abundance were related with habitat structure. A total of 35 species were registered, among which sardine Astyanax aeneus (Characidae) and livebearer Alfaro cultratus (Poeciliidae) were the most abundant fish (71%). The highest species richness was observed in Caño Crucitas (s=19) and Minas Creek (s=18). Significant differences in fish communities structure and composition from Infiernillo river and Minas creek were observed (lamda = 0.0, F(132, 66) = 2.24, p < 0.001). Presence and/or absence of certain species such as Dormitor gobiomorus, Rhamdia nicaraguensis, Parachromis loiseillei and Atractosteus tropicus explained most of the spatial variation among sites. Habitat structure also contributed to explain differences among sites (lamda = 0.004, F(60.183) = 5.52, p < 0.001). Substratum (soft and hard bottom types) and habitat attributes (elevation, width and depth) explained most of the variability observed in Infiernillo River, Caño Crucitas and Tamagá Creek. In addition, a significant association between fish species and habitat structure was observed. This study reveals a high complexity in tropical fish communities that inhabit a gold mine area. Furthermore, it highlights the importance of habitat heterogeneity in fish community dynamics. The loss and degradation of aquatic systems in Cerro Crucitas can have a strong negative effect on fish community structure and composition of local species. A better understanding of the use of specific habitats that serve as essential fish habitats can improve tropical fish conservation and management strategies, thus increasing local diversity, and thereby, the biological importance of the area.

Better concrete mixes for rapid repair in Wisconsin : research brief.

DOT National Transportation Integrated Search

2017-07-04

Research Benefits : Confirmed that Wisconsins current CIP rapid-repair concretes perform adequately : Recommended mixture improvements to alleviate construction difficulties : Determined that increasing the durability of rapid repair c...

A rapid method to characterize seabed habitats and associated macro-organisms

USGS Publications Warehouse

Anderson, T.J.; Cochrane, G.R.; Roberts, D.A.; Chezar, H.; Hatcher, G.; ,

2007-01-01

This study presents a method for rapidly collecting, processing, and interrogating real-time abiotic and biotic seabed data to determine seabed habitat classifications. This is done from data collected over a large area of an acoustically derived seabed map, along multidirectional transects, using a towed small camera-sled. The seabed, within the newly designated Point Harris Marine Reserve on the northern coast of San Miguel Island, California, was acoustically imaged using sidescan sonar then ground-truthed using a towed small camera-sled. Seabed characterizations were made from video observations, and were logged to a laptop computer (PC) in real time. To ground-truth the acoustic mosaic, and to characterize abiotic and biotic aspects of the seabed, a three-tiered characterization scheme was employed that described the substratum type, physical structure (i.e., bedform or vertical relief), and the occurrence of benthic macrofauna and flora. A crucial advantage of the method described here, is that preliminary seabed characterizations can be interrogated and mapped over the sidescan mosaic and other seabed information within hours of data collection. This ability to rapidly process seabed data is invaluable to scientists and managers, particularly in modifying concurrent or planning subsequent surveys.

Enabling Rapid and Robust Structural Analysis During Conceptual Design

NASA Technical Reports Server (NTRS)

Eldred, Lloyd B.; Padula, Sharon L.; Li, Wu

2015-01-01

This paper describes a multi-year effort to add a structural analysis subprocess to a supersonic aircraft conceptual design process. The desired capabilities include parametric geometry, automatic finite element mesh generation, static and aeroelastic analysis, and structural sizing. The paper discusses implementation details of the new subprocess, captures lessons learned, and suggests future improvements. The subprocess quickly compares concepts and robustly handles large changes in wing or fuselage geometry. The subprocess can rank concepts with regard to their structural feasibility and can identify promising regions of the design space. The automated structural analysis subprocess is deemed robust and rapid enough to be included in multidisciplinary conceptual design and optimization studies.

Fast Response, Open-Celled Porous, Shape Memory Effect Actuators with Integrated Attachments

NASA Technical Reports Server (NTRS)

Jardine, Andrew Peter (Inventor)

2015-01-01

This invention relates to the exploitation of porous foam articles exhibiting the Shape Memory Effect as actuators. Each foam article is composed of a plurality of geometric shapes, such that some geometric shapes can fit snugly into or around rigid mating connectors that attach the Shape Memory foam article intimately into the load path between a static structure and a moveable structure. The foam is open-celled, composed of a plurality of interconnected struts whose mean diameter can vary from approximately 50 to 500 microns. Gases and fluids flowing through the foam transfer heat rapidly with the struts, providing rapid Shape Memory Effect transformations. Embodiments of porous foam articles as torsional actuators and approximately planar structures are disposed. Simple, integral connection systems exploiting the ability to supply large loads to a structure, and that can also supply hot and cold gases and fluids to effect rapid actuation are also disposed.

Electron backscatter diffraction analysis of Nb3Al multifilamentary strands prepared by rapid heating, quenching and transformation annealing

NASA Astrophysics Data System (ADS)

Takeuchi, T.; Tsuchiya, K.; Saeda, M.; Banno, N.; Kikuchi, A.; Iijima, Y.

2010-12-01

To enhance the non-Cu critical current density Jc at 15 T and 4.2 K (1000 A mm - 2 at present) we have endeavoured to refine the grain size of rapid heating, quenching and transformation (RHQT)-processed Nb3Al. In the present study, the grain boundary structures of RHQT-processed Nb3Al were examined by electron backscatter diffraction (EBSD) because transgranular fracture prevents the observation of fractured cross sections of Nb3Al to statistically determine the grain size. The grain size distributions of body-centred-cubic supersaturated-solid-solution Nb(Al)ss and A15 Nb3Al filaments were measured for grains misoriented by more than 2°, 5° and 15°. A mixed grain structure, which consists of a few large grains (>25 µm) and many small grains (<1 µm), was observed for an Nb3Al filament that had been transformed from non-deformed Nb(Al)ss. Plastic deformation that had been made between the rapid heating and quenching steps and the transformation step apparently homogenized the grain size distribution and then reduced the average grain size. The misorientation angle distributions of Nb(Al)ss and Nb3Al were also measured and compared with each other. A clear relationship between the Jc and the inverse grain size was not confirmed for the RHQT Nb3Al conductors examined in the present study, which indicates the importance of making a filament compositionally homogeneous to obtain a high Jc.

Rapid and accurate peripheral nerve detection using multipoint Raman imaging (Conference Presentation)

NASA Astrophysics Data System (ADS)

Kumamoto, Yasuaki; Minamikawa, Takeo; Kawamura, Akinori; Matsumura, Junichi; Tsuda, Yuichiro; Ukon, Juichiro; Harada, Yoshinori; Tanaka, Hideo; Takamatsu, Tetsuro

2017-02-01

Nerve-sparing surgery is essential to avoid functional deficits of the limbs and organs. Raman scattering, a label-free, minimally invasive, and accurate modality, is one of the best candidate technologies to detect nerves for nerve-sparing surgery. However, Raman scattering imaging is too time-consuming to be employed in surgery. Here we present a rapid and accurate nerve visualization method using a multipoint Raman imaging technique that has enabled simultaneous spectra measurement from different locations (n=32) of a sample. Five sec is sufficient for measuring n=32 spectra with good S/N from a given tissue. Principal component regression discriminant analysis discriminated spectra obtained from peripheral nerves (n=863 from n=161 myelinated nerves) and connective tissue (n=828 from n=121 tendons) with sensitivity and specificity of 88.3% and 94.8%, respectively. To compensate the spatial information of a multipoint-Raman-derived tissue discrimination image that is too sparse to visualize nerve arrangement, we used morphological information obtained from a bright-field image. When merged with the sparse tissue discrimination image, a morphological image of a sample shows what portion of Raman measurement points in arbitrary structure is determined as nerve. Setting a nerve detection criterion on the portion of "nerve" points in the structure as 40% or more, myelinated nerves (n=161) and tendons (n=121) were discriminated with sensitivity and specificity of 97.5%. The presented technique utilizing a sparse multipoint Raman image and a bright-field image has enabled rapid, safe, and accurate detection of peripheral nerves.

Structural analysis of a set of proteins resulting from a bacterial genomics project.

PubMed

Badger, J; Sauder, J M; Adams, J M; Antonysamy, S; Bain, K; Bergseid, M G; Buchanan, S G; Buchanan, M D; Batiyenko, Y; Christopher, J A; Emtage, S; Eroshkina, A; Feil, I; Furlong, E B; Gajiwala, K S; Gao, X; He, D; Hendle, J; Huber, A; Hoda, K; Kearins, P; Kissinger, C; Laubert, B; Lewis, H A; Lin, J; Loomis, K; Lorimer, D; Louie, G; Maletic, M; Marsh, C D; Miller, I; Molinari, J; Muller-Dieckmann, H J; Newman, J M; Noland, B W; Pagarigan, B; Park, F; Peat, T S; Post, K W; Radojicic, S; Ramos, A; Romero, R; Rutter, M E; Sanderson, W E; Schwinn, K D; Tresser, J; Winhoven, J; Wright, T A; Wu, L; Xu, J; Harris, T J R

2005-09-01

The targets of the Structural GenomiX (SGX) bacterial genomics project were proteins conserved in multiple prokaryotic organisms with no obvious sequence homolog in the Protein Data Bank of known structures. The outcome of this work was 80 structures, covering 60 unique sequences and 49 different genes. Experimental phase determination from proteins incorporating Se-Met was carried out for 45 structures with most of the remainder solved by molecular replacement using members of the experimentally phased set as search models. An automated tool was developed to deposit these structures in the Protein Data Bank, along with the associated X-ray diffraction data (including refined experimental phases) and experimentally confirmed sequences. BLAST comparisons of the SGX structures with structures that had appeared in the Protein Data Bank over the intervening 3.5 years since the SGX target list had been compiled identified homologs for 49 of the 60 unique sequences represented by the SGX structures. This result indicates that, for bacterial structures that are relatively easy to express, purify, and crystallize, the structural coverage of gene space is proceeding rapidly. More distant sequence-structure relationships between the SGX and PDB structures were investigated using PDB-BLAST and Combinatorial Extension (CE). Only one structure, SufD, has a truly unique topology compared to all folds in the PDB. Copyright 2005 Wiley-Liss, Inc.

Structured triglycerides were well tolerated and induced increased whole body fat oxidation compared with long-chain triglycerides in postoperative patients.

PubMed

Sandström, R; Hyltander, A; Körner, U; Lundholm, K

1995-01-01

It has been proposed, on the basis of animal experiments, that medium-chain triglycerides (MCT) may exert more favorable effects on whole body metabolism of injured animals than long-chain triglycerides (LCT). Therefore, the present study was designed to evaluate whether structured triglycerides are associated with increased whole body fat oxidation without promotion of ketogenesis in postoperative patients. A structured lipid emulsion (73403 Pharmacia, Sweden) containing medium- and long-chain fatty acids, esterified randomly to glycerol in a triglyceride structure, was used. Whole body fat oxidation was determined by indirect calorimetry in the postoperative period. Patients were randomized to receive structured lipids 1 day followed by LCT (Intralipid, Pharmacia) the next day or vice versa during 6 postoperative days. In part 1 of the study patients received fat at 1.0 g/kg per day in the presence of 80% of the basal requirement of nonprotein calories. In part 2 patients received fat at 1.5 g/kg per day in the presence of 120% of the nonprotein caloric requirement. Amino acids were always provided at 0.15 g N/kg per day. Structured lipids were not associated with any side effects, were rapidly cleared from the plasma compartment, and were rapidly oxidized without any significant hyperlipidemia or ketosis. Provision of structured lipids in the presence of excess of nonprotein calories (part 2) caused a significantly higher whole body fat oxidation (2.4 +/- 0.05 g/kg per day) compared with LCT provision (1.9 +/- 0.06 g/kg per day) (p < .0001) examined in the same patients. The results demonstrated for the first time in man that provision of structured triglycerides were associated with increased whole body fat oxidation in stressed postoperative patients, which is in line with the original metabolic and biochemical concept for structured triglycerides. The study provided evidence to support that structured lipids may represent a next generation of IV fat emulsions that may be clinically advantageous compared with conventional LCT emulsions in certain clinical conditions.

Determination of HIV Status in African Adults With Discordant HIV Rapid Tests.

PubMed

Fogel, Jessica M; Piwowar-Manning, Estelle; Donohue, Kelsey; Cummings, Vanessa; Marzinke, Mark A; Clarke, William; Breaud, Autumn; Fiamma, Agnès; Donnell, Deborah; Kulich, Michal; Mbwambo, Jessie K K; Richter, Linda; Gray, Glenda; Sweat, Michael; Coates, Thomas J; Eshleman, Susan H

2015-08-01

In resource-limited settings, HIV infection is often diagnosed using 2 rapid tests. If the results are discordant, a third tie-breaker test is often used to determine HIV status. This study characterized samples with discordant rapid tests and compared different testing strategies for determining HIV status in these cases. Samples were previously collected from 173 African adults in a population-based survey who had discordant rapid test results. Samples were classified as HIV positive or HIV negative using a rigorous testing algorithm that included two fourth-generation tests, a discriminatory test, and 2 HIV RNA tests. Tie-breaker tests were evaluated, including rapid tests (1 performed in-country), a third-generation enzyme immunoassay, and two fourth-generation tests. Selected samples were further characterized using additional assays. Twenty-nine samples (16.8%) were classified as HIV positive and 24 of those samples (82.8%) had undetectable HIV RNA. Antiretroviral drugs were detected in 1 sample. Sensitivity was 8.3%-43% for the rapid tests; 24.1% for the third-generation enzyme immunoassay; 95.8% and 96.6% for the fourth-generation tests. Specificity was lower for the fourth-generation tests than the other tests. Accuracy ranged from 79.5% to 91.3%. In this population-based survey, most HIV-infected adults with discordant rapid tests were virally suppressed without antiretroviral drugs. Use of individual assays as tie-breaker tests was not a reliable method for determining HIV status in these individuals. More extensive testing algorithms that use a fourth-generation screening test with a discriminatory test and HIV RNA test are preferable for determining HIV status in these cases.

Damage identification of beam structures using free response shapes obtained by use of a continuously scanning laser Doppler vibrometer system

NASA Astrophysics Data System (ADS)

Xu, Y. F.; Chen, Da-Ming; Zhu, W. D.

2017-08-01

Spatially dense operating deflection shapes and mode shapes can be rapidly obtained by use of a continuously scanning laser Doppler vibrometer (CSLDV) system, which sweeps its laser spot over a vibrating structure surface. This paper introduces a new type of vibration shapes called a free response shape (FRS) that can be obtained by use of a CSLDV system, and a new damage identification methodology using FRSs is developed for beam structures. An analytical expression of FRSs of a damped beam structure is derived, and FRSs from the analytical expression compare well with those from a finite element model. In the damage identification methodology, a free-response damage index (FRDI) is proposed, and damage regions can be identified near neighborhoods with consistently high values of FRDIs associated with different modes; an auxiliary FRDI is defined to assist identification of the neighborhoods. A FRDI associated with a mode consists of differences between curvatures of FRSs associated with the mode in a number of half-scan periods of a CSLDV system and those from polynomials that fit the FRSs with properly determined orders. A convergence index is proposed to determine the proper order of a polynomial fit. One advantage of the methodology is that the FRDI does not require any baseline information of an undamaged beam structure, if it is geometrically smooth and made of materials that have no stiffness and mass discontinuities. Another advantage is that FRDIs associated with multiple modes can be obtained using free response of a beam structure measured by a CSLDV system in one scan. The number of half-scan periods for calculation of the FRDI associated with a mode can be determined by use of the short-time Fourier transform. The proposed methodology was numerically and experimentally applied to identify damage in beam structures; effects of the scan frequency of a CSLDV system on qualities of obtained FRSs were experimentally investigated.

Effect of rapid thermal annealing on the electrical, optical and structural properties of ZnO-doped In2O3 films grown by linear facing target sputtering.

PubMed

Cho, Chung-Ki; Kim, Han-Ki

2012-04-01

We investigated the effect of rapid thermal annealing on the electrical, optical, and structural properties of ZnO-doped In2O3 (ZIO) films grown at different Ar/O2 flow ratios (15/0 and 15/1 sccm) by using linear facing target sputtering. It was found that the ZIO films grown at different Ar/O2, flow ratios showed different electrical and optical behavior with increasing rapid thermal annealing temperature. Synchrotron X-ray scattering examination showed that the different electrical and optical properties of the ZIO films could be attributed to the difference in preferred orientation with an increase in rapid thermal annealing temperature.

Rapid search for tertiary fragments reveals protein sequence–structure relationships

PubMed Central

Zhou, Jianfu; Grigoryan, Gevorg

2015-01-01

Finding backbone substructures from the Protein Data Bank that match an arbitrary query structural motif, composed of multiple disjoint segments, is a problem of growing relevance in structure prediction and protein design. Although numerous protein structure search approaches have been proposed, methods that address this specific task without additional restrictions and on practical time scales are generally lacking. Here, we propose a solution, dubbed MASTER, that is both rapid, enabling searches over the Protein Data Bank in a matter of seconds, and provably correct, finding all matches below a user-specified root-mean-square deviation cutoff. We show that despite the potentially exponential time complexity of the problem, running times in practice are modest even for queries with many segments. The ability to explore naturally plausible structural and sequence variations around a given motif has the potential to synthesize its design principles in an automated manner; so we go on to illustrate the utility of MASTER to protein structural biology. We demonstrate its capacity to rapidly establish structure–sequence relationships, uncover the native designability landscapes of tertiary structural motifs, identify structural signatures of binding, and automatically rewire protein topologies. Given the broad utility of protein tertiary fragment searches, we hope that providing MASTER in an open-source format will enable novel advances in understanding, predicting, and designing protein structure. PMID:25420575

The development of an annotated library of neutral human milk oligosaccharides

PubMed Central

Wu, Shuai; Tao, Nannan; German, J. Bruce; Grimm, Rudolf; Lebrilla, Carlito B.

2010-01-01

Human milk oligosaccharides (HMOs)a perform a number of functions including serving as prebiotics to stimulate the growth of beneficial intestinal bacteria, as receptor analogs to inhibit binding of pathogens, and as substances that promote postnatal brain development. There is further evidence that HMOs participate in modulating the human immune system. Because the absorption, catabolism and biological function of oligosaccharides (OS) have strong correlations with their structures, structure elucidation is key to advancing this research. Oligosaccharides are produced by competing enzymes that provide the large structural diversity and heterogeneity that characterizes this class of compounds. Unlike the proteome, there is no template for oligosaccharides making it difficult to rapidly identify oligosaccharide structures. In this research, the annotation of the neutral free oligosaccharides in milk is performed to develop a database for the rapid identification of oligosaccharide structures. Our strategy incorporates high performance nanoflow liquid chromatography and mass spectrometry for characterizing HMO structures. HPLC-Chip/TOF MS provides a sensitive and quantitative method for sample profiling. The reproducible retention time and accurate mass can be used to rapidly identify the OS structures in HMO samples. A library with 45 neutral OS structures has been constructed. The structures include information regarding the epitopes such as Lewis type as well as information regarding the secretor status. PMID:20578730

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 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.

Noise-tolerant inverse analysis models for nondestructive evaluation of transportation infrastructure systems using neural networks

NASA Astrophysics Data System (ADS)

Ceylan, Halil; Gopalakrishnan, Kasthurirangan; Birkan Bayrak, Mustafa; Guclu, Alper

2013-09-01

The need to rapidly and cost-effectively evaluate the present condition of pavement infrastructure is a critical issue concerning the deterioration of ageing transportation infrastructure all around the world. Nondestructive testing (NDT) and evaluation methods are well-suited for characterising materials and determining structural integrity of pavement systems. The falling weight deflectometer (FWD) is a NDT equipment used to assess the structural condition of highway and airfield pavement systems and to determine the moduli of pavement layers. This involves static or dynamic inverse analysis (referred to as backcalculation) of FWD deflection profiles in the pavement surface under a simulated truck load. The main objective of this study was to employ biologically inspired computational systems to develop robust pavement layer moduli backcalculation algorithms that can tolerate noise or inaccuracies in the FWD deflection data collected in the field. Artificial neural systems, also known as artificial neural networks (ANNs), are valuable computational intelligence tools that are increasingly being used to solve resource-intensive complex engineering problems. Unlike the linear elastic layered theory commonly used in pavement layer backcalculation, non-linear unbound aggregate base and subgrade soil response models were used in an axisymmetric finite element structural analysis programme to generate synthetic database for training and testing the ANN models. In order to develop more robust networks that can tolerate the noisy or inaccurate pavement deflection patterns in the NDT data, several network architectures were trained with varying levels of noise in them. The trained ANN models were capable of rapidly predicting the pavement layer moduli and critical pavement responses (tensile strains at the bottom of the asphalt concrete layer, compressive strains on top of the subgrade layer and the deviator stresses on top of the subgrade layer), and also pavement surface deflections with very low average errors comparable with those obtained directly from the finite element analyses.

Assessment and Challenges of Ligand Docking into Comparative Models of G-Protein Coupled Receptors

PubMed Central

Frimurer, Thomas M.; Meiler, Jens

2013-01-01

The rapidly increasing number of high-resolution X-ray structures of G-protein coupled receptors (GPCRs) creates a unique opportunity to employ comparative modeling and docking to provide valuable insight into the function and ligand binding determinants of novel receptors, to assist in virtual screening and to design and optimize drug candidates. However, low sequence identity between receptors, conformational flexibility, and chemical diversity of ligands present an enormous challenge to molecular modeling approaches. It is our hypothesis that rapid Monte-Carlo sampling of protein backbone and side-chain conformational space with Rosetta can be leveraged to meet this challenge. This study performs unbiased comparative modeling and docking methodologies using 14 distinct high-resolution GPCRs and proposes knowledge-based filtering methods for improvement of sampling performance and identification of correct ligand-receptor interactions. On average, top ranked receptor models built on template structures over 50% sequence identity are within 2.9 Å of the experimental structure, with an average root mean square deviation (RMSD) of 2.2 Å for the transmembrane region and 5 Å for the second extracellular loop. Furthermore, these models are consistently correlated with low Rosetta energy score. To predict their binding modes, ligand conformers of the 14 ligands co-crystalized with the GPCRs were docked against the top ranked comparative models. In contrast to the comparative models themselves, however, it remains difficult to unambiguously identify correct binding modes by score alone. On average, sampling performance was improved by 103 fold over random using knowledge-based and energy-based filters. In assessing the applicability of experimental constraints, we found that sampling performance is increased by one order of magnitude for every 10 residues known to contact the ligand. Additionally, in the case of DOR, knowledge of a single specific ligand-protein contact improved sampling efficiency 7 fold. These findings offer specific guidelines which may lead to increased success in determining receptor-ligand complexes. PMID:23844000

How Do Normal Faults Grow?

NASA Astrophysics Data System (ADS)

Jackson, C. A. L.; Bell, R. E.; Rotevatn, A.; Tvedt, A. B. M.

2015-12-01

Normal faulting accommodates stretching of the Earth's crust and is one of the fundamental controls on landscape evolution and sediment dispersal in rift basins. Displacement-length scaling relationships compiled from global datasets suggest normal faults grow via a sympathetic increase in these two parameters (the 'isolated fault model'). This model has dominated the structural geology literature for >20 years and underpins the structural and tectono-stratigraphic models developed for active rifts. However, relatively recent analysis of high-quality 3D seismic reflection data suggests faults may grow by rapid establishment of their near-final length prior to significant displacement accumulation (the 'coherent fault model'). The isolated and coherent fault models make very different predictions regarding the tectono-stratigraphic evolution of rift basin, thus assessing their applicability is important. To-date, however, very few studies have explicitly set out to critically test the coherent fault model thus, it may be argued, it has yet to be widely accepted in the structural geology community. Displacement backstripping is a simple graphical technique typically used to determine how faults lengthen and accumulate displacement; this technique should therefore allow us to test the competing fault models. However, in this talk we use several subsurface case studies to show that the most commonly used backstripping methods (the 'original' and 'modified' methods) are, however, of limited value, because application of one over the other requires an a priori assumption of the model most applicable to any given fault; we argue this is illogical given that the style of growth is exactly what the analysis is attempting to determine. We then revisit our case studies and demonstrate that, in the case of seismic-scale growth faults, growth strata thickness patterns and relay zone kinematics, rather than displacement backstripping, should be assessed to directly constrain fault length and thus tip behaviour through time. We conclude that rapid length establishment prior to displacement accumulation may be more common than is typically assumed, thus challenging the well-established, widely cited and perhaps overused, isolated fault model.

Rapid, sensitive and simultaneous determination of fluorescence-labeled polyamines in human hair by high-pressure liquid chromatography coupled with electrospray-ionization time-of-flight mass spectrometry.

PubMed

Sugiura, Koichi; Min, Jun Zhe; Toyo'oka, Toshimasa; Inagaki, Shinsuke

2008-09-26

The rapid, sensitive and simultaneous determination of six polyamines, i.e., ornithine (ORN), 1,3-diaminopropane (DAP), putrescine (PUT), cadaverine (CAD), spermidine (SPD) and spermine (SPM), in human hairs was performed by ultra-performance liquid chromatography (UPLC) with fluorescence (FL) detection and electrospray-ionization time-of-flight mass spectrometry (ESI-TOF-MS). The primary (-NH(2)) and secondary (-NH) amines in the polyamine structures were first labeled with 4-(N,N-dimethylaminosulfonyl)-7-fluoro-2,1,3-benzoxadiazole (DBD-F) at 60 degrees C for 30 min in the mixture of 0.1M borax (pH 9.3) and acetonitrile (CH(3)CN). The resulting derivatives were perfectly separated using an ACQUITY UPLC BEH C(18) column (1.7 microm, 100 mm x 2.1mm i.d.) by a gradient elution with a mixture of water-acetonitrile containing 0.1% formic acid (HCOOH). The separated polyamine derivatives were sensitively detected with both FL and TOF-MS. The detection limits in FL and TOF-MS were 11-86 and 2-5 fmol, respectively. However, the determination of several polyamines by FL detection was interfered with by endogenous substances in the hair. Therefore, the simultaneous determination in hair was carried out by the combination of UPLC separation and the ESI-TOF-MS detection. The structures of the polyamines were identified from the protonated-molecular ions [M+H](+) obtained from the TOF-MS measurement. A good linearity was achieved from the calibration curves, that was obtained by plotting the peak area ratios of the analytes relative to the internal standard (IS), i.e., 1,6-diaminohexane (DAH), against the injected amounts of each polyamine (0.05-50 pmol, r(2)>0.999). The proposed method was applied to the determination in the hairs of healthy volunteers. The mean concentrations of ORN, DAP, PUT, CAD, SPD and SPM in 1mg of human hairs (n=20) were 1.46, 0.18, 1.18, 0.11, 1.97 and 0.98 pmol, respectively. Because the proposed method provides a good mass accuracy and the trace detection of the polyamines in hair, this analytical technique seems to be applicable for the determination of various biological compounds in hair.

Evaluation of the Rapid Polymyxin NP Test for Polymyxin B Resistance Detection Using Enterobacter cloacae and Enterobacter aerogenes Isolates.

PubMed

Simar, Shelby; Sibley, Diane; Ashcraft, Deborah; Pankey, George

2017-10-01

Polymyxin resistance is an increasing problem worldwide. Currently, determining susceptibility to polymyxins is problematic and lengthy. Polymyxins diffuse poorly into agar, potentially giving inaccurate disk diffusion and Etest results. A rapid screening test (2 h) for the detection of polymyxin resistance in Enterobacteriaceae , developed by P. Nordmann and L. Poirel (rapid polymyxin NP test) in 2016, detects glucose metabolization in the presence of polymyxin E (PE) and PB via pH-induced color change. The sensitivity and specificity were 99.3 and 95.4%, respectively, with results obtained in ≤2 h. Our goal was to evaluate this test using PB against larger numbers of Enterobacter A total of 143 nonduplicate Enterobacter isolates (102 E. cloacae complex, 41 E. aerogenes ) were tested, including 136 collected from Ochsner Health System patients from March to May 2016 and 7 previously determined PB-resistant E. cloacae isolates from JMI Laboratories. MICs were determined via broth microdilution. For the rapid polymyxin NP test, a color change from orange to yellow is positive; a weak/no color change is deemed negative after 4 h. Of 143 Enterobacter isolates, 25 were determined to be PB resistant by broth microdilution (MIC > 2 μg/ml), including all 7 JMI isolates. Of these 25, 7 were positive by the rapid polymyxin NP test (included 3/7 JMI isolates). All 118 isolates determined to be PB susceptible by broth microdilution were NP test negative. The sensitivity and specificity for the rapid polymyxin NP test were 25 and 100%, respectively, compared to broth microdilution. Although the rapid polymyxin NP test is a much faster method (2 to 4 h) for polymyxin resistance determination compared to broth microdilution (16 to 20 h), our study indicates that it may be subject to limitations when testing Enterobacter . Copyright © 2017 American Society for Microbiology.

The effects of temperature and diet on age grading and population age structure determination in Drosophila.

PubMed

Aw, Wen C; Ballard, J William O

2013-10-01

The age structure of natural population is of interest in physiological, life history and ecological studies but it is often difficult to determine. One methodological problem is that samples may need to be invasively sampled preventing subsequent taxonomic curation. A second problem is that it can be very expensive to accurately determine the age structure of given population because large sample sizes are often necessary. In this study, we test the effects of temperature (17 °C, 23 °C and 26 °C) and diet (standard cornmeal and low calorie diet) on the accuracy of the non-invasive, inexpensive and high throughput near-infrared spectroscopy (NIRS) technique to determine the age of Drosophila flies. Composite and simplified calibration models were developed for each sex. Independent sets for each temperature and diet treatments with flies not involved in calibration model were then used to validate the accuracy of the calibration models. The composite NIRS calibration model was generated by including flies reared under all temperatures and diets. This approach permits rapid age measurement and age structure determination in large population of flies as less than or equal to 9 days, or more than 9 days old with 85-97% and 64-99% accuracy, respectively. The simplified calibration models were generated by including flies reared at 23 °C on standard diet. Low accuracy rates were observed when simplified calibration models were used to identify (a) Drosophila reared at 17 °C and 26 °C and (b) 23 °C with low calorie diet. These results strongly suggest that appropriate calibration models need to be developed in the laboratory before this technique can be reliably used in field. These calibration models should include the major environmental variables that change across space and time in the particular natural population to be studied. Copyright © 2013 Elsevier Ltd. All rights reserved.

Structure-seq2: sensitive and accurate genome-wide profiling of RNA structure in vivo

PubMed Central

Ritchey, Laura E.; Su, Zhao; Tang, Yin; Tack, David C.

2017-01-01

Abstract RNA serves many functions in biology such as splicing, temperature sensing, and innate immunity. These functions are often determined by the structure of RNA. There is thus a pressing need to understand RNA structure and how it changes during diverse biological processes both in vivo and genome-wide. Here, we present Structure-seq2, which provides nucleotide-resolution RNA structural information in vivo and genome-wide. This optimized version of our original Structure-seq method increases sensitivity by at least 4-fold and improves data quality by minimizing formation of a deleterious by-product, reducing ligation bias, and improving read coverage. We also present a variation of Structure-seq2 in which a biotinylated nucleotide is incorporated during reverse transcription, which greatly facilitates the protocol by eliminating two PAGE purification steps. We benchmark Structure-seq2 on both mRNA and rRNA structure in rice (Oryza sativa). We demonstrate that Structure-seq2 can lead to new biological insights. Our Structure-seq2 datasets uncover hidden breaks in chloroplast rRNA and identify a previously unreported N1-methyladenosine (m1A) in a nuclear-encoded Oryza sativa rRNA. Overall, Structure-seq2 is a rapid, sensitive, and unbiased method to probe RNA in vivo and genome-wide that facilitates new insights into RNA biology. PMID:28637286

Age and Stress Prediction

NASA Technical Reports Server (NTRS)

2000-01-01

Genoa is a software product that predicts progressive aging and failure in a variety of materials. It is the result of a SBIR contract between the Glenn Research Center and Alpha Star Corporation. Genoa allows designers to determine if the materials they plan on applying to a structure are up to the task or if alternate materials should be considered. Genoa's two feature applications are its progressive failure simulations and its test verification. It allows for a reduction in inspection frequency, rapid design solutions, and manufacturing with low cost materials. It will benefit the aerospace, airline, and automotive industries, with future applications for other uses.

Ion current in a magnetic neutral region - Generation of an incipient magnetopause

NASA Technical Reports Server (NTRS)

Whipple, E. C.; Silevitch, M. B.

1982-01-01

The current contributed by ions trapped in the vicinity of a magnetic X line is calculated. The three dimensional configuration of the neutral region is found to be critical in determining the current in that the escape mechanism and trapping times depend on the three-dimensional aspects. A trapping criterion is defined. In the neutral region the ions can gain substantial kinetic energy, and the current will change the X line configuration in such a way that there will be a positive feedback effect, rapidly forming an extended magnetopauselike structure for even very small incident plasma densities.

Molecular Evolutionary Constraints that Determine the Avirulence State of Clostridium botulinum C2 Toxin.

PubMed

Prisilla, A; Prathiviraj, R; Chellapandi, P

2017-04-01

Clostridium botulinum (group-III) is an anaerobic bacterium producing C2 toxin along with botulinum neurotoxins. C2 toxin is belonged to binary toxin A family in bacterial ADP-ribosylation superfamily. A structural and functional diversity of binary toxin A family was inferred from different evolutionary constraints to determine the avirulence state of C2 toxin. Evolutionary genetic analyses revealed evidence of C2 toxin cluster evolution through horizontal gene transfer from the phage or plasmid origins, site-specific insertion by gene divergence, and homologous recombination event. It has also described that residue in conserved NAD-binding core, family-specific domain structure, and functional motifs found to predetermine its virulence state. Any mutational changes in these residues destabilized its structure-function relationship. Avirulent mutants of C2 toxin were screened and selected from a crucial site required for catalytic function of C2I and pore-forming function of C2II. We found coevolved amino acid pairs contributing an essential role in stabilization of its local structural environment. Avirulent toxins selected in this study were evaluated by detecting evolutionary constraints in stability of protein backbone structure, folding and conformational dynamic space, and antigenic peptides. We found 4 avirulent mutants of C2I and 5 mutants of C2II showing more stability in their local structural environment and backbone structure with rapid fold rate, and low conformational flexibility at mutated sites. Since, evolutionary constraints-free mutants with lack of catalytic and pore-forming function suggested as potential immunogenic candidates for treating C. botulinum infected poultry and veterinary animals. Single amino acid substitution in C2 toxin thus provides a major importance to understand its structure-function link, not only of a molecule but also of the pathogenesis.

A crystallographic study of human NONO (p54nrb): overcoming pathological problems with purification, data collection and noncrystallographic symmetry

PubMed Central

Knott, Gavin J.; Panjikar, Santosh; Thorn, Andrea; Fox, Archa H.; Conte, Maria R.; Lee, Mihwa; Bond, Charles S.

2016-01-01

Non-POU domain-containing octamer-binding protein (NONO, a.k.a. p54nrb) is a central player in nuclear gene regulation with rapidly emerging medical significance. NONO is a member of the highly conserved Drosophila behaviour/human splicing (DBHS) protein family, a dynamic family of obligatory dimeric nuclear regulatory mediators. However, work with the NONO homodimer has been limited by rapid irreversible sample aggregation. Here, it is reported that l-proline stabilizes purified NONO homodimers, enabling good-quality solution small-angle X-ray structure determination and crystallization. NONO crystallized in the apparent space group P21 with a unique axis (b) of 408.9 Å and with evidence of twinning, as indicated by the cumulative intensity distribution L statistic, suggesting the possibility of space group P1. Structure solution by molecular replacement shows a superhelical arrangement of six NONO homodimers (or 12 in P1) oriented parallel to the long axis, resulting in extensive noncrystallographic symmetry. Further analysis revealed that the crystal was not twinned, but the collected data suffered from highly overlapping reflections that obscured the L-test. Optimized data collection on a new crystal using higher energy X-rays, a smaller beam width and an increased sample-to-detector distance produced non-overlapping reflections to 2.6 Å resolution. The steps taken to analyse and overcome this series of practical difficulties and to produce a biologically informative structure are discussed. PMID:27303796

Emplacement, rapid burial, and exhumation of 90-Ma plutons in southeastern Alaska

USGS Publications Warehouse

Himmelberg, G.R.; Haeussler, Peter J.; Brew, D.A.

2004-01-01

In southeastern Alaska, granodiorite-tonalite plutons of the Admiralty-Revillagigedo belt intruded the Jurassic-Cretaceous Gravina belt along the eastern side of the Alexander terrane around 90 Ma. These plutons postdate some deformation related to a major contractional event between the previously amalgamated Wrangellia and Alexander terranes and the previously accreted terranes of the North American margin. We studied the aureole mineral assemblages of these plutons near Petersburg, Alaska, determined pressure and temperature of equilibration, and examined structures that developed within and adjacent to these plutons. Parallelism of magmatic and submagmatic fabrics with fabrics in the country rock indicates synchroneity of pluton emplacement with regional deformation and suggests that magma transport to higher crustal levels was assisted by regional deformation. Replacement of andalusite by kyanite or sillimanite indicates crustal thickening soon after pluton emplacement. Regional structural analysis indicates the crustal thickening was accomplished by thrust burial. Thermobarometric analyses indicate the aureoles reached near-peak temperatures of 525 to 635 ??C at pressures of 570 to 630 MPa. Consideration of the rate of thermal decay of the aureoles suggests that burial was rapid and occurred at rates around 5 to 8 mm/year. Structural observations indicate there was contractional deformation before, during, and after emplacement of the 90-Ma plutons. Initial exhumation of the Admiralty-Revillagedo belt in the Petersburg area may have occurred along a thrust west of the pluton belt within the Gravina belt. ?? 2004 NRC Canada.

Stream channel erosion in a rapidly urbanizing region of the US-Mexico border: documenting importance of channel hardpoints with structure-from-motion

USDA-ARS?s Scientific Manuscript database

A combination of field surveys and Structure-from-Motion (SfM) techniques were used to document spatial patterns in stream channel geometry in a rapidly urbanizing watershed, Los Laureles Canyon (LLCW), in Tijuana, Mexico. Ground-based SfM was used to map channel dimensions with 10 cm vertical accur...

Research and Development of Rapid Design Systems for Aerospace Structure

NASA Technical Reports Server (NTRS)

Schaeffer, Harry G.

1999-01-01

This report describes the results of research activities associated with the development of rapid design systems for aerospace structures in support of the Intelligent Synthesis Environment (ISE). The specific subsystems investigated were the interface between model assembly and analysis; and, the high performance NASA GPS equation solver software system in the Windows NT environment on low cost high-performance PCs.

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).

Stochastic Simulation Tool for Aerospace Structural Analysis

NASA Technical Reports Server (NTRS)

Knight, Norman F.; Moore, David F.

2006-01-01

Stochastic simulation refers to incorporating the effects of design tolerances and uncertainties into the design analysis model and then determining their influence on the design. A high-level evaluation of one such stochastic simulation tool, the MSC.Robust Design tool by MSC.Software Corporation, has been conducted. This stochastic simulation tool provides structural analysts with a tool to interrogate their structural design based on their mathematical description of the design problem using finite element analysis methods. This tool leverages the analyst's prior investment in finite element model development of a particular design. The original finite element model is treated as the baseline structural analysis model for the stochastic simulations that are to be performed. A Monte Carlo approach is used by MSC.Robust Design to determine the effects of scatter in design input variables on response output parameters. The tool was not designed to provide a probabilistic assessment, but to assist engineers in understanding cause and effect. It is driven by a graphical-user interface and retains the engineer-in-the-loop strategy for design evaluation and improvement. The application problem for the evaluation is chosen to be a two-dimensional shell finite element model of a Space Shuttle wing leading-edge panel under re-entry aerodynamic loading. MSC.Robust Design adds value to the analysis effort by rapidly being able to identify design input variables whose variability causes the most influence in response output parameters.

The application of compressive sampling in rapid ultrasonic computerized tomography (UCT) technique of steel tube slab (STS)

PubMed Central

Jiang, Baofeng; Jia, Pengjiao; Zhao, Wen; Wang, Wentao

2018-01-01

This paper explores a new method for rapid structural damage inspection of steel tube slab (STS) structures along randomly measured paths based on a combination of compressive sampling (CS) and ultrasonic computerized tomography (UCT). In the measurement stage, using fewer randomly selected paths rather than the whole measurement net is proposed to detect the underlying damage of a concrete-filled steel tube. In the imaging stage, the ℓ1-minimization algorithm is employed to recover the information of the microstructures based on the measurement data related to the internal situation of the STS structure. A numerical concrete tube model, with the various level of damage, was studied to demonstrate the performance of the rapid UCT technique. Real-world concrete-filled steel tubes in the Shenyang Metro stations were detected using the proposed UCT technique in a CS framework. Both the numerical and experimental results show the rapid UCT technique has the capability of damage detection in an STS structure with a high level of accuracy and with fewer required measurements, which is more convenient and efficient than the traditional UCT technique. PMID:29293593

Rapid construction of mechanically- confined multi- cellular structures using dendrimeric intercellular linker.

PubMed

Mo, Xuejun; Li, Qiushi; Yi Lui, Lena Wai; Zheng, Baixue; Kang, Chiang Huen; Nugraha, Bramasta; Yue, Zhilian; Jia, Rui Rui; Fu, Hong Xia; Choudhury, Deepak; Arooz, Talha; Yan, Jie; Lim, Chwee Teck; Shen, Shali; Hong Tan, Choon; Yu, Hanry

2010-10-01

Tissue constructs that mimic the in vivo cell-cell and cell-matrix interactions are especially useful for applications involving the cell- dense and matrix- poor internal organs. Rapid and precise arrangement of cells into functional tissue constructs remains a challenge in tissue engineering. We demonstrate rapid assembly of C3A cells into multi- cell structures using a dendrimeric intercellular linker. The linker is composed of oleyl- polyethylene glycol (PEG) derivatives conjugated to a 16 arms- polypropylenimine hexadecaamine (DAB) dendrimer. The positively charged multivalent dendrimer concentrates the linker onto the negatively charged cell surface to facilitate efficient insertion of the hydrophobic oleyl groups into the cellular membrane. Bringing linker- treated cells into close proximity to each other via mechanical means such as centrifugation and micromanipulation enables their rapid assembly into multi- cellular structures within minutes. The cells exhibit high levels of viability, proliferation, three- dimensional (3D) cell morphology and other functions in the constructs. We constructed defined multi- cellular structures such as rings, sheets or branching rods that can serve as potential tissue building blocks to be further assembled into complex 3D tissue constructs for biomedical applications. 2010 Elsevier Ltd. All rights reserved.

Use of hydrologic budgets and hydrochemistry to determine ground-water and surface-water interactions for Rapid Creek, Western South Dakota

USGS Publications Warehouse

Anderson, Mark T.

1995-01-01

The study of ground-water and surface-water interactions often employs streamflow-gaging records and hydrologic budgets to determine ground-water seepage. Because ground-water seepage usually is computed as a residual in the hydrologic budget approach, all uncertainty of measurement and estimation of budget components is associated with the ground-water seepage. This uncertainty can exceed the estimate, especially when streamflow and its associated error of measurement, is large relative to other budget components. In a study of Rapid Creek in western South Dakota, the hydrologic budget approach with hydrochemistry was combined to determine ground-water seepage. The City of Rapid City obtains most of its municipal water from three infiltration galleries (Jackson Springs, Meadowbrook, and Girl Scout) constructed in the near-stream alluvium along Rapid Creek. The reach of Rapid Creek between Pactola Reservoir and Rapid City and, in particular the two subreaches containing the galleries, were studied intensively to identify the sources of water to each gallery. Jackson Springs Gallery was found to pump predominantly ground water with a minor component of surface water. Meadowbrook and Girl Scout Galleries induce infiltration of surface water from Rapid Creek but also have a significant component of ground water.

Mid-Cretaceous oblique rifting of West Antarctica: Emplacement and rapid cooling of the Fosdick Mountains migmatite-cored gneiss dome

USGS Publications Warehouse

McFadden, Rory; Teyssier, Christian; Siddoway, Christine; Cosca, Michael A.; Fanning, C. Mark

2015-01-01

In Marie Byrd Land, West Antarctica, the Fosdick Mountains migmatite-cored gneiss dome was exhumed from mid- to lower middle crustal depths during the incipient stage of the West Antarctic Rift system in the mid-Cretaceous. Prior to and during exhumation, major crustal melting and deformation included transfer and emplacement of voluminous granitic material and numerous intrusions of mantle-derived diorite in dikes. A succession of melt- and magma-related structures formed at temperatures in excess of 665 ± 50 °C based on Ti-in-zircon thermometry. These record a transition from wrench to oblique extensional deformation that culminated in the development of the oblique South Fosdick Detachment zone. Solid-state fabrics within the detachment zone and overprinting brittle structures record translation of the detachment zone and dome to shallow levels.To determine the duration of exhumation and cooling, we sampled granite and gneisses at high spatial resolution for U–Pb zircon geochronology and 40Ar/39Ar hornblende and biotite thermochronology. U–Pb zircon crystallization ages for the youngest granites are 102 Ma. Three hornblende ages are 103 to 100 Ma and 12 biotite ages are 101 to 99 Ma. All overlap within uncertainty. The coincidence of zircon crystallization ages with 40Ar/39Ar cooling ages indicates cooling rates > 100 °C/m.y. that, when considered together with overprinting structures, indicates rapid exhumation of granite and migmatite from deep to shallow crustal levels within a transcurrent setting. Orientations of structures and age-constrained crosscutting relationships indicate counterclockwise rotation of stretching axes from oblique extension into nearly orthogonal extension with respect to the Marie Byrd Land margin. The rotation may be a result of localized extension arising from unroofing and arching of the Fosdick dome, extensional opening within a pull-apart zone, or changes in plate boundary configuration.The rapid tectonic and temperature evolution of the Fosdick Mountains dome lends support to recently developed numerical models of crustal flow and cooling in orogenic crust undergoing extension/transtension, and accords with numerous studies of migmatite-cored gneiss domes in transcurrent settings.

Deconstruction Rapid Assessment Tool

EPA Pesticide Factsheets

Deconstruction Rapid Assessment Tool (EPA 905-F-15-001) instructions, form and spreadsheet for assessing and triaging structures being considered for deconstruction. Promote environmental stewardship and economic revitalization through deconstruction.

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.

Protein Structure Validation and Refinement Using Amide Proton Chemical Shifts Derived from Quantum Mechanics

PubMed Central

Christensen, Anders S.; Linnet, Troels E.; Borg, Mikael; Boomsma, Wouter; Lindorff-Larsen, Kresten; Hamelryck, Thomas; Jensen, Jan H.

2013-01-01

We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond (h3 JNC') spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to obtain this agreement. The ProCS method thus offers a powerful new tool for refining the structures of hydrogen bonding networks to high accuracy with many potential applications such as protein flexibility in ligand binding. PMID:24391900

[Rapid fabrication of molecularly imprinted polymer fibers for solid phase microextraction of bisphenol A].

PubMed

Hu, Mei; Zhang, Yijun; Yang, Jinghua; Zhou, Xiaomao; Wei, Zhuqing; Ding, Xiaoqing; Zhang, Yuping

2015-02-01

The rapid preparation of molecularly imprinted polymer (MIP) fibers was reported using bisphenol A (BPA) as the template molecular, acetonitrile (ACN) as the porogenic solvent, α-methacrylic acid (MAA) as the functional monomer, ethylene dimethacrylate (EDMA) as the crosslinker, and azodiisobutyronitrile (AIBN) as the thermal initiator. It was carried out within a capillary of 530 µm inner diameter (I. D.) by microwave irradiation in 7 min. The resulted BPA-MIP fibers were pushed out from the capillary, eluted in a vial and inserted in the capillary again followed by the application of the solid phase microextraction (SPME) procedure. The extraction performance was investigated in detail by varying the molar ratios between the template and the monomer (BPA/MAA), the concentration of NaCl, the extraction and desorption time, the pH value and the desorption solvents. The selectivity of the prepared MIP and non-molecularly imprinted polymer (NIP) fibers was comparatively evaluated by selecting two structurally-related compounds, phenol (P) and 4-phenylphenol (PP), and non-analogue dicyandiamide (DCD). The established method was successfully applied for the pretreatment and determination of BPA from beverage samples coupled to high performance liquid chromatography (HPLC). Under the optimal conditions, the linear range of BPA was 10-400 µg/L; the detection limit (LOD) was 0.45 µg/L and the recoveries spiked in the mineral water were 88.4%-102. 8%. The results demonstrated that the developed method can determine BPA in real samples with some advantages of simple pretreatment, rapid analysis, low limit of detection and low consumption of materials.

Solidification of undercooled liquids

NASA Technical Reports Server (NTRS)

Perepezko, J. H.; Shiohara, Y.; Paik, J. S.; Flemmings, M. C.

1982-01-01

During rapid solidification processing (RSP) the amount of liquid undercooling is an important factor in determining microstructural development by controlling phase selection during nucleation and morphological evolution during crystal growth. While undercooling is an inherent feature of many techniques of RSP, the deepest undercoolings and most controlled studies have been possible in carefully prepared fine droplet samples. From past work and recent advances in studies of nucleation kinetics it has become clear that the initiation of crystallization during RSP is governed usually by heterogeneous sites located at surfaces. With known nucleant sites, it has been possible to identify specific pathways of metastable phase formation and microstructural development in alloys. These advances have allowed for a clearer assessment of the interplay between undercooling, cooling rate and particle size statistics in structure formation. New approaches to the examination of growth processes have been developed to follow the thermal behavior and morphology in small samples in the period of rapid crystallization and recalescence. Based upon the new experimental information from these studies, useful models can be developed for the overall solidification process to include nucleation behavior, thermodynamic constraints, thermal history, growth kinetics, solute redistribution and resulting structures. From the refinement of knowledge concerning the underlying factors that govern RSP a basis is emerging for an effective alloy design and processing strategy.

Localized Temperature Variations in Laser-Irradiated Composites with Embedded Fiber Bragg Grating Sensors.

PubMed

Jenkins, R Brian; Joyce, Peter; Mechtel, Deborah

2017-01-27

Fiber Bragg grating (FBG) temperature sensors are embedded in composites to detect localized temperature gradients resulting from high energy infrared laser radiation. The goal is to detect the presence of radiation on a composite structure as rapidly as possible and to identify its location, much the same way human skin senses heat. A secondary goal is to determine how a network of sensors can be optimized to detect thermal damage in laser-irradiated composite materials or structures. Initial tests are conducted on polymer matrix composites reinforced with either carbon or glass fiber with a single optical fiber embedded into each specimen. As many as three sensors in each optical fiber measure the temporal and spatial thermal response of the composite to high energy radiation incident on the surface. Additional tests use a 2 × 2 × 3 array of 12 sensors embedded in a carbon fiber/epoxy composite to simultaneously measure temperature variations at locations on the composite surface and through the thickness. Results indicate that FBGs can be used to rapidly detect temperature gradients in a composite and their location, even for a direct strike of laser radiation on a sensor, when high temperatures can cause a non-uniform thermal response and FBG decay.

Split green fluorescent protein as a modular binding partner for protein crystallization

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

Nguyen, Hau B.; Hung, Li-Wei; Yeates, Todd O.

2013-12-01

A strategy using a new split green fluorescent protein (GFP) as a modular binding partner to form stable protein complexes with a target protein is presented. The modular split GFP may open the way to rapidly creating crystallization variants. A modular strategy for protein crystallization using split green fluorescent protein (GFP) as a crystallization partner is demonstrated. Insertion of a hairpin containing GFP β-strands 10 and 11 into a surface loop of a target protein provides two chain crossings between the target and the reconstituted GFP compared with the single connection afforded by terminal GFP fusions. This strategy was testedmore » by inserting this hairpin into a loop of another fluorescent protein, sfCherry. The crystal structure of the sfCherry-GFP(10–11) hairpin in complex with GFP(1–9) was determined at a resolution of 2.6 Å. Analysis of the complex shows that the reconstituted GFP is attached to the target protein (sfCherry) in a structurally ordered way. This work opens the way to rapidly creating crystallization variants by reconstituting a target protein bearing the GFP(10–11) hairpin with a variety of GFP(1–9) mutants engineered for favorable crystallization.« less

Localized Temperature Variations in Laser-Irradiated Composites with Embedded Fiber Bragg Grating Sensors

PubMed Central

Jenkins, R. Brian; Joyce, Peter; Mechtel, Deborah

2017-01-01

Fiber Bragg grating (FBG) temperature sensors are embedded in composites to detect localized temperature gradients resulting from high energy infrared laser radiation. The goal is to detect the presence of radiation on a composite structure as rapidly as possible and to identify its location, much the same way human skin senses heat. A secondary goal is to determine how a network of sensors can be optimized to detect thermal damage in laser-irradiated composite materials or structures. Initial tests are conducted on polymer matrix composites reinforced with either carbon or glass fiber with a single optical fiber embedded into each specimen. As many as three sensors in each optical fiber measure the temporal and spatial thermal response of the composite to high energy radiation incident on the surface. Additional tests use a 2 × 2 × 3 array of 12 sensors embedded in a carbon fiber/epoxy composite to simultaneously measure temperature variations at locations on the composite surface and through the thickness. Results indicate that FBGs can be used to rapidly detect temperature gradients in a composite and their location, even for a direct strike of laser radiation on a sensor, when high temperatures can cause a non-uniform thermal response and FBG decay. PMID:28134815

Mass spectrometry-driven drug discovery for development of herbal medicine.

PubMed

Zhang, Aihua; Sun, Hui; Wang, Xijun

2018-05-01

Herbal medicine (HM) has made a major contribution to the drug discovery process with regard to identifying products compounds. Currently, more attention has been focused on drug discovery from natural compounds of HM. Despite the rapid advancement of modern analytical techniques, drug discovery is still a difficult and lengthy process. Fortunately, mass spectrometry (MS) can provide us with useful structural information for drug discovery, has been recognized as a sensitive, rapid, and high-throughput technology for advancing drug discovery from HM in the post-genomic era. It is essential to develop an efficient, high-quality, high-throughput screening method integrated with an MS platform for early screening of candidate drug molecules from natural products. We have developed a new chinmedomics strategy reliant on MS that is capable of capturing the candidate molecules, facilitating their identification of novel chemical structures in the early phase; chinmedomics-guided natural product discovery based on MS may provide an effective tool that addresses challenges in early screening of effective constituents of herbs against disease. This critical review covers the use of MS with related techniques and methodologies for natural product discovery, biomarker identification, and determination of mechanisms of action. It also highlights high-throughput chinmedomics screening methods suitable for lead compound discovery illustrated by recent successes. © 2016 Wiley Periodicals, Inc.

Rapid fluctuations in extracellular brain glucose levels induced by natural arousing stimuli and intravenous cocaine: fueling the brain during neural activation

PubMed Central

Lenoir, Magalie

2012-01-01

Glucose, a primary energetic substrate for neural activity, is continuously influenced by two opposing forces that tend to either decrease its extracellular levels due to enhanced utilization in neural cells or increase its levels due to entry from peripheral circulation via enhanced cerebral blood flow. How this balance is maintained under physiological conditions and changed during neural activation remains unclear. To clarify this issue, enzyme-based glucose sensors coupled with high-speed amperometry were used in freely moving rats to evaluate fluctuations in extracellular glucose levels induced by brief audio stimulus, tail pinch (TP), social interaction with another rat (SI), and intravenous cocaine (1 mg/kg). Measurements were performed in nucleus accumbens (NAcc) and substantia nigra pars reticulata (SNr), which drastically differ in neuronal activity. In NAcc, where most cells are powerfully excited after salient stimulation, glucose levels rapidly (latency 2–6 s) increased (30–70 μM or 6–14% over baseline) by all stimuli; the increase differed in magnitude and duration for each stimulus. In SNr, where most cells are transiently inhibited by salient stimuli, TP, SI, and cocaine induced a biphasic glucose response, with the initial decrease (−20–40 μM or 5–10% below baseline) followed by a reboundlike increase. The critical role of neuronal activity in mediating the initial glucose response was confirmed by monitoring glucose currents after local microinjections of glutamate (GLU) or procaine (PRO). While intra-NAcc injection of GLU transiently increased glucose levels in this structure, intra-SNr PRO injection resulted in rapid, transient decreases in SNr glucose. Therefore, extracellular glucose levels in the brain change very rapidly after physiological and pharmacological stimulation, the response is structure specific, and the pattern of neuronal activity appears to be a critical factor determining direction and magnitude of physiological fluctuations in glucose levels. PMID:22723672

Impact of food processing on rye product properties and their in vitro digestion.

PubMed

Johansson, Daniel P; Gutiérrez, José L Vázquez; Landberg, Rikard; Alminger, Marie; Langton, Maud

2018-06-01

Rye products have been reported to elicit postprandial insulin and glucose responses which may be beneficial for prevention of type-2 diabetes. However, mechanisms underlying variations in responses related to processing techniques are not fully understood. Five differently processed rye products (sourdough-fermented bread, fermented and unfermented crispbread, extrusion-cooked rye, and porridge) and refined wheat bread were characterised. Two in vitro methods, a dynamic method simulating digestion in the stomach and small intestine and a static method, simulating conditions in the stomach were used to determine viscosity development, structural changes and release of glucose during digestion. Structural and compositional differences induced by processing influenced product digestion. Gastric disintegration and digesta particle size were related to characteristics of the starch/protein matrix, while digesta viscosity was reduced due to fibre degradation during fermentation. More cohesive boluses were associated with slower glucose release. Sourdough fermentation increased amylose leakage and appeared to inhibit starch hydrolysis despite low digesta viscosity and rapid disintegration. The net release of glucose during digestion of foods is determined by several factors which may vary in their importance depending on product specific properties.

Microwave spectroscopy and curious molecular dynamics of ethyl trifluoroacetate

NASA Astrophysics Data System (ADS)

Bohn, Robert K.; Montgomery, John A.; Harvey Michels, H.; Acharte, Christian

2017-05-01

The first ethyl ester whose structure was determined by microwave spectroscopy is ethyl formate. It exists in two conformations. In the 1970s, that study was used as a model to determine the structures of other ethyl esters, ethyl cyanoformate, chloroformate, and trifluoroacetate. They display the same conformations as ethyl formate. But under the experimental conditions used, Stark modulation with a maximum electric field, static low pressure gas, rapid sweeping, and long detector time constants, each of those esters displays bands of an additional third species. A careful, high resolution study of ethyl cyanoformate only observed two conformers. A model has been proposed that the third species derives from a dense array of torsionally excited states with broadened transitions due to short lifetimes. The present study of ethyl trifluoroacetate in a pulsed jet Fourier Transform spectrometer is intended to clarify the earlier results. Two conformers are observed including all their monosubstituted 13C and 18O isotopologs. In a pulsed jet Fourier Transform spectrometer using argon as the carrier gas, only one conformer is observed. Switching to helium as the carrier gas, another, higher energy conformer is also observed.

MASS ESTIMATES OF RAPIDLY MOVING PROMINENCE MATERIAL FROM HIGH-CADENCE EUV IMAGES

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

Williams, David R.; Baker, Deborah; Van Driel-Gesztelyi, Lidia, E-mail: d.r.williams@ucl.ac.uk

We present a new method for determining the column density of erupting filament material using state-of-the-art multi-wavelength imaging data. Much of the prior work on filament/prominence structure can be divided between studies that use a polychromatic approach with targeted campaign observations and those that use synoptic observations, frequently in only one or two wavelengths. The superior time resolution, sensitivity, and near-synchronicity of data from the Solar Dynamics Observatory's Advanced Imaging Assembly allow us to combine these two techniques using photoionization continuum opacity to determine the spatial distribution of hydrogen in filament material. We apply the combined techniques to SDO/AIA observationsmore » of a filament that erupted during the spectacular coronal mass ejection on 2011 June 7. The resulting 'polychromatic opacity imaging' method offers a powerful way to track partially ionized gas as it erupts through the solar atmosphere on a regular basis, without the need for coordinated observations, thereby readily offering regular, realistic mass-distribution estimates for models of these erupting structures.« less

The molecular basis of the specificity of action of KATP channel openers

PubMed Central

Moreau, Christophe; Jacquet, Hélène; Prost, Anne-Lise; D’hahan, Nathalie; Vivaudou, Michel

2000-01-01

KATP channels incorporate a regulatory subunit of the ATP-binding cassette (ABC) transporter family, the sulfonylurea receptor (SUR), which defines their pharmacology. The therapeutically important K+ channel openers (e.g. pinacidil, cromakalim, nicorandil) act specifically on the SUR2 muscle isoforms but, except for diazoxide, remain ineffective on the SUR1 neuronal/pancreatic isoform. This SUR1/2 dichotomy underpinned a chimeric strategy designed to identify the structural determinants of opener action, which led to a minimal set of two residues within the last transmembrane helix of SUR. Transfer of either residue from SUR2A to SUR1 conferred opener sensitivity to SUR1, while the reverse operation abolished SUR2A sensitivity. It is therefore likely that these residues form part of the site of interaction of openers with the channel. Thus, openers would target a region that, in other ABC transporters, is known to be tightly involved with the binding of substrates and other ligands. This first glimpse of the site of action of pharmacological openers should permit rapid progress towards understanding the structural determinants of their affinity and specificity. PMID:11118199

Quantitation of Permethylated N-Glycans through Multiple-Reaction Monitoring (MRM) LC-MS/MS

PubMed Central

Zhou, Shiyue; Hu, Yunli; DeSantos-Garcia, Janie L.; Mechref, Yehia

2015-01-01

The important biological roles of glycans and their implications in disease development and progression have created a demand for the development of sensitive quantitative glycomics methods. Quantitation of glycans existing at low abundance is still analytically challenging. In this study, an N-linked glycans quantitation method using multiple reaction monitoring (MRM) on a triple quadrupole instrument was developed. Optimum normalized collision energy (CE) for both sialylated and fucosylated N-glycan structures was determined to be 30% while it was found to be 35% for either fucosylated or sialylated structures The optimum CE for mannose and complex type N-glycan structures was determined to be 35%. Additionally, the use of three transitions was shown to facilitate reliable quantitation. A total of 88 N-glycan structures in human blood serum were quantified using this MRM approach. Reliable detection and quantitation of these structures was achieved when the equivalence of 0.005 μL of blood serum was analyzed. Accordingly, N-glycans down to the 100th of a μL level can be reliably quantified in pooled human blood serum, spanning a dynamic concentration range of three orders of magnitudes. MRM was also effectively utilized to quantitatively compare the expression of N-glycans derived from brain-targeting breast carcinoma cells (MDA-MB-231BR) and metastatic breast cancer cells (MDA-MB-231). Thus, the described MRM method of permethylated N-glycan structures enables a rapid and reliable identification and quantitation of glycans derived from glycoproteins purified or present in complex biological samples. PMID:25698222

Macrozooplankton biomass in a warm-core Gulf Stream ring: Time series changes in size structure, taxonomic composition, and vertical distribution

NASA Astrophysics Data System (ADS)

Davis, Cabell S.; Wiebe, Peter H.

1985-01-01

Macrozooplankton size structure and taxonomic composition in warm-core ring 82B was examined from a time series (March, April, June) of ring center MOCNESS (1 m) samples. Size distributions of 15 major taxonomic groups were determined from length measurements digitized from silhouette photographs of the samples. Silhouette digitization allows rapid quantification of Zooplankton size structure and taxonomic composition. Length/weight regressions, determined for each taxon, were used to partition the biomass (displacement volumes) of each sample among the major taxonomic groups. Zooplankton taxonomic composition and size structure varied with depth and appeared to coincide with the hydrographic structure of the ring. In March and April, within the thermostad region of the ring, smaller herbivorous/omnivorous Zooplankton, including copepods, crustacean larvae, and euphausiids, were dominant, whereas below this region, larger carnivores, such as medusae, ctenophores, fish, and decapods, dominated. Copepods were generally dominant in most samples above 500 m. Total macrozooplankton abundance and biomass increased between March and April, primarily because of increases in herbivorous taxa, including copepods, crustacean larvae, and larvaceans. A marked increase in total macrozooplankton abundance and biomass between April and June was characterized by an equally dramatic shift from smaller herbivores (1.0-3.0 mm) in April to large herbivores (5.0-6.0 mm) and carnivores (>15 mm) in June. Species identifications made directly from the samples suggest that changes in trophic structure resulted from seeding type immigration and subsequent in situ population growth of Slope Water zooplankton species.

Fuel cell system logic for differentiating between rapid and normal shutdown commands

DOEpatents

Keskula, Donald H.; Doan, Tien M.; Clingerman, Bruce J.

2000-01-01

A method of controlling the operation of a fuel cell system wherein each shutdown command for the system is subjected to decision logic which determines whether the command should be a normal shutdown command or rapid shutdown command. If the logic determines that the shutdown command should be a normal shutdown command, then the system is shutdown in a normal step-by-step process in which the hydrogen stream is consumed within the system. If the logic determines that the shutdown command should be a rapid shutdown command, the hydrogen stream is removed from the system either by dumping to atmosphere or routing to storage.

Microstructural properties and evolution of nanoclusters in liquid Si during a rapid cooling process

NASA Astrophysics Data System (ADS)

Gao, T.; Hu, X.; Li, Y.; Tian, Z.; Xie, Q.; Chen, Q.; Liang, Y.; Luo, X.; Ren, L.; Luo, J.

2017-11-01

The formation of amorphous structures in Si during the rapid quenching process was studied based on molecular dynamics simulation by using the Stillinger-Weber potential. The evolution characteristics of nanoclusters during the solidification were analyzed by several structural analysis methods. The amorphous Si has been formed with many tetrahedral clusters and few nanoclusters. During the solidification, tetrahedral polyhedrons affect the local structures by their different positions and connection modes. The main kinds of polyhedrons randomly linked with one another to form an amorphous network structures in the system. The structural evolution of crystal nanocluster demonstrates that the nanocluster has difficulty to growth because of the high cooling rate of 1012 K/s.

AN ENVIRONMENTAL TECHNOLOGY VERIFICATION (ETV) TESTING OF SEVEN TECHNOLOGIES DETECTING TOXICITY IN DRINKING WATER (R2)

EPA Science Inventory

Rapid toxicity technologies can detect certain toxins and with testing it can be determined their susceptibility to interfering chemical in controlled experimental matrix. Rapid toxicity technologies do not identify or determine the concentrations of specific contaminants, but s...

Trends in the Electron Microscopy Data Bank (EMDB).

PubMed

Patwardhan, Ardan

2017-06-01

Recent technological advances, such as the introduction of the direct electron detector, have transformed the field of cryo-EM and the landscape of molecular and cellular structural biology. This study analyses these trends from the vantage point of the Electron Microscopy Data Bank (EMDB), the public archive for three-dimensional EM reconstructions. Over 1000 entries were released in 2016, representing almost a quarter of the total number of entries (4431). Structures at better than 6 Å resolution now represent one of the fastest-growing categories, while the share of annually released tomography-related structures is approaching 20%. The use of direct electron detectors is growing very rapidly: they were used for 70% of the structures released in 2016, in contrast to none before 2011. Microscopes from FEI have an overwhelming lead in terms of usage, and the use of the RELION software package continues to grow rapidly after having attained a leading position in the field. China is rapidly emerging as a major player in the field, supplementing the US, Germany and the UK as the big four. Similarly, Tsinghua University ranks only second to the MRC Laboratory for Molecular Biology in terms of involvement in publications associated with cryo-EM structures at better than 4 Å resolution. Overall, the numbers point to a rapid democratization of the field, with more countries and institutes becoming involved.

Justification of rapid prototyping in the development cycle of thermoplastic-based lab-on-a-chip.

PubMed

Preywisch, Regina; Ritzi-Lehnert, Marion; Drese, Klaus S; Röser, Tina

2011-11-01

During the developmental cycle of lab-on-a-chip devices, various microstructuring techniques are required. While in the designing and assay implementation phase direct structuring or so-called rapid-prototyping methods such as milling or laser ablation are applied, replication methods like hot embossing or injection moulding are favourable for large quantity manufacturing. This work investigated the applicability of rapid-prototyping techniques for thermoplastic chip development in general, and the reproducibility of performances in dependency of the structuring technique. A previously published chip for prenatal diagnosis that preconcentrates DNA via electrokinetic trapping and field-amplified-sample-stacking and afterwards separates it in CGE was chosen as a model. The impact of structuring, sealing, and the integration of membranes on the mobility of the EOF, DNA preconcentration, and DNA separation was studied. Structuring methods were found to significantly change the location where preconcentration of DNA occurs. However, effects on the mobility of the EOF and the separation quality of DNA were not observed. Exchange of the membrane has no effect on the chip performance, whereas the sealing method impairs the separation of DNA within the chip. The overall assay performance is not significantly influenced by different structuring methods; thus, the application of rapid-prototyping methods during a chip development cycle is well justified. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Trends in the Electron Microscopy Data Bank (EMDB)

PubMed Central

Patwardhan, Ardan

2017-01-01

Recent technological advances, such as the introduction of the direct electron detector, have transformed the field of cryo-EM and the landscape of molecular and cellular structural biology. This study analyses these trends from the vantage point of the Electron Microscopy Data Bank (EMDB), the public archive for three-dimensional EM reconstructions. Over 1000 entries were released in 2016, representing almost a quarter of the total number of entries (4431). Structures at better than 6 Å resolution now represent one of the fastest-growing categories, while the share of annually released tomography-related structures is approaching 20%. The use of direct electron detectors is growing very rapidly: they were used for 70% of the structures released in 2016, in contrast to none before 2011. Microscopes from FEI have an overwhelming lead in terms of usage, and the use of the RELION software package continues to grow rapidly after having attained a leading position in the field. China is rapidly emerging as a major player in the field, supplementing the US, Germany and the UK as the big four. Similarly, Tsinghua University ranks only second to the MRC Laboratory for Molecular Biology in terms of involvement in publications associated with cryo-EM structures at better than 4 Å resolution. Overall, the numbers point to a rapid democratization of the field, with more countries and institutes becoming involved. PMID:28580912

75 FR 20792 - Airworthiness Directives; The Boeing Company Model 747-100, 747-100B, 747-100B SUD, 747-200B, 747...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-21

... develop in the adjacent frame structure and skin, resulting in a rapid loss of cabin pressure. DATES: We... the following methods: Federal eRulemaking Portal: Go to http://www.regulations.gov . Follow the... severed, cracks could develop in the adjacent frame structure and skin, resulting in rapid loss of cabin...

A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction

PubMed Central

Spencer, Matt; Eickholt, Jesse; Cheng, Jianlin

2014-01-01

Ab initio protein secondary structure (SS) predictions are utilized to generate tertiary structure predictions, which are increasingly demanded due to the rapid discovery of proteins. Although recent developments have slightly exceeded previous methods of SS prediction, accuracy has stagnated around 80% and many wonder if prediction cannot be advanced beyond this ceiling. Disciplines that have traditionally employed neural networks are experimenting with novel deep learning techniques in attempts to stimulate progress. Since neural networks have historically played an important role in SS prediction, we wanted to determine whether deep learning could contribute to the advancement of this field as well. We developed an SS predictor that makes use of the position-specific scoring matrix generated by PSI-BLAST and deep learning network architectures, which we call DNSS. Graphical processing units and CUDA software optimize the deep network architecture and efficiently train the deep networks. Optimal parameters for the training process were determined, and a workflow comprising three separately trained deep networks was constructed in order to make refined predictions. This deep learning network approach was used to predict SS for a fully independent test data set of 198 proteins, achieving a Q3 accuracy of 80.7% and a Sov accuracy of 74.2%. PMID:25750595

A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction.

PubMed

Spencer, Matt; Eickholt, Jesse; Jianlin Cheng

2015-01-01

Ab initio protein secondary structure (SS) predictions are utilized to generate tertiary structure predictions, which are increasingly demanded due to the rapid discovery of proteins. Although recent developments have slightly exceeded previous methods of SS prediction, accuracy has stagnated around 80 percent and many wonder if prediction cannot be advanced beyond this ceiling. Disciplines that have traditionally employed neural networks are experimenting with novel deep learning techniques in attempts to stimulate progress. Since neural networks have historically played an important role in SS prediction, we wanted to determine whether deep learning could contribute to the advancement of this field as well. We developed an SS predictor that makes use of the position-specific scoring matrix generated by PSI-BLAST and deep learning network architectures, which we call DNSS. Graphical processing units and CUDA software optimize the deep network architecture and efficiently train the deep networks. Optimal parameters for the training process were determined, and a workflow comprising three separately trained deep networks was constructed in order to make refined predictions. This deep learning network approach was used to predict SS for a fully independent test dataset of 198 proteins, achieving a Q3 accuracy of 80.7 percent and a Sov accuracy of 74.2 percent.

A Practical Probabilistic Graphical Modeling Tool for Weighing ...

EPA Pesticide Factsheets

Past weight-of-evidence frameworks for adverse ecological effects have provided soft-scoring procedures for judgments based on the quality and measured attributes of evidence. Here, we provide a flexible probabilistic structure for weighing and integrating lines of evidence for ecological risk determinations. Probabilistic approaches can provide both a quantitative weighing of lines of evidence and methods for evaluating risk and uncertainty. The current modeling structure wasdeveloped for propagating uncertainties in measured endpoints and their influence on the plausibility of adverse effects. To illustrate the approach, we apply the model framework to the sediment quality triad using example lines of evidence for sediment chemistry measurements, bioassay results, and in situ infauna diversity of benthic communities using a simplified hypothetical case study. We then combine the three lines evidence and evaluate sensitivity to the input parameters, and show how uncertainties are propagated and how additional information can be incorporated to rapidly update the probability of impacts. The developed network model can be expanded to accommodate additional lines of evidence, variables and states of importance, and different types of uncertainties in the lines of evidence including spatial and temporal as well as measurement errors. We provide a flexible Bayesian network structure for weighing and integrating lines of evidence for ecological risk determinations

Sketch on the structural geology and vulcanism in the Central High Plateau of the Bolivian Andes

NASA Technical Reports Server (NTRS)

Brockmann, C. E. (Principal Investigator)

1973-01-01

The author has identified the following significant results. The Earth Resources Technology Satellite Program has as an objective the development of tectonic maps for Bolivia. Maps were prepared using the images of ERTS-1 in a preliminary study of alignments observed and rapidly interpreted in images 1010-14033-3-4-5-6-7 on a scale of 1:1,000,000, and later verified on the ground with corresponding fault zones. This information was not shown on existing geologial maps. The ERTS-1 imagery was used in volcanology research for drawing the regional limits of volcanic formations as soon as the alignment and the extent of the volcanoes could be determined. The extensive coverage of ERTS-1 images provides an excellent opportunity for developing studies of regional structures.

Rational Protein Engineering Guided by Deep Mutational Scanning

PubMed Central

Shin, HyeonSeok; Cho, Byung-Kwan

2015-01-01

Sequence–function relationship in a protein is commonly determined by the three-dimensional protein structure followed by various biochemical experiments. However, with the explosive increase in the number of genome sequences, facilitated by recent advances in sequencing technology, the gap between protein sequences available and three-dimensional structures is rapidly widening. A recently developed method termed deep mutational scanning explores the functional phenotype of thousands of mutants via massive sequencing. Coupled with a highly efficient screening system, this approach assesses the phenotypic changes made by the substitution of each amino acid sequence that constitutes a protein. Such an informational resource provides the functional role of each amino acid sequence, thereby providing sufficient rationale for selecting target residues for protein engineering. Here, we discuss the current applications of deep mutational scanning and consider experimental design. PMID:26404267

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.

Identification and structural characterisation of triterpene saponins from the root of Ardisia mamillata Hance by HPLC-ESI-QTOF-MS/MS.

PubMed

Zhang, Er-Fei; Ling, Yun; Yin, Zi; Zhang, Qing

2018-04-01

Triterpene saponins in medicinal plants attract scientific attentions for their structural diversity and significant bioactivities. In this work, a high-performance liquid chromatography coupled to electrospray ionisation and quadrupole time-of-flight mass spectrometry (HPLC-ESI-QTOF-MS/MS) method is used to rapidly separate and identify triterpene saponins from the extract of Ardisia mamillata Hance (AMH). In the full scan mass spectrum, the accurate determination of molecular formula is obtained by the predominant ion [M + HCOO] - in negative ion mode. As a result, 30 triterpene saponins are identified or tentatively identified in the plant extract. Of these, 17 triterpene saponins are new compounds. In conclusion, the HPLC-ESI-QTOF-MS/MS is an efficient technique to separate and identify triterpene saponins in complex matrices of medicinal plant.

Cellular automaton simulation examining progenitor hierarchy structure effects on mammary ductal carcinoma in situ.

PubMed

Bankhead, Armand; Magnuson, Nancy S; Heckendorn, Robert B

2007-06-07

A computer simulation is used to model ductal carcinoma in situ, a form of non-invasive breast cancer. The simulation uses known histological morphology, cell types, and stochastic cell proliferation to evolve tumorous growth within a duct. The ductal simulation is based on a hybrid cellular automaton design using genetic rules to determine each cell's behavior. The genetic rules are a mutable abstraction that demonstrate genetic heterogeneity in a population. Our goal was to examine the role (if any) that recently discovered mammary stem cell hierarchies play in genetic heterogeneity, DCIS initiation and aggressiveness. Results show that simpler progenitor hierarchies result in greater genetic heterogeneity and evolve DCIS significantly faster. However, the more complex progenitor hierarchy structure was able to sustain the rapid reproduction of a cancer cell population for longer periods of time.

Centrality dependence of charged jet production in p-Pb collisions at [Formula: see text] = 5.02 TeV.

PubMed

Adam, J; Adamová, D; Aggarwal, M M; Aglieri Rinella, G; Agnello, M; Agrawal, N; Ahammed, Z; Ahmad, S; Ahn, S U; Aiola, S; Akindinov, A; Alam, S N; Albuquerque, D S D; Aleksandrov, D; Alessandro, B; Alexandre, D; Alfaro Molina, R; Alici, A; Alkin, A; Almaraz, J R M; Alme, J; Alt, T; Altinpinar, S; Altsybeev, I; Alves Garcia Prado, C; Andrei, C; Andronic, A; Anguelov, V; Antičić, T; Antinori, F; Antonioli, P; Aphecetche, L; Appelshäuser, H; Arcelli, S; Arnaldi, R; Arnold, O W; Arsene, I C; Arslandok, M; Audurier, B; Augustinus, A; Averbeck, R; Azmi, M D; Badalà, A; Baek, Y W; Bagnasco, S; Bailhache, R; Bala, R; Balasubramanian, S; Baldisseri, A; Baral, R C; Barbano, A M; Barbera, R; Barile, F; Barnaföldi, G G; Barnby, L S; Barret, V; Bartalini, P; Barth, K; Bartke, J; Bartsch, E; Basile, M; Bastid, N; Basu, S; Bathen, B; Batigne, G; Batista Camejo, A; Batyunya, B; Batzing, P C; Bearden, I G; Beck, H; Bedda, C; Behera, N K; Belikov, I; Bellini, F; Bello Martinez, H; Bellwied, R; Belmont, R; Belmont-Moreno, E; Belyaev, V; Bencedi, G; Beole, S; Berceanu, I; Bercuci, A; Berdnikov, Y; Berenyi, D; Bertens, R A; Berzano, D; Betev, L; Bhasin, A; Bhat, I R; Bhati, A K; Bhattacharjee, B; Bhom, J; Bianchi, L; Bianchi, N; Bianchin, C; Bielčík, J; Bielčíková, J; Bilandzic, A; Biro, G; Biswas, R; Biswas, S; Bjelogrlic, S; Blair, J T; Blau, D; Blume, C; Bock, F; Bogdanov, A; Bøggild, H; Boldizsár, L; Bombara, M; Book, J; Borel, H; Borissov, A; Borri, M; Bossú, F; Botta, E; Bourjau, C; Braun-Munzinger, P; Bregant, M; Breitner, T; Broker, T A; Browning, T A; Broz, M; Brucken, E J; Bruna, E; Bruno, G E; Budnikov, D; Buesching, H; Bufalino, S; Buncic, P; Busch, O; Buthelezi, Z; Butt, J B; Buxton, J T; Cabala, J; Caffarri, D; Cai, X; Caines, H; Calero Diaz, L; Caliva, A; Calvo Villar, E; Camerini, P; Carena, F; Carena, W; Carnesecchi, F; Castillo Castellanos, J; Castro, A J; Casula, E A R; Ceballos Sanchez, C; Cepila, J; Cerello, P; Cerkala, J; Chang, B; Chapeland, S; Chartier, M; Charvet, J L; Chattopadhyay, S; Chattopadhyay, S; Chauvin, A; Chelnokov, V; Cherney, M; Cheshkov, C; Cheynis, B; Chibante Barroso, V; Chinellato, D D; Cho, S; Chochula, P; Choi, K; Chojnacki, M; Choudhury, S; Christakoglou, P; Christensen, C H; Christiansen, P; Chujo, T; Chung, S U; Cicalo, C; Cifarelli, L; Cindolo, F; Cleymans, J; Colamaria, F; Colella, D; Collu, A; Colocci, M; Conesa Balbastre, G; Conesa Del Valle, Z; Connors, M E; Contreras, J G; Cormier, T M; Corrales Morales, Y; Cortés Maldonado, I; Cortese, P; Cosentino, M R; Costa, F; Crochet, P; Cruz Albino, R; Cuautle, E; Cunqueiro, L; Dahms, T; Dainese, A; Danisch, M C; Danu, A; Das, D; Das, I; Das, S; Dash, A; Dash, S; De, S; De Caro, A; de Cataldo, G; de Conti, C; de Cuveland, J; De Falco, A; De Gruttola, D; De Marco, N; De Pasquale, S; Deisting, A; Deloff, A; Dénes, E; Deplano, C; Dhankher, P; Di Bari, D; Di Mauro, A; Di Nezza, P; Diaz Corchero, M A; Dietel, T; Dillenseger, P; Divià, R; Djuvsland, Ø; Dobrin, A; Domenicis Gimenez, D; Dönigus, B; Dordic, O; Drozhzhova, T; Dubey, A K; Dubla, A; Ducroux, L; Dupieux, P; Ehlers, R J; Elia, D; Endress, E; Engel, H; Epple, E; Erazmus, B; Erdemir, I; Erhardt, F; Espagnon, B; Estienne, M; Esumi, S; Eum, J; Evans, D; Evdokimov, S; Eyyubova, G; Fabbietti, L; Fabris, D; Faivre, J; Fantoni, A; Fasel, M; Feldkamp, L; Feliciello, A; Feofilov, G; Ferencei, J; Fernández Téllez, A; Ferreiro, E G; Ferretti, A; Festanti, A; Feuillard, V J G; Figiel, J; Figueredo, M A S; Filchagin, S; Finogeev, D; Fionda, F M; Fiore, E M; Fleck, M G; Floris, M; Foertsch, S; Foka, P; Fokin, S; Fragiacomo, E; Francescon, A; Frankenfeld, U; Fronze, G G; Fuchs, U; Furget, C; Furs, A; Fusco Girard, M; Gaardhøje, J J; Gagliardi, M; Gago, A M; Gallio, M; Gangadharan, D R; Ganoti, P; Gao, C; Garabatos, C; Garcia-Solis, E; Gargiulo, C; Gasik, P; Gauger, E F; Germain, M; Gheata, M; Ghosh, P; Ghosh, S K; Gianotti, P; Giubellino, P; Giubilato, P; Gladysz-Dziadus, E; Glässel, P; Goméz Coral, D M; Gomez Ramirez, A; Gonzalez, A S; Gonzalez, V; González-Zamora, P; Gorbunov, S; Görlich, L; Gotovac, S; Grabski, V; Grachov, O A; Graczykowski, L K; Graham, K L; Grelli, A; Grigoras, A; Grigoras, C; Grigoriev, V; Grigoryan, A; Grigoryan, S; Grinyov, B; Grion, N; Gronefeld, J M; Grosse-Oetringhaus, J F; Grosso, R; Guber, F; Guernane, R; Guerzoni, B; Gulbrandsen, K; Gunji, T; Gupta, A; Gupta, R; Haake, R; Haaland, Ø; Hadjidakis, C; Haiduc, M; Hamagaki, H; Hamar, G; Hamon, J C; Harris, J W; Harton, A; Hatzifotiadou, D; Hayashi, S; Heckel, S T; Hellbär, E; Helstrup, H; Herghelegiu, A; Herrera Corral, G; Hess, B A; Hetland, K F; Hillemanns, H; Hippolyte, B; Horak, D; Hosokawa, R; Hristov, P; Humanic, T J; Hussain, N; Hussain, T; Hutter, D; Hwang, D S; Ilkaev, R; Inaba, M; Incani, E; Ippolitov, M; Irfan, M; Ivanov, M; Ivanov, V; Izucheev, V; Jacazio, N; Jacobs, P M; Jadhav, M B; Jadlovska, S; Jadlovsky, J; Jahnke, C; Jakubowska, M J; Jang, H J; Janik, M A; Jayarathna, P H S Y; Jena, C; Jena, S; Jimenez Bustamante, R T; Jones, P G; Jusko, A; Kalinak, P; Kalweit, A; Kamin, J; Kang, J H; Kaplin, V; Kar, S; Karasu Uysal, A; Karavichev, O; Karavicheva, T; Karayan, L; Karpechev, E; Kebschull, U; Keidel, R; Keijdener, D L D; Keil, M; Mohisin Khan, M; Khan, P; Khan, S A; Khanzadeev, A; Kharlov, Y; Kileng, B; Kim, D W; Kim, D J; Kim, D; Kim, H; Kim, J S; Kim, M; Kim, S; Kim, T; Kirsch, S; Kisel, I; Kiselev, S; Kisiel, A; Kiss, G; Klay, J L; Klein, C; Klein, J; Klein-Bösing, C; Klewin, S; Kluge, A; Knichel, M L; Knospe, A G; Kobdaj, C; Kofarago, M; Kollegger, T; Kolojvari, A; Kondratiev, V; Kondratyeva, N; Kondratyuk, E; Konevskikh, A; Kopcik, M; Kostarakis, P; Kour, M; Kouzinopoulos, C; Kovalenko, O; Kovalenko, V; Kowalski, M; Koyithatta Meethaleveedu, G; Králik, I; Kravčáková, A; Krivda, M; Krizek, F; Kryshen, E; Krzewicki, M; Kubera, A M; Kučera, V; Kuhn, C; Kuijer, P G; Kumar, A; Kumar, J; Kumar, L; Kumar, S; Kurashvili, P; Kurepin, A; Kurepin, A B; Kuryakin, A; Kweon, M J; Kwon, Y; La Pointe, S L; La Rocca, P; Ladron de Guevara, P; Lagana Fernandes, C; Lakomov, I; Langoy, R; Lapidus, K; Lara, C; Lardeux, A; Lattuca, A; Laudi, E; Lea, R; Leardini, L; Lee, G R; Lee, S; Lehas, F; Lehner, S; Lemmon, R C; Lenti, V; Leogrande, E; León Monzón, I; León Vargas, H; Leoncino, M; Lévai, P; Li, S; Li, X; Lien, J; Lietava, R; Lindal, S; Lindenstruth, V; Lippmann, C; Lisa, M A; Ljunggren, H M; Lodato, D F; Loenne, P I; Loginov, V; Loizides, C; Lopez, X; López Torres, E; Lowe, A; Luettig, P; Lunardon, M; Luparello, G; Lutz, T H; Maevskaya, A; Mager, M; Mahajan, S; Mahmood, S M; Maire, A; Majka, R D; Malaev, M; Maldonado Cervantes, I; Malinina, L; Mal'Kevich, D; Malzacher, P; Mamonov, A; Manko, V; Manso, F; Manzari, V; Marchisone, M; Mareš, J; Margagliotti, G V; Margotti, A; Margutti, J; Marín, A; Markert, C; Marquard, M; Martin, N A; Martin Blanco, J; Martinengo, P; Martínez, M I; Martínez García, G; Martinez Pedreira, M; Mas, A; Masciocchi, S; Masera, M; Masoni, A; Mastroserio, A; Matyja, A; Mayer, C; Mazer, J; Mazzoni, M A; Mcdonald, D; Meddi, F; Melikyan, Y; Menchaca-Rocha, A; Meninno, E; Mercado Pérez, J; Meres, M; Miake, Y; Mieskolainen, M M; Mikhaylov, K; Milano, L; Milosevic, J; Mischke, A; Mishra, A N; Miśkowiec, D; Mitra, J; Mitu, C M; Mohammadi, N; Mohanty, B; Molnar, L; Montaño Zetina, L; Montes, E; Moreira De Godoy, D A; Moreno, L A P; Moretto, S; Morreale, A; Morsch, A; Muccifora, V; Mudnic, E; Mühlheim, D; Muhuri, S; Mukherjee, M; Mulligan, J D; Munhoz, M G; Munzer, R H; Murakami, H; Murray, S; Musa, L; Musinsky, J; Naik, B; Nair, R; Nandi, B K; Nania, R; Nappi, E; Naru, M U; Natal da Luz, H; Nattrass, C; Navarro, S R; Nayak, K; Nayak, R; Nayak, T K; Nazarenko, S; Nedosekin, A; Nellen, L; Ng, F; Nicassio, M; Niculescu, M; Niedziela, J; Nielsen, B S; Nikolaev, S; Nikulin, S; Nikulin, V; Noferini, F; Nomokonov, P; Nooren, G; Noris, J C C; Norman, J; Nyanin, A; Nystrand, J; Oeschler, H; Oh, S; Oh, S K; Ohlson, A; Okatan, A; Okubo, T; Olah, L; Oleniacz, J; Oliveira Da Silva, A C; Oliver, M H; Onderwaater, J; Oppedisano, C; Orava, R; Oravec, M; Ortiz Velasquez, A; Oskarsson, A; Otwinowski, J; Oyama, K; Ozdemir, M; Pachmayer, Y; Pagano, D; Pagano, P; Paić, G; Pal, S K; Pan, J; Pandey, A K; Papikyan, V; Pappalardo, G S; Pareek, P; Park, W J; Parmar, S; Passfeld, A; Paticchio, V; Patra, R N; Paul, B; Pei, H; Peitzmann, T; Pereira Da Costa, H; Peresunko, D; Perez Lezama, E; Peskov, V; Pestov, Y; Petráček, V; Petrov, V; Petrovici, M; Petta, C; Piano, S; Pikna, M; Pillot, P; Pimentel, L O D L; Pinazza, O; Pinsky, L; Piyarathna, D B; Płoskoń, M; Planinic, M; Pluta, J; Pochybova, S; Podesta-Lerma, P L M; Poghosyan, M G; Polichtchouk, B; Poljak, N; Poonsawat, W; Pop, A; Porteboeuf-Houssais, S; Porter, J; Pospisil, J; Prasad, S K; Preghenella, R; Prino, F; Pruneau, C A; Pshenichnov, I; Puccio, M; Puddu, G; Pujahari, P; Punin, V; Putschke, J; Qvigstad, H; Rachevski, A; Raha, S; Rajput, S; Rak, J; Rakotozafindrabe, A; Ramello, L; Rami, F; Raniwala, R; Raniwala, S; Räsänen, S S; Rascanu, B T; Rathee, D; Read, K F; Redlich, K; Reed, R J; Rehman, A; Reichelt, P; Reidt, F; Ren, X; Renfordt, R; Reolon, A R; Reshetin, A; Reygers, K; Riabov, V; Ricci, R A; Richert, T; Richter, M; Riedler, P; Riegler, W; Riggi, F; Ristea, C; Rocco, E; Rodríguez Cahuantzi, M; Rodriguez Manso, A; Røed, K; Rogochaya, E; Rohr, D; Röhrich, D; Ronchetti, F; Ronflette, L; Rosnet, P; Rossi, A; Roukoutakis, F; Roy, A; Roy, C; Roy, P; Rubio Montero, A J; Rui, R; Russo, R; Ruzza, B D; Ryabinkin, E; Ryabov, Y; Rybicki, A; Saarinen, S; Sadhu, S; Sadovsky, S; Šafařík, K; Sahlmuller, B; Sahoo, P; Sahoo, R; Sahoo, S; Sahu, P K; Saini, J; Sakai, S; Saleh, M A; Salzwedel, J; Sambyal, S; Samsonov, V; Šándor, L; Sandoval, A; Sano, M; Sarkar, D; Sarkar, N; Sarma, P; Scapparone, E; Scarlassara, F; Schiaua, C; Schicker, R; Schmidt, C; Schmidt, H R; Schmidt, M; Schuchmann, S; Schukraft, J; Schulc, M; Schutz, Y; Schwarz, K; Schweda, K; Scioli, G; Scomparin, E; Scott, R; Šefčík, M; Seger, J E; Sekiguchi, Y; Sekihata, D; Selyuzhenkov, I; Senosi, K; Senyukov, S; Serradilla, E; Sevcenco, A; Shabanov, A; Shabetai, A; Shadura, O; Shahoyan, R; Shahzad, M I; Shangaraev, A; Sharma, A; Sharma, M; Sharma, M; Sharma, N; Sheikh, A I; Shigaki, K; Shou, Q; Shtejer, K; Sibiriak, Y; Siddhanta, S; Sielewicz, K M; Siemiarczuk, T; Silvermyr, D; Silvestre, C; Simatovic, G; Simonetti, G; Singaraju, R; Singh, R; Singha, S; Singhal, V; Sinha, B C; Sinha, T; Sitar, B; Sitta, M; Skaali, T B; Slupecki, M; Smirnov, N; Snellings, R J M; Snellman, T W; Song, J; Song, M; Song, Z; Soramel, F; Sorensen, S; Souza, R D de; Sozzi, F; Spacek, M; Spiriti, E; Sputowska, I; Spyropoulou-Stassinaki, M; Stachel, J; Stan, I; Stankus, P; Stenlund, E; Steyn, G; Stiller, J H; Stocco, D; Strmen, P; Suaide, A A P; Sugitate, T; Suire, C; Suleymanov, M; Suljic, M; Sultanov, R; Šumbera, M; Sumowidagdo, S; Szabo, A; Szarka, I; Szczepankiewicz, A; Szymanski, M; Tabassam, U; Takahashi, J; Tambave, G J; Tanaka, N; Tarhini, M; Tariq, M; Tarzila, M G; Tauro, A; Tejeda Muñoz, G; Telesca, A; Terasaki, K; Terrevoli, C; Teyssier, B; Thäder, J; Thakur, D; Thomas, D; Tieulent, R; Tikhonov, A; Timmins, A R; Toia, A; Trogolo, S; Trombetta, G; Trubnikov, V; Trzaska, W H; Tsuji, T; Tumkin, A; Turrisi, R; Tveter, T S; Ullaland, K; Uras, A; Usai, G L; Utrobicic, A; Vala, M; Valencia Palomo, L; Vallero, S; Van Der Maarel, J; Van Hoorne, J W; van Leeuwen, M; Vanat, T; Vande Vyvre, P; Varga, D; Vargas, A; Vargyas, M; Varma, R; Vasileiou, M; Vasiliev, A; Vauthier, A; Vázquez Doce, O; Vechernin, V; Veen, A M; Veldhoen, M; Velure, A; Vercellin, E; Vergara Limón, S; Vernet, R; Verweij, M; Vickovic, L; Viinikainen, J; Vilakazi, Z; Villalobos Baillie, O; Villatoro Tello, A; Vinogradov, A; Vinogradov, L; Vinogradov, Y; Virgili, T; Vislavicius, V; Viyogi, Y P; Vodopyanov, A; Völkl, M A; Voloshin, K; Voloshin, S A; Volpe, G; Haller, B von; Vorobyev, I; Vranic, D; Vrláková, J; Vulpescu, B; Wagner, B; Wagner, J; Wang, H; Wang, M; Watanabe, D; Watanabe, Y; Weber, M; Weber, S G; Weiser, D F; Wessels, J P; Westerhoff, U; Whitehead, A M; Wiechula, J; Wikne, J; Wilk, G; Wilkinson, J; Williams, M C S; Windelband, B; Winn, M; Yang, P; Yano, S; Yasin, Z; Yin, Z; Yokoyama, H; Yoo, I-K; Yoon, J H; Yurchenko, V; Zaborowska, A; Zaccolo, V; Zaman, A; Zampolli, C; Zanoli, H J C; Zaporozhets, S; Zardoshti, N; Zarochentsev, A; Závada, P; Zaviyalov, N; Zbroszczyk, H; Zgura, I S; Zhalov, M; Zhang, H; Zhang, X; Zhang, Y; Zhang, C; Zhang, Z; Zhao, C; Zhigareva, N; Zhou, D; Zhou, Y; Zhou, Z; Zhu, H; Zhu, J; Zichichi, A; Zimmermann, A; Zimmermann, M B; Zinovjev, G; Zyzak, M

2016-01-01

Measurements of charged jet production as a function of centrality are presented for  p-Pb  collisions recorded at [Formula: see text] TeV with the ALICE detector. Centrality classes are determined via the energy deposit in neutron calorimeters at zero degree, close to the beam direction, to minimise dynamical biases of the selection. The corresponding number of participants or binary nucleon-nucleon collisions is determined based on the particle production in the Pb-going rapidity region. Jets have been reconstructed in the central rapidity region from charged particles with the anti-[Formula: see text] algorithm for resolution parameters [Formula: see text] and [Formula: see text] in the transverse momentum range 20 to 120 GeV/ c . The reconstructed jet momentum and yields have been corrected for detector effects and underlying-event background. In the five centrality bins considered, the charged jet production in  p-Pb   collisions is consistent with the production expected from binary scaling from pp collisions. The ratio of jet yields reconstructed with the two different resolution parameters is also independent of the centrality selection, demonstrating the absence of major modifications of the radial jet structure in the reported centrality classes.

Attrition Rate of Oxygen Carriers in Chemical Looping Combustion Systems

NASA Astrophysics Data System (ADS)

Feilen, Harry Martin

This project developed an evaluation methodology for determining, accurately and rapidly, the attrition resistance of oxygen carrier materials used in chemical looping technologies. Existing test protocols, to evaluate attrition resistance of granular materials, are conducted under non-reactive and ambient temperature conditions. They do not accurately reflect the actual behavior under the unique process conditions of chemical looping, including high temperatures and cyclic operation between oxidizing and reducing atmospheres. This project developed a test method and equipment that represented a significant improvement over existing protocols. Experimental results obtained from this project have shown that hematite exhibits different modes of attrition, including both due to mechanical stresses and due to structural changes in the particles due to chemical reaction at high temperature. The test methodology has also proven effective in providing reactivity changes of the material with continued use, a property, which in addition to attrition, determines material life. Consumption/replacement cost due to attrition or loss of reactivity is a critical factor in the economic application of the chemical looping technology. This test method will allow rapid evaluation of a wide range of materials that are best suited for this technology. The most important anticipated public benefit of this project is the acceleration of the development of chemical looping technology for lowering greenhouse gas emissions from fossil fuel combustion.

Centrality dependence of charged jet production in p–Pb collisions at $$\\sqrt{s_\\mathrm{NN}}$$ = 5.02 TeV

DOE PAGES

Adam, J.; Adamová, D.; Aggarwal, M. M.; ...

2016-05-17

Measurements of charged jet production as a function of centrality are presented for p–Pb collisions recorded atmore » $$\\sqrt{s_\\mathrm{NN}}$$= 5.02 TeV with the ALICE detector. Centrality classes are determined via the energy deposit in neutron calorimeters at zero degree, close to the beam direction, to minimise dynamical biases of the selection. The corresponding number of participants or binary nucleon–nucleon collisions is determined based on the particle production in the Pb-going rapidity region. Jets have been reconstructed in the central rapidity region from charged particles with the anti-k T algorithm for resolution parameters R = 0.2 and R = 0.4 in the transverse momentum range 20 to 120 GeV/c. The reconstructed jet momentum and yields have been corrected for detector effects and underlying-event background. In the five centrality bins considered, the charged jet production in p–Pb collisions is consistent with the production expected from binary scaling from pp collisions. The ratio of jet yields reconstructed with the two different resolution parameters is also independent of the centrality selection, demonstrating the absence of major modifications of the radial jet structure in the reported centrality classes.« less

75 FR 20396 - Terex USA, LLC, Cedar Rapids, IA; Notice of Negative Determination Regarding Application for...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-19

... DEPARTMENT OF LABOR Employment and Training Administration [TA-W-72,103] Terex USA, LLC, Cedar Rapids, IA; Notice of Negative Determination Regarding Application for Reconsideration By application dated March 8, 2010, the State of Iowa Trade Adjustment Assistance (TAA) Coordinator requested...

Microbial Protein-Antigenome Determination (MAD) Technology: A Proteomics-Based Strategy for Rapid Identification of Microbial Targets of Host Humoral Immune Responses

USDA-ARS?s Scientific Manuscript database

Immunogenic, pathogen-specific proteins have excellent potential for development of novel management modalities. Here, we describe an innovative application of proteomics called Microbial protein-Antigenome Determination (MAD) Technology for rapid identification of native microbial proteins that el...

Microbial Protein-Antigenome Determination (MAD) Technology: A Proteomics-Based Strategy for Rapid Identification of Microbial Targets of Host Humoral Immune Responses

USDA-ARS?s Scientific Manuscript database

Immunogenic, pathogen-specific proteins have excellent potential for development of novel management modalities. Here, we describe an innovative application of proteomics called Microbial protein-Antigenome Determination (MAD) Technology for rapid identification of native microbial proteins that eli...

Contribution of the mu loop to the structure and function of rat glutathione transferase M1-1

PubMed Central

Hearne, Jennifer L.; Colman, Roberta F.

2006-01-01

The “mu loop,” an 11-residue loop spanning amino acid residues 33–43, is a characteristic structural feature of the mu class of glutathione transferases. To assess the contribution of the mu loop to the structure and function of rat GST M1-1, amino acid residues 35–44 (35GDAPDYDRSQ44) were excised by deletion mutagenesis, resulting in the “Deletion Enzyme.” Kinetic studies reveal that the Km values of the Deletion Enzyme are markedly increased compared with those of the wild-type enzyme: 32-fold for 1-chloro-2,4-dinitrobenzene, 99-fold for glutathione, and 880-fold for monobromobimane, while the Vmax value for each substrate is increased only modestly. Results from experiments probing the structure of the Deletion Enzyme, in comparison with that of the wild-type enzyme, suggest that the secondary and quaternary structures have not been appreciably perturbed. Thermostability studies indicate that the Deletion Enzyme is as stable as the wild-type enzyme at 4°C and 10°C, but it rapidly loses activity at 25°C, unlike the wild-type enzyme. In the temperature range of 4°C through 25°C, the loss of activity of the Deletion Enzyme is not the result of a change in its structure, as determined by circular dichroism spectroscopy and sedimentation equilibrium centrifugation. Collectively, these results indicate that the mu loop is not essential for GST M1-1 to maintain its structure nor is it required for the enzyme to retain some catalytic activity. However, it is an important determinant of the enzyme's affinity for its substrates. PMID:16672236

Porous silicon based photoluminescence immunosensor for rapid and highly-sensitive detection of Ochratoxin A.

PubMed

Myndrul, Valerii; Viter, Roman; Savchuk, Maryna; Shpyrka, Nelya; Erts, Donats; Jevdokimovs, Daniels; Silamiķelis, Viesturs; Smyntyna, Valentyn; Ramanavicius, Arunas; Iatsunskyi, Igor

2018-04-15

A rapid and low cost photoluminescence (PL) immunosensor for the determination of low concentrations of Ochratoxin A (OTA) has been developed. This immunosensor was based on porous silicon (PSi) and modified by antibodies against OTA (anti-OTA). PSi layer was fabricated by metal-assisted chemical etching (MACE) procedure. Main structural parameters (pore size, layer thickness, morphology and nanograins size) and composition of PSi were investigated by means of X-Ray diffraction (XRD), scanning electron microscopy (SEM) and Raman spectroscopy. PL-spectroscopy of PSi was performed at room temperature and showed a wide emission band centered at 680 ± 20nm. Protein A was covalently immobilized on the surface of PSi, which in next steps was modified by anti-OTA and BSA in this way a anti-OTA/Protein-A/PSi structure sensitive towards OTA was designed. The anti-OTA/Protein-A/PSi-based immunosensors were tested in a wide range of OTA concentrations from 0.001 upto 100ng/ml. Interaction of OTA with anti-OTA/Protein-A/PSi surface resulted in the quenching of photoluminescence in comparison to bare PSi. The limit of detection (LOD) and the sensitivity range of anti-OTA/Protein-A/PSi immunosensors were estimated. Association constant and Gibbs free energy for the interaction of anti-OTA/Protein-A/PSi with OTA were calculated and analyzed using the interaction isotherms. Response time of the anti-OTA/Protein-A/PSi-based immunosensor toward OTA was in the range of 500-700s. These findings are very promising for the development of highly sensitive, and potentially portable immunosensors suitable for fast determination of OTA in food and beverages. Copyright © 2017 Elsevier B.V. All rights reserved.

Structure and properties of carbon black particles

NASA Astrophysics Data System (ADS)

Xu, Wei

Structure and properties of carbon black particles were investigated using atomic force microscopy, gas adsorption, Raman spectroscopy, and X-ray diffraction. Supplementary information was obtained using TEM and neutron scattering. The AFM imaging of carbon black aggregates provided qualitative visual information on their morphology, complementary to that obtained by 3-D modeling based on TEM images. Our studies showed that carbon black aggregates were relatively flat. The surface of all untreated carbon black particles was found to be rough and its fractal dimension was 2.2. Heating reduced the roughness and fractal dimension for all samples heat treated at above 1300 K to 2.0. Once the samples were heat treated rapid cooling did not affect the surface roughness. However, rapid cooling reduced crystallite sizes, and different Raman spectra were obtained for carbon blacks of various history of heat treatment. By analyzing the Raman spectra we determined the crystallite sizes and identified amorphous carbon. The concentration of amorphous carbon depends on hydrogen content. Once hydrogen was liberated at increased temperature, the concentration of amorphous carbon was reduced and crystallites started to grow. Properties of carbon blacks at high pressure were also studied. Hydrostatic pressure did not affect the size of the crystallites in carbon black particles. The pressure induced shift in Raman frequency of the graphitic component was a result of increased intermolecular forces and not smaller crystallites. Two methods of determining the fractal dimension, the FHH model and the yardstick technique based on the BET theory were used in the literature. Our study proved that the FHH model is sensitive to numerous assumptions and leads to wrong conclusions. On the other hand the yardstick method gave correct results, which agreed with the AFM results.

Comparison of the effects of rapid maxillary expansion caused by treatment with either a memory screw or a Hyrax screw on the dentofacial structures--transversal effects.

PubMed

Halıcıoğlu, Koray; Yavuz, Ibrahim

2014-04-01

The aim of the present study was to investigate and compare the effects of conventional Hyrax screw treatment and memory screw treatment on skeletal and dentoalveolar structures. Thirty-two patients with maxillary transversal deficiency were divided into two groups. The memory-screw group included 17 patients (nine females and eight males), while the Hyrax-screw group comprised 15 patients (eight females and seven males). Mean ages of the subjects in the memory-screw and Hyrax-screw groups were 13.00 ± 1.29 and 12.58 ± 1.50 years, respectively. Plaster models and postero-anterior cephalograms were taken from the patients at the beginning of the treatment (T1) and at the end of expansion (T2) and retention periods (T3). The mean expansion period was 7.76 ± 1.04 days in the memory-screw group and 35.46 ± 9.39 days in the Hyrax-screw group. 'Shapiro-Wilk Normality test' was used to determine whether the investigated parameters were homogeneous or not. To determine the treatment changes within the group, 'paired t-test' and 'Wilcoxon signed-ranks test' were applied to the homogeneous and non-homogeneous parameters, respectively. Comparison between the groups was carried out using 'Student's t-test' for homogeneous parameters and 'Mann-Whitney U-test' for the rest. Rapid maxillary expansion was carried out successfully in both the groups. However, the use of memory screw may be advantageous because it shortens the maxillary expansion period, provides additional expansion in the retention period, and generates light forces relative to the conventional Hyrax screw.

Challenges Facing Chinese PE Curriculum Reform--Teachers' Talk

ERIC Educational Resources Information Center

Jin, Aijing

2009-01-01

China has attracted a huge amount of interest from around the world over the last two decades because of its rapid and vigorous development. Rapid economic growth has brought with it significant structural reforms in all trades and professions across China. Within this context of rapid social change, the Chinese basic education system has been…

Using travel socialization and underlying motivations to better understand motorcycle usage in Taiwan.

PubMed

Chang, Hsin-Li; Lai, Chi-Yen

2015-06-01

This study introduces self-determination theory (SDT) to refine previous models of vehicle usage motivation. We add travel socialization theory regarding parental influence on vehicle usage to enhance previous structural models describing motorcycle usage behavior. Our newly developed model was empirically verified in a sample of 721 motorcycle users in Taiwan. In addition to instrumental, symbolic, and affective motivations, perceived parental attitudes (PPAs) towards motorcycle riding were found to have a significant effect on individuals' motorcycle use habits. Additionally, participants who perceived their parents to have more positive attitudes toward motorcycles were found to have more experience being chauffeured on motorcycles by their parents. Based on these results, we suggest means to confront the challenges brought on by the rapid growth of motorcycle usage, especially serious motorcycle traffic accidents. These results improve our understanding motorcycle usage in Taiwan and can be used by transportation professionals who are seeking solutions to the rapid growth of motorcycle usage. Copyright © 2015 Elsevier Ltd. All rights reserved.

A building-block approach to 3D printing a multichannel, organ-regenerative scaffold.

PubMed

Wang, Xiaohong; Rijff, Boaz Lloyd; Khang, Gilson

2017-05-01

Multichannel scaffolds, formed by rapid prototyping technologies, retain a high potential for regenerative medicine and the manufacture of complex organs. This study aims to optimize several parameters for producing poly(lactic-co-glycolic acid) (PLGA) scaffolds by a low-temperature, deposition manufacturing, three-dimensional printing (3DP, or rapid prototyping) system. Concentration of the synthetic polymer solution, nozzle speed and extrusion rate were analysed and discussed. Polymer solution with a concentration of 12% w/v was determined as optimal for formation; large deviation of this figure failed to maintain the desired structure. The extrusion rate was also modified for better construct quality. Finally, several solid organ scaffolds, such as the liver, with proper wall thickness and intact contour were printed. This study gives basic instruction to design and fabricate scaffolds with de novo material systems, particularly by showing the approximation of variables for manufacturing multichannel PLGA scaffolds. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

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.

Effect of pectin methylesterase on carrot (Daucus carota) juice cloud stability.

PubMed

Schultz, Alison K; Anthon, Gordon E; Dungan, Stephanie R; Barrett, Diane M

2014-02-05

To determine the effect of residual enzyme activity on carrot juice cloud, 0 to 1 U/g pectin methylesterase (PME) was added to pasteurized carrot juice. Cloud stability and particle diameters were measured to quantify juice cloud stability and clarification for 56 days of storage. All levels of PME addition resulted in clarification; higher amounts had a modest effect in causing more rapid clarification, due to a faster increase in particle size. The cloud initially exhibited a trimodal distribution of particle sizes. For enzyme-containing samples, particles in the smallest-sized mode initially aggregated to merge with the second peak over 5-10 days. This larger population then continued to aggregate more slowly over longer times. This observation of a more rapid destabilization process initially, followed by slower subsequent changes in the cloud, was also manifested in measurements of sedimentation extent and in turbidity tests. Optical microscopy showed that aggregation created elongated, fractal particle structures over time.

High-fidelity large area nano-patterning of silicon with femtosecond light sheet

NASA Astrophysics Data System (ADS)

Sidhu, Mehra S.; Munjal, Pooja; Singh, Kamal P.

2018-01-01

We employ a femtosecond light sheet generated by a cylindrical lens to rapidly produce high-fidelity nano-structures over large area on silicon surface. The Fourier analysis of electron microscopy images of the laser-induced surface structures reveals sharp peaks indicating good homogeneity. We observed an emergence of second-order spatial periodicity on increasing the scan speed. Our reliable approach may rapidly nano-pattern curved solid surfaces and tiny objects for diverse potential applications in optical devices, structural coloring, plasmonic substrates and in high-harmonic generation.

Rapid identification of Keap1-Nrf2 small-molecule inhibitors through structure-based virtual screening and hit-based substructure search.

PubMed

Zhuang, Chunlin; Narayanapillai, Sreekanth; Zhang, Wannian; Sham, Yuk Yin; Xing, Chengguo

2014-02-13

In this study, rapid structure-based virtual screening and hit-based substructure search were utilized to identify small molecules that disrupt the interaction of Keap1-Nrf2. Special emphasis was placed toward maximizing the exploration of chemical diversity of the initial hits while economically establishing informative structure-activity relationship (SAR) of novel scaffolds. Our most potent noncovalent inhibitor exhibits three times improved cellular activation in Nrf2 activation than the most active noncovalent Keap1 inhibitor known to date.

Determination of the Structure and Catalytic Mechanism of Sorghum bicolor Caffeic Acid O-Methyltransferase and the Structural Impact of Three brown midrib12 Mutations.

PubMed

Green, Abigail R; Lewis, Kevin M; Barr, John T; Jones, Jeffrey P; Lu, Fachuang; Ralph, John; Vermerris, Wilfred; Sattler, Scott E; Kang, ChulHee

2014-08-01

Using S-adenosyl-methionine as the methyl donor, caffeic acid O-methyltransferase from sorghum (Sorghum bicolor; SbCOMT) methylates the 5-hydroxyl group of its preferred substrate, 5-hydroxyconiferaldehyde. In order to determine the mechanism of SbCOMT and understand the observed reduction in the lignin syringyl-to-guaiacyl ratio of three brown midrib12 mutants that carry COMT gene missense mutations, we determined the apo-form and S-adenosyl-methionine binary complex SbCOMT crystal structures and established the ternary complex structure with 5-hydroxyconiferaldehyde by molecular modeling. These structures revealed many features shared with monocot ryegrass (Lolium perenne) and dicot alfalfa (Medicago sativa) COMTs. SbCOMT steady-state kinetic and calorimetric data suggest a random bi-bi mechanism. Based on our structural, kinetic, and thermodynamic results, we propose that the observed reactivity hierarchy among 4,5-dihydroxy-3-methoxycinnamyl (and 3,4-dihydroxycinnamyl) aldehyde, alcohol, and acid substrates arises from the ability of the aldehyde to stabilize the anionic intermediate that results from deprotonation of the 5-hydroxyl group by histidine-267. Additionally, despite the presence of other phenylpropanoid substrates in vivo, sinapaldehyde is the preferential product, as demonstrated by its low K m for 5-hydroxyconiferaldehyde. Unlike its acid and alcohol substrates, the aldehydes exhibit product inhibition, and we propose that this is due to nonproductive binding of the S-cis-form of the aldehydes inhibiting productive binding of the S-trans-form. The S-cis-aldehydes most likely act only as inhibitors, because the high rotational energy barrier around the 2-propenyl bond prevents S-trans-conversion, unlike alcohol substrates, whose low 2-propenyl bond rotational energy barrier enables rapid S-cis/S-trans-interconversion. © 2014 American Society of Plant Biologists. All Rights Reserved.

Structural Configuration Analysis of Crew Exploration Vehicle Concepts

NASA Technical Reports Server (NTRS)

Mukhopadhyay, V.

2006-01-01

Structural configuration modeling and finite element analysis of crew exploration vehicle (CEV) concepts are presented. In the structural configuration design approach, parametric solid models of the pressurized shell and tanks are developed. The CEV internal cabin pressure is same as in the International Space Station (ISS) to enable docking with the ISS without an intermediate airlock. Effects of this internal pressure load on the stress distribution, factor of safety, mass and deflections are investigated. Uniform 7 mm thick skin shell, 5 mm thick shell with ribs and frames, and isogrid skin construction options are investigated. From this limited study, the isogrid construction appears to provide most strength/mass ratio. Initial finite element analysis results on the service module tanks are also presented. These rapid finite element analyses, stress and factor of safety distribution results are presented as a part of lessons learned and to build up a structural mass estimation and sizing database for future technology support. This rapid structural analysis process may also facilitate better definition of the vehicles and components for rapid prototyping. However, these structural analysis results are highly conceptual and exploratory in nature and do not reflect current configuration designs being conducted at the program level by NASA and industry.

Flytrap-inspired robot using structurally integrated actuation based on bistability and a developable surface.

PubMed

Kim, Seung-Won; Koh, Je-Sung; Lee, Jong-Gu; Ryu, Junghyun; Cho, Maenghyo; Cho, Kyu-Jin

2014-09-01

The Venus flytrap uses bistability, the structural characteristic of its leaf, to actuate the leaf's rapid closing motion for catching its prey. This paper presents a flytrap-inspired robot and novel actuation mechanism that exploits the structural characteristics of this structure and a developable surface. We focus on the concept of exploiting structural characteristics for actuation. Using shape memory alloy (SMA), the robot actuates artificial leaves made from asymmetrically laminated carbon fiber reinforced prepregs. We exploit two distinct structural characteristics of the leaves. First, the bistability acts as an implicit actuator enabling rapid morphing motion. Second, the developable surface has a kinematic constraint that constrains the curvature of the artificial leaf. Due to this constraint, the curved artificial leaf can be unbent by bending the straight edge orthogonal to the curve. The bending propagates from one edge to the entire surface and eventually generates an overall shape change. The curvature change of the artificial leaf is 18 m(-1) within 100 ms when closing. Experiments show that these actuation mechanisms facilitate the generation of a rapid and large morphing motion of the flytrap robot by one-way actuation of the SMA actuators at a local position.

2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update

PubMed Central

Duff, Anthony P.; Durand, Dominique; Gabel, Frank; Hendrickson, Wayne A.; Hura, Greg L.; Jacques, David A.; Kirby, Nigel M.; Kwan, Ann H.; Pérez, Javier; Pollack, Lois; Ryan, Timothy M.; Sali, Andrej; Schneidman-Duhovny, Dina; Vachette, Patrice; Westbrook, John

2017-01-01

In 2012, preliminary guidelines were published addressing sample quality, data acquisition and reduction, presentation of scattering data and validation, and modelling for biomolecular small-angle scattering (SAS) experiments. Bio­molecular SAS has since continued to grow and authors have increasingly adopted the preliminary guidelines. In parallel, integrative/hybrid determination of biomolecular structures is a rapidly growing field that is expanding the scope of structural biology. For SAS to contribute maximally to this field, it is essential to ensure open access to the information required for evaluation of the quality of SAS samples and data, as well as the validity of SAS-based structural models. To this end, the preliminary guidelines for data presentation in a publication are reviewed and updated, and the deposition of data and associated models in a public archive is recommended. These guidelines and recommendations have been prepared in consultation with the members of the International Union of Crystallography (IUCr) Small-Angle Scattering and Journals Commissions, the Worldwide Protein Data Bank (wwPDB) Small-Angle Scattering Validation Task Force and additional experts in the field. PMID:28876235

Expressing the human proteome for affinity proteomics: optimising expression of soluble protein domains and in vivo biotinylation.

PubMed

Keates, Tracy; Cooper, Christopher D O; Savitsky, Pavel; Allerston, Charles K; Phillips, Claire; Hammarström, Martin; Daga, Neha; Berridge, Georgina; Mahajan, Pravin; Burgess-Brown, Nicola A; Müller, Susanne; Gräslund, Susanne; Gileadi, Opher

2012-06-15

The generation of affinity reagents to large numbers of human proteins depends on the ability to express the target proteins as high-quality antigens. The Structural Genomics Consortium (SGC) focuses on the production and structure determination of human proteins. In a 7-year period, the SGC has deposited crystal structures of >800 human protein domains, and has additionally expressed and purified a similar number of protein domains that have not yet been crystallised. The targets include a diversity of protein domains, with an attempt to provide high coverage of protein families. The family approach provides an excellent basis for characterising the selectivity of affinity reagents. We present a summary of the approaches used to generate purified human proteins or protein domains, a test case demonstrating the ability to rapidly generate new proteins, and an optimisation study on the modification of >70 proteins by biotinylation in vivo. These results provide a unique synergy between large-scale structural projects and the recent efforts to produce a wide coverage of affinity reagents to the human proteome. Copyright © 2011 Elsevier B.V. All rights reserved.

Developments in seismic monitoring for risk reduction

USGS Publications Warehouse

Celebi, M.

2007-01-01

This paper presents recent state-of-the-art developments to obtain displacements and drift ratios for seismic monitoring and damage assessment of buildings. In most cases, decisions on safety of buildings following seismic events are based on visual inspections of the structures. Real-time instrumental measurements using GPS or double integration of accelerations, however, offer a viable alternative. Relevant parameters, such as the type of connections and structural characteristics (including storey geometry), can be estimated to compute drifts corresponding to several pre-selected threshold stages of damage. Drift ratios determined from real-time monitoring can then be compared to these thresholds in order to estimate damage conditions drift ratios. This approach is demonstrated in three steel frame buildings in San Francisco, California. Recently recorded data of strong shaking from these buildings indicate that the monitoring system can be a useful tool in rapid assessment of buildings and other structures following an earthquake. Such systems can also be used for risk monitoring, as a method to assess performance-based design and analysis procedures, for long-term assessment of structural characteristics of a building, and as a possible long-term damage detection tool.

A Structural Model for a Self-Assembled Nanotube Provides Insight into Its Exciton Dynamics

PubMed Central

2016-01-01

The design and synthesis of functional self-assembled nanostructures is frequently an empirical process fraught with critical knowledge gaps about atomic-level structure in these noncovalent systems. Here, we report a structural model for a semiconductor nanotube formed via the self-assembly of naphthalenediimide-lysine (NDI-Lys) building blocks determined using experimental 13C–13C and 13C–15N distance restraints from solid-state nuclear magnetic resonance supplemented by electron microscopy and X-ray powder diffraction data. The structural model reveals a two-dimensional-crystal-like architecture of stacked monolayer rings each containing ∼50 NDI-Lys molecules, with significant π-stacking interactions occurring both within the confines of the ring and along the long axis of the tube. Excited-state delocalization and energy transfer are simulated for the nanotube based on time-dependent density functional theory and an incoherent hopping model. Remarkably, these calculations reveal efficient energy migration from the excitonic bright state, which is in agreement with the rapid energy transfer within NDI-Lys nanotubes observed previously using fluorescence spectroscopy. PMID:26120375

Topography of the casein micelle surface by surface plasmon resonance (SPR) using a selection of specific monoclonal antibodies.

PubMed

Dupont, Didier; Johansson, Annette; Marchin, Stephane; Rolet-Repecaud, Odile; Marchesseau, Sylvie; Leonil, Joelle

2011-08-10

Several theoretical models of the casein micelle structure have been proposed in the past, but the exact organization of the four individual caseins (α(s1), α(s2), β, and κ) within this supramolecular structure remains unknown. The present study aims at determining the topography of the casein micelle surface by following the interaction between 44 monoclonal antibodies specific for different epitopes of α(s1)-, α(s2)-, β-, and κ-casein and the casein micelle in real time and no labeling using a surface plasmon resonance (SPR)-based biosensor. Although the four individual caseins were found to be accessible for antibody binding, data confirmed that the C-terminal extremity of κ-casein was highly accessible and located at the periphery of the structure. When casein micelles were submitted to proteolysis, the C-terminal extremity of κ-casein was rapidly hydrolyzed. Disintegration of the micellar structure resulted in an increased access for antibodies to hydrophobic areas of α(s1)- and α(s2)-casein.

Temperature Dependence of the Structural Parameters in the Transformation of Aragonite to Calcite, as Determined from In Situ Synchrotron Powder X-ray-Diffratction Data

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

Antao, Sytle M.; Hassan, Ishmael; West Indies)

The temperature dependency of the crystal structure and the polymorphic transition of CaCO{sub 3} from aragonite to calcite were studied using Rietveld structure refinement and high-temperature in situ synchrotron powder X-ray-diffraction data at ambient pressure, P. The orthorhombic metastable aragonite at room P, space group Pmcn, transforms to trigonal calcite, space group R{bar 3}c, at about T{sub c} = 468 C. This transformation occurs rapidly; it starts at about 420 C and is completed by 500 C, an 80 C interval that took about 10 minutes using a heating rate of 8 C/min. Structurally, from aragonite to calcite, the distributionmore » of the Ca atom changes from approximately hexagonal to cubic close-packing. A 5.76% discontinuous increase in volume accompanies the reconstructive first-order transition. Besides the change in coordination of the Ca atom from nine to six from aragonite to calcite, the CO{sub 3} groups change by a 30{sup o} rotation across the transition.« less

Decoding structural complexity in conical carbon nanofibers.

PubMed

Zhu, Yi-An; Wang, Zi-Jun; Cheng, Hong-Ye; Yang, Qin-Min; Sui, Zhi-Jun; Zhou, Xing-Gui; Chen, De

2017-06-07

Conical carbon nanofibers (CNFs) exist primarily as graphitic ribbons that fold into a cylindrical structure with the formation of a hollow core. Structural analysis aided by molecular modeling proves useful for obtaining a full picture of how the size of the central channel varies from fiber to fiber. From a geometrical perspective, conical CNFs possibly have cone tips that are nearly closed. On the other hand, their fiber wall thickness can be reduced to a minimum possible value that is determined solely by the apex angle, regardless of the outer diameter. A formula has been developed to express the number of carbon atoms present in conical CNFs in terms of measurable structural parameters. It appears that the energetically preferred fiber wall thickness increases not only with the apex angle, but also with the number of atoms in the constituent graphitic cones. The origin of the empirical observation that conical CNFs with small apex angles tend to have a large hollow core lies in the fact that in graphene sheets that are more highly curved the curvature-induced strain energy rises more rapidly as the fiber wall thickens.

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.

Expressing the human proteome for affinity proteomics: optimising expression of soluble protein domains and in vivo biotinylation

PubMed Central

Keates, Tracy; Cooper, Christopher D.O.; Savitsky, Pavel; Allerston, Charles K.; Phillips, Claire; Hammarström, Martin; Daga, Neha; Berridge, Georgina; Mahajan, Pravin; Burgess-Brown, Nicola A.; Müller, Susanne; Gräslund, Susanne; Gileadi, Opher

2012-01-01

The generation of affinity reagents to large numbers of human proteins depends on the ability to express the target proteins as high-quality antigens. The Structural Genomics Consortium (SGC) focuses on the production and structure determination of human proteins. In a 7-year period, the SGC has deposited crystal structures of >800 human protein domains, and has additionally expressed and purified a similar number of protein domains that have not yet been crystallised. The targets include a diversity of protein domains, with an attempt to provide high coverage of protein families. The family approach provides an excellent basis for characterising the selectivity of affinity reagents. We present a summary of the approaches used to generate purified human proteins or protein domains, a test case demonstrating the ability to rapidly generate new proteins, and an optimisation study on the modification of >70 proteins by biotinylation in vivo. These results provide a unique synergy between large-scale structural projects and the recent efforts to produce a wide coverage of affinity reagents to the human proteome. PMID:22027370

The Role of Phase Changes in TiO2/Pt/TiO2 Filaments

NASA Astrophysics Data System (ADS)

Bíró, Ferenc; Hajnal, Zoltán; Dücső, Csaba; Bársony, István

2018-04-01

This work analyses the role of phase changes in TiO2/Pt/TiO2 layer stacks for micro-heater application regarding their stability and reliable operation. The polycrystalline Pt layer wrapped in a TiO2 adhesion layer underwent a continuous recrystallisation in a self-heating operation causing a drift in the resistance ( R) versus temperature ( T) performance. Simultaneously, the TiO2 adhesion layer also deteriorates at high temperature by phase changes from amorphous to anatase and rutile crystallite formation, which not only influences the Pt diffusion in different migration phenomena, but also reduces the cross section of the Pt heater wire. Thorough scanning electron microscopy, energy dispersive spectroscopy, cross-sectional transmission electron microscopy (XTEM) and electron beam diffraction analysis of the structures operated at increasing temperature revealed the elemental structural processes leading to the instabilities and the accelerated degradation, resulting in rapid breakdown of the heater wire. Owing to stability and reliability criteria, the conditions for safe operation of these layer structures could be determined.

Automation process for morphometric analysis of volumetric CT data from pulmonary vasculature in rats.

PubMed

Shingrani, Rahul; Krenz, Gary; Molthen, Robert

2010-01-01

With advances in medical imaging scanners, it has become commonplace to generate large multidimensional datasets. These datasets require tools for a rapid, thorough analysis. To address this need, we have developed an automated algorithm for morphometric analysis incorporating A Visualization Workshop computational and image processing libraries for three-dimensional segmentation, vascular tree generation and structural hierarchical ordering with a two-stage numeric optimization procedure for estimating vessel diameters. We combine this new technique with our mathematical models of pulmonary vascular morphology to quantify structural and functional attributes of lung arterial trees. Our physiological studies require repeated measurements of vascular structure to determine differences in vessel biomechanical properties between animal models of pulmonary disease. Automation provides many advantages including significantly improved speed and minimized operator interaction and biasing. The results are validated by comparison with previously published rat pulmonary arterial micro-CT data analysis techniques, in which vessels were manually mapped and measured using intense operator intervention. Published by Elsevier Ireland Ltd.

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

Reverse osmosis membrane composition, structure and performance modification by bisulphite, iron(III), bromide and chlorite exposure.

PubMed

Ferrer, O; Gibert, O; Cortina, J L

2016-10-15

Reverse osmosis (RO) membrane exposure to bisulphite, chlorite, bromide and iron(III) was assessed in terms of membrane composition, structure and performance. Membrane composition was determined by Rutherford backscattering spectrometry (RBS) and membrane performance was assessed by water and chloride permeation, using a modified version of the solution-diffusion model. Iron(III) dosage in presence of bisulphite led to an autooxidation of the latter, probably generating free radicals which damaged the membrane. It comprised a significant raise in chloride passage (chloride permeation coefficient increased 5.3-5.1 fold compared to the virgin membrane under the conditions studied) rapidly. No major differences in terms of water permeability and membrane composition were observed. Nevertheless, an increase in the size of the network pores, and a raise in the fraction of aggregate pores of the polyamide (PA) layer were identified, but no amide bond cleavage was observed. These structural changes were therefore, in accordance with the transport properties observed. Copyright © 2016 Elsevier Ltd. All rights reserved.

High-pressure phase transition makes B 4.3 C boron carbide a wide-gap semiconductor

DOE PAGES

Hushur, Anwar; Manghnani, Murli H.; Werheit, Helmut; ...

2016-01-11

Single-crystal B4.3C boron carbide is investigated concerning the pressure-dependence of optical properties and of Raman-active phonons up to ~70 GPa. The high concentration of structural defects determining the electronic properties of boron carbide at ambient conditions initially decrease and finally vanish with pressure increasing. We obtain this immediately from transparency photos, allowing to estimate the pressure-dependent variation of the absorption edge rapidly increasing around 55 GPa. Glass-like transparency at pressures exceeding 60 GPa indicate that the width of the band exceeds ~3.1 eV thus making boron carbide a wide-gap semiconductor. Furthermore, the spectra of Raman–active phonons indicate a pressure-dependent phasemore » transition in single-crystal natB4.3C boron carbide near 35 GPa., particularly related to structural changes in connection with the C-B-C chains, while the basic icosahedral structure remains largely unaffected.« less

Rapid saccharification for production of cellulosic biofuels.

PubMed

Lee, Dae-Seok; Wi, Seung Gon; Lee, Soo Jung; Lee, Yoon-Gyo; Kim, Yeong-Suk; Bae, Hyeun-Jong

2014-04-01

The economical production of biofuels is hindered by the recalcitrance of lignocellulose to processing, causing high consumption of processing enzymes and impeding hydrolysis of pretreated lignocellulosic biomass. We determined the major rate-limiting factor in the hydrolysis of popping pre-treated rice straw (PPRS) by examining cellulase adsorption to lignin and cellulose, amorphogenesis of PPRS, and re-hydrolysis. Based on the results, equivalence between enzyme loading and the open structural area of cellulose was required to significantly increase productive adsorption of cellulase and to accelerate enzymatic saccharification of PPRS. Amorphogenesis of PPRS by phosphoric acid treatment to expand open structural area of the cellulose fibers resulted in twofold higher cellulase adsorption and increased the yield of the first re-hydrolysis step from 13% to 46%. The total yield from PPRS was increased to 84% after 3h. These results provide evidence that cellulose structure is one of major effects on the enzymatic hydrolysis. Copyright © 2014 Elsevier Ltd. All rights reserved.

Effects of HMW-GS Ax1 or Dx2 absence on the glutenin polymerization and gluten micro structure of wheat (Triticum aestivum L.).

PubMed

Gao, Xin; Liu, Tianhong; Ding, Mengyun; Wang, Jun; Li, Chunlian; Wang, Zhonghua; Li, Xuejun

2018-02-01

Wheat (Triticum aestivum L.) dough strength and extensibility are mainly determined by the polymerization of glutenin. The number of high-molecular-weight glutenin subunits (HMW-GS) differs in various wheat varieties due to the silencing of some genes. The effects of Ax1 or Dx2 subunit absence on glutenin polymerization, dough mixing properties and gluten micro structure were investigated with two groups of near-isogenic lines. The results showed that Ax1 or Dx2 absence decreased the accumulation rate of glutenin polymers and thus delayed the rapid increase period for glutenin polymerization by at least ten days, which led to lower percentage of polymeric protein in mature grain. Ax1 or Dx2 absence significantly decreased the dough development time and dough stability, but increased the uniformity of micro structure. Lacunarity, derived from quantitative analysis of gluten network, is suggested as a new indicator for wheat quality. Copyright © 2017 Elsevier Ltd. All rights reserved.

High-Throughput, Data-Rich Cellular RNA Device Engineering

PubMed Central

Townshend, Brent; Kennedy, Andrew B.; Xiang, Joy S.; Smolke, Christina D.

2015-01-01

Methods for rapidly assessing sequence-structure-function landscapes and developing conditional gene-regulatory devices are critical to our ability to manipulate and interface with biology. We describe a framework for engineering RNA devices from preexisting aptamers that exhibit ligand-responsive ribozyme tertiary interactions. Our methodology utilizes cell sorting, high-throughput sequencing, and statistical data analyses to enable parallel measurements of the activities of hundreds of thousands of sequences from RNA device libraries in the absence and presence of ligands. Our tertiary interaction RNA devices exhibit improved performance in terms of gene silencing, activation ratio, and ligand sensitivity as compared to optimized RNA devices that rely on secondary structure changes. We apply our method to building biosensors for diverse ligands and determine consensus sequences that enable ligand-responsive tertiary interactions. These methods advance our ability to develop broadly applicable genetic tools and to elucidate understanding of the underlying sequence-structure-function relationships that empower rational design of complex biomolecules. PMID:26258292

Single-Molecule Tracking Photoactivated Localization Microscopy to Map Nano-Scale Structure and Dynamics in Living Spines

PubMed Central

MacGillavry, Harold D.; Blanpied, Thomas A.

2013-01-01

Super-resolution microscopy has rapidly become an indispensable tool in cell biology and neuroscience by enabling measurement in live cells of structures smaller than the classical limit imposed by diffraction. The most widely applied super-resolution method currently is localization microscopy, which takes advantage of the ability to determine the position of individual fluorescent molecules with nanometer accuracy even in cells. By iteratively measuring sparse subsets of photoactivatable fluorescent proteins, protein distribution in macromolecular structures can be accurately reconstructed. Moreover, the motion trajectories of individual molecules within cells can be measured, providing unique ability to measure transport kinetics, exchange rates, and binding affinities of even small subsets of molecules with high temporal resolution and great spatial specificity. This unit describes protocols to measure and quantify the distribution of scaffold proteins within single synapses of cultured hippocampal neurons, and to track and measure the diffusion of intracellular constituents of the neuronal plasma membrane. PMID:25429311

Microscopic origin of entropy-driven polymorphism in hybrid organic-inorganic perovskite materials

NASA Astrophysics Data System (ADS)

Butler, Keith T.; Svane, Katrine; Kieslich, Gregor; Cheetham, Anthony K.; Walsh, Aron

2016-11-01

Entropy is a critical, but often overlooked, factor in determining the relative stabilities of crystal phases. The importance of entropy is most pronounced in softer materials, where small changes in free energy can drive phase transitions, which has recently been demonstrated in the case of organic-inorganic hybrid-formate perovskites. In this Rapid Communication we demonstrate the interplay between composition and crystal structure that is responsible for the particularly pronounced role of entropy in determining polymorphism in hybrid organic-inorganic materials. Using ab initio based lattice dynamics, we probe the origins and effects of vibrational entropy of four archetype perovskite (A B X3 ) structures. We consider an inorganic material (SrTiO3), an A -site hybrid-halide material (CH3NH3) PbI3 , a X -site hybrid material KSr (BH4)3 , and a mixed A - and X -site hybrid-formate material (N2H5) Zn (HCO2)3 , comparing the differences in entropy between two common polymorphs. The results demonstrate the importance of low-frequency intermolecular modes in determining the phase stability in these materials. The understanding gained allows us to propose a general principle for the relative stability of different polymorphs of hybrid materials as temperature is increased.

[Experimental rationale for the parameters of a rapid method for oxidase activity determination].

PubMed

Butorina, N N

2010-01-01

Experimental rationale is provided for the parameters of a rapid (1-2-min) test to concurrently determine the oxidase activity of all bacteria grown on the membrane filter after water filtration. Oxidase reagents that are the aqueous solutions of tetramethyl-p-phenylenediamine dihydrochloride and demethyl-p-phenylenediamine dihydrochloride have been first ascertained to exert no effect on the viability and enzymatic activity of bacteria after one-hour contact. An algorithm has been improved for the rapid oxidase activity test: the allowable time for bacteria to contact oxidase reagents and procedures for minimizing the effect on bacterial biochemical activity following the contact. An accelerated method based on lactose medium with tergitol 7 and Endo agar has been devised to determine coliform bacteria, by applying the rapid oxidase test: the time of a final response is 18-24 hours. The method has been included into GOST 52426-2005.

Bacterial structures and ecosystem functions in glaciated floodplains: contemporary states and potential future shifts

PubMed Central

Freimann, Remo; Bürgmann, Helmut; Findlay, Stuart EG; Robinson, Christopher T

2013-01-01

Glaciated alpine floodplains are responding quickly to climate change through shrinking ice masses. Given the expected future changes in their physicochemical environment, we anticipated variable shifts in structure and ecosystem functioning of hyporheic microbial communities in proglacial alpine streams, depending on present community characteristics and landscape structures. We examined microbial structure and functioning during different hydrologic periods in glacial (kryal) streams and, as contrasting systems, groundwater-fed (krenal) streams. Three catchments were chosen to cover an array of landscape features, including interconnected lakes, differences in local geology and degree of deglaciation. Community structure was assessed by automated ribosomal intergenic spacer analysis and microbial function by potential enzyme activities. We found each catchment to contain a distinct bacterial community structure and different degrees of separation in structure and functioning that were linked to the physicochemical properties of the waters within each catchment. Bacterial communities showed high functional plasticity, although achieved by different strategies in each system. Typical kryal communities showed a strong linkage of structure and function that indicated a major prevalence of specialists, whereas krenal sediments were dominated by generalists. With the rapid retreat of glaciers and therefore altered ecohydrological characteristics, lotic microbial structure and functioning are likely to change substantially in proglacial floodplains in the future. The trajectory of these changes will vary depending on contemporary bacterial community characteristics and landscape structures that ultimately determine the sustainability of ecosystem functioning. PMID:23842653

Bacterial structures and ecosystem functions in glaciated floodplains: contemporary states and potential future shifts.

PubMed

Freimann, Remo; Bürgmann, Helmut; Findlay, Stuart E G; Robinson, Christopher T

2013-12-01

Glaciated alpine floodplains are responding quickly to climate change through shrinking ice masses. Given the expected future changes in their physicochemical environment, we anticipated variable shifts in structure and ecosystem functioning of hyporheic microbial communities in proglacial alpine streams, depending on present community characteristics and landscape structures. We examined microbial structure and functioning during different hydrologic periods in glacial (kryal) streams and, as contrasting systems, groundwater-fed (krenal) streams. Three catchments were chosen to cover an array of landscape features, including interconnected lakes, differences in local geology and degree of deglaciation. Community structure was assessed by automated ribosomal intergenic spacer analysis and microbial function by potential enzyme activities. We found each catchment to contain a distinct bacterial community structure and different degrees of separation in structure and functioning that were linked to the physicochemical properties of the waters within each catchment. Bacterial communities showed high functional plasticity, although achieved by different strategies in each system. Typical kryal communities showed a strong linkage of structure and function that indicated a major prevalence of specialists, whereas krenal sediments were dominated by generalists. With the rapid retreat of glaciers and therefore altered ecohydrological characteristics, lotic microbial structure and functioning are likely to change substantially in proglacial floodplains in the future. The trajectory of these changes will vary depending on contemporary bacterial community characteristics and landscape structures that ultimately determine the sustainability of ecosystem functioning.

Preparation of core-shell structured CaCO3 microspheres as rapid and recyclable adsorbent for anionic dyes

NASA Astrophysics Data System (ADS)

Zhao, Mengen; Chen, Zhenhua; Lv, Xinyan; Zhou, Kang; Zhang, Jie; Tian, Xiaohan; Ren, Xiuli; Mei, Xifan

2017-09-01

Core-shell structured CaCO3 microspheres (MSs) were prepared by a facile, one-pot method at room temperature. The adsorbent dosage and adsorption time of the obtained CaCO3 MSs were investigated. The results suggest that these CaCO3 MSs can rapidly and efficiently remove 99-100% of anionic dyes within the first 2 min. The obtained CaCO3 MSs have a high Brunauer-Emmett-Teller surface area (211.77 m2 g-1). In addition, the maximum adsorption capacity of the obtained CaCO3 MSs towards Congo red was 99.6 mg g-1. We also found that the core-shell structured CaCO3 MSs have a high recycling capability for removing dyes from water. Our results demonstrate that the prepared core-shell structured CaCO3 MSs can be used as an ideal, rapid, efficient and recyclable adsorbent to remove dyes from aqueous solution.

Stimulation Induced Changes in Frog Neuromuscular Junctions: A Quantitative Ultrastructural Comparison of Rapid-Frozen and Chemically Fixed Nerve Terminals

DTIC Science & Technology

1984-03-06

study was conducted to determine the presynaptic morphological changes due to neural activity in rapidly stimulated neuromuscular junctions...Control preparations were unstimulated and preserved either by chemical fixation or rapid-freezing. This study provides evidence that most of the...tissue. The rapid-frozen preparations in the present study showed, in addition, that rapid stimulation produces an increase in synaptic vesicle

Landscape approaches for determining the ensemble of folding transition states: Success and failure hinge on the degree of frustration

NASA Astrophysics Data System (ADS)

Nymeyer, Hugh; Socci, Nicholas D.; Onuchic, José Nelson

2000-01-01

* Department of Physics, University of California at San Diego, La Jolla, CA 92093-0319; and § Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10021 Edited by R. Stephen Berry, University of Chicago, Chicago, IL, and approved November 5, 1999 (received for review July 2, 1999) We present a method for determining structural properties of the ensemble of folding transition states from protein simulations. This method relies on thermodynamic quantities (free energies as a function of global reaction coordinates, such as the percentage of native contacts) and not on "kinetic" measurements (rates, transmission coefficients, complete trajectories); consequently, it requires fewer computational resources compared with otherapproaches, making it more suited to large and complex models. We explain the theoretical framework that underlies this method and use it to clarify the connection between the experimentally determined value, a quantity determined by the ratio of rate and stability changes due to point mutations, and the average structure of the transition state ensemble. To determine the accuracy of this thermodynamic approach, we apply it to minimalist protein models and compare these results with the ones obtained by using the standard experimental procedure for determining values. We show that the accuracy of both methods depends sensitively on the amount of frustration. In particular, the results are similar when applied to models with minimal amounts of frustration, characteristic of rapid-folding, single-domain globular proteins.

Peculiar features of boron distribution in high temperature fracture area of rapidly quenched heat-resistant nickel alloy

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

Shulga, A. V., E-mail: avshulga@mephi.ru

This article comprises the results of comprehensive study of the structure and distribution in the high temperature fracture area of rapidly quenched heat-resistant superalloy of grade EP741NP after tensile tests. The structure and boron distribution in the fracture area are studied in detail by means of direct track autoradiography in combination with metallography of macro- and microstructure. A rather extensive region of microcracks generation and intensive boron redistribution is detected in the high temperature fracture area of rapidly quenched nickel superalloy of grade EP741NP. A significant decrease in boron content in the fracture area and formation of elliptically arranged boridemore » precipitates are revealed. The mechanism of intense boron migration and stability violation of the structural and phase state in the fracture area of rapidly quenched heat-resistant nickel superalloy of grade EP741NP is proposed on the basis of accounting for deformation occurring in the fracture area and analysis of the stressed state near a crack.« less

Western North Pacific Tropical Cyclone Formation and Structure Change in TCS08

DTIC Science & Technology

2013-09-30

transition to a fast-moving and rapidly- developing extratropical cyclone that may contain gale-, storm -, or hurricane-force winds, there is a need to...improve understanding and prediction of the extratropical transition phase of a decaying tropical cyclone. The structural evolution of the transition from...a tropical to an extratropical circulation involves rapid changes to the wind, cloud, and precipitation patterns that potentially impact maritime

Western North Pacific Tropical Cyclone Formation and Structure Change in TCS-08

DTIC Science & Technology

2012-09-30

cyclones often transition to a fast-moving and rapidly- developing extratropical cyclone that may contain gale-, storm -, or hurricane-force winds...there is a need to improve understanding and prediction of the extratropical transition phase of a decaying tropical cyclone. The structural evolution...of the transition from a tropical to an extratropical circulation involves rapid changes to the wind, cloud, and precipitation patterns that

Plant Growth and Development: An Outline for a Unit Structured Around the Life Cycle of Rapid-Cycling Brassica Rapa.

ERIC Educational Resources Information Center

Becker, Wayne M.

This outline is intended for use in a unit of 10-12 lectures on plant growth and development at the introductory undergraduate level as part of a course on organismal biology. The series of lecture outlines is structured around the life cycle of rapid-cycling Brassica rapa (RCBr). The unit begins with three introductory lectures on general plant…

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.

Luria in Uzbekistan: the vicissitudes of cross-cultural neuropsychology.

PubMed

Nell, V

1999-03-01

If the material conditions of culture shape cognitive structures, as Luria and Vygotsky argued, the "extraordinarily deep and rapid restructuring of historical forms" (Luria, 1971, 265) in the Soviet Republics that followed the Bolshevik revolution of 1917 provided a natural laboratory to determine whether processes of modernization changed traditional ways of thinking. This was the purpose of Luria's 1931 expedition to the Soviet Republic of Uzbekistan in central Asia. Luria's initial reports attracted vitriolic criticism because he had allegedly belittled "primitive" Uzbeki culture. The lasting importance of the Uzbek expedition is its emphasis on culture as a determinant of cognitive processes that remains valid to the present: in 1984, Gilbert replicated Luria's field studies in South Africa with near-identical results. Yet current neuropsychology has been slow to recognize the need for culturally sensitive assessment.

Determination of total monomeric anthocyanin pigment content of fruit juices, beverages, natural colorants, and wines by the pH differential method: collaborative study.

PubMed

Lee, Jungmin; Durst, Robert W; Wrolstad, Ronald E

2005-01-01

This collaborative study was conducted to determine the total monomeric anthocyanin concentration by the pH differential method, which is a rapid and simple spectrophotometric method based on the anthocyanin structural transformation that occurs with a change in pH (colored at pH 1.0 and colorless at pH 4.5). Eleven collaborators representing commercial laboratories, academic institutions, and government laboratories participated. Seven Youden pair materials representing fruit juices, beverages, natural colorants, and wines were tested. The repeatability relative standard deviation (RSDr) varied from 1.06 to 4.16%. The reproducibility relative standard deviation (RSDR) ranged from 2.69 to 10.12%. The HorRat values were < or = 1.33 for all materials. The Study Director recommends that the method be adopted Official First Action.

Rapid Analysis of Mass Distribution of Radiation Shielding

NASA Technical Reports Server (NTRS)

Zapp, Edward

2007-01-01

Radiation Shielding Evaluation Toolset (RADSET) is a computer program that rapidly calculates the spatial distribution of mass of an arbitrary structure for use in ray-tracing analysis of the radiation-shielding properties of the structure. RADSET was written to be used in conjunction with unmodified commercial computer-aided design (CAD) software that provides access to data on the structure and generates selected three-dimensional-appearing views of the structure. RADSET obtains raw geometric, material, and mass data on the structure from the CAD software. From these data, RADSET calculates the distribution(s) of the masses of specific materials about any user-specified point(s). The results of these mass-distribution calculations are imported back into the CAD computing environment, wherein the radiation-shielding calculations are performed.

CD4+ T-cell recovery with suppressive ART-induced rapid sequence evolution in hepatitis C virus envelope but not NS3.

PubMed

Liu, Lin; Nardo, David; Li, Eric; Wang, Gary P

2016-03-13

CD4 T-cell depletion from HIV infection leads to a global decline in anti-hepatitis C virus (HCV) envelope neutralizing antibody (nAb) response, which may play a role in accelerating liver fibrosis. An increase in anti-HCV nAb titers has been reported during antiretroviral therapy (ART) but its impact on HCV remains poorly understood. The objective of this study is to determine the effects of ART on long-term HCV evolution. We examined HCV quasispecies structure and long-term evolution in HIV/HCV coinfected patients with ART-induced CD4 T-cell recovery, and compared with patients with CD4 T-cell depletion from delayed ART. We applied a single-variant sequencing (SVS) method to construct authentic viral quasispecies and compared sequence evolution in HCV envelope, the primary target for humoral immune responses, and NS3, a target for cellular immunity, between the two cohorts. The SVS method corrected biases known to skew the proportions of viral variants, revealing authentic HCV quasispeices structures. We observed higher rates of HCV envelope sequence evolution in patients with ART-induced CD4 T-cell recovery, compared with patients with CD4 T-cell depletion from delayed ART (P = 0.03). Evolutionary rates for NS3 were considerably lower than the rates for envelope (P < 0.01), with no significant difference observed between the two groups. ART-induced CD4 T-cell recovery results in rapid sequence evolution in HCV envelope, but not in NS3. These results suggest that suppressive ART disproportionally enhances HCV-specific humoral responses more than cellular responses, resulting in rapid sequence evolution in HCV envelope but not NS3.

Optofluidic refractive-index sensors employing bent waveguide structures for low-cost, rapid chemical and biomedical sensing.

PubMed

Liu, I-Chen; Chen, Pin-Chuan; Chau, Lai-Kwan; Chang, Guo-En

2018-01-08

We propose and develop an intensity-detection-based refractive-index (RI) sensor for low-cost, rapid RI sensing. The sensor is composed of a polymer bent ridge waveguide (BRWG) structure on a low-cost glass substrate and is integrated with a microfluidic channel. Different-RI solutions flowing through the BRWG sensing region induce output optical power variations caused by optical bend losses, enabling simple and real-time RI detection. Additionally, the sensors are fabricated using rapid and cost-effective vacuum-less processes, attaining the low cost and high throughput required for mass production. A good RI solution of 5.31 10 -4 × RIU -1 is achieved from the RI experiments. This study demonstrates mass-producible and compact RI sensors for rapid and sensitive chemical analysis and biomedical sensing.

Turning limited experimental information into 3D models of RNA.

PubMed

Flores, Samuel Coulbourn; Altman, Russ B

2010-09-01

Our understanding of RNA functions in the cell is evolving rapidly. As for proteins, the detailed three-dimensional (3D) structure of RNA is often key to understanding its function. Although crystallography and nuclear magnetic resonance (NMR) can determine the atomic coordinates of some RNA structures, many 3D structures present technical challenges that make these methods difficult to apply. The great flexibility of RNA, its charged backbone, dearth of specific surface features, and propensity for kinetic traps all conspire with its long folding time, to challenge in silico methods for physics-based folding. On the other hand, base-pairing interactions (either in runs to form helices or isolated tertiary contacts) and motifs are often available from relatively low-cost experiments or informatics analyses. We present RNABuilder, a novel code that uses internal coordinate mechanics to satisfy user-specified base pairing and steric forces under chemical constraints. The code recapitulates the topology and characteristic L-shape of tRNA and obtains an accurate noncrystallographic structure of the Tetrahymena ribozyme P4/P6 domain. The algorithm scales nearly linearly with molecule size, opening the door to the modeling of significantly larger structures.

Regulation of skeletal myotube formation and alignment by nanotopographically controlled cell-secreted extracellular matrix.

PubMed

Jiao, Alex; Moerk, Charles T; Penland, Nisa; Perla, Mikael; Kim, Jinsung; Smith, Alec S T; Murry, Charles E; Kim, Deok-Ho

2018-06-01

Skeletal muscle has a well-organized tissue structure comprised of aligned myofibers and an encasing extracellular matrix (ECM) sheath or lamina, within which reside satellite cells. We hypothesize that the organization of skeletal muscle tissues in culture can affect both the structure of the deposited ECM and the differentiation potential of developing myotubes. Furthermore, we posit that cellular and ECM cues can be a strong determinant of myoblast fusion and morphology in 3D tissue culture environments. To test these, we utilized a thermoresponsive nanofabricated substratum to engineer anisotropic sheets of myoblasts which could then be transferred and stacked into multilayered tissues. Within such engineered tissues, we found that myoblasts rapidly sense topography and deposit structurally organized ECM proteins. Furthermore, the initial tissue structure was found to exert significant control over myoblast fusion and eventual myotube organization. These results highlight the importance of ECM structure on myoblast fusion and organization, and provide insights into substrate-mediated control of myotube formation in the development of novel, more effective, engineered skeletal muscle tissues. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 106A: 1543-1551, 2018. © 2018 Wiley Periodicals, Inc.

Structural and Computational Biology in the Design of Immunogenic Vaccine Antigens

PubMed Central

Liljeroos, Lassi; Malito, Enrico; Ferlenghi, Ilaria; Bottomley, Matthew James

2015-01-01

Vaccination is historically one of the most important medical interventions for the prevention of infectious disease. Previously, vaccines were typically made of rather crude mixtures of inactivated or attenuated causative agents. However, over the last 10–20 years, several important technological and computational advances have enabled major progress in the discovery and design of potently immunogenic recombinant protein vaccine antigens. Here we discuss three key breakthrough approaches that have potentiated structural and computational vaccine design. Firstly, genomic sciences gave birth to the field of reverse vaccinology, which has enabled the rapid computational identification of potential vaccine antigens. Secondly, major advances in structural biology, experimental epitope mapping, and computational epitope prediction have yielded molecular insights into the immunogenic determinants defining protective antigens, enabling their rational optimization. Thirdly, and most recently, computational approaches have been used to convert this wealth of structural and immunological information into the design of improved vaccine antigens. This review aims to illustrate the growing power of combining sequencing, structural and computational approaches, and we discuss how this may drive the design of novel immunogens suitable for future vaccines urgently needed to increase the global prevention of infectious disease. PMID:26526043

Symmetry-lowering lattice distortion at the spin reorientation in MnBi single crystals

DOE PAGES

McGuire, Michael A.; Cao, Huibo; Chakoumakos, Bryan C.; ...

2014-11-18

Here we report structural and physical properties determined by measurements on large single crystals of the anisotropic ferromagnet MnBi. The findings support the importance of magnetoelastic effects in this material. X-ray diffraction reveals a structural phase transition at the spin reorientation temperature T SR = 90 K. The distortion is driven by magneto-elastic coupling, and upon cooling transforms the structure from hexagonal to orthorhombic. Heat capacity measurements show a thermal anomaly at the crystallographic transition, which is suppressed rapidly by applied magnetic fields. Effects on the transport and anisotropic magnetic properties of the single crystals are also presented. Increasing anisotropymore » of the atomic displacement parameters for Bi with increasing temperature above T SR is revealed by neutron diffraction measurements. It is likely that this is directly related to the anisotropic thermal expansion in MnBi, which plays a key role in the spin reorientation and magnetocrystalline anisotropy. Finally, the identification of the true ground state crystal structure reported here may be important for future experimental and theoretical studies of this permanent magnet material, which have to date been performed and interpreted using only the high temperature structure.« less

Structure and organization of heteromeric AMPA-type glutamate receptors.

PubMed

Herguedas, Beatriz; García-Nafría, Javier; Cais, Ondrej; Fernández-Leiro, Rafael; Krieger, James; Ho, Hinze; Greger, Ingo H

2016-04-29

AMPA-type glutamate receptors (AMPARs), which are central mediators of rapid neurotransmission and synaptic plasticity, predominantly exist as heteromers of the subunits GluA1 to GluA4. Here we report the first AMPAR heteromer structures, which deviate substantially from existing GluA2 homomer structures. Crystal structures of the GluA2/3 and GluA2/4 N-terminal domains reveal a novel compact conformation with an alternating arrangement of the four subunits around a central axis. This organization is confirmed by cysteine cross-linking in full-length receptors, and it permitted us to determine the structure of an intact GluA2/3 receptor by cryogenic electron microscopy. Two models in the ligand-free state, at resolutions of 8.25 and 10.3 angstroms, exhibit substantial vertical compression and close associations between domain layers, reminiscent of N-methyl-D-aspartate receptors. Model 1 resembles a resting state and model 2 a desensitized state, thus providing snapshots of gating transitions in the nominal absence of ligand. Our data reveal organizational features of heteromeric AMPARs and provide a framework to decipher AMPAR architecture and signaling. Copyright © 2016, American Association for the Advancement of Science.

Structural and Computational Biology in the Design of Immunogenic Vaccine Antigens.

PubMed

Liljeroos, Lassi; Malito, Enrico; Ferlenghi, Ilaria; Bottomley, Matthew James

2015-01-01

Vaccination is historically one of the most important medical interventions for the prevention of infectious disease. Previously, vaccines were typically made of rather crude mixtures of inactivated or attenuated causative agents. However, over the last 10-20 years, several important technological and computational advances have enabled major progress in the discovery and design of potently immunogenic recombinant protein vaccine antigens. Here we discuss three key breakthrough approaches that have potentiated structural and computational vaccine design. Firstly, genomic sciences gave birth to the field of reverse vaccinology, which has enabled the rapid computational identification of potential vaccine antigens. Secondly, major advances in structural biology, experimental epitope mapping, and computational epitope prediction have yielded molecular insights into the immunogenic determinants defining protective antigens, enabling their rational optimization. Thirdly, and most recently, computational approaches have been used to convert this wealth of structural and immunological information into the design of improved vaccine antigens. This review aims to illustrate the growing power of combining sequencing, structural and computational approaches, and we discuss how this may drive the design of novel immunogens suitable for future vaccines urgently needed to increase the global prevention of infectious disease.

Chimaeric sounds reveal dichotomies in auditory perception

PubMed Central

Smith, Zachary M.; Delgutte, Bertrand; Oxenham, Andrew J.

2008-01-01

By Fourier's theorem1, signals can be decomposed into a sum of sinusoids of different frequencies. This is especially relevant for hearing, because the inner ear performs a form of mechanical Fourier transform by mapping frequencies along the length of the cochlear partition. An alternative signal decomposition, originated by Hilbert2, is to factor a signal into the product of a slowly varying envelope and a rapidly varying fine time structure. Neurons in the auditory brainstem3–6 sensitive to these features have been found in mammalian physiological studies. To investigate the relative perceptual importance of envelope and fine structure, we synthesized stimuli that we call ‘auditory chimaeras’, which have the envelope of one sound and the fine structure of another. Here we show that the envelope is most important for speech reception, and the fine structure is most important for pitch perception and sound localization. When the two features are in conflict, the sound of speech is heard at a location determined by the fine structure, but the words are identified according to the envelope. This finding reveals a possible acoustic basis for the hypothesized ‘what’ and ‘where’ pathways in the auditory cortex7–10. PMID:11882898

A rapid method for determining salinomycin and monensin sensitivity in Eimeria tenella

USDA-ARS?s Scientific Manuscript database

Standard methods of determining the ionophore sensitivity of Eimeria rely on infecting chickens with an isolate or a mixture of Eimeria spp. oocysts in the presence of different anti-coccidial drugs. The purpose of this study was to develop a rapid in vitro method for assessing salinomycin and mone...

A critical analysis of methods for rapid and nondestructive determination of wood density in standing trees

Treesearch

Shan Gao; Xiping Wang; Michael C. Wiemann; Brian K. Brashaw; Robert J. Ross; Lihai Wang

2017-01-01

Key message Field methods for rapid determination of wood density in trees have evolved from increment borer, torsiometer, Pilodyn, and nail withdrawal into sophisticated electronic tools of resistance drilling measurement. A partial resistance drilling approach coupled with knowledge of internal tree density distribution may...

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

Rapid Characterisation of Vegetation Structure to Predict Refugia and Climate Change Impacts across a Global Biodiversity Hotspot

PubMed Central

Schut, Antonius G. T.; Wardell-Johnson, Grant W.; Yates, Colin J.; Keppel, Gunnar; Baran, Ireneusz; Franklin, Steven E.; Hopper, Stephen D.; Van Niel, Kimberley P.; Mucina, Ladislav; Byrne, Margaret

2014-01-01

Identification of refugia is an increasingly important adaptation strategy in conservation planning under rapid anthropogenic climate change. Granite outcrops (GOs) provide extraordinary diversity, including a wide range of taxa, vegetation types and habitats in the Southwest Australian Floristic Region (SWAFR). However, poor characterization of GOs limits the capacity of conservation planning for refugia under climate change. A novel means for the rapid identification of potential refugia is presented, based on the assessment of local-scale environment and vegetation structure in a wider region. This approach was tested on GOs across the SWAFR. Airborne discrete return Light Detection And Ranging (LiDAR) data and Red Green and Blue (RGB) imagery were acquired. Vertical vegetation profiles were used to derive 54 structural classes. Structural vegetation types were described in three areas for supervised classification of a further 13 GOs across the region. Habitat descriptions based on 494 vegetation plots on and around these GOs were used to quantify relationships between environmental variables, ground cover and canopy height. The vegetation surrounding GOs is strongly related to structural vegetation types (Kappa = 0.8) and to its spatial context. Water gaining sites around GOs are characterized by taller and denser vegetation in all areas. The strong relationship between rainfall, soil-depth, and vegetation structure (R2 of 0.8–0.9) allowed comparisons of vegetation structure between current and future climate. Significant shifts in vegetation structural types were predicted and mapped for future climates. Water gaining areas below granite outcrops were identified as important putative refugia. A reduction in rainfall may be offset by the occurrence of deeper soil elsewhere on the outcrop. However, climate change interactions with fire and water table declines may render our conclusions conservative. The LiDAR-based mapping approach presented enables the integration of site-based biotic assessment with structural vegetation types for the rapid delineation and prioritization of key refugia. PMID:24416149

Rapid characterisation of vegetation structure to predict refugia and climate change impacts across a global biodiversity hotspot.

PubMed

Schut, Antonius G T; Wardell-Johnson, Grant W; Yates, Colin J; Keppel, Gunnar; Baran, Ireneusz; Franklin, Steven E; Hopper, Stephen D; Van Niel, Kimberley P; Mucina, Ladislav; Byrne, Margaret

2014-01-01

Identification of refugia is an increasingly important adaptation strategy in conservation planning under rapid anthropogenic climate change. Granite outcrops (GOs) provide extraordinary diversity, including a wide range of taxa, vegetation types and habitats in the Southwest Australian Floristic Region (SWAFR). However, poor characterization of GOs limits the capacity of conservation planning for refugia under climate change. A novel means for the rapid identification of potential refugia is presented, based on the assessment of local-scale environment and vegetation structure in a wider region. This approach was tested on GOs across the SWAFR. Airborne discrete return Light Detection And Ranging (LiDAR) data and Red Green and Blue (RGB) imagery were acquired. Vertical vegetation profiles were used to derive 54 structural classes. Structural vegetation types were described in three areas for supervised classification of a further 13 GOs across the region. Habitat descriptions based on 494 vegetation plots on and around these GOs were used to quantify relationships between environmental variables, ground cover and canopy height. The vegetation surrounding GOs is strongly related to structural vegetation types (Kappa = 0.8) and to its spatial context. Water gaining sites around GOs are characterized by taller and denser vegetation in all areas. The strong relationship between rainfall, soil-depth, and vegetation structure (R(2) of 0.8-0.9) allowed comparisons of vegetation structure between current and future climate. Significant shifts in vegetation structural types were predicted and mapped for future climates. Water gaining areas below granite outcrops were identified as important putative refugia. A reduction in rainfall may be offset by the occurrence of deeper soil elsewhere on the outcrop. However, climate change interactions with fire and water table declines may render our conclusions conservative. The LiDAR-based mapping approach presented enables the integration of site-based biotic assessment with structural vegetation types for the rapid delineation and prioritization of key refugia.

Fine-scale genetic structure arises during range expansion of an invasive gecko.

PubMed

Short, Kristen Harfmann; Petren, Kenneth

2011-01-01

Processes of range expansion are increasingly important in light of current concerns about invasive species and range shifts due to climate change. Theoretical studies suggest that genetic structuring may occur during range expansion. Ephemeral genetic structure can have important evolutionary implications, such as propagating genetic changes along the wave front of expansion, yet few studies have shown evidence of such structure. We tested the hypothesis that genetic structure arises during range expansion in Hemidactylus mabouia, a nocturnal African gecko recently introduced to Florida, USA. Twelve highly variable microsatellite loci were used to screen 418 individuals collected from 43 locations from four sampling sites across Florida, representing a gradient from earlier (∼1990s) to very recent colonization. We found earlier colonized locations had little detectable genetic structure and higher allelic richness than more recently colonized locations. Genetic structuring was pronounced among locations at spatial scales of tens to hundreds of meters near the leading edge of range expansion. Despite the rapid pace of range expansion in this introduced gecko, dispersal is limited among many suitable habitat patches. Fine-scale genetic structure is likely the result of founder effects during colonization of suitable habitat patches. It may be obscured over time and by scale-dependent modes of dispersal. Further studies are needed to determine if such genetic structure affects adaptation and trait evolution in range expansions and range shifts.

Rapid method to determine actinides and 89/90Sr in limestone and marble samples

DOE PAGES

Maxwell, Sherrod L.; Culligan, Brian; Hutchison, Jay B.; ...

2016-04-12

A new method for the determination of actinides and radiostrontium in limestone and marble samples has been developed that utilizes a rapid sodium hydroxide fusion to digest the sample. Following rapid pre-concentration steps to remove sample matrix interferences, the actinides and 89/90Sr are separated using extraction chromatographic resins and measured radiometrically. The advantages of sodium hydroxide fusion versus other fusion techniques will be discussed. Lastly, this approach has a sample preparation time for limestone and marble samples of <4 hours.

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.

​Plant centromeres​.

PubMed

Comai, Luca; Maheshwari, Shamoni; Marimuthu, Mohan P A

2017-04-01

Plant centromeres, which are determined epigenetically by centromeric histone 3 (CENH3) have revealed surprising structural diversity, ranging from the canonical monocentric seen in vertebrates, to polycentric, and holocentric. Normally stable, centromeres can change position over evolutionary times or upon genomic stress, such as when chromosomes are broken. At the DNA level, centromeres can be based on single copy DNA or more commonly on repeats. Rapid evolution of centromeric sequences and of CENH3 protein remains a mystery, as evidence of co-adaptation is lacking. Epigenetic differences between parents can trigger uniparental centromere failure and genome elimination, contributing to postzygotic hybridization barriers.​. Copyright © 2017 Elsevier Ltd. All rights reserved.

Suicide and the selfish gene.

PubMed

Satora, Leszek

2005-01-01

The application of an evolutionary perspective to human behaviour generates philosophical, political and scientific controversy. Modern human symbolic consciousness is not the cumulation of the long trend that natural selection would predict. The new archaeological data suggested the anatomical and behavioural innovation has been episodic and rare separated by long periods of stagnate. New behavioural mode and the new skeletal structure of modem human arose as an incidental exaptation. Additionally the genetic basis dysfunction connected with suicide behaviour and growing statistic suicide among teenager is contradictory to the theory that our behaviour are programmed in any detail by selfish genes. In this cases genetically determined suicidal behaviour should be rapidly eliminated by natural selection.

90-kilobar diamond-anvil high-pressure cell for use on an automatic diffractometer.

PubMed

Schiferl, D; Jamieson, J C; Lenko, J E

1978-03-01

A gasketed diamond-anvil high-pressure cell is described which can be used on a four-circle automatic diffractometer to collect x-ray intensity data from single-crystal samples subjected to truly hydrostatic pressures of over 90 kilobars. The force generating system exerts only forces normal to the diamond faces to obtain maximum reliability. A unique design allows exceptionally large open areas for maximum x-ray access and is particularly well suited for highly absorbing materials, as the x rays are not transmitted through the sample. Studies on ruby show that high-pressure crystal structure determinations may be done rapidly, reliably, and routinely with this system.

Magneto-optical properties of cerium substituted yttrium iron garnet films with reduced thermal budget for monolithic photonic integrated circuits.

PubMed

Goto, Taichi; Onbaşlı, Mehmet C; Ross, C A

2012-12-17

Thin films of polycrystalline cerium substituted yttrium iron garnet (CeYIG) were grown on an yttrium iron garnet (YIG) seed layer on Si and Si-on-insulator substrates by pulsed laser deposition, and their optical and magneto-optical properties in the near-IR region were measured. A YIG seed layer of ~30 nm thick processed by rapid thermal anneal at 800°C provided a virtual substrate to promote crystallization of the CeYIG. The effect of the thermal budget of the YIG/CeYIG growth process on the film structure, magnetic and magnetooptical properties was determined.

Nondestructive, real-time determination and visualization of cellulose, hemicellulose and lignin by luminescent oligothiophenes

NASA Astrophysics Data System (ADS)

Choong, Ferdinand X.; Bäck, Marcus; Steiner, Svava E.; Melican, Keira; Nilsson, K. Peter R.; Edlund, Ulrica; Richter-Dahlfors, Agneta

2016-10-01

Enabling technologies for efficient use of the bio-based feedstock are crucial to the replacement of oil-based products. We investigated the feasibility of luminescent conjugated oligothiophenes (LCOs) for non-destructive, rapid detection and quality assessment of lignocellulosic components in complex biomass matrices. A cationic pentameric oligothiophene denoted p-HTEA (pentamer hydrogen thiophene ethyl amine) showed unique binding affinities to cellulose, lignin, hemicelluloses, and cellulose nanofibrils in crystal, liquid and paper form. We exploited this finding using spectrofluorometric methods and fluorescence confocal laser scanning microscopy, for sensitive, simultaneous determination of the structural and compositional complexities of native lignocellulosic biomass. With exceptional photostability, p-HTEA is also demonstrated as a dynamic sensor for real-time monitoring of enzymatic cellulose degradation in cellulolysis. These results demonstrate the use of p-HTEA as a non-destructive tool for the determination of cellulose, hemicellulose and lignin in complex biomass matrices, thereby aiding in the optimization of biomass-converting technologies.

Nondestructive, real-time determination and visualization of cellulose, hemicellulose and lignin by luminescent oligothiophenes

PubMed Central

Choong, Ferdinand X.; Bäck, Marcus; Steiner, Svava E.; Melican, Keira; Nilsson, K. Peter R.; Edlund, Ulrica; Richter-Dahlfors, Agneta

2016-01-01

Enabling technologies for efficient use of the bio-based feedstock are crucial to the replacement of oil-based products. We investigated the feasibility of luminescent conjugated oligothiophenes (LCOs) for non-destructive, rapid detection and quality assessment of lignocellulosic components in complex biomass matrices. A cationic pentameric oligothiophene denoted p-HTEA (pentamer hydrogen thiophene ethyl amine) showed unique binding affinities to cellulose, lignin, hemicelluloses, and cellulose nanofibrils in crystal, liquid and paper form. We exploited this finding using spectrofluorometric methods and fluorescence confocal laser scanning microscopy, for sensitive, simultaneous determination of the structural and compositional complexities of native lignocellulosic biomass. With exceptional photostability, p-HTEA is also demonstrated as a dynamic sensor for real-time monitoring of enzymatic cellulose degradation in cellulolysis. These results demonstrate the use of p-HTEA as a non-destructive tool for the determination of cellulose, hemicellulose and lignin in complex biomass matrices, thereby aiding in the optimization of biomass-converting technologies. PMID:27759105

Effects of Rapid Weight Loss on Systemic and Adipose Tissue Inflammation and Metabolism in Obese Postmenopausal Women.

PubMed

Alemán, José O; Iyengar, Neil M; Walker, Jeanne M; Milne, Ginger L; Da Rosa, Joel Correa; Liang, Yupu; Giri, Dilip D; Zhou, Xi Kathy; Pollak, Michael N; Hudis, Clifford A; Breslow, Jan L; Holt, Peter R; Dannenberg, Andrew J

2017-06-01

Obesity is associated with subclinical white adipose tissue inflammation, as defined by the presence of crown-like structures (CLSs) consisting of dead or dying adipocytes encircled by macrophages. In humans, bariatric surgery-induced weight loss leads to a decrease in CLSs, but the effects of rapid diet-induced weight loss on CLSs and metabolism are unclear. To determine the effects of rapid very-low-calorie diet-induced weight loss on CLS density, systemic biomarkers of inflammation, and metabolism in obese postmenopausal women. Prospective cohort study. Rockefeller University Hospital, New York, NY. Ten obese, postmenopausal women with a mean age of 60.6 years (standard deviation, ±3.6 years). Effects on CLS density and gene expression in abdominal subcutaneous adipose tissue, cardiometabolic risk factors, white blood count, circulating metabolites, and oxidative stress (urinary isoprostane-M) were measured. Obese subjects lost approximately 10% body weight over a mean of 46 days. CLS density increased in subcutaneous adipose tissue without an associated increase in proinflammatory gene expression. Weight loss was accompanied by decreased fasting blood levels of high-sensitivity C-reactive protein, glucose, lactate, and kynurenine, and increased circulating levels of free fatty acids, glycerol, β -hydroxybutyrate, and 25 hydroxyvitamin D. Levels of urinary isoprostane-M declined. Rapid weight loss stimulated lipolysis and an increase in CLS density in subcutaneous adipose tissue in association with changes in levels of circulating metabolites, and improved systemic biomarkers of inflammation and insulin resistance. The observed change in levels of metabolites ( i.e. , lactate, β -hydroxybutyrate, 25 hydroxyvitamin D) may contribute to the anti-inflammatory effect of rapid weight loss.

Effects of Rapid Weight Loss on Systemic and Adipose Tissue Inflammation and Metabolism in Obese Postmenopausal Women

PubMed Central

Iyengar, Neil M.; Walker, Jeanne M.; Milne, Ginger L.; Da Rosa, Joel Correa; Liang, Yupu; Giri, Dilip D.; Zhou, Xi Kathy; Pollak, Michael N.; Hudis, Clifford A.; Breslow, Jan L.; Holt, Peter R.; Dannenberg, Andrew J.

2017-01-01

Context: Obesity is associated with subclinical white adipose tissue inflammation, as defined by the presence of crown-like structures (CLSs) consisting of dead or dying adipocytes encircled by macrophages. In humans, bariatric surgery-induced weight loss leads to a decrease in CLSs, but the effects of rapid diet-induced weight loss on CLSs and metabolism are unclear. Objective: To determine the effects of rapid very-low-calorie diet-induced weight loss on CLS density, systemic biomarkers of inflammation, and metabolism in obese postmenopausal women. Design: Prospective cohort study. Setting: Rockefeller University Hospital, New York, NY. Participants: Ten obese, postmenopausal women with a mean age of 60.6 years (standard deviation, ±3.6 years). Main Outcome Measures: Effects on CLS density and gene expression in abdominal subcutaneous adipose tissue, cardiometabolic risk factors, white blood count, circulating metabolites, and oxidative stress (urinary isoprostane-M) were measured. Results: Obese subjects lost approximately 10% body weight over a mean of 46 days. CLS density increased in subcutaneous adipose tissue without an associated increase in proinflammatory gene expression. Weight loss was accompanied by decreased fasting blood levels of high-sensitivity C-reactive protein, glucose, lactate, and kynurenine, and increased circulating levels of free fatty acids, glycerol, β-hydroxybutyrate, and 25 hydroxyvitamin D. Levels of urinary isoprostane-M declined. Conclusion: Rapid weight loss stimulated lipolysis and an increase in CLS density in subcutaneous adipose tissue in association with changes in levels of circulating metabolites, and improved systemic biomarkers of inflammation and insulin resistance. The observed change in levels of metabolites (i.e., lactate, β-hydroxybutyrate, 25 hydroxyvitamin D) may contribute to the anti-inflammatory effect of rapid weight loss. PMID:29264516

Human Tolerance to Rapidly Applied Accelerations: A Summary of the Literature

NASA Technical Reports Server (NTRS)

Eiband, A. Martin

1959-01-01

The literature is surveyed to determine human tolerance to rapidly applied accelerations. Pertinent human and animal experiments applicable to space flight and to crash impact forces are analyzed and discussed. These data are compared and presented on the basis of a trapezoidal pulse. The effects of body restraint and of acceleration direction, onset rate, and plateau duration on the maximum tolerable and survivable rapidly applied accelerations are shown. Results of the survey indicate that adequate torso and extremity restraint is the primary variable in tolerance to rapidly applied accelerations. The harness, or restraint system, must be arranged to transmit the major portion of the accelerating force directly to the pelvic structure and not via the vertebral column. When the conditions of adequate restraint have been met, then the other variables, direction, magnitude, and onset rate of rapidly applied accelerations, govern maximum tolerance and injury limits. The results also indicate that adequately stressed aft-faced passenger seats offer maximum complete body support with minimum objectionable harnessing. Such a seat, whether designed for 20-, 30-, or 40-G dynamic loading, would include lap strap, chest (axillary) strap, and winged-back seat to increase headward and lateral G protection, full-height integral head rest, arm rests (load-bearing) with recessed hand-holds and provisions to prevent arms from slipping either laterally or beyond the seat back, and leg support to keep the legs from being wedged under the seat. For crew members and others whose duties require forward-facing seats, maximum complete body support requires lap, shoulder, and thigh straps, lap-belt tie-down strap, and full-height seat back with integral head support.

Fabrication of scalable and structured tissue engineering scaffolds using water dissolvable sacrificial 3D printed moulds.

PubMed

Mohanty, Soumyaranjan; Larsen, Layla Bashir; Trifol, Jon; Szabo, Peter; Burri, Harsha Vardhan Reddy; Canali, Chiara; Dufva, Marin; Emnéus, Jenny; Wolff, Anders

2015-10-01

One of the major challenges in producing large scale engineered tissue is the lack of ability to create large highly perfused scaffolds in which cells can grow at a high cell density and viability. Here, we explore 3D printed polyvinyl alcohol (PVA) as a sacrificial mould in a polymer casting process. The PVA mould network defines the channels and is dissolved after curing the polymer casted around it. The printing parameters determined the PVA filament density in the sacrificial structure and this density resulted in different stiffness of the corresponding elastomer replica. It was possible to achieve 80% porosity corresponding to about 150 cm(2)/cm(3) surface to volume ratio. The process is easily scalable as demonstrated by fabricating a 75 cm(3) scaffold with about 16,000 interconnected channels (about 1m(2) surface area) and with a channel to channel distance of only 78 μm. To our knowledge this is the largest scaffold ever to be produced with such small feature sizes and with so many structured channels. The fabricated scaffolds were applied for in-vitro culturing of hepatocytes over a 12-day culture period. Smaller scaffolds (6×4 mm) were tested for cell culturing and could support homogeneous cell growth throughout the scaffold. Presumably, the diffusion of oxygen and nutrient throughout the channel network is rapid enough to support cell growth. In conclusion, the described process is scalable, compatible with cell culture, rapid, and inexpensive. Copyright © 2015. Published by Elsevier B.V.

CTER-rapid estimation of CTF parameters with error assessment.

PubMed

Penczek, Pawel A; Fang, Jia; Li, Xueming; Cheng, Yifan; Loerke, Justus; Spahn, Christian M T

2014-05-01

In structural electron microscopy, the accurate estimation of the Contrast Transfer Function (CTF) parameters, particularly defocus and astigmatism, is of utmost importance for both initial evaluation of micrograph quality and for subsequent structure determination. Due to increases in the rate of data collection on modern microscopes equipped with new generation cameras, it is also important that the CTF estimation can be done rapidly and with minimal user intervention. Finally, in order to minimize the necessity for manual screening of the micrographs by a user it is necessary to provide an assessment of the errors of fitted parameters values. In this work we introduce CTER, a CTF parameters estimation method distinguished by its computational efficiency. The efficiency of the method makes it suitable for high-throughput EM data collection, and enables the use of a statistical resampling technique, bootstrap, that yields standard deviations of estimated defocus and astigmatism amplitude and angle, thus facilitating the automation of the process of screening out inferior micrograph data. Furthermore, CTER also outputs the spatial frequency limit imposed by reciprocal space aliasing of the discrete form of the CTF and the finite window size. We demonstrate the efficiency and accuracy of CTER using a data set collected on a 300kV Tecnai Polara (FEI) using the K2 Summit DED camera in super-resolution counting mode. Using CTER we obtained a structure of the 80S ribosome whose large subunit had a resolution of 4.03Å without, and 3.85Å with, inclusion of astigmatism parameters. Copyright © 2014 Elsevier B.V. All rights reserved.

Initialization, Prediction and Diagnosis of the Rapid Intensification of Tropical Cyclones using the Australian Community Climate and Earth System Simulator, ACCESS

DTIC Science & Technology

2012-10-12

structure on the evolving storm behaviour. 13 7. Large scale influences on Rapid Intensification and Extratropical Transition: RI and ET...assimilation techniques to better initialize and validate TC structures (including the intense inner core and storm asymmetries) consistent with the large...Without vortex specification, initial conditions usually contain a weak and misplaced circulation. Based on estimates of central pressure and storm size

ROSA: Distributed Joint Routing and Dynamic Spectrum Allocation in Cognitive Radio Ad Hoc Networks

DTIC Science & Technology

2010-03-01

Aug. 1999. [20] I. N. Psaromiligkos and S. N. Batalama. Rapid Combined Synchronization/Demodulation Structures for DS - CDMA Systems - Part II: Finite...Medley. Rapid Combined Synchronization/Demodulation Structures for DS - CDMA Systems - Part I: Algorithmic developments. IEEE Transactions on...multiple access ( CDMA ) [21][20] al- low concurrent co-located communications so that a message from node i to node j can be correctly received even if

Structural damage to periodontal tissues at varying rate of anesthetic injection.

PubMed

Sarapultseva, Maria; Sarapultsev, Alexey; Medvedeva, Svetlana; Danilova, Irina

2018-04-01

Incorrect administration of an anesthetic during local anesthesia is one of the most important causes of pain symptoms in patients scheduled for dental procedures. The current study assessed the severity of damage to periodontal tissue following different rates of anesthetic administration. The research was conducted on 50 outbred male rats with a body mass of 180-240 g. The anesthetic used was 1% articaine. The results showed that administration of the anesthetic at a rapid pace caused structural damage to the periodontal tissue. Further, signs of impaired microcirculation were noted at all rates of administration. Biochemical studies demonstrated changes in the level of glucose and enzymes with the rapid introduction of the anesthetic, indicating severe systemic stress response of the body. Injection of local anesthetic at any rate of introduction induces vascular congestion in the microcirculatory bloodstream and exudative reactions. Rapid introduction of an anesthetic causes progression of structural changes in the gingival tissue.

Properties of tetrahedral clusters and medium range order in GaN during rapid solidification

NASA Astrophysics Data System (ADS)

Gao, Tinghong; Li, Yidan; Yao, Zhenzhen; Hu, Xuechen; Xie, Quan

2017-12-01

The solidification process of liquid gallium nitride has been studied by molecular dynamics simulation using the Stillinger-Weber potential at cooling rate of 10 K/ps. The structural properties of gallium nitride during the rapid cooling process were investigated in detail by the radial distribution functions, Voronoi polyhedron index and the visualization technology. The amorphous structures were formed with many medium range order structures at 200 K. The <4 0 0 0> polyhedron as the main polyhedron was more stable than other polyhedron in GaN during the quenching process. The cubic and hexahedral medium range order structures were formed by the close link between <4 0 0 0> polyhedron. The cubic crystal structures grew up through the crystalline surface by a layer-by-layer method to become more stable structures during the quenching process.

Sucrose-Metabolizing Enzymes in Transport Tissues and Adjacent Sink Structures in Developing Citrus Fruit 1

PubMed Central

Lowell, Cadance A.; Tomlinson, Patricia T.; Koch, Karen E.

1989-01-01

Juice tissues of citrus lack phloem; therefore, photosynthates enroute to juice sacs exit the vascular system on the surface of each segment. Areas of extensive phloem unloading and transport (vascular bundles + segment epidermis) can thus be separated from those of assimilate storage (juice sacs) and adjacent tissues where both processes occur (peel). Sugar composition, dry weight accumulation, and activities of four sucrose-metabolizing enzymes (soluble and cell-wall-bound acid invertase, alkaline invertase, sucrose synthase, and sucrose phosphate synthase) were measured in these transport and sink tissues of grapefruit (Citrus paradisi Macf.) to determine more clearly whether a given enzyme appeared to be more directly associated with assimilate transport versus deposition or utilization. Results were compared at three developmental stages. Activity of sucrose (per gram fresh weight and per milligram protein) extracted from zones of extensive phloem unloading and transport was significantly greater than from adjacent sink tissues during the stages (II and III) when juice sacs grow most rapidly. In stage II fruit, activity of sucrose synthase also significantly surpassed that of all other sucrose-metabolizing enzymes in extracts from the transport tissues (vascular bundles + segment epidermis). In contrast, sucrose phosphate synthase and alkaline invertase at this stage of growth were the most active enzymes from adjacent, rapidly growing, phloem-free sink tissues (juice sacs). Activity of these two enzymes in extracts from juice sacs was significantly greater than that form the transport tissues (vascular bundles + segment epidermis). Soluble acid invertase was the most active enzyme in extracts from all tissues of very young fruit (stage I), including nonvascular regions, but nearly disappeared prior to the onset of juice sac sugar accumulation. The physiological function of high sucrose synthase activity in the transport tissues during rapid sucrose import remains to be determined. PMID:16666942

Volcanic glasses, their origins and alteration processes

USGS Publications Warehouse

Friedman, I.; Long, W.

1984-01-01

Natural glass can be formed by volcanic processes, lightning (fulgarites) burning coal, and by meteorite impact. By far the most common process is volcanic - basically the glass is rapidly chilled molten rock. All natural glasses are thermodynamically unstable and tend to alter chemically or to crystallize. The rate of these processes is determined by the chemical composition of the magma. The hot and fluid basaltic melts have a structure that allows for rapid crystal growth, and seldom forms glass selvages greater than a few centimeters thick, even when the melt is rapidly cooled by extrusion in the deep sea. In contrast the cooler and very viscous rhyolitic magmas can yield bodies of glass that are tens of meters thick. These highly polymerized magmas have a high silica content - often 71-77% SiO2. Their high viscosity inhibits diffusive crystal growth. Basalt glass in sea water forms an alteration zone called palagonite whose thickness increases linearly with time. The rate of diffusion of water into rhyolitic glass, which follows the relationship - thickness = k (time) 1 2, has been determined as a function of the glass composition and temperature. Increased SiO2 increases the rate, whereas increased CaO, MgO and H2O decrease the rate. The activation energy of water diffusion varies from about 19 to 22 kcal/mol. for the glasses studied. The diffusion of alkali out of rhyolite glass occurs simultaneously with water diffusion into the glass. The rate of devitrification of rhyolitic glass is a function of the glass viscosity, which in turn is a function of water content and temperature. Although all of the aforementioned processes tend to destroy natural glasses, the slow rates of these processes, particularly for rhyolitic glass, has allowed samples of glass to persist for 60 million years. ?? 1984.

Structural Changes in Isometrically Contracting Insect Flight Muscle Trapped following a Mechanical Perturbation

PubMed Central

Wu, Shenping; Liu, Jun; Perz-Edwards, Robert J.; Tregear, Richard T.; Winkler, Hanspeter; Franzini-Armstrong, Clara; Sasaki, Hiroyuki; Goldman, Yale E.; Reedy, Michael K.; Taylor, Kenneth A.

2012-01-01

The application of rapidly applied length steps to actively contracting muscle is a classic method for synchronizing the response of myosin cross-bridges so that the average response of the ensemble can be measured. Alternatively, electron tomography (ET) is a technique that can report the structure of the individual members of the ensemble. We probed the structure of active myosin motors (cross-bridges) by applying 0.5% changes in length (either a stretch or a release) within 2 ms to isometrically contracting insect flight muscle (IFM) fibers followed after 5–6 ms by rapid freezing against a liquid helium cooled copper mirror. ET of freeze-substituted fibers, embedded and thin-sectioned, provides 3-D cross-bridge images, sorted by multivariate data analysis into ∼40 classes, distinct in average structure, population size and lattice distribution. Individual actin subunits are resolved facilitating quasi-atomic modeling of each class average to determine its binding strength (weak or strong) to actin. ∼98% of strong-binding acto-myosin attachments present after a length perturbation are confined to “target zones” of only two actin subunits located exactly midway between successive troponin complexes along each long-pitch helical repeat of actin. Significant changes in the types, distribution and structure of actin-myosin attachments occurred in a manner consistent with the mechanical transients. Most dramatic is near disappearance, after either length perturbation, of a class of weak-binding cross-bridges, attached within the target zone, that are highly likely to be precursors of strong-binding cross-bridges. These weak-binding cross-bridges were originally observed in isometrically contracting IFM. Their disappearance following a quick stretch or release can be explained by a recent kinetic model for muscle contraction, as behaviour consistent with their identification as precursors of strong-binding cross-bridges. The results provide a detailed model for contraction in IFM that may be applicable to contraction in other types of muscle. PMID:22761792

The Molecular Volcano Revisited: Determination of Crack Propagation and Distribution During the Crystallization of Nanoscale Amorphous Solid Water Films.

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

May, Robert A.; Smith, R. Scott; Kay, Bruce D.

2012-02-02

Temperature programmed desorption (TPD) is utilized to determine the length distribution of cracks formed through amorphous solid water (ASW) during crystallization. This distribution is determined by monitoring how the thickness of an ASW overlayer alters desorption of an underlayer of O2. As deposited the ASW overlayer prevents desorption of O2. During crystallization, cracks form through the ASW overlayer and open a path to vacuum which allows O2 to escape in a rapid episodic release known as the 'molecular volcano'. Sufficiently thick ASW overlayers further trap O2 resulting in a second O2 desorption peak commensurate with desorption of the last ofmore » the ASW overlayer. The evolution of this trapping peak with overlayer thickness is the basis for determining the distribution of crystallization induced cracks through the ASW. Reflection adsorption infrared spectroscopy (RAIRS) and TPD of multicomponent parfait structures of ASW, O2 and Kr indicate that a preponderance of these cracks propagate down from the outer surface of the ASW.« less

Cumulates, Dykes and Pressure Solution in the Ice-Salt Mantle of Europa: Geological Consequences of Pressure Dependent Liquid Compositions and Volume Changes During Ice-Salt Melting Reactions.

NASA Astrophysics Data System (ADS)

Day, S.; Asphaug, E.; Bruesch, L.

2002-12-01

Water-salt analogue experiments used to investigate cumulate processes in silicate magmas, along with observations of sea ice and ice shelf behaviour, indicate that crystal-melt separation in water-salt systems is a rapid and efficient process even on scales of millimetres and minutes. Squeezing-out of residual melts by matrix compaction is also predicted to be rapid on geological timescales. We predict that the ice-salt mantle of Europa is likely to be strongly stratified, with a layered structure predictable from density and phase relationships between ice polymorphs, aqueous saline solutions and crystalline salts such as hydrated magnesium sulphates (determined experimentally by, inter alia, Hogenboom et al). A surface layer of water ice flotation cumulate will be separated from denser salt cumulates by a cotectic horizon. This cotectic horizon will be both the site of subsequent lowest-temperature melting and a level of neutral buoyancy for the saline melts produced. Initial melting will be in a narrow depth range owing to increasing melting temperature with decreasing pressure: the phase relations argue against direct melt-though to the surface unless vesiculation occurs. Overpressuring of dense melts due to volume expansion on cotectic melting is predicted to lead to lateral dyke emplacement and extension above the dyke tips. Once the liquid leaves the cotectic, melting of water ice will involve negative volume change. Impact-generated melts will drain downwards through the fractured zones beneath crater floors. A feature in the complex crater Mannan'an, with elliptical ring fractures around a conical depression with a central pit, bears a close resemblance to Icelandic glacier collapse cauldrons produced by subglacial eruptions. Other structures resembling Icelandic cauldrons occur along Europan banded structures, while resurgence of ice rubble within collapse structures may produce certain types of chaos region. More general contraction of the ice mantle due to melting may be accommodated across banded structures by deformation and pressure solution. Expansion and contraction during different parts of a melting (and freezing) episode may account for the complexity of banded structures on Europa and inconsistent offsets of older structures across them.

An Examination of Four Successes in the Coast Guard’s Innovation Program and Implications for Innovation within Homeland Security

DTIC Science & Technology

2008-03-01

patterns, determine positive directions, and rapidly drive process improvements. This thesis examines literature related to leadership, strategic...an effective mechanism to sense emerging patterns, determine positive directions, and rapidly drive process improvements. This thesis examines...VESSEL SIGHTING APPLICATION - MISLE LITE .............................42 B. RUGGEDIZED TABLET COMPUTER

Controlled Synthesis and Fluorescence Tracking of Highly Uniform Poly(N-isopropylacrylamide) Microgels.

PubMed

Virtanen, Otto L J; Purohit, Ashvini; Brugnoni, Monia; Wöll, Dominik; Richtering, Walter

2016-09-08

Stimuli-sensitive poly(N-isopropylacrylamide) (PNIPAM) microgels have various prospective practical applications and uses in fundamental research. In this work, we use single particle tracking of fluorescently labeled PNIPAM microgels as a showcase for tuning microgel size by a rapid non-stirred precipitation polymerization procedure. This approach is well suited for prototyping new reaction compositions and conditions or for applications that do not require large amounts of product. Microgel synthesis, particle size and structure determination by dynamic and static light scattering are detailed in the protocol. It is shown that the addition of functional comonomers can have a large influence on the particle nucleation and structure. Single particle tracking by wide-field fluorescence microscopy allows for an investigation of the diffusion of labeled tracer microgels in a concentrated matrix of non-labeled microgels, a system not easily investigated by other methods such as dynamic light scattering.

Supramolecular structure of 5-aminosalycilic acid/halloysite composites.

PubMed

Viseras, Maria-Teresa; Aguzzi, Carola; Cerezo, Pilar; Cultrone, Giuseppe; Viseras, Cesar

2009-05-01

This paper assesses the supramolecular structure of nanocomposites prepared by including the anti-inflammatory drug 5-aminosalycilic acid in halloysite nanotubes. Halloysite tubes have sub-micron individual lengths with outer diameters ∼0.1 µm, as observed by FESEM. The mercury intrusion plots showed bimodal profiles with pore dimensions ∼10 and 0.06 µm. X-ray diffraction and thermogravimetric results revealed changes in the hydration form of the clay after the interaction. The groups associated to the interaction were studied by FTIR. The location of the drug in the composites was determined after uranium staining of its amino groups by X-EDS microanalysis coupled with HREM. The drug was located both inside and on the surface of the halloysite nanotubes. These results confirm the occurrence of two concomitant interaction mechanisms: rapid adsorption of 5-ASA at the external halloysite surface followed by slow adsorption of the drug inside the tubes.

Study of Different Sol-Gel Coatings to Enhance the Lifetime of PDMS Devices: Evaluation of Their Biocompatibility.

PubMed

Aymerich, María; Gómez-Varela, Ana I; Álvarez, Ezequiel; Flores-Arias, María T

2016-08-25

A study of PDMS (polydimethylsiloxane) sol-gel-coated channels fabricated using soft lithography and a laser direct writing technique is presented. PDMS is a biocompatible material that presents a high versatility to reproduce several structures. It is widely employed in the fabrication of preclinical devices due to its advantages but it presents a rapid chemical deterioration to organic solvents. The use of sol-gel layers to cover the PDMS overcomes this problem since it provides the robustness of glass for the structures made with PDMS, decreasing its deterioration and changing the biocompatibility of the surface. In this work, PDMS channels are coated with three different kinds of sol-gel compositions (60MTES/40TEOS, 70MTES/30TISP and 80MTES/20TISP). The endothelial cell adhesion to the different coated devices is evaluated in order to determine the most suitable sol-gel preparation conditions to enhance cellular adhesion.

Design and Evaluation of a Boron Dipyrrin Electrophore for Redox Flow Batteries.

PubMed

Heiland, Niklas; Cidarér, Clemens; Rohr, Camilla; Piescheck, Mathias; Ahrens, Johannes; Bröring, Martin; Schröder, Uwe

2017-08-29

A boron dipyrrin (BODIPY) dye was designed as a molecular single-component electrophore for redox flow batteries. All positions of the BODIPY core were assessed on the basis of literature data, in particular cyclic voltammetry and density functional calculations, and a minimum required substitution pattern was designed to provide solubility, aggregation, radical cation and anion stabilities, a large potential window, and synthetic accessibility. In-depth electrochemical and physical studies of this electrophore revealed suitable cathodic behavior and stability of the radical anion but rapid anodic decomposition of the radical cation. The three products that formed under the conditions of controlled oxidative electrolysis were isolated, and their structures were determined by spectroscopy and comparison with a synthetic model compound. From these structures, a benzylic radical reactivity, initiated by one-electron oxidation, was concluded to play the major role in this unexpected decomposition. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Plasmon-exciton polaritons in two-dimensional semiconductor/metal interfaces

NASA Astrophysics Data System (ADS)

Gonçalves, P. A. D.; Bertelsen, L. P.; Xiao, Sanshui; Mortensen, N. Asger

2018-01-01

The realization and control of polaritons is of paramount importance in the prospect of novel photonic devices. Here, we investigate the emergence of plasmon-exciton polaritons in hybrid structures consisting of a two-dimensional transition-metal dichalcogenide (TMDC) deposited onto a metal substrate or coating a metallic thin film. We determine the polaritonic spectrum and show that, in the former case, the addition of a top dielectric layer and, in the latter case, the thickness of the metal film can be used to tune and promote plasmon-exciton interactions well within the strong-coupling regime. Our results demonstrate that Rabi splittings exceeding 100 meV can readily be achieved in planar dielectric/TMDC/metal structures under ambient conditions. We thus believe that this Rapid Communication provides a simple and intuitive picture to tailor strong coupling in plexcitonics with potential applications for engineering compact photonic devices with tunable optical properties.

Shock initiation of 2,4-dinitroimidazole (2,4-DNI)

NASA Astrophysics Data System (ADS)

Urtiew, P. A.; Tarver, C. M.; Simpson, R. L.

1996-05-01

The shock sensitivity of the pressed solid explosive 2,4-dinitroimidazole (2,4-DNI) was determined using the embedded manganin pressure gauge technique. At an initial shock pressure of 2 GPa, several microseconds were required before any exothermic reaction was observed. At 4 GPa, 2,4-DNI reacted more rapidly but did not transition to detonation at the 12 mm deep gauge position. At 6 GPa, detonation occurred in less than 6 mm of shock propagation. Thus, 2,4-DNI is more shock sensitive than TATB-based explosives but is considerably less shock sensitive than HMX-based explosives. An Ignition and Growth reactive flow model for 2,4-DNI based on these gauge records showed that 2,4-DNI exhibits shock initiation characteristics similar to TATB but reacts faster. The chemical structure of 2,4-DNI suggests that it may exhibit thermal decomposition reactions similar to nitroguanine and explosives with similar ring structures, such as ANTA and NTO.

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.

A new tool for the rapid remote detection of leaks from subsea pipelines during remotely operated vehicle inspections

NASA Astrophysics Data System (ADS)

McStay, D.; McIlroy, J.; Forte, A.; Lunney, F.; Greenway, T.; Thabeth, K.; Dean, G.

2005-06-01

A new 2000 m depth rated subsea sensor that can effectively, rapidly and remotely detect leaks of fluorescein dye, leak detection chemicals and hydraulic fluids from underwater structures is reported. The system utilizes ultra-bright LED technology to project a structured beam of light, at a wavelength suitable to excite the fluorescence of the target material, into the water column. The resultant fluorescence is collected and digital signal processing used to extract the intensity. The system is capable of detecting ppm concentrations of fluorescein at a range of 2.5 m in water in real time. The ability to stand-off from subsea structures, while rapidly detecting the chemicals makes the system highly suited to subsea leak inspections with remotely operated vehicles or autonomous underwater vehicles, as it allows the vehicles to be flown quickly and safely over the structure to be inspected. This increases both the speed and effectiveness of the inspection. The remote detection capability is also highly effective for probing complex underwater structures. The system has been successfully used in real subsea survey applications and has been found to be effective, user friendly and to dramatically reduce inspection times and hence costs.

Structural studies of RNA-protein complexes: A hybrid approach involving hydrodynamics, scattering, and computational methods.

PubMed

Patel, Trushar R; Chojnowski, Grzegorz; Astha; Koul, Amit; McKenna, Sean A; Bujnicki, Janusz M

2017-04-15

The diverse functional cellular roles played by ribonucleic acids (RNA) have emphasized the need to develop rapid and accurate methodologies to elucidate the relationship between the structure and function of RNA. Structural biology tools such as X-ray crystallography and Nuclear Magnetic Resonance are highly useful methods to obtain atomic-level resolution models of macromolecules. However, both methods have sample, time, and technical limitations that prevent their application to a number of macromolecules of interest. An emerging alternative to high-resolution structural techniques is to employ a hybrid approach that combines low-resolution shape information about macromolecules and their complexes from experimental hydrodynamic (e.g. analytical ultracentrifugation) and solution scattering measurements (e.g., solution X-ray or neutron scattering), with computational modeling to obtain atomic-level models. While promising, scattering methods rely on aggregation-free, monodispersed preparations and therefore the careful development of a quality control pipeline is fundamental to an unbiased and reliable structural determination. This review article describes hydrodynamic techniques that are highly valuable for homogeneity studies, scattering techniques useful to study the low-resolution shape, and strategies for computational modeling to obtain high-resolution 3D structural models of RNAs, proteins, and RNA-protein complexes. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Structure-based Insights into the Catalytic Power and Conformational Dexterity of Peroxiredoxins

PubMed Central

Hall, Andrea; Nelson, Kimberly; Poole, Leslie B.

2011-01-01

Abstract Peroxiredoxins (Prxs), some of nature's dominant peroxidases, use a conserved Cys residue to reduce peroxides. They are highly expressed in organisms from all kingdoms, and in eukaryotes they participate in hydrogen peroxide signaling. Seventy-two Prx structures have been determined that cover much of the diversity of the family. We review here the current knowledge and show that Prxs can be effectively classified by a structural/evolutionary organization into six subfamilies followed by specification of a 1-Cys or 2-Cys mechanism, and for 2-Cys Prxs, the structural location of the resolving Cys. We visualize the varied catalytic structural transitions and highlight how they differ depending on the location of the resolving Cys. We also review new insights into the question of how Prxs are such effective catalysts: the enzyme activates not only the conserved Cys thiolate but also the peroxide substrate. Moreover, the hydrogen-bonding network created by the four residues conserved in all Prx active sites stabilizes the transition state of the peroxidatic SN2 displacement reaction. Strict conservation of the peroxidatic active site along with the variation in structural transitions provides a fascinating picture of how the diverse Prxs function to break down peroxide substrates rapidly. Antioxid. Redox Signal. 15, 795–815. PMID:20969484

Rapid water disinfection over a Ag/AgBr/covalent triazine-based framework composite under visible light.

PubMed

Li, Liuyi; Li, Xiaofen; Cheng, Zhi; Bi, Jinhong; Liang, Shijing; Zhang, Zizhong; Yu, Yan; Wu, Ling

2018-05-22

Development of visible-light-induced and rapid water disinfection is of significant importance. Covalent triazine-based frameworks (CTFs) with pre-designable structures and favorable semiconductive behaviors hold great promise for photocatalytic water disinfection. Here, we report an Ag/AgBr/CTF composite with a layered structure, which serves as an efficient photocatalyst for rapid water disinfection. Water disinfection with >99.99% inactivation of Escherichia coli within 12 min was achieved by using a small amount of Ag/AgBr/CTF under visible light irradiation. The inactivation efficiency of Ag/AgBr/CTF was ∼10 times better than that of bare Ag/AgBr. Rapid water disinfection by the Ag/AgBr/CTF composite mainly results from the greatly improved generation of reactive oxygen species through the synergistic effects among the three components and the affinity of CTF to the cell wall of bacteria.

Practical computational toolkits for dendrimers and dendrons structure design.

PubMed

Martinho, Nuno; Silva, Liana C; Florindo, Helena F; Brocchini, Steve; Barata, Teresa; Zloh, Mire

2017-09-01

Dendrimers and dendrons offer an excellent platform for developing novel drug delivery systems and medicines. The rational design and further development of these repetitively branched systems are restricted by difficulties in scalable synthesis and structural determination, which can be overcome by judicious use of molecular modelling and molecular simulations. A major difficulty to utilise in silico studies to design dendrimers lies in the laborious generation of their structures. Current modelling tools utilise automated assembly of simpler dendrimers or the inefficient manual assembly of monomer precursors to generate more complicated dendrimer structures. Herein we describe two novel graphical user interface toolkits written in Python that provide an improved degree of automation for rapid assembly of dendrimers and generation of their 2D and 3D structures. Our first toolkit uses the RDkit library, SMILES nomenclature of monomers and SMARTS reaction nomenclature to generate SMILES and mol files of dendrimers without 3D coordinates. These files are used for simple graphical representations and storing their structures in databases. The second toolkit assembles complex topology dendrimers from monomers to construct 3D dendrimer structures to be used as starting points for simulation using existing and widely available software and force fields. Both tools were validated for ease-of-use to prototype dendrimer structure and the second toolkit was especially relevant for dendrimers of high complexity and size.

Practical computational toolkits for dendrimers and dendrons structure design

NASA Astrophysics Data System (ADS)

Martinho, Nuno; Silva, Liana C.; Florindo, Helena F.; Brocchini, Steve; Barata, Teresa; Zloh, Mire

2017-09-01

Dendrimers and dendrons offer an excellent platform for developing novel drug delivery systems and medicines. The rational design and further development of these repetitively branched systems are restricted by difficulties in scalable synthesis and structural determination, which can be overcome by judicious use of molecular modelling and molecular simulations. A major difficulty to utilise in silico studies to design dendrimers lies in the laborious generation of their structures. Current modelling tools utilise automated assembly of simpler dendrimers or the inefficient manual assembly of monomer precursors to generate more complicated dendrimer structures. Herein we describe two novel graphical user interface toolkits written in Python that provide an improved degree of automation for rapid assembly of dendrimers and generation of their 2D and 3D structures. Our first toolkit uses the RDkit library, SMILES nomenclature of monomers and SMARTS reaction nomenclature to generate SMILES and mol files of dendrimers without 3D coordinates. These files are used for simple graphical representations and storing their structures in databases. The second toolkit assembles complex topology dendrimers from monomers to construct 3D dendrimer structures to be used as starting points for simulation using existing and widely available software and force fields. Both tools were validated for ease-of-use to prototype dendrimer structure and the second toolkit was especially relevant for dendrimers of high complexity and size.

Navigating 3D electron microscopy maps with EM-SURFER.

PubMed

Esquivel-Rodríguez, Juan; Xiong, Yi; Han, Xusi; Guang, Shuomeng; Christoffer, Charles; Kihara, Daisuke

2015-05-30

The Electron Microscopy DataBank (EMDB) is growing rapidly, accumulating biological structural data obtained mainly by electron microscopy and tomography, which are emerging techniques for determining large biomolecular complex and subcellular structures. Together with the Protein Data Bank (PDB), EMDB is becoming a fundamental resource of the tertiary structures of biological macromolecules. To take full advantage of this indispensable resource, the ability to search the database by structural similarity is essential. However, unlike high-resolution structures stored in PDB, methods for comparing low-resolution electron microscopy (EM) density maps in EMDB are not well established. We developed a computational method for efficiently searching low-resolution EM maps. The method uses a compact fingerprint representation of EM maps based on the 3D Zernike descriptor, which is derived from a mathematical series expansion for EM maps that are considered as 3D functions. The method is implemented in a web server named EM-SURFER, which allows users to search against the entire EMDB in real-time. EM-SURFER compares the global shapes of EM maps. Examples of search results from different types of query structures are discussed. We developed EM-SURFER, which retrieves structurally relevant matches for query EM maps from EMDB within seconds. The unique capability of EM-SURFER to detect 3D shape similarity of low-resolution EM maps should prove invaluable in structural biology.

The Beginning and End of the Universe

NASA Technical Reports Server (NTRS)

Gardner, Jonathan P.

2007-01-01

Cosmology is the scientific study of how the Universe began more than 13 billion years ago, how its properties have changed, and what its future might be. The balance of forces and energy cause the Universe to expand, first accelerating, then decelerating and then accelerating again. Within this overall structure, the interplay of atoms and light with the mysterious dark matter and dark energy causes stars and galaxies to form and evolve, leading to galaxies like our own home, the Milky Way. Observational cosmology uses telescopes on Earth and in space to reach back in time to find the faint remaining echoes of the Big Bang and to trace the formation and evolution of the galaxies and structures that fill the Universe. In this lecture, Dr. Gardner will give an overview of cosmology, outlining the 13-billion year history of the Universe, and highlighting the very rapid progress this field has made in the last decade. He will discuss the role that NASA space telescopes have played in this progress and will continue to play in the years to come. He will give a time-based history of the Universe, discussing the successive processes that formed matter, particles, atoms, stars and galaxies. In particular, he will focus on cosmological inflation, the rapid accelerated expansion that marks the beginning of the Universe, and dark energy, a tenuous substance that overcomes gravity and whose properties will determine its final fate.

The Beginning and End of the Universe

NASA Technical Reports Server (NTRS)

Gardner, Jonathan

2008-01-01

Cosmology is the scientific study of how the Universe began more than 13 billion years ago, how its properties have changed, and what its future might be. The balance of forces and energy cause the Universe to expand, first accelerating, then decelerating and then accelerating again. Within this overall structure, the interplay of atoms and light with the mysterious dark matter and dark energy causes stars and galaxies to form and evolve, leading to galaxies like our own home, the Milky Way. Observational cosmology uses telescopes on Earth and in space to reach back in time to find the faint remaining echoes of the Big Bang and to trace the formation and evolution of the galaxies and structures that fill the Universe. In this lecture, Dr. Gradner will give an overview of cosmology, outlining the 13-billion year history of the Universe, and highlighting the very rapid progress this field has made i the last decade. He will discuss the role that NASA space telescopes have played in this progress and wil continue to play in the years to come. He will give a time-based history of the Universe, discussing the successive processes that formed matter, particles, atoms, stars and galaxies. In particular, he will focus on cosmological inflation, the rapid accelerated expansion that marks the beginning of the Universe, and dark energy, a tenuous substance that overcomes gravity and whose properties will determine its final fate.

Synthesis of the 3-sulfates of S-acyl glutathione conjugated bile acids and their biotransformation by a rat liver cytosolic fraction.

PubMed

Mitamura, Kuniko; Hori, Naohiro; Mino, Shiori; Iida, Takashi; Hofmann, Alan F; Ikegawa, Shigeo

2012-04-01

The 3-sulfates of the S-acyl glutathione (GSH) conjugates of five natural bile acids (cholic, chenodeoxycholic, deoxycholic, ursodeoxycholic, and lithocholic) were synthesized as reference standards in order to investigate their possible formation by a rat liver cytosolic fraction. Their structures were confirmed by proton nuclear magnetic resonance, as well as by means of electrospray ionization-linear ion-trap mass spectrometry with negative-ion detection. Upon collision-induced dissociation, structurally informative product ions were observed. Using a triple-stage quadrupole instrument, selected reaction monitoring analyses by monitoring characteristic transition ions allowed the achievement of a highly sensitive and specific assay. This method was used to determine whether the 3-sulfates of the bile acid-GSH conjugates (BA-GSH) were formed when BA-GSH were incubated with a rat liver cytosolic fraction to which 3'-phosphoadenosine 5'-phosphosulfate had been added. The S-acyl linkage was rapidly hydrolyzed to form the unconjugated bile acid. A little sulfation of the GSH conjugates occurred, but greater sulfation at C-3 of the liberated bile acid occurred. Sulfation was proportional to the hydrophobicity of the unconjugated bile acid. Thus GSH conjugates of bile acids as well as their C-3 sulfates if formed in vivo are rapidly hydrolyzed by cytosolic enzymes. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Prenatal Alcohol Exposure Affects Progenitor Cell Numbers in Olfactory Bulbs and Dentate Gyrus of Vervet Monkeys.

PubMed

Burke, Mark W; Inyatkin, Alexey; Ptito, Maurice; Ervin, Frank R; Palmour, Roberta M

2016-10-27

Fetal alcohol exposure (FAE) alters hippocampal cell numbers in rodents and primates, and this may be due, in part, to a reduction in the number or migration of neuronal progenitor cells. The olfactory bulb exhibits substantial postnatal cellular proliferation and a rapid turnover of newly formed cells in the rostral migratory pathway, while production and migration of postnatal neurons into the dentate gyrus may be more complex. The relatively small size of the olfactory bulb, compared to the hippocampus, potentially makes this structure ideal for a rapid analysis. This study used the St. Kitts vervet monkey ( Chlorocebus sabeus ) to (1) investigate the normal developmental sequence of post-natal proliferation in the olfactory bulb and dentate gyrus and (2) determine the effects of naturalistic prenatal ethanol exposure on proliferation at three different ages (neonate, five months and two years). Using design-based stereology, we found an age-related decrease of actively proliferating cells in the olfactory bulb and dentate gyrus for both control and FAE groups. Furthermore, at the neonatal time point, the FAE group had fewer actively proliferating cells as compared to the control group. These data are unique with respect to fetal ethanol effects on progenitor proliferation in the primate brain and suggest that the olfactory bulb may be a useful structure for studies of cellular proliferation.

[On some characteristics of the population development in the Shenzhen Special Economic Region].

PubMed

Zhang, Z; Yang, Q; An, H; Fang, D

1984-03-29

Shenzhen was originally a town in Guandong Province. In 1979, it was made into a Special Economic Region in order to cope with the needs of modernization. Because of rapid economic development, the population has also been growing rapidly. Before 1979, the total population of Shenzhen was only 20,000, both industry and agriculture were backward, and the living standard was low. After it was made a Special Economic Region, its population figure reached 200,000 according to a 1982 report. The age structure of the local population is young, and there are more males than females. In the last two years, because of family planning measures, the natural population growth rate has shown an obvious downward trend. The population development of Shenzhen has several characteristics: 1) the pace of population growth is very fast; 2) the educational level for the population is high, and investment in education is emphasized; 3) population mobility is strong, and it has an extensive impact on the local market, transportation, and social order; 4) the social and economic systems of Hong Kong have a special influence on its population development. Special studies and discussions concerning how to control Shenzhen's population growth, how to determine the trends toward change in age structure, and how to promote population quality and spiritual civilization should be conducted according to characteristics of the local population development.

Fast de novo discovery of low-energy protein loop conformations.

PubMed

Wong, Samuel W K; Liu, Jun S; Kou, S C

2017-08-01

In the prediction of protein structure from amino acid sequence, loops are challenging regions for computational methods. Since loops are often located on the protein surface, they can have significant roles in determining protein functions and binding properties. Loop prediction without the aid of a structural template requires extensive conformational sampling and energy minimization, which are computationally difficult. In this article we present a new de novo loop sampling method, the Parallely filtered Energy Targeted All-atom Loop Sampler (PETALS) to rapidly locate low energy conformations. PETALS explores both backbone and side-chain positions of the loop region simultaneously according to the energy function selected by the user, and constructs a nonredundant ensemble of low energy loop conformations using filtering criteria. The method is illustrated with the DFIRE potential and DiSGro energy function for loops, and shown to be highly effective at discovering conformations with near-native (or better) energy. Using the same energy function as the DiSGro algorithm, PETALS samples conformations with both lower RMSDs and lower energies. PETALS is also useful for assessing the accuracy of different energy functions. PETALS runs rapidly, requiring an average time cost of 10 minutes for a length 12 loop on a single 3.2 GHz processor core, comparable to the fastest existing de novo methods for generating an ensemble of conformations. Proteins 2017; 85:1402-1412. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Polyethylene glycol promotes autoxidation of cytochrome c.

PubMed

Sato, Wataru; Uchida, Takeshi; Saio, Tomohide; Ishimori, Koichiro

2018-06-01

Cytochrome c (Cyt c) was rapidly oxidized by molecular oxygen in the presence, but not absence of PEG. The redox potential of heme c was determined by the potentiometric titration to be +236 ± 3 mV in the absence of PEG, which was negatively shifted to +200 ± 4 mV in the presence of PEG. The underlying the rapid oxidation was explored by examining the structural changes in Cyt c in the presence of PEG using UV-visible absorption, circular dichroism, resonance Raman, and fluorescence spectroscopies. These spectroscopic analyses suggested that heme oxidation was induced by a modest tertiary structural change accompanied by a slight shift in the heme position (<1.0 Å) rather than by partial denaturation, as is observed in the presence of cardiolipin. The near-infrared spectra showed that PEG induced dehydration from Cyt c, which triggered heme displacement. The primary dehydration site was estimated to be around surface-exposed hydrophobic residues near the heme center: Ile81 and Val83. These findings and our previous studies, which showed that hydrated water molecules around Ile81 and Val83 are expelled when Cyt c forms a complex with CcO, proposed that dehydration of these residues is functionally significant to electron transfer from Cyt c to CcO. Copyright © 2018 Elsevier B.V. All rights reserved.

Rapid method to determine 89Sr/ 90Sr in large concrete samples

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

Maxwell, Sherrod L.; Culligan, Brian; Hutchison, Jay B.

Here, a new rapid method has been developed that provides high quality low-level measurements of 89,90Sr in concrete samples with an MDA (Minimum Detectable Activity) of <1 mBq g -1. The new method is fast, meets new decommissioning regulatory limits and is robust even if refractory particles are present. The method utilizes a rapid fusion to ensure total dissolution of samples and rapid preconcentration and separation of 89,90Sr from 5-10 g concrete samples. When, the 89Sr/ 90Sr ratio is high, Sr can be isolated from up to 5g concrete samples, total 89/90Sr measured, and then 90Sr determined via 90Y separatedmore » after a period of ingrowth. Another approach allows the immediate determination of 90Sr in 10 g concrete aliquots without waiting for 90Y ingrowth, in instances where the shorter lived 89Sr is unlikely to be encountered.« less

Rapid method to determine 89Sr/ 90Sr in large concrete samples

DOE PAGES

Maxwell, Sherrod L.; Culligan, Brian; Hutchison, Jay B.; ...

2016-03-24

Here, a new rapid method has been developed that provides high quality low-level measurements of 89,90Sr in concrete samples with an MDA (Minimum Detectable Activity) of <1 mBq g -1. The new method is fast, meets new decommissioning regulatory limits and is robust even if refractory particles are present. The method utilizes a rapid fusion to ensure total dissolution of samples and rapid preconcentration and separation of 89,90Sr from 5-10 g concrete samples. When, the 89Sr/ 90Sr ratio is high, Sr can be isolated from up to 5g concrete samples, total 89/90Sr measured, and then 90Sr determined via 90Y separatedmore » after a period of ingrowth. Another approach allows the immediate determination of 90Sr in 10 g concrete aliquots without waiting for 90Y ingrowth, in instances where the shorter lived 89Sr is unlikely to be encountered.« less

Physical and Chemical Characterization of Therapeutic Iron Containing Materials: A Study of Several Superparamagnetic Drug Formulations with the β-FeOOH or Ferrihydrite Structure

NASA Astrophysics Data System (ADS)

Funk, Felix; Long, Gary J.; Hautot, Dimitri; Büchi, Ruth; Christl, Iso; Weidler, Peter G.

2001-03-01

The effectiveness of therapeutically used iron compounds is related to their physical and chemical properties. Four different iron compounds used in oral, intravenous, and intramuscular therapy have been examined by X-ray powder diffraction, iron-57 Mössbauer spectroscopy, transmission electron microscopy, BET surface area measurement, potentiometric titration and studied through dissolution kinetics determinations using acid, reducing and chelating agents. All compounds are nanosized with particle diameters, as determined by X-ray diffraction, ranging from 1 to 4.1 nm. The superparamagnetic blocking temperatures, as determined by Mössbauer spectroscopy, indicate that the relative diameters of the aggregates range from 2.5 to 4.1 nm. Three of the iron compounds have an akaganeite-like structure, whereas one has a ferrihydrite-like structure. As powders the particles form large and dense aggregates which have a very low surface area on the order of 1 m2 g-1. There is evidence, however, that in a colloidal solution the surface area is increased by two to three orders of magnitude, presumably as a result of the break up of the aggregates. Iron release kinetics by acid, chelating and reducing agents reflect the high surface area, the size and crystallinity of the particles, and the presence of the protective carbohydrate layer coating the iron compound. Within a physiologically relevant time period, the iron release produced by acid or large chelating ligands is small. In contrast, iron is rapidly mobilized by small organic chelating agents, such as oxalate, or by chelate-forming reductants, such as thioglycolate.

Effects of rapid temperature fluctuations prior to breeding on reproductive efficiency in replacement gilts

USDA-ARS?s Scientific Manuscript database

Recently, we determined that rapidly cooling pigs after acute heat stress (HS) resulted in a pathological condition, and because rapid temperature fluctuations are often associated with reduced reproductive success in sows it lends itself to the hypothesis that these conditions may be linked. Study ...

Magnetron magnetic priming for rapid startup and noise reduction

NASA Astrophysics Data System (ADS)

Neculaes, Vasile Bogdan

The magnetron is a vacuum electronics crossed-field device: perpendicular electric and magnetic fields determine the electron dynamics. Compactness, efficiency and reliability make magnetrons suitable for a wide range of military and civilian applications: radar, industrial heating, plasma sources, and medical accelerators. The most ubiquitous use of magnetrons is as the microwave power source in microwave ovens, operating at 2.45 GHz and delivering about 800--1000 W. University of Michigan and several other research programs are actively pursuing the development of GW range relativistic magnetrons. This dissertation presents experimental and computational results concerning innovative techniques to improve magnetron noise, startup and mode stability. The DC-operated oven magnetron studies performed at University of Michigan opened new directions by utilizing azimuthally varying magnetic fields (magnetic priming). Magnetic priming for rapid startup in an N-cavity magnetron operating in the pi-mode is based on implementation of an axial magnetic field with N/2 azimuthal periods, to prebunch the electrons in the desired number of spokes (N/2). Experiments with magnetic priming on DC oven magnetrons using perturbing magnets added on the upper existing magnet of the magnetron showed rapid startup (pi-mode oscillation observed at low currents) and up to 35 dB noise reduction (close to the carrier and in sidebands). A complex 3-dimensional (3D) ICEPIC computational model recovered the oven magnetron magnetic priming experimental results: rapid electron prebunching due to presence of perturbing magnets, fast startup and tendency towards a lower noise state. Simulations in 6-cavity relativistic magnetrons show that ideal magnetic priming causes fast startup, rapid mode growth (with radial electron diffusion) and suppression of mode competition. A highly idealized model (planar, crossed-field, non-resonant, non-relativistic structure) using single particle dynamics showed that magnetic priming causes rapid electron prebunching, specific symmetries in the electron cloud and an orbital parametric instability (radial exponential growth).