Cell biochemistry studied by single-molecule imaging.

PubMed

Mashanov, G I; Nenasheva, T A; Peckham, M; Molloy, J E

2006-11-01

Over the last decade, there have been remarkable developments in live-cell imaging. We can now readily observe individual protein molecules within living cells and this should contribute to a systems level understanding of biological pathways. Direct observation of single fluorophores enables several types of molecular information to be gathered. Temporal and spatial trajectories enable diffusion constants and binding kinetics to be deduced, while analyses of fluorescence lifetime, intensity, polarization or spectra give chemical and conformational information about molecules in their cellular context. By recording the spatial trajectories of pairs of interacting molecules, formation of larger molecular complexes can be studied. In the future, multicolour and multiparameter imaging of single molecules in live cells will be a powerful analytical tool for systems biology. Here, we discuss measurements of single-molecule mobility and residency at the plasma membrane of live cells. Analysis of diffusional paths at the plasma membrane gives information about its physical properties and measurement of temporal trajectories enables rates of binding and dissociation to be derived. Meanwhile, close scrutiny of individual fluorophore trajectories enables ideas about molecular dimerization and oligomerization related to function to be tested directly.

How memory of direct animal interactions can lead to territorial pattern formation.

PubMed

Potts, Jonathan R; Lewis, Mark A

2016-05-01

Mechanistic home range analysis (MHRA) is a highly effective tool for understanding spacing patterns of animal populations. It has hitherto focused on populations where animals defend their territories by communicating indirectly, e.g. via scent marks. However, many animal populations defend their territories using direct interactions, such as ritualized aggression. To enable application of MHRA to such populations, we construct a model of direct territorial interactions, using linear stability analysis and energy methods to understand when territorial patterns may form. We show that spatial memory of past interactions is vital for pattern formation, as is memory of 'safe' places, where the animal has visited but not suffered recent territorial encounters. Additionally, the spatial range over which animals make decisions to move is key to understanding the size and shape of their resulting territories. Analysis using energy methods, on a simplified version of our system, shows that stability in the nonlinear system corresponds well to predictions of linear analysis. We also uncover a hysteresis in the process of territory formation, so that formation may depend crucially on initial space-use. Our analysis, in one dimension and two dimensions, provides mathematical groundwork required for extending MHRA to situations where territories are defended by direct encounters. © 2016 The Author(s).

Geological Sequestration of CO2 by Hydrous Carbonate Formation with Reclaimed Slag

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

Von L. Richards; Kent Peaslee; Jeffrey Smith

The concept of this project is to develop a process that improves the kinetics of the hydrous carbonate formation reaction enabling steelmakers to directly remove CO2 from their furnace exhaust gas. It is proposed to bring the furnace exhaust stream containing CO2 in contact with reclaimed steelmaking slag in a reactor that has an environment near the unit activity of water resulting in the production of carbonates. The CO2 emissions from the plant would be reduced by the amount sequestered in the formation of carbonates. The main raw materials for the process are furnace exhaust gases and specially prepared slag.

Formation pathways of mesoporous silica nanoparticles with dodecagonal tiling

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

Sun, Yao; Ma, Kai; Kao, Teresa

Considerable progress in the fabrication of quasicrystals demonstrates that they can be realized in a broad range of materials. However, the development of chemistries enabling direct experimental observation of early quasicrystal growth pathways remains challenging. Here, we report the synthesis of four surfactant-directed mesoporous silica nanoparticle structures, including dodecagonal quasicrystalline nanoparticles, as a function of micelle pore expander concentration or stirring rate. We demonstrate that the early formation stages of dodecagonal quasicrystalline mesoporous silica nanoparticles can be preserved, where precise control of mesoporous silica nanoparticle size down to <30 nm facilitates comparison between mesoporous silica nanoparticles and simulated single-particle growthmore » trajectories beginning with a single tiling unit. Our results reveal details of the building block size distributions during early growth and how they promote quasicrystal formation. This work identifies simple synthetic parameters, such as stirring rate, that may be exploited to design other quasicrystal-forming self-assembly chemistries and processes.« less

Formation pathways of mesoporous silica nanoparticles with dodecagonal tiling

DOE PAGES

Sun, Yao; Ma, Kai; Kao, Teresa; ...

2017-08-15

Considerable progress in the fabrication of quasicrystals demonstrates that they can be realized in a broad range of materials. However, the development of chemistries enabling direct experimental observation of early quasicrystal growth pathways remains challenging. Here, we report the synthesis of four surfactant-directed mesoporous silica nanoparticle structures, including dodecagonal quasicrystalline nanoparticles, as a function of micelle pore expander concentration or stirring rate. We demonstrate that the early formation stages of dodecagonal quasicrystalline mesoporous silica nanoparticles can be preserved, where precise control of mesoporous silica nanoparticle size down to <30 nm facilitates comparison between mesoporous silica nanoparticles and simulated single-particle growthmore » trajectories beginning with a single tiling unit. Our results reveal details of the building block size distributions during early growth and how they promote quasicrystal formation. This work identifies simple synthetic parameters, such as stirring rate, that may be exploited to design other quasicrystal-forming self-assembly chemistries and processes.« less

Development and application of bond cleavage reactions in bioorthogonal chemistry.

PubMed

Li, Jie; Chen, Peng R

2016-03-01

Bioorthogonal chemical reactions are a thriving area of chemical research in recent years as an unprecedented technique to dissect native biological processes through chemistry-enabled strategies. However, current concepts of bioorthogonal chemistry have largely centered on 'bond formation' reactions between two mutually reactive bioorthogonal handles. Recently, in a reverse strategy, a collection of 'bond cleavage' reactions has emerged with excellent biocompatibility. These reactions have expanded our bioorthogonal chemistry repertoire, enabling an array of exciting new biological applications that range from the chemically controlled spatial and temporal activation of intracellular proteins and small-molecule drugs to the direct manipulation of intact cells under physiological conditions. Here we highlight the development and applications of these bioorthogonal cleavage reactions. Furthermore, we lay out challenges and propose future directions along this appealing avenue of research.

Amide to Alkyne Interconversion via a Nickel/Copper-Catalyzed Deamidative Cross-Coupling of Aryl and Alkenyl Amides.

PubMed

Srimontree, Watchara; Chatupheeraphat, Adisak; Liao, Hsuan-Hung; Rueping, Magnus

2017-06-16

A nickel-catalyzed deamidative cross-coupling reaction of amides with terminal alkynes as coupling partners was disclosed. This newly developed methodology allows the direct interconversion of amides to alkynes and enables a facile route for C(sp2)-C(sp) bond formation in a straightforward and mild fashion.

Cell-Type Specific Inactivation of Hippocampal CA1 Disrupts Location-Dependent Object Recognition in the Mouse

ERIC Educational Resources Information Center

Haettig, Jakob; Sun, Yanjun; Wood, Marcelo A.; Xu, Xiangmin

2013-01-01

The allatostatin receptor (AlstR)/ligand inactivation system enables potent regulation of neuronal circuit activity. To examine how different cell types participate in memory formation, we have used this system through Cre-directed, cell-type specific expression in mouse hippocampal CA1 in vivo and examined functional effects of inactivation of…

Enabling and Integrating Online Formative Assessment in a Flipped Calculus Course

ERIC Educational Resources Information Center

Schroeder, Larissa Bucchi; Dorn, Brian

2016-01-01

The increased use of videos in mathematics courses means that direct instruction, traditionally part of class lectures, now often occurs outside of the classroom. Although students come to class with some baseline level of understanding, instructors lose opportunities to assess students' understanding of content as it is seen for the first time.…

Enantioselective Copper-Catalyzed Carboetherification of Unactivated Alkenes**

PubMed Central

Bovino, Michael T.; Liwosz, Timothy W.; Kendel, Nicole E.; Miller, Yan; Tyminska, Nina

2014-01-01

Chiral saturated oxygen heterocycles are important components of bioactive compounds. Cyclization of alcohols onto pendant alkenes is a direct route to their synthesis, but few catalytic enantioselective methods enabling cyclization onto unactivated alkenes exist. Herein is reported a highly efficient copper-catalyzed cyclization of γ-unsaturated pentenols that terminates in C-C bond formation, a net alkene carboetherification. Both intra- and intermolecular C-C bond formations are demonstrated, yielding functionalized chiral tetrahydrofurans as well as fused-ring and bridged-ring oxabicyclic products. Transition state calculations support a cis-oxycupration stereochemistry-determining step. PMID:24798697

Modular protein expression by RNA trans-splicing enables flexible expression of antibody formats in mammalian cells from a dual-host phage display vector.

PubMed

Shang, Yonglei; Tesar, Devin; Hötzel, Isidro

2015-10-01

A recently described dual-host phage display vector that allows expression of immunoglobulin G (IgG) in mammalian cells bypasses the need for subcloning of phage display clone inserts to mammalian vectors for IgG expression in large antibody discovery and optimization campaigns. However, antibody discovery and optimization campaigns usually need different antibody formats for screening, requiring reformatting of the clones in the dual-host phage display vector to an alternative vector. We developed a modular protein expression system mediated by RNA trans-splicing to enable the expression of different antibody formats from the same phage display vector. The heavy-chain region encoded by the phage display vector is directly and precisely fused to different downstream heavy-chain sequences encoded by complementing plasmids simply by joining exons in different pre-mRNAs by trans-splicing. The modular expression system can be used to efficiently express structurally correct IgG and Fab fragments or other antibody formats from the same phage display clone in mammalian cells without clone reformatting. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Controlling formation and suppression of fiber-optical rogue waves.

PubMed

Brée, Carsten; Steinmeyer, Günter; Babushkin, Ihar; Morgner, Uwe; Demircan, Ayhan

2016-08-01

Fiber-optical rogue waves appear as rare but extreme events during optical supercontinuum generation in photonic crystal fibers. This process is typically initiated by the decay of a high-order fundamental soliton into fundamental solitons. Collisions between these solitons as well as with dispersive radiation affect the soliton trajectory in frequency and time upon further propagation. Launching an additional dispersive wave at carefully chosen delay and wavelength enables statistical manipulation of the soliton trajectory in such a way that the probability of rogue wave formation is either enhanced or reduced. To enable efficient control, parameters of the dispersive wave have to be chosen to allow trapping of dispersive radiation in the nonlinear index depression created by the soliton. Under certain conditions, direct manipulation of soliton properties is possible by the dispersive wave. In other more complex scenarios, control is possible via increasing or decreasing the number of intersoliton collisions. The control mechanism reaches a remarkable efficiency, enabling control of relatively large soliton energies. This scenario appears promising for highly dynamic all-optical control of supercontinua.

Addressable Direct-Write Nanoscale Filament Formation and Dissolution by Nanoparticle-Mediated Bipolar Electrochemistry.

PubMed

Crouch, Garrison M; Han, Donghoon; Fullerton-Shirey, Susan K; Go, David B; Bohn, Paul W

2017-05-23

Nanoscale conductive filaments, usually associated with resistive memory or memristor technology, may also be used for chemical sensing and nanophotonic applications; however, realistic implementation of the technology requires precise knowledge of the conditions that control the formation and dissolution of filaments. Here we describe and characterize an addressable direct-write nanoelectrochemical approach to achieve repeatable formation/dissolution of Ag filaments across a ∼100 nm poly(ethylene oxide) (PEO) film containing either Ag + alone or Ag + together with 50 nm Ag-nanoparticles acting as bipolar electrodes. Using a conductive AFM tip, formation occurs when the PEO film is subjected to a forward bias, and dissolution occurs under reverse bias. Formation-dissolution kinetics were studied for three film compositions: Ag|PEO-Ag + , Ag|poly(ethylene glycol) monolayer-PEO-Ag + , and Ag|poly(ethylene glycol) monolayer-PEO-Ag + /Ag-nanoparticle. Statistical analysis shows that the distribution of formation times exhibits Gaussian behavior, and the fastest average initial formation time occurs for the Ag|PEO-Ag + system. In contrast, formation in the presence of Ag nanoparticles likely proceeds by a noncontact bipolar electrochemical mechanism, exhibiting the slowest initial filament formation. Dissolution times are log-normal for all three systems, and repeated reformation of filaments from previously formed structures is characterized by rapid regrowth. The direct-write bipolar electrochemical deposition/dissolution strategy developed here presents an approach to reconfigurable, noncontact in situ wiring of nanoparticle arrays-thereby enabling applications where actively controlled connectivity of nanoparticle arrays is used to manipulate nanoelectronic and nanophotonic behavior. The system further allows for facile manipulation of experimental conditions while simultaneously characterizing surface conditions and filament formation/dissolution kinetics.

Direct imaging search for the "missing link" in giant planet formation

NASA Astrophysics Data System (ADS)

Ngo, Henry; Mawet, Dimitri; Ruane, Garreth; Xuan, Wenhao; Bowler, Brendan; Cook, Therese; Zawol, Zoe

2018-01-01

While transit and radial velocity detection techniques have probed giant planet populations at close separations (within a few au), current direct imaging surveys are finding giant planets at separations of 10s-100s au. Furthermore, these directly imaged planets are very massive, including some with masses above the deuterium burning limit. It is not certain whether these objects represent the high mass end of planet formation scenarios or the low mass end of star formation. We present a direct imaging survey to search for the "missing link" population between the close-in RV and transiting giant planets and the extremely distant directly imaged giant planets (i.e. giant planets between 5-10 au). Finding and characterizing this population allows for comparisons with the formation models of closer-in planets and connects directly imaged planets with closer-in planets in semi-major axis phase space. In addition, microlensing surveys have suggested a large reservoir of giant planets exist in this region. To find these "missing link" giant planets, our survey searches for giant planets around M-stars. The ubiquity of M-stars provide a large number of nearby targets and their L-band contrast with planets allow for sensitivities to smaller planet masses than surveys conducted at shorter wavelengths. Along with careful target selection, we use Keck's L-band vector vortex coronagraph to enable sensitivities of a few Jupiter masses as close as 4 au to their host stars. We present our completed 2-year survey targeting 200 young (10-150 Myr), nearby M-stars and our ongoing work to follow-up over 40 candidate objects.

Separate elements of episodic memory subserved by distinct hippocampal-prefrontal connections.

PubMed

Barker, Gareth R I; Banks, Paul J; Scott, Hannah; Ralph, G Scott; Mitrophanous, Kyriacos A; Wong, Liang-Fong; Bashir, Zafar I; Uney, James B; Warburton, E Clea

2017-02-01

Episodic memory formation depends on information about a stimulus being integrated within a precise spatial and temporal context, a process dependent on the hippocampus and prefrontal cortex. Investigations of putative functional interactions between these regions are complicated by multiple direct and indirect hippocampal-prefrontal connections. Here application of a pharmacogenetic deactivation technique enabled us to investigate the mnemonic contributions of two direct hippocampal-medial prefrontal cortex (mPFC) pathways, one arising in the dorsal CA1 (dCA1) and the other in the intermediate CA1 (iCA1). While deactivation of either pathway impaired episodic memory, the resulting pattern of mnemonic deficits was different: deactivation of the dCA1→mPFC pathway selectively disrupted temporal order judgments while iCA1→mPFC pathway deactivation disrupted spatial memory. These findings reveal a previously unsuspected division of function among CA1 neurons that project directly to the mPFC. Such subnetworks may enable the distinctiveness of contextual information to be maintained in an episodic memory circuit.

Femtosecond laser inscription of asymmetric directional couplers for in-fiber optical taps and fiber cladding photonics.

PubMed

Grenier, Jason R; Fernandes, Luís A; Herman, Peter R

2015-06-29

Precise alignment of femtosecond laser tracks in standard single mode optical fiber is shown to enable controllable optical tapping of the fiber core waveguide light with fiber cladding photonic circuits. Asymmetric directional couplers are presented with tunable coupling ratios up to 62% and bandwidths up to 300 nm at telecommunication wavelengths. Real-time fiber monitoring during laser writing permitted a means of controlling the coupler length to compensate for micron-scale alignment errors and to facilitate tailored design of coupling ratio, spectral bandwidth and polarization properties. Laser induced waveguide birefringence was harnessed for polarization dependent coupling that led to the formation of in-fiber polarization-selective taps with 32 dB extinction ratio. This technology enables the interconnection of light propagating in pre-existing waveguides with laser-formed devices, thereby opening a new practical direction for the three-dimensional integration of optical devices in the cladding of optical fibers and planar lightwave circuits.

Direct laser writing of polymeric nanostructures via optically induced local thermal effect

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

Tong, Quang Cong; Institute of Materials Science, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, 10000 Hanoi; Nguyen, Dam Thuy Trang

We demonstrate the fabrication of desired structures with feature size below the diffraction limit by use of a positive photoresist. The direct laser writing technique employing a continuous-wave laser was used to optically induce a local thermal effect in a positive photoresist, which then allowed the formation of solid nanostructures. This technique enabled us to realize multi-dimensional sub-microstructures by use of a positive photoresist, with a feature size down to 57 nm. This mechanism acting on positive photoresists opens a simple and low-cost way for nanofabrication.

Dioctyl sulfosuccinate analysis in near-shore Gulf of Mexico water by direct-injection liquid chromatography-tandem mass spectrometry.

PubMed

Mathew, Johnson; Schroeder, David L; Zintek, Lawrence B; Schupp, Caitlin R; Kosempa, Michael G; Zachary, Adam M; Schupp, George C; Wesolowski, Dennis J

2012-03-30

Dioctyl sulfosuccinate (DOSS) was a major component of the dispersants most used in the 2010 Deepwater Horizon Oil Spill incident response. This analytical method quantifies salt water DOSS concentrations to a reporting limit of 20 μg/L, which was below the United States Environmental Protection Agency's (U.S. EPA) 40 μg/L DOSS Aquatic Life Benchmark. DOSS in Gulf of Mexico water samples were analyzed by direct-injection reversed-phase liquid chromatography-tandem mass spectrometry (LC-MS/MS). Sample preparation with 50% acetonitrile (ACN) enabled quantitative transfer of DOSS and increased DOSS response 20-fold by reducing aggregation. This increased sensitivity enabled the detection of a confirmatory transition over the calibration range of 10-200 μg/L. U.S. EPA Region 5 and Region 6 laboratories analyzed hundreds of near-shore surface Gulf of Mexico water samples, none contained more than the 20 ppb reporting limit. The matrix spike DOSS/deuterated surrogate (DOSS-D34) correlation of determination varied with mobile phase modifier (ammonium formate R(2)=0.95 and formic acid R(2)=0.27). Using ammonium formate, DOSS-D34 accurately measured DOSS matrix effect. The near-shore sodium concentrations varied more than 10,000-fold, but were not strongly correlated with DOSS recovery. DOSS detection by LC-MS/MS enabled rapid analysis which was valuable in guiding incident response. Published by Elsevier B.V.

Enantioselective copper-catalyzed carboetherification of unactivated alkenes.

PubMed

Bovino, Michael T; Liwosz, Timothy W; Kendel, Nicole E; Miller, Yan; Tyminska, Nina; Zurek, Eva; Chemler, Sherry R

2014-06-16

Chiral saturated oxygen heterocycles are important components of bioactive compounds. Cyclization of alcohols onto pendant alkenes is a direct route to their synthesis, but few catalytic enantioselective methods enabling cyclization onto unactivated alkenes exist. Herein reported is a highly efficient copper-catalyzed cyclization of γ-unsaturated pentenols which terminates in C-C bond formation, a net alkene carboetherification. Both intra- and intermolecular C-C bond formations are demonstrated, thus yielding functionalized chiral tetrahydrofurans as well as fused-ring and bridged-ring oxabicyclic products. Transition-state calculations support a cis-oxycupration stereochemistry-determining step. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Investigation of laser irradiation of WC-Co cemented carbides inside a scanning electron microscope (LASEM)

NASA Astrophysics Data System (ADS)

Schultrich, B.; Wetzig, K.

1987-09-01

A combination of SEM and laser enables direct observation of structural modifications by a high-energy input. With this new device, melting phenomena and fracture processes in a WC-6 percent Co hard metal were investigated. The first laser pulse leads to melting of a thin surface layer with the formation of blisters and craters. Cracking is induced by the relaxation of compressive surface stresses during the high-temperature stage and the appearance of tensile stresses during cooling. Besides crack formation and extension, complete welding of crack surfaces was observed after repeated laser irradiation.

PeakML/mzMatch: a file format, Java library, R library, and tool-chain for mass spectrometry data analysis.

PubMed

Scheltema, Richard A; Jankevics, Andris; Jansen, Ritsert C; Swertz, Morris A; Breitling, Rainer

2011-04-01

The recent proliferation of high-resolution mass spectrometers has generated a wealth of new data analysis methods. However, flexible integration of these methods into configurations best suited to the research question is hampered by heterogeneous file formats and monolithic software development. The mzXML, mzData, and mzML file formats have enabled uniform access to unprocessed raw data. In this paper we present our efforts to produce an equally simple and powerful format, PeakML, to uniformly exchange processed intermediary and result data. To demonstrate the versatility of PeakML, we have developed an open source Java toolkit for processing, filtering, and annotating mass spectra in a customizable pipeline (mzMatch), as well as a user-friendly data visualization environment (PeakML Viewer). The PeakML format in particular enables the flexible exchange of processed data between software created by different groups or companies, as we illustrate by providing a PeakML-based integration of the widely used XCMS package with mzMatch data processing tools. As an added advantage, downstream analysis can benefit from direct access to the full mass trace information underlying summarized mass spectrometry results, providing the user with the means to rapidly verify results. The PeakML/mzMatch software is freely available at http://mzmatch.sourceforge.net, with documentation, tutorials, and a community forum.

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

Bowen, Benjamin; Ruebel, Oliver; Fischer, Curt Fischer R.

BASTet is an advanced software library written in Python. BASTet serves as the analysis and storage library for the OpenMSI project. BASTet is an integrate framework for: i) storage of spectral imaging data, ii) storage of derived analysis data, iii) provenance of analyses, iv) integration and execution of analyses via complex workflows. BASTet implements the API for the HDF5 storage format used by OpenMSI. Analyses that are developed using BASTet benefit from direct integration with storage format, automatic tracking of provenance, and direct integration with command-line and workflow execution tools. BASTet also defines interfaces to enable developers to directly integratemore » their analysis with OpenMSI's web-based viewing infrastruture without having to know OpenMSI. BASTet also provides numerous helper classes and tools to assist with the conversion of data files, ease parallel implementation of analysis algorithms, ease interaction with web-based functions, description methods for data reduction. BASTet also includes detailed developer documentation, user tutorials, iPython notebooks, and other supporting documents.« less

An application of the geophysical methods and ALS DTM for the identification of the geological structure in the Kraśnik region - Lublin Upland, Poland

NASA Astrophysics Data System (ADS)

Kamiński, Mirosław

2017-11-01

The purpose of the study was the assessment of the viability of selected geophysical methods and the Airborne Laser Scanning (ALS) for the identification and interpretation of the geological structure. The studied area is covered with a dense forest. For this reason, the ALS numerical terrain model was applied for the analysis of the topography. Three geophysical methods were used: gravimetric, in the form of a semi-detailed gravimetric photograph, Vertical Electrical Sounding (VES), and Electrical Resistivity Tomography (ERT). The numerical terrain model enabled the identification of Jurassic limestone outcrops and interpretation of the directions of the faults network. The geological interpretation of the digitally processed gravimetric data enabled the determination of the spatial orientation of the synclines and anticlines axes and of the course directions of main faults. Vertical Electrical Sounding carried along the section line perpendicular to the Gościeradów anticline axis enabled the interpretation of the lithology of this structure and identification of its complex tectonic structure. The shallow geophysical surveys using the ERT method enabled the estimation of the thickness of Quaternary formations deposited unconformably on the highly eroded Jurassic limestone outcrop. The lithology of Quaternary, Cretaceous and Jurassic rocks was also interpreted.

Three-dimensional photonic crystals created by single-step multi-directional plasma etching.

PubMed

Suzuki, Katsuyoshi; Kitano, Keisuke; Ishizaki, Kenji; Noda, Susumu

2014-07-14

We fabricate 3D photonic nanostructures by simultaneous multi-directional plasma etching. This simple and flexible method is enabled by controlling the ion-sheath in reactive-ion-etching equipment. We realize 3D photonic crystals on single-crystalline silicon wafers and show high reflectance (>95%) and low transmittance (<-15dB) at optical communication wavelengths, suggesting the formation of a complete photonic bandgap. Moreover, our method simply demonstrates Si-based 3D photonic crystals that show the photonic bandgap effect in a shorter wavelength range around 0.6 μm, where further fine structures are required.

MICA: Multiple interval-based curve alignment

NASA Astrophysics Data System (ADS)

Mann, Martin; Kahle, Hans-Peter; Beck, Matthias; Bender, Bela Johannes; Spiecker, Heinrich; Backofen, Rolf

2018-01-01

MICA enables the automatic synchronization of discrete data curves. To this end, characteristic points of the curves' shapes are identified. These landmarks are used within a heuristic curve registration approach to align profile pairs by mapping similar characteristics onto each other. In combination with a progressive alignment scheme, this enables the computation of multiple curve alignments. Multiple curve alignments are needed to derive meaningful representative consensus data of measured time or data series. MICA was already successfully applied to generate representative profiles of tree growth data based on intra-annual wood density profiles or cell formation data. The MICA package provides a command-line and graphical user interface. The R interface enables the direct embedding of multiple curve alignment computation into larger analyses pipelines. Source code, binaries and documentation are freely available at https://github.com/BackofenLab/MICA

Improving the Accessibility and Use of NASA Earth Science Data

NASA Technical Reports Server (NTRS)

Tisdale, Matthew; Tisdale, Brian

2015-01-01

Many of the NASA Langley Atmospheric Science Data Center (ASDC) Distributed Active Archive Center (DAAC) multidimensional tropospheric and atmospheric chemistry data products are stored in HDF4, HDF5 or NetCDF format, which traditionally have been difficult to analyze and visualize with geospatial tools. With the rising demand from the diverse end-user communities for geospatial tools to handle multidimensional products, several applications, such as ArcGIS, have refined their software. Many geospatial applications now have new functionalities that enable the end user to: Store, serve, and perform analysis on each individual variable, its time dimension, and vertical dimension. Use NetCDF, GRIB, and HDF raster data formats across applications directly. Publish output within REST image services or WMS for time and space enabled web application development. During this webinar, participants will learn how to leverage geospatial applications such as ArcGIS, OPeNDAP and ncWMS in the production of Earth science information, and in increasing data accessibility and usability.

Structure–property relationships in atomic-scale junctions: Histograms and beyond

DOE PAGES

Mark S. Hybertsen; Venkataraman, Latha

2016-03-03

Over the past 10 years, there has been tremendous progress in the measurement, modeling and understanding of structure–function relationships in single molecule junctions. Numerous research groups have addressed significant scientific questions, directed both to conductance phenomena at the single molecule level and to the fundamental chemistry that controls junction functionality. Many different functionalities have been demonstrated, including single-molecule diodes, optically and mechanically activated switches, and, significantly, physical phenomena with no classical analogues, such as those based on quantum interference effects. Experimental techniques for reliable and reproducible single molecule junction formation and characterization have led to this progress. In particular, themore » scanning tunneling microscope based break-junction (STM-BJ) technique has enabled rapid, sequential measurement of large numbers of nanoscale junctions allowing a statistical analysis to readily distinguish reproducible characteristics. Furthermore, harnessing fundamental link chemistry has provided the necessary chemical control over junction formation, enabling measurements that revealed clear relationships between molecular structure and conductance characteristics.« less

Structure–property relationships in atomic-scale junctions: Histograms and beyond

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

Mark S. Hybertsen; Venkataraman, Latha

Over the past 10 years, there has been tremendous progress in the measurement, modeling and understanding of structure–function relationships in single molecule junctions. Numerous research groups have addressed significant scientific questions, directed both to conductance phenomena at the single molecule level and to the fundamental chemistry that controls junction functionality. Many different functionalities have been demonstrated, including single-molecule diodes, optically and mechanically activated switches, and, significantly, physical phenomena with no classical analogues, such as those based on quantum interference effects. Experimental techniques for reliable and reproducible single molecule junction formation and characterization have led to this progress. In particular, themore » scanning tunneling microscope based break-junction (STM-BJ) technique has enabled rapid, sequential measurement of large numbers of nanoscale junctions allowing a statistical analysis to readily distinguish reproducible characteristics. Furthermore, harnessing fundamental link chemistry has provided the necessary chemical control over junction formation, enabling measurements that revealed clear relationships between molecular structure and conductance characteristics.« less

Highly Stable Operation of Lithium Metal Batteries Enabled by the Formation of a Transient High Concentration Electrolyte Layer

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

Zheng, Jianming; Yan, Pengfei; Mei, Donghai

2016-02-08

Lithium (Li) metal has been extensively investigated as an anode for rechargeable battery applications due to its ultrahigh specific capacity and the lowest redox potential. However, significant challenges including dendrite growth and low Coulombic efficiency are still hindering the practical applications of rechargeable Li metal batteries. Here, we demonstrate that long-term cycling of Li metal batteries can be realized by the formation of a transient high concentration electrolyte layer near the surface of Li metal anode during high rate discharge process. The highly concentrated Li+ ions in this transient layer will immediately solvate with the available solvent molecules and facilitatemore » the formation of a stable and flexible SEI layer composed of a poly(ethylene carbonate) framework integrated with other organic/inorganic lithium salts. This SEI layer largely suppresses the corrosion of Li metal anode by free organic solvents and enables the long-term operation of Li metal batteries. The fundamental findings in this work provide a new direction for the development and operation of Li metal batteries that could be operated at high current densities for a wide range of applications.« less

Morphogenesis at the inflorescence shoot apex of Anagallis arvensis: surface geometry and growth in comparison with the vegetative shoot.

PubMed

Kwiatkowska, Dorota; Routier-Kierzkowska, Anne-Lise

2009-01-01

Quantitative analysis of geometry and surface growth based on the sequential replica method is used to compare morphogenesis at the shoot apex of Anagallis arvensis in the reproductive and vegetative phases of development. Formation of three types of lateral organs takes place at the Anagallis shoot apical meristem (SAM): vegetative leaf primordia are formed during the vegetative phase and leaf-like bracts and flower primordia during the reproductive phase. Although the shapes of all the three types of primordia are very similar during their early developmental stages, areal growth rates and anisotropy of apex surface growth accompanying formation of leaf or bract primordia are profoundly different from those during formation of flower primordia. This provides an example of different modes of de novo formation of a given shape. Moreover, growth accompanying the formation of the boundary between the SAM and flower primordium is entirely different from growth at the adaxial leaf or bract primordium boundary. In the latter, areal growth rates at the future boundary are the lowest of all the apex surface, while in the former they are relatively very high. The direction of maximal growth rate is latitudinal (along the future boundary) in the case of leaf or bract primordium but meridional (across the boundary) in the case of flower. The replica method does not enable direct analysis of growth in the direction perpendicular to the apex surface (anticlinal direction). Nevertheless, the reconstructed surfaces of consecutive replicas taken from an individual apex allow general directions of SAM surface bulging accompanying primordium formation to be recognized. Precise alignment of consecutive reconstructions shows that the direction of initial bulging during the leaf or bract formation is nearly parallel to the shoot axis (upward bulging), while in the case of flower it is perpendicular to the axis (lateral bulging). In future, such 3D reconstructions can be used to assess displacement velocity fields so that growth in the anticlinal direction can be assessed. In terms of self-perpetuation, the inflorescence SAM of Anagallis differs from the SAM in the vegetative phase in that the centrally located region of slow growth is less distinct in the inflorescence SAM. Moreover, the position of this slowly growing zone with respect to cells is not stable in the course of the meristem ontogeny.

Structure and Dynamics of Dinucleosomes Assessed by Atomic Force Microscopy

DOE PAGES

Filenko, Nina A.; Palets, Dmytro B.; Lyubchenko, Yuri L.

2012-01-01

Dynamics of nucleosomes and their interactions are important for understanding the mechanism of chromatin assembly. Internucleosomal interaction is required for the formation of higher-order chromatin structures. Although H1 histone is critically involved in the process of chromatin assembly, direct internucleosomal interactions contribute to this process as well. To characterize the interactions of nucleosomes within the nucleosome array, we designed a dinucleosome and performed direct AFM imaging. The analysis of the AFM data showed dinucleosomes are very dynamic systems, enabling the nucleosomes to move in a broad range along the DNA template. Di-nucleosomes in close proximity were observed, but their populationmore » was low. The use of the zwitterionic detergent, CHAPS, increased the dynamic range of the di-nucleosome, facilitating the formation of tight di-nucleosomes. The role of CHAPS and similar natural products in chromatin structure and dynamics is also discussed.« less

Free-Energy Landscape of the Dissolution of Gibbsite at High pH.

PubMed

Shen, Zhizhang; Kerisit, Sebastien N; Stack, Andrew G; Rosso, Kevin M

2018-04-05

The individual elementary reactions involved in the dissolution of a solid into solution remain mostly speculative due to a lack of direct experimental probes. In this regard, we have applied atomistic simulations to map the free-energy landscape of the dissolution of gibbsite from a step edge as a model of metal hydroxide dissolution. The overall reaction combines kink formation and kink propagation. Two individual reactions were found to be rate-limiting for kink formation, that is, the displacement of Al from a step site to a ledge adatom site and its detachment from ledge/terrace adatom sites into the solution. As a result, a pool of mobile and labile adsorbed species, or adatoms, exists before the release of Al into solution. Because of the quasi-hexagonal symmetry of gibbsite, kink site propagation can occur in multiple directions. Overall, our results will enable the development of microscopic mechanistic models of metal oxide dissolution.

Direct observation of mineral–organic composite formation reveals occlusion mechanism

DOE PAGES

Cho, Kang Rae; Kim, Yi -Yeoun; Yang, Pengcheng; ...

2016-01-06

Manipulation of inorganic materials with organic macromolecules enables organisms to create biominerals such as bones and seashells, where occlusion of biomacromolecules within individual crystals generates superior mechanical properties. Current understanding of this process largely comes from studying the entrapment of micron-size particles in cooling melts. Here, by investigating micelle incorporation in calcite with atomic force microscopy and micromechanical simulations, we show that different mechanisms govern nanoscale occlusion. By simultaneously visualizing the micelles and propagating step edges, we demonstrate that the micelles experience significant compression during occlusion, which is accompanied by cavity formation. This generates local lattice strain, leading to enhancedmore » mechanical properties. Furthermore, these results give new insight into the formation of occlusions in natural and synthetic crystals, and will facilitate the synthesis of multifunctional nanocomposite crystals.« less

Active Learning and Engagement with the Wireless Indoor Location Device (WILD) Learning System

NASA Astrophysics Data System (ADS)

Moldwin, M.; Samson, P. J.; Ojeda, L.; Miller, T.; Yu, J.

2016-12-01

The Wireless Indoor Location Device (WILD) Learning System being developed at the University of Michigan and the Education Technology company A2 Motus LLC provides a unique platform for social learning by allowing students to become active participants in live simulations of complex systems, like hurricane formation. The WILD Learning System enables teachers to engage students in kinesthetic activities that explore complex models from a wide variety of STEAM (Science, Technology, Engineering, Art and Math) disciplines. The system provides students' location, orientation and motion within the classroom and assigns each student different parameters depending on the activity. For example, students learning about hurricanes could be assigned atmospheric pressure levels and asked to arrange themselves around the room to simulate a hurricane. The Wild Learning System software then takes the students' pressure readings and locations and projects their locations overlaid onto a real-time generated simulated pressure weather map enabling the observation of how their arrangement influences the pressure structure. The teacher then could have the students orient themselves in the direction they think the resulting wind field will be based on the pressure contours as the system can show an arrow originating from each of the students position in the direction that they are facing. The system also could incorporate a student response-type system for the instructor to then directly question students about other concepts and record their response to both the kinesthetic activity and other formative assessment questions. The WILD Learning System consists of a sensor package for each student in the class, beacons to enable precise localization of the students, software to calculate student location information, and educational software for a variety of activities. In addition, a software development kit (SDK) is under development that would allow others to create additional learning activities using the WILD Learning System. (WILD Learning System development has been partially supported by NASA's CYGNSS Mission EPO, the NSF and the University of Michigan).

Star & Planet Formation Studies and Opportunities with SOFIA

NASA Technical Reports Server (NTRS)

Smith, Kimberly Ennico

2018-01-01

Star formation, the most fundamental process in the universe, is linked to planet formation and thus to the origin and evolution of life. We have a general outline of how planets and stars form, yet unraveling the details of the physics and chemistry continues to challenge us. The infrared and submillimeter part of the spectrum hold the most promise for studying the beginnings of star formation. The observational landscape recently shaped by Spitzer, Herschel and ALMA, continues to challenge our current theories. SOFIA, the Stratospheric Observatory for Infrared Astronomy, equipped with state-of-the-art infrared instrumentation to a vantage point at 45,000 feet (13.7 kilometers) flight altitude that is above 99.9 percent of the Earth's water vapor, enables observations in the infrared through terahertz frequencies not possible from the ground. SOFIA is a community observatory, about to start its sixth annual observing cycle. My talk will focus on recent results in advancing star and planet formation processes using SOFIA's imaging and polarimetric capabilities, and the upcoming science enabled by the 3rd generation instrument High-Resolution Mid-Infrared Spectrometer (HIRMES) to be commissioned in 2019. I will show how mid-infrared imaging is used to test massive star formation theories, how far-infrared polarimetry on sub-parsec scales is directly testing the role of magnetic fields in molecular clouds, and how velocity-resolved high-resolution spectroscopy will push forward our understanding of proto-planetary disk science. I will also summarize upcoming opportunities with the SOFIA observatory. For the latest news about your flying observatory, see https://sofia.usra.edu/.

Interactions of UNC-34 Enabled With Rac GTPases and the NIK Kinase MIG-15 in Caenorhabditis elegans Axon Pathfinding and Neuronal Migration

PubMed Central

Shakir, M. Afaq; Gill, Jason S.; Lundquist, Erik A.

2006-01-01

Many genes that affect axon pathfinding and cell migration have been identified. Mechanisms by which these genes and the molecules they encode interact with one another in pathways and networks to control developmental events are unclear. Rac GTPases, the cytoskeletal signaling molecule Enabled, and NIK kinase have all been implicated in regulating axon pathfinding and cell migration. Here we present evidence that, in Caenorhabditis elegans, three Rac GTPases, CED-10, RAC-2, and MIG-2, define three redundant pathways that each control axon pathfinding, and that the NIK kinase MIG-15 acts in each Rac pathway. Furthermore, we show that the Enabled molecule UNC-34 defines a fourth partially redundant pathway that acts in parallel to Rac/MIG-15 signaling in axon pathfinding. Enabled and the three Racs also act redundantly to mediate AQR and PQR neuronal cell migration. The Racs and UNC-34 Ena might all control the formation of actin-based protrusive structures (lamellipodia and filopodia) that mediate growth cone outgrowth and cell migration. MIG-15 does not act with the three Racs in execution of cell migration. Rather, MIG-15 affects direction of PQR neuronal migration, similar to UNC-40 and DPY-19, which control initial Q cell polarity, and Wnt signaling, which acts later to control Q cell-directed migration. MIG-2 Rac, which acts with CED-10 Rac, RAC-2 Rac, and UNC-34 Ena in axon pathfinding and cell migration, also acts with MIG-15 in PQR directional migration. PMID:16204220

Local formation of nitrogen-vacancy centers in diamond by swift heavy ions

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

Schwartz, J.; Aloni, S.; Ogletree, D. F.

2014-12-03

In this paper, we exposed nitrogen-implanted diamonds to beams of swift heavy ions (~1 GeV, ~4 MeV/u) and find that these irradiations lead directly to the formation of nitrogen vacancy (NV) centers, without thermal annealing. We compare the photoluminescence intensities of swift heavy ion activated NV - centers to those formed by irradiation with low-energy electrons and by thermal annealing. NV - yields from irradiations with swift heavy ions are 0.1 of yields from low energy electrons and 0.02 of yields from thermal annealing. We discuss possible mechanisms of NV center formation by swift heavy ions such as electronic excitationsmore » and thermal spikes. While forming NV centers with low efficiency, swift heavy ions could enable the formation of three dimensional NV - assemblies over relatively large distances of tens of micrometers. Finally and further, our results show that NV center formation is a local probe of (partial) lattice damage relaxation induced by electronic excitations from swift heavy ions in diamond.« less

MEAs and 3D nanoelectrodes: electrodeposition as tool for a precisely controlled nanofabrication.

PubMed

Weidlich, Sabrina; Krause, Kay J; Schnitker, Jan; Wolfrum, Bernhard; Offenhäusser, Andreas

2017-01-31

Microelectrode arrays (MEAs) are gaining increasing importance for the investigation of signaling processes between electrogenic cells. However, efficient cell-chip coupling for robust and long-term electrophysiological recording and stimulation still remains a challenge. A possible approach for the improvement of the cell-electrode contact is the utilization of three-dimensional structures. In recent years, various 3D electrode geometries have been developed, but we are still lacking a fabrication approach that enables the formation of different 3D structures on a single chip in a controlled manner. This, however, is needed to enable a direct and reliable comparison of the recording capabilities of the different structures. Here, we present a method for a precisely controlled deposition of nanoelectrodes, enabling the fabrication of multiple, well-defined types of structures on our 64 electrode MEAs towards a rapid-prototyping approach to 3D electrodes.

Vitreous carbon mask substrate for X-ray lithography

DOEpatents

Aigeldinger, Georg [Livermore, CA; Skala, Dawn M [Fremont, CA; Griffiths, Stewart K [Livermore, CA; Talin, Albert Alec [Livermore, CA; Losey, Matthew W [Livermore, CA; Yang, Chu-Yeu Peter [Dublin, CA

2009-10-27

The present invention is directed to the use of vitreous carbon as a substrate material for providing masks for X-ray lithography. The new substrate also enables a small thickness of the mask absorber used to pattern the resist, and this enables improved mask accuracy. An alternative embodiment comprised the use of vitreous carbon as a LIGA substrate wherein the VC wafer blank is etched in a reactive ion plasma after which an X-ray resist is bonded. This surface treatment provides a surface enabling good adhesion of the X-ray photoresist and subsequent nucleation and adhesion of the electrodeposited metal for LIGA mold-making while the VC substrate practically eliminates secondary radiation effects that lead to delamination of the X-ray resist form the substrate, the loss of isolated resist features, and the formation of a resist layer adjacent to the substrate that is insoluble in the developer.

Phototropism: translating light into directional growth.

PubMed

Hohm, Tim; Preuten, Tobias; Fankhauser, Christian

2013-01-01

Phototropism allows plants to align their photosynthetic tissues with incoming light. The direction of incident light is sensed by the phototropin family of blue light photoreceptors (phot1 and phot2 in Arabidopsis), which are light-activated protein kinases. The kinase activity of phototropins and phosphorylation of residues in the activation loop of their kinase domains are essential for the phototropic response. These initial steps trigger the formation of the auxin gradient across the hypocotyl that leads to asymmetric growth. The molecular events between photoreceptor activation and the growth response are only starting to be elucidated. In this review, we discuss the major steps leading from light perception to directional growth concentrating on Arabidopsis. In addition, we highlight links that connect these different steps enabling the phototropic response.

In Vitro Screening of Synthetic Fluorogenic Substrates for Detection of Cancer Procoagulant Activity.

PubMed

Krause, Jason; Frost, Carminita L

2018-04-01

Cancer procoagulant (CP), a direct activator of coagulation factor X, is among one of the tumour cell products or activities which may promote fibrin formation and has been suggested to be selectively associated with the malignant phenotype. At present, the most reliable assay for the quantification of CP activity is the three-stage chromogenic assay which utilises the ability of CP to activate factor X. In this assay, the activation of factor X leads to the formation of activated thrombin from prothrombin and the eventual hydrolyses of a thrombin chromogenic substrate which contains a p-nitroaniline leaving group. The complexity of the three-stage chromogenic assay suggests a need for a direct method of assaying CP activity. This study focuses on the design of a fluorogenic substrate that would enable the direct quantification of CP activity. The results of the study show two promising substrates for the determination of CP activity: Boc-PQVR-AMC and PQVR-AMC. Further analysis showed that Boc-PQVR-AMC could be excluded as a potential substrate for CP since it was also cleaved by collagenase.

An enzyme cascade synthesis of ε-caprolactone and its oligomers.

PubMed

Schmidt, Sandy; Scherkus, Christian; Muschiol, Jan; Menyes, Ulf; Winkler, Till; Hummel, Werner; Gröger, Harald; Liese, Andreas; Herz, Hans-Georg; Bornscheuer, Uwe T

2015-02-23

Poly-ε-caprolactone (PCL) is chemically produced on an industrial scale in spite of the need for hazardous peracetic acid as an oxidation reagent. Although Baeyer-Villiger monooxygenases (BVMO) in principle enable the enzymatic synthesis of ε-caprolactone (ε-CL) directly from cyclohexanone with molecular oxygen, current systems suffer from low productivity and are subject to substrate and product inhibition. The major limitations for such a biocatalytic route to produce this bulk chemical were overcome by combining an alcohol dehydrogenase with a BVMO to enable the efficient oxidation of cyclohexanol to ε-CL. Key to success was a subsequent direct ring-opening oligomerization of in situ formed ε-CL in the aqueous phase by using lipase A from Candida antarctica, thus efficiently solving the product inhibition problem and leading to the formation of oligo-ε-CL at more than 20 g L(-1) when starting from 200 mM cyclohexanol. This oligomer is easily chemically polymerized to PCL. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Gro2mat: a package to efficiently read gromacs output in MATLAB.

PubMed

Dien, Hung; Deane, Charlotte M; Knapp, Bernhard

2014-07-30

Molecular dynamics (MD) simulations are a state-of-the-art computational method used to investigate molecular interactions at atomic scale. Interaction processes out of experimental reach can be monitored using MD software, such as Gromacs. Here, we present the gro2mat package that allows fast and easy access to Gromacs output files from Matlab. Gro2mat enables direct parsing of the most common Gromacs output formats including the binary xtc-format. No openly available Matlab parser currently exists for this format. The xtc reader is orders of magnitudes faster than other available pdb/ascii workarounds. Gro2mat is especially useful for scientists with an interest in quick prototyping of new mathematical and statistical approaches for Gromacs trajectory analyses. © 2014 Wiley Periodicals, Inc. Copyright © 2014 Wiley Periodicals, Inc.

Turbine airfoil with a compliant outer wall

DOEpatents

Campbell, Christian X [Oviedo, FL; Morrison, Jay A [Oviedo, FL

2012-04-03

A turbine airfoil usable in a turbine engine with a cooling system and a compliant dual wall configuration configured to enable thermal expansion between inner and outer layers while eliminating stress formation in the outer layer is disclosed. The compliant dual wall configuration may be formed a dual wall formed from inner and outer layers separated by a support structure. The outer layer may be a compliant layer configured such that the outer layer may thermally expand and thereby reduce the stress within the outer layer. The outer layer may be formed from a nonplanar surface configured to thermally expand. In another embodiment, the outer layer may be planar and include a plurality of slots enabling unrestricted thermal expansion in a direction aligned with the outer layer.

Remote carboxylation of halogenated aliphatic hydrocarbons with carbon dioxide

NASA Astrophysics Data System (ADS)

Juliá-Hernández, Francisco; Moragas, Toni; Cornella, Josep; Martin, Ruben

2017-05-01

Catalytic carbon-carbon bond formation has enabled the streamlining of synthetic routes when assembling complex molecules. It is particularly important when incorporating saturated hydrocarbons, which are common motifs in petrochemicals and biologically relevant molecules. However, cross-coupling methods that involve alkyl electrophiles result in catalytic bond formation only at specific and previously functionalized sites. Here we describe a catalytic method that is capable of promoting carboxylation reactions at remote and unfunctionalized aliphatic sites with carbon dioxide at atmospheric pressure. The reaction occurs via selective migration of the catalyst along the hydrocarbon side-chain with excellent regio- and chemoselectivity, representing a remarkable reactivity relay when compared with classical cross-coupling reactions. Our results demonstrate that site-selectivity can be switched and controlled, enabling the functionalization of less-reactive positions in the presence of a priori more reactive ones. Furthermore, we show that raw materials obtained in bulk from petroleum processing, such as alkanes and unrefined mixtures of olefins, can be used as substrates. This offers an opportunity to integrate a catalytic platform en route to valuable fatty acids by transforming petroleum-derived feedstocks directly.

How an improved implementation of H2 self-shielding influences the formation of massive stars and black holes

NASA Astrophysics Data System (ADS)

Hartwig, Tilman; Glover, Simon C. O.; Klessen, Ralf S.; Latif, Muhammad A.; Volonteri, Marta

2015-09-01

High-redshift quasars at z > 6 have masses up to ˜109 M⊙. One of the pathways to their formation includes direct collapse of gas, forming a supermassive star, precursor of the black hole seed. The conditions for direct collapse are more easily achievable in metal-free haloes, where atomic hydrogen cooling operates and molecular hydrogen (H2) formation is inhibited by a strong external (ultraviolet) UV flux. Above a certain value of UV flux (Jcrit), the gas in a halo collapses isothermally at ˜104 K and provides the conditions for supermassive star formation. However, H2 can self-shield, reducing the effect of photodissociation. So far, most numerical studies used the local Jeans length to calculate the column densities for self-shielding. We implement an improved method for the determination of column densities in 3D simulations and analyse its effect on the value of Jcrit. This new method captures the gas geometry and velocity field and enables us to properly determine the direction-dependent self-shielding factor of H2 against photodissociating radiation. We find a value of Jcrit that is a factor of 2 smaller than with the Jeans approach (˜2000 J21 versus ˜4000 J21). The main reason for this difference is the strong directional dependence of the H2 column density. With this lower value of Jcrit, the number of haloes exposed to a flux > Jcrit is larger by more than an order of magnitude compared to previous studies. This may translate into a similar enhancement in the predicted number density of black hole seeds.

Effect of Annealing on the Passive Film Stability and Corrosion Resistance of New Families of Iron-Based Amorphous Metals

DTIC Science & Technology

2011-06-01

metallic glass easier to create and more stable once formed, thus improving the corrosion resistance. Adding titanium will enable the formation of...glass easier to create and more stable once formed, thus improving the corrosion resistance. Adding titanium will enable the formation of an extremely...research, it was hypothesized that additions of titanium could enable the formation of a protective titanium oxide film on the surface of the alloy

Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment.

PubMed

Bohler, Anwesha; Eijssen, Lars M T; van Iersel, Martijn P; Leemans, Christ; Willighagen, Egon L; Kutmon, Martina; Jaillard, Magali; Evelo, Chris T

2015-08-23

Biological pathways are descriptive diagrams of biological processes widely used for functional analysis of differentially expressed genes or proteins. Primary data analysis, such as quality control, normalisation, and statistical analysis, is often performed in scripting languages like R, Perl, and Python. Subsequent pathway analysis is usually performed using dedicated external applications. Workflows involving manual use of multiple environments are time consuming and error prone. Therefore, tools are needed that enable pathway analysis directly within the same scripting languages used for primary data analyses. Existing tools have limited capability in terms of available pathway content, pathway editing and visualisation options, and export file formats. Consequently, making the full-fledged pathway analysis tool PathVisio available from various scripting languages will benefit researchers. We developed PathVisioRPC, an XMLRPC interface for the pathway analysis software PathVisio. PathVisioRPC enables creating and editing biological pathways, visualising data on pathways, performing pathway statistics, and exporting results in several image formats in multiple programming environments. We demonstrate PathVisioRPC functionalities using examples in Python. Subsequently, we analyse a publicly available NCBI GEO gene expression dataset studying tumour bearing mice treated with cyclophosphamide in R. The R scripts demonstrate how calls to existing R packages for data processing and calls to PathVisioRPC can directly work together. To further support R users, we have created RPathVisio simplifying the use of PathVisioRPC in this environment. We have also created a pathway module for the microarray data analysis portal ArrayAnalysis.org that calls the PathVisioRPC interface to perform pathway analysis. This module allows users to use PathVisio functionality online without having to download and install the software and exemplifies how the PathVisioRPC interface can be used by data analysis pipelines for functional analysis of processed genomics data. PathVisioRPC enables data visualisation and pathway analysis directly from within various analytical environments used for preliminary analyses. It supports the use of existing pathways from WikiPathways or pathways created using the RPC itself. It also enables automation of tasks performed using PathVisio, making it useful to PathVisio users performing repeated visualisation and analysis tasks. PathVisioRPC is freely available for academic and commercial use at http://projects.bigcat.unimaas.nl/pathvisiorpc.

Direct printing of microstructures by femtosecond laser excitation of nanocrystals in solution

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

Shou, Wan; Pan, Heng, E-mail: hp5c7@mst.edu

2016-05-23

We report direct printing of micro/sub-micron structures by femtosecond laser excitation of semiconductor nanocrystals (NCs) in solution. Laser excitation with moderate intensity (10{sup 11}–10{sup 12} W/cm{sup 2}) induces 2D and 3D deposition of CdTe nanocrystals in aqueous solution, which can be applied for direct printing of microstructures. It is believed that laser irradiation induces charge formation on nanocrystals leading to deposition. Furthermore, it is demonstrated that the charged nanocrystals can respond to external electrical bias, enabling a printing approach based on selective laser induced electrophoretic deposition. Finally, energy dispersive X-ray analysis of deposited structures shows oxidation occurs and deposited structure mainlymore » consists of Cd{sub x}O.« less

Nanoscale growth twins in sputtered metal films

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

Misra, Amit; Anderoglu, Osman; Hoagland, Richard G

2008-01-01

We review recent studies on the mechanical properties of sputtered Cu and 330 stainless steel films with {l_brace}1 1 1{r_brace} nanoscale growth twins preferentially oriented perpendicular to growth direction. The mechanisms of formation of growth twins during sputtering and the deformation mechanisms that enable usually high strengths in nanotwinned structures are highlighted. Growth twins in sputtered films possess good thermal stability at elevated temperature, providing an approach to extend the application of high strength nanostructured metals to higher temperatures.

Ka-Band Autonomous Formation Flying Sensor

NASA Technical Reports Server (NTRS)

Tien, Jeffrey; Purcell, George, Jr.; Srinivasan, Jeffrey; Ciminera, Michael; Srinivasan, Meera; Meehan, Thomas; Young, Lawrence; Aung, MiMi; Amaro, Luis; Chong, Yong;

G protein-coupled receptor internalization assays in the high-content screening format.

PubMed

Haasen, Dorothea; Schnapp, Andreas; Valler, Martin J; Heilker, Ralf

2006-01-01

High-content screening (HCS), a combination of fluorescence microscopic imaging and automated image analysis, has become a frequently applied tool to study test compound effects in cellular disease-modeling systems. This chapter describes the measurement of G protein-coupled receptor (GPCR) internalization in the HCS format using a high-throughput, confocal cellular imaging device. GPCRs are the most successful group of therapeutic targets on the pharmaceutical market. Accordingly, the search for compounds that interfere with GPCR function in a specific and selective way is a major focus of the pharmaceutical industry today. This chapter describes methods for the ligand-induced internalization of GPCRs labeled previously with either a fluorophore-conjugated ligand or an antibody directed against an N-terminal tag of the GPCR. Both labeling techniques produce robust assay formats. Complementary to other functional GPCR drug discovery assays, internalization assays enable a pharmacological analysis of test compounds. We conclude that GPCR internalization assays represent a valuable medium/high-throughput screening format to determine the cellular activity of GPCR ligands.

Free-Energy Landscape of the Dissolution of Gibbsite at High pH

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

Shen, Zhizhang; Kerisit, Sebastien N.; Stack, Andrew G.

The individual elementary reactions involved in the dissolution of a solid into solution remain mostly speculative due to a lack of suitable, direct experimental probes. In this regard, we have applied atomistic simulations to map the free energy landscape of the dissolution of gibbsite from a step edge, as a model of metal hydroxide dissolution. The overall reaction combines kink site formation and kink site propagation. Two individual reactions were found to be rate-limiting for kink site formation, that is, the displacement of Al from a step site to a ledge adatom site and its detachment from ledge/terrace adatom sitesmore » into the solution. As a result, a pool of mobile and labile Al adsorbed species, or adatoms, exists before the release of Al into solution. Because of the quasi-hexagonal symmetry of gibbsite, kink site propagation can occur in multiple directions. Overall, the simulation results will enable the development of microscopic mechanistic models of metal oxide dissolution.« less

Direct Metal Deposition of H13 Tool Steel on Copper Alloy Substrate: Parametric Investigation

NASA Astrophysics Data System (ADS)

Imran, M. Khalid; Masood, S. H.; Brandt, Milan

2015-12-01

Over the past decade, researchers have demonstrated interest in tribology and prototyping by the laser aided material deposition process. Laser aided direct metal deposition (DMD) enables the formation of a uniform clad by melting the powder to form desired component from metal powder materials. In this research H13 tool steel has been used to clad on a copper alloy substrate using DMD. The effects of laser parameters on the quality of DMD deposited clad have been investigated and acceptable processing parameters have been determined largely through trial-and-error approaches. The relationships between DMD process parameters and the product characteristics such as porosity, micro-cracks and microhardness have been analysed using scanning electron microscope (SEM), image analysis software (ImageJ) and microhardness tester. It has been found that DMD parameters such as laser power, powder mass flow rate, feed rate and focus size have an important role in clad quality and crack formation.

The force-sensing peptide VemP employs extreme compaction and secondary structure formation to induce ribosomal stalling.

PubMed

Su, Ting; Cheng, Jingdong; Sohmen, Daniel; Hedman, Rickard; Berninghausen, Otto; von Heijne, Gunnar; Wilson, Daniel N; Beckmann, Roland

2017-05-30

Interaction between the nascent polypeptide chain and the ribosomal exit tunnel can modulate the rate of translation and induce translational arrest to regulate expression of downstream genes. The ribosomal tunnel also provides a protected environment for initial protein folding events. Here, we present a 2.9 Å cryo-electron microscopy structure of a ribosome stalled during translation of the extremely compacted VemP nascent chain. The nascent chain forms two α-helices connected by an α-turn and a loop, enabling a total of 37 amino acids to be observed within the first 50-55 Å of the exit tunnel. The structure reveals how α-helix formation directly within the peptidyltransferase center of the ribosome interferes with aminoacyl-tRNA accommodation, suggesting that during canonical translation, a major role of the exit tunnel is to prevent excessive secondary structure formation that can interfere with the peptidyltransferase activity of the ribosome.

Nitric oxide coupling to generate N2O promoted by a single-heme system as examined by density functional theory.

PubMed

Yi, Jun; Campbell, Adam L O; Richter-Addo, George B

2016-11-30

Bacteria utilize a heme/non-heme enzyme system to detoxify nitric oxide (NO) to N 2 O. In order to probe the capacity of a single-heme system to mediate this NO-to-N 2 O transformation, various scenarios for addition of electrons, protons, and a second NO molecule to a heme nitrosyl to generate N 2 O were explored by density functional theory calculations. We describe, utilizing this single-heme system, several stepwise intermediates along pathways that enable the critical N-N bond formation step yielding the desired Fe-N 2 O product. We also report a hitherto unreported directional second protonation that results in either productive N 2 O formation with loss of water, or formation of a non-productive hyponitrous acid adduct Fe{HONNOH}. Copyright © 2016 Elsevier Inc. All rights reserved.

Thrombus Formation at High Shear Rates.

PubMed

Casa, Lauren D C; Ku, David N

2017-06-21

The final common pathway in myocardial infarction and ischemic stroke is occlusion of blood flow from a thrombus forming under high shear rates in arteries. A high-shear thrombus forms rapidly and is distinct from the slow formation of coagulation that occurs in stagnant blood. Thrombosis at high shear rates depends primarily on the long protein von Willebrand factor (vWF) and platelets, with hemodynamics playing an important role in each stage of thrombus formation, including vWF binding, platelet adhesion, platelet activation, and rapid thrombus growth. The prediction of high-shear thrombosis is a major area of biofluid mechanics in which point-of-care testing and computational modeling are promising future directions for clinically relevant research. Further research in this area will enable identification of patients at high risk for arterial thrombosis, improve prevention and treatment based on shear-dependent biological mechanisms, and improve blood-contacting device design to reduce thrombosis risk.

Nanopores formed by DNA origami: a review.

PubMed

Bell, Nicholas A W; Keyser, Ulrich F

2014-10-01

Nanopores have emerged over the past two decades to become an important technique in single molecule experimental physics and biomolecule sensing. Recently DNA nanotechnology, in particular DNA origami, has been used for the formation of nanopores in insulating materials. DNA origami is a very attractive technique for the formation of nanopores since it enables the construction of 3D shapes with precise control over geometry and surface functionality. DNA origami has been applied to nanopore research by forming hybrid architectures with solid state nanopores and by direct insertion into lipid bilayers. This review discusses recent experimental work in this area and provides an outlook for future avenues and challenges. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Rate-dependent inverse-addition beta-selective mannosylation and contiguous sequential glycosylation involving beta-mannosidic bond formation.

PubMed

Chang, Shih-Sheng; Shih, Che-Hao; Lai, Kwun-Cheng; Mong, Kwok-Kong Tony

2010-05-03

The beta-selectivity of mannosylation has been found to be dependent on the addition rate of the mannosyl trichloroacetimidate donor in an inverse-addition (I-A) procedure. This rate dependent I-A procedure can improve the selectivity of direct beta-mannosylation and is applicable to orthogonal glycosylations of thioglycoside acceptors. Further elaboration of this novel procedure enables the development of the contiguous sequential glycosylation strategy, which streamlines the preparation of oligosaccharides invoking beta-mannosidic bond formation. The synthetic utility of the contiguous glycosylation strategy was demonstrated by the preparation of the trisaccharide core of human N-linked glycoproteins and the trisaccharide repeating unit of the O-specific polysaccharide found in the cellular capsule of Salmonelle bacteria.

Local formation of nitrogen-vacancy centers in diamond by swift heavy ions

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

Schwartz, J.; Ilmenau University of Technology, Department of Microelectronics and Nanoelectric Systems, 98684 Ilmenau; Aloni, S.

2014-12-07

We exposed nitrogen-implanted diamonds to beams of swift heavy ions (∼1 GeV, ∼4 MeV/u) and find that these irradiations lead directly to the formation of nitrogen vacancy (NV) centers, without thermal annealing. We compare the photoluminescence intensities of swift heavy ion activated NV{sup −} centers to those formed by irradiation with low-energy electrons and by thermal annealing. NV{sup −} yields from irradiations with swift heavy ions are 0.1 of yields from low energy electrons and 0.02 of yields from thermal annealing. We discuss possible mechanisms of NV center formation by swift heavy ions such as electronic excitations and thermal spikes. While formingmore » NV centers with low efficiency, swift heavy ions could enable the formation of three dimensional NV{sup −} assemblies over relatively large distances of tens of micrometers. Further, our results show that NV center formation is a local probe of (partial) lattice damage relaxation induced by electronic excitations from swift heavy ions in diamond.« less

Aza-heterocyclic Receptors for Direct Electron Transfer Hemoglobin Biosensor

NASA Astrophysics Data System (ADS)

Kumar, Vinay; Kashyap, D. M. Nikhila; Hebbar, Suraj; Swetha, R.; Prasad, Sujay; Kamala, T.; Srikanta, S. S.; Krishnaswamy, P. R.; Bhat, Navakanta

2017-02-01

Direct Electron Transfer biosensors, facilitating direct communication between the biomolecule of interest and electrode surface, are preferable compared to enzymatic and mediator based sensors. Although hemoglobin (Hb) contains four redox active iron centres, direct detection is not possible due to inaccessibility of iron centres and formation of dimers, blocking electron transfer. Through the coordination of iron with aza-heterocyclic receptors - pyridine and imidazole - we report a cost effective, highly sensitive and simple electrochemical Hb sensor using cyclic voltammetry and chronoamperometry. The receptor can be either in the form of liquid micro-droplet mixed with blood or dry chemistry embedded in paper membrane on top of screen printed carbon electrodes. We demonstrate excellent linearity and robustness against interference using clinical samples. A truly point of care technology is demonstrated by integrating disposable test strips with handheld reader, enabling finger prick to result in less than a minute.

Advancing the global proteome survey platform by using an oriented single chain antibody fragment immobilization approach.

PubMed

Säll, Anna; Persson, Helena; Ohlin, Mats; Borrebaeck, Carl A K; Wingren, Christer

2016-09-25

Increasing the understanding of a proteome and how its protein composition is affected by for example different diseases, such as cancer, has the potential to improve strategies for early diagnosis and therapeutics. The Global Proteome Survey or GPS is a method that combines mass spectrometry and affinity enrichment with the use of antibodies. The technology enables profiling of complex proteomes in a species independent manner. The sensitivity of GPS, and other methods relying on affinity enrichment, is largely affected by the activity of the exploited affinity reagent. We here present an improvement of the GPS platform by utilizing an antibody immobilization approach which ensures a controlled immobilization process of the antibody to the magnetic bead support. More specifically, we make use of an antibody format that enables site-directed biotinylation and use this in combination with streptavidin coated magnetic beads. The performance of the expanded GPS platform was evaluated by profiling yeast proteome samples. We demonstrate that the oriented antibody immobilization strategy increases the ability of the GPS platform and results in larger fraction of functional antibodies. Additionally, we show that this new antibody format enabled in-solution capture, i.e. immobilization of the antibodies after sample incubation. A workflow has been established that permit the use of an oriented immobilization strategy for the GPS platform. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Imaging Exoplanets with the Exo-S Starshade Mission: Key Enabling Technologies

NASA Astrophysics Data System (ADS)

Kasdin, N. Jeremy; Lisman, Doug; Shaklan, Stuart; Thomson, Mark; Webb, David; Cady, Eric; Exo-S Science; Technology Definition Team, Exoplanet Program Probe Study Design Team

2015-01-01

There is increasing interest in the use of a starshade, a spacecraft employing a large screen flying in formation with a space telescope, for providing the starlight suppression needed to detect and characterize exoplanets. In particular, Exo-S is a NASA study directed at designing a probe-scale exoplanet mission employing a starshade. In this poster we present the enabling technologies needed to make a starshade mission a reality: flight-like petals, a deployable truss to support the petals, optical edges, optical diffraction studies, and formation sensing and control. We show the status of each technology gap and summarize our progress over the past 5 years with plans for the next 3 years in demonstrating feasibility in all these areas. In particular, since no optical end-to-end test is possible, it is necessary to both show that a starshade can be built and deployed to the required accuracy and, via laboratory experiments at smaller scale, that the optical modeling upon which the accuracy requirements are based is validated. We show our progress verifying key enabling technologies, including demonstrating that a starshade petal made from flight-like materials can be manufactured to the needed accuracy and that a central truss with attached petals can be deployed with the needed precision. We also summarize our sub-scale lab experiments that demonstrate we can achieve the contrast predicted by our optical models.

New SPDF Directions and Evolving Services Supporting Heliophysics Research

NASA Technical Reports Server (NTRS)

McGuire, Robert E.; Candey, Robert M.; Bilitza, D.; Chimiak, Reine A.; Cooper, John F.; Fung, Shing F.; Han, David B.; Harris, Bernie; Johnson R.; Klipsch, C.;

Ion-beam nanopatterning: experimental results with chemically-assisted beam

NASA Astrophysics Data System (ADS)

Pochon, Sebastien C. R.

2018-03-01

The need for forming gratings (for example used in VR headsets) in materials such as SiO2 has seen a recent surge in the use of Ion beam etching techniques. However, when using an argon-only beam, the selectivity is limited as it is a physical process. Typically, gases such as CHF3, SF6, O2 and Cl2 can be added to argon in order to increase selectivity; depending on where the gas is injected, the process is known as Reactive Ion Beam Etching (RIBE) or Chemically Assisted Ion Beam Etching (CAIBE). The substrate holder can rotate in order to provide an axisymmetric etch rate profile. It can also be tilted over a range of angles to the beam direction. This enables control over the sidewall profile as well as radial uniformity optimisation. Ion beam directionality in conjunction with variable incident beam angle via platen angle setting enables profile control and feature shaping during nanopatterning. These hardware features unique to the Ion Beam etching methods can be used to create angled etch features. The CAIBE technique is also well suited to laser diode facet etch (for optoelectronic devices); these typically use III-V materials like InP. Here, we report on materials such as SiO2 etched without rotation and at a fixed platen angle allowing the formation of gratings and InP etched at a fixed angle with rotation allowing the formation of nanopillars and laser facets.

Adaptability of Protein Structures to Enable Functional Interactions and Evolutionary Implications

PubMed Central

Haliloglu, Turkan; Bahar, Ivet

2015-01-01

Several studies in recent years have drawn attention to the ability of proteins to adapt to intermolecular interactions by conformational changes along structure-encoded collective modes of motions. These so-called soft modes, primarily driven by entropic effects, facilitate, if not enable, functional interactions. They represent excursions on the conformational space along principal low-ascent directions/paths away from the original free energy minimum, and they are accessible to the protein even prior to protein-protein/ligand interactions. An emerging concept from these studies is the evolution of structures or modular domains to favor such modes of motion that will be recruited or integrated for enabling functional interactions. Structural dynamics, including the allosteric switches in conformation that are often stabilized upon formation of complexes and multimeric assemblies, emerge as key properties that are evolutionarily maintained to accomplish biological activities, consistent with the paradigm sequence → structure → dynamics → function where ‘dynamics’ bridges structure and function. PMID:26254902

Enabling Large Focal Plane Arrays Through Mosaic Hybridization

NASA Technical Reports Server (NTRS)

Miller, TImothy M.; Jhabvala, Christine A.; Leong, Edward; Costen, Nicholas P.; Sharp, Elmer; Adachi, Tomoko; Benford, Dominic

2012-01-01

We have demonstrated advances in mosaic hybridization that will enable very large format far-infrared detectors. Specifically we have produced electrical detector models via mosaic hybridization yielding superconducting circuit paths by hybridizing separately fabricated sub-units onto a single detector unit. The detector model was made on a 100mm diameter wafer while four model readout quadrant chips were made from a separate 100mm wafer. The individually fabricated parts were hybridized using a flip-chip bonder to assemble the detector-readout stack. Once all of the hybridized readouts were in place, a single, large and thick silicon substrate was placed on the stack and attached with permanent epoxy to provide strength and a Coefficient of Thermal Expansion match to the silicon components underneath. Wirebond pads on the readout chips connect circuits to warm readout electronics; and were used to validate the successful superconducting electrical interconnection of the model mosaic-hybrid detector. This demonstration is directly scalable to 150 mm diameter wafers, enabling pixel areas over ten times the area currently available.

SketchBio: a scientist's 3D interface for molecular modeling and animation.

PubMed

Waldon, Shawn M; Thompson, Peter M; Hahn, Patrick J; Taylor, Russell M

2014-10-30

Because of the difficulties involved in learning and using 3D modeling and rendering software, many scientists hire programmers or animators to create models and animations. This both slows the discovery process and provides opportunities for miscommunication. Working with multiple collaborators, a tool was developed (based on a set of design goals) to enable them to directly construct models and animations. SketchBio is presented, a tool that incorporates state-of-the-art bimanual interaction and drop shadows to enable rapid construction of molecular structures and animations. It includes three novel features: crystal-by-example, pose-mode physics, and spring-based layout that accelerate operations common in the formation of molecular models. Design decisions and their consequences are presented, including cases where iterative design was required to produce effective approaches. The design decisions, novel features, and inclusion of state-of-the-art techniques enabled SketchBio to meet all of its design goals. These features and decisions can be incorporated into existing and new tools to improve their effectiveness.

Schwann cells induce cancer cell dispersion and invasion

PubMed Central

Deborde, Sylvie; Lyubchik, Anna; Zhou, Yi; He, Shizhi; McNamara, William F.; Chernichenko, Natalya; Lee, Sei-Young; Barajas, Fernando; Chen, Chun-Hao; Bakst, Richard L.; Vakiani, Efsevia; He, Shuangba; Hall, Alan; Wong, Richard J.

2016-01-01

Nerves enable cancer progression, as cancers have been shown to extend along nerves through the process of perineural invasion, which carries a poor prognosis. Furthermore, the innervation of some cancers promotes growth and metastases. It remains unclear, however, how nerves mechanistically contribute to cancer progression. Here, we demonstrated that Schwann cells promote cancer invasion through direct cancer cell contact. Histological evaluation of murine and human cancer specimens with perineural invasion uncovered a subpopulation of Schwann cells that associates with cancer cells. Coculture of cancer cells with dorsal root ganglion extracts revealed that Schwann cells direct cancer cells to migrate toward nerves and promote invasion in a contact-dependent manner. Upon contact, Schwann cells induced the formation of cancer cell protrusions in their direction and intercalated between the cancer cells, leading to cancer cell dispersion. The formation of these processes was dependent on Schwann cell expression of neural cell adhesion molecule 1 (NCAM1) and ultimately promoted perineural invasion. Moreover, NCAM1-deficient mice showed decreased neural invasion and less paralysis. Such Schwann cell behavior reflects normal Schwann cell programs that are typically activated in nerve repair but are instead exploited by cancer cells to promote perineural invasion and cancer progression. PMID:26999607

PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets.

PubMed

Perez-Riverol, Yasset; Xu, Qing-Wei; Wang, Rui; Uszkoreit, Julian; Griss, Johannes; Sanchez, Aniel; Reisinger, Florian; Csordas, Attila; Ternent, Tobias; Del-Toro, Noemi; Dianes, Jose A; Eisenacher, Martin; Hermjakob, Henning; Vizcaíno, Juan Antonio

2016-01-01

The original PRIDE Inspector tool was developed as an open source standalone tool to enable the visualization and validation of mass-spectrometry (MS)-based proteomics data before data submission or already publicly available in the Proteomics Identifications (PRIDE) database. The initial implementation of the tool focused on visualizing PRIDE data by supporting the PRIDE XML format and a direct access to private (password protected) and public experiments in PRIDE.The ProteomeXchange (PX) Consortium has been set up to enable a better integration of existing public proteomics repositories, maximizing its benefit to the scientific community through the implementation of standard submission and dissemination pipelines. Within the Consortium, PRIDE is focused on supporting submissions of tandem MS data. The increasing use and popularity of the new Proteomics Standards Initiative (PSI) data standards such as mzIdentML and mzTab, and the diversity of workflows supported by the PX resources, prompted us to design and implement a new suite of algorithms and libraries that would build upon the success of the original PRIDE Inspector and would enable users to visualize and validate PX "complete" submissions. The PRIDE Inspector Toolsuite supports the handling and visualization of different experimental output files, ranging from spectra (mzML, mzXML, and the most popular peak lists formats) and peptide and protein identification results (mzIdentML, PRIDE XML, mzTab) to quantification data (mzTab, PRIDE XML), using a modular and extensible set of open-source, cross-platform libraries. We believe that the PRIDE Inspector Toolsuite represents a milestone in the visualization and quality assessment of proteomics data. It is freely available at http://github.com/PRIDE-Toolsuite/. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets*

PubMed Central

Perez-Riverol, Yasset; Xu, Qing-Wei; Wang, Rui; Uszkoreit, Julian; Griss, Johannes; Sanchez, Aniel; Reisinger, Florian; Csordas, Attila; Ternent, Tobias; del-Toro, Noemi; Dianes, Jose A.; Eisenacher, Martin; Hermjakob, Henning; Vizcaíno, Juan Antonio

2016-01-01

The original PRIDE Inspector tool was developed as an open source standalone tool to enable the visualization and validation of mass-spectrometry (MS)-based proteomics data before data submission or already publicly available in the Proteomics Identifications (PRIDE) database. The initial implementation of the tool focused on visualizing PRIDE data by supporting the PRIDE XML format and a direct access to private (password protected) and public experiments in PRIDE. The ProteomeXchange (PX) Consortium has been set up to enable a better integration of existing public proteomics repositories, maximizing its benefit to the scientific community through the implementation of standard submission and dissemination pipelines. Within the Consortium, PRIDE is focused on supporting submissions of tandem MS data. The increasing use and popularity of the new Proteomics Standards Initiative (PSI) data standards such as mzIdentML and mzTab, and the diversity of workflows supported by the PX resources, prompted us to design and implement a new suite of algorithms and libraries that would build upon the success of the original PRIDE Inspector and would enable users to visualize and validate PX “complete” submissions. The PRIDE Inspector Toolsuite supports the handling and visualization of different experimental output files, ranging from spectra (mzML, mzXML, and the most popular peak lists formats) and peptide and protein identification results (mzIdentML, PRIDE XML, mzTab) to quantification data (mzTab, PRIDE XML), using a modular and extensible set of open-source, cross-platform libraries. We believe that the PRIDE Inspector Toolsuite represents a milestone in the visualization and quality assessment of proteomics data. It is freely available at http://github.com/PRIDE-Toolsuite/. PMID:26545397

Horizontal natural gas storage caverns and methods for producing same

DOEpatents

Russo, Anthony

1995-01-01

The invention provides caverns and methods for producing caverns in bedded salt deposits for the storage of materials that are not solvents for salt. The contemplated salt deposits are of the bedded, non-domed variety, more particularly salt found in layered formations that are sufficiently thick to enable the production of commercially usefully sized caverns completely encompassed by walls of salt of the formation. In a preferred method, a first bore hole is drilled into the salt formation and a cavity for receiving insolubles is leached from the salt formation. Thereafter, at a predetermined distance away from the first bore hole, a second bore hole is drilled towards the salt formation. As this drill approaches the salt, the drill assumes a slant approach and enters the salt and drills through it in a horizontal direction until it intersects the cavity for receiving insolubles. This produces a substantially horizontal conduit from which solvent is controlledly supplied to the surrounding salt formation, leaching the salt and producing a concentrated brine which is removed through the first bore hole. Insolubles are collected in the cavity for receiving insolubles. By controlledly supplying solvent, a horizontal cavern is produced with two bore holes extending therefrom.

Elongation factor Ts directly facilitates the formation and disassembly of the Escherichia coli elongation factor Tu·GTP·aminoacyl-tRNA ternary complex.

PubMed

Burnett, Benjamin J; Altman, Roger B; Ferrao, Ryan; Alejo, Jose L; Kaur, Navdep; Kanji, Joshua; Blanchard, Scott C

2013-05-10

Aminoacyl-tRNA (aa-tRNA) enters the ribosome in a ternary complex with the G-protein elongation factor Tu (EF-Tu) and GTP. EF-Tu·GTP·aa-tRNA ternary complex formation and decay rates are accelerated in the presence of the nucleotide exchange factor elongation factor Ts (EF-Ts). EF-Ts directly facilitates the formation and disassociation of ternary complex. This system demonstrates a novel function of EF-Ts. Aminoacyl-tRNA enters the translating ribosome in a ternary complex with elongation factor Tu (EF-Tu) and GTP. Here, we describe bulk steady state and pre-steady state fluorescence methods that enabled us to quantitatively explore the kinetic features of Escherichia coli ternary complex formation and decay. The data obtained suggest that both processes are controlled by a nucleotide-dependent, rate-determining conformational change in EF-Tu. Unexpectedly, we found that this conformational change is accelerated by elongation factor Ts (EF-Ts), the guanosine nucleotide exchange factor for EF-Tu. Notably, EF-Ts attenuates the affinity of EF-Tu for GTP and destabilizes ternary complex in the presence of non-hydrolyzable GTP analogs. These results suggest that EF-Ts serves an unanticipated role in the cell of actively regulating the abundance and stability of ternary complex in a manner that contributes to rapid and faithful protein synthesis.

Multi-messenger studies of compact binary mergers in the in the ngVLA era

NASA Astrophysics Data System (ADS)

Corsi, Alessandra

2018-01-01

We explore some of the scientific opportunities that the next generation Very Large Array (ngVLA) will open in the field of multi-messenger time-domain astronomy. We focus on compact binary mergers, golden astrophysical targets of ground-based gravitational wave (GW) detectors such as advanced LIGO. A decade from now, a large number of these mergers is likely to be discovered by a world-wide network of GW detectors. We discuss how a radio array with 10 times the sensitivity of the current Karl G. Jansky VLA and 10 times the resolution, would enable resolved radio continuum studies of binary merger hosts, probing regions of the galaxy undergoing star formation (which can be heavily obscured by dust and gas), AGN components, and mapping the offset distribution of the mergers with respect to the host galaxy light. For compact binary mergers containing at least one neutron star (NS), from which electromagnetic counterparts are expected to exist, we show how the ngVLA would enable direct size measurements of the relativistic merger ejecta and probe, for the first time directly, their dynamics.

New physiologically-relevant liver tissue model based on hierarchically cocultured primary rat hepatocytes with liver endothelial cells.

PubMed

Xiao, Wenjin; Perry, Guillaume; Komori, Kikuo; Sakai, Yasuyuki

2015-11-01

To develop an in vitro liver tissue equivalent, hepatocytes should be cocultured with liver non-parenchymal cells to mimic the in vivo physiological microenvironments. In this work, we describe a physiologically-relevant liver tissue model by hierarchically organizing layers of primary rat hepatocytes and human liver sinusoidal endothelial cells (TMNK-1) on an oxygen-permeable polydimethylsiloxane (PDMS) membrane, which facilitates direct oxygenation by diffusion through the membrane. This in vivo-mimicking hierarchical coculture was obtained by simply proceeding the overlay of TMNK-1 cells on the hepatocyte layer re-formed on the collagen immobilized PDMS membranes. The comparison of hepatic functionalities was achieved between coculture and sandwich culture with Matrigel, in the presence and absence of direct oxygenation. A complete double-layered structure of functional liver cells with vertical contact between hepatocytes and TMNK-1 was successfully constructed in the coculture with direct oxygen supply and was well-maintained for 14 days. The hepatocytes in this hierarchical culture exhibited improved survival, functional bile canaliculi formation, cellular level polarization and maintenance of metabolic activities including Cyp1A1/2 activity and albumin production. By contrast, the two cell populations formed discontinuous monolayers on the same surfaces in the non-oxygen-permeable cultures. These results demonstrate that (i) the direct oxygenation through the PDMS membranes enables very simple formation of a hierarchical structure consisting of a hepatocyte layer and a layer of TMNK-1 and (ii) we may include other non-parenchymal cells in this format easily, which can be widely applicable to other epithelial organs.

Chemical signal activation of an organocatalyst enables control over soft material formation.

PubMed

Trausel, Fanny; Maity, Chandan; Poolman, Jos M; Kouwenberg, D S J; Versluis, Frank; van Esch, Jan H; Eelkema, Rienk

2017-10-12

Cells can react to their environment by changing the activity of enzymes in response to specific chemical signals. Artificial catalysts capable of being activated by chemical signals are rare, but of interest for creating autonomously responsive materials. We present an organocatalyst that is activated by a chemical signal, enabling temporal control over reaction rates and the formation of materials. Using self-immolative chemistry, we design a deactivated aniline organocatalyst that is activated by the chemical signal hydrogen peroxide and catalyses hydrazone formation. Upon activation of the catalyst, the rate of hydrazone formation increases 10-fold almost instantly. The responsive organocatalyst enables temporal control over the formation of gels featuring hydrazone bonds. The generic design should enable the use of a large range of triggers and organocatalysts, and appears a promising method for the introduction of signal response in materials, constituting a first step towards achieving communication between artificial chemical systems.Enzymes regulated by chemical signals are common in biology, but few such artificial catalysts exist. Here, the authors design an aniline catalyst that, when activated by a chemical trigger, catalyses formation of hydrazone-based gels, demonstrating signal response in a soft material.

DIRECT secure messaging as a common transport layer for reporting structured and unstructured lab results to outpatient providers.

PubMed

Sujansky, Walter; Wilson, Tom

2015-04-01

This report describes a grant-funded project to explore the use of DIRECT secure messaging for the electronic delivery of laboratory test results to outpatient physicians and electronic health record systems. The project seeks to leverage the inherent attributes of DIRECT secure messaging and electronic provider directories to overcome certain barriers to the delivery of lab test results in the outpatient setting. The described system enables laboratories that generate test results as HL7 messages to deliver these results as structured or unstructured documents attached to DIRECT secure messages. The system automatically analyzes generated HL7 messages and consults an electronic provider directory to determine the appropriate DIRECT address and delivery format for each indicated recipient. The system also enables lab results delivered to providers as structured attachments to be consumed by HL7 interface engines and incorporated into electronic health record systems. Lab results delivered as unstructured attachments may be printed or incorporated into patient records as PDF files. The system receives and logs acknowledgement messages to document the status of each transmitted lab result, and a graphical interface allows searching and review of this logged information. The described system is a fully implemented prototype that has been tested in a laboratory setting. Although this approach is promising, further work is required to pilot test the system in production settings with clinical laboratories and outpatient provider organizations. Copyright © 2015 Elsevier Inc. All rights reserved.

Collaborative Planning of Robotic Exploration

NASA Technical Reports Server (NTRS)

Norris, Jeffrey; Backes, Paul; Powell, Mark; Vona, Marsette; Steinke, Robert

2004-01-01

The Science Activity Planner (SAP) software system includes an uplink-planning component, which enables collaborative planning of activities to be undertaken by an exploratory robot on a remote planet or on Earth. Included in the uplink-planning component is the SAP-Uplink Browser, which enables users to load multiple spacecraft activity plans into a single window, compare them, and merge them. The uplink-planning component includes a subcomponent that implements the Rover Markup Language Activity Planning format (RML-AP), based on the Extensible Markup Language (XML) format that enables the representation, within a single document, of planned spacecraft and robotic activities together with the scientific reasons for the activities. Each such document is highly parseable and can be validated easily. Another subcomponent of the uplink-planning component is the Activity Dictionary Markup Language (ADML), which eliminates the need for two mission activity dictionaries - one in a human-readable format and one in a machine-readable format. Style sheets that have been developed along with the ADML format enable users to edit one dictionary in a user-friendly environment without compromising

Additive direct-write microfabrication for MEMS: A review

NASA Astrophysics Data System (ADS)

Teh, Kwok Siong

2017-12-01

Direct-write additive manufacturing refers to a rich and growing repertoire of well-established fabrication techniques that builds solid objects directly from computer- generated solid models without elaborate intermediate fabrication steps. At the macroscale, direct-write techniques such as stereolithography, selective laser sintering, fused deposition modeling ink-jet printing, and laminated object manufacturing have significantly reduced concept-to-product lead time, enabled complex geometries, and importantly, has led to the renaissance in fabrication known as the maker movement. The technological premises of all direct-write additive manufacturing are identical—converting computer generated three-dimensional models into layers of two-dimensional planes or slices, which are then reconstructed sequentially into threedimensional solid objects in a layer-by-layer format. The key differences between the various additive manufacturing techniques are the means of creating the finished layers and the ancillary processes that accompany them. While still at its infancy, direct-write additive manufacturing techniques at the microscale have the potential to significantly lower the barrier-of-entry—in terms of cost, time and training—for the prototyping and fabrication of MEMS parts that have larger dimensions, high aspect ratios, and complex shapes. In recent years, significant advancements in materials chemistry, laser technology, heat and fluid modeling, and control systems have enabled additive manufacturing to achieve higher resolutions at the micrometer and nanometer length scales to be a viable technology for MEMS fabrication. Compared to traditional MEMS processes that rely heavily on expensive equipment and time-consuming steps, direct-write additive manufacturing techniques allow for rapid design-to-prototype realization by limiting or circumventing the need for cleanrooms, photolithography and extensive training. With current direct-write additive manufacturing technologies, it is possible to fabricate unsophisticated micrometer scale structures at adequate resolutions and precisions using materials that range from polymers, metals, ceramics, to composites. In both academia and industry, direct-write additive manufacturing offers extraordinary promises to revolutionize research and development in microfabrication and MEMS technologies. Importantly, direct-write additive manufacturing could appreciably augment current MEMS fabrication technologies, enable faster design-to-product cycle, empower new paradigms in MEMS designs, and critically, encourage wider participation in MEMS research at institutions or for individuals with limited or no access to cleanroom facilities. This article aims to provide a limited review of the current landscape of direct-write additive manufacturing techniques that are potentially applicable for MEMS microfabrication.

In situ measurements of soot formation in simple flames using small angle X-ray scattering

NASA Astrophysics Data System (ADS)

Gardner, C.; Greaves, G. N.; Hargrave, G. K.; Jarvis, S.; Wildman, P.; Meneau, F.; Bras, W.; Thomas, G.

2005-08-01

Direct SAXS measurements of soot formation from ethylene have been made using laminar pre-mixed flames for the first time. The slot burner was configured to maximise the signal from particulates. The geometry also enabled the thermal background from the surrounding hot gasses to be accurately removed. With cold flame speeds of 40 cm s-1 we have been able to identify particle sizes and densities from moderately sooty to rich flame conditions. By adjusting the height of the burner in the beam, the development of particles as a function of position above the flame tip and therefore as a function of time from ignition have been obtained. These reveal evidence for bimodal particle nucleation and growth at different stages in the continuous combustion of ethylene.

Quantum memory receiver for superadditive communication using binary coherent states

NASA Astrophysics Data System (ADS)

Klimek, Aleksandra; Jachura, Michał; Wasilewski, Wojciech; Banaszek, Konrad

2016-11-01

We propose a simple architecture based on multimode quantum memories for collective readout of classical information keyed using a pair coherent states, exemplified by the well-known binary phase shift keying format. Such a configuration enables demonstration of the superadditivity effect in classical communication over quantum channels, where the transmission rate becomes enhanced through joint detection applied to multiple channel uses. The proposed scheme relies on the recently introduced idea to prepare Hadamard sequences of input symbols that are mapped by a linear optical transformation onto the pulse position modulation format [Guha, S. Phys. Rev. Lett. 2011, 106, 240502]. We analyze two versions of readout based on direct detection and an optional Dolinar receiver which implements the minimum-error measurement for individual detection of a binary coherent state alphabet.

Quantum memory receiver for superadditive communication using binary coherent states.

PubMed

Klimek, Aleksandra; Jachura, Michał; Wasilewski, Wojciech; Banaszek, Konrad

2016-11-12

We propose a simple architecture based on multimode quantum memories for collective readout of classical information keyed using a pair coherent states, exemplified by the well-known binary phase shift keying format. Such a configuration enables demonstration of the superadditivity effect in classical communication over quantum channels, where the transmission rate becomes enhanced through joint detection applied to multiple channel uses. The proposed scheme relies on the recently introduced idea to prepare Hadamard sequences of input symbols that are mapped by a linear optical transformation onto the pulse position modulation format [Guha, S. Phys. Rev. Lett. 2011 , 106 , 240502]. We analyze two versions of readout based on direct detection and an optional Dolinar receiver which implements the minimum-error measurement for individual detection of a binary coherent state alphabet.

Structural features of silver-doped phosphate glasses in zone of femtosecond laser-induced modification

NASA Astrophysics Data System (ADS)

Vasileva, A. A.; Nazarov, I. A.; Olshin, P. K.; Povolotskiy, A. V.; Sokolov, I. A.; Manshina, A. A.

2015-10-01

Femtosecond (fs) laser writing of two-dimensional microstructures (waveguides) is demonstrated in bulk phosphate glasses doped with silver ions. Silver-content phosphate and silver-content niobium-phosphate glasses with high concentration of silver oxide 55 mol% were used as samples for fs laser writing. The chemical network structure of the synthesized samples is analyzed through Raman spectroscopy and was found to be strongly sensitive to Nb incorporation. It was found that the direct laser writing process enables not only reorganization of glass network, but also formation of color centers and silver nanoparticles that are revealed in appearance of luminescence signal and plasmon absorption. The process of NPs' formation is more efficient for Nb-phosphate glass, while color centers are preferably formed in phosphate glass.

3D-Printed Transparent Glass

DOE PAGES

Nguyen, Du T.; Meyers, Cameron; Yee, Timothy D.; ...

2017-04-28

In this study, silica inks are developed, which may be 3D printed and thermally processed to produce optically transparent glass structures with sub-millimeter features in forms ranging from scaffolds to monoliths. The inks are composed of silica powder suspended in a liquid and are printed using direct ink writing. The printed structures are then dried and sintered at temperatures well below the silica melting point to form amorphous, solid, transparent glass structures. This technique enables the mold-free formation of transparent glass structures previously inaccessible using conventional glass fabrication processes.

3D-Printed Transparent Glass

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

Nguyen, Du T.; Meyers, Cameron; Yee, Timothy D.

In this study, silica inks are developed, which may be 3D printed and thermally processed to produce optically transparent glass structures with sub-millimeter features in forms ranging from scaffolds to monoliths. The inks are composed of silica powder suspended in a liquid and are printed using direct ink writing. The printed structures are then dried and sintered at temperatures well below the silica melting point to form amorphous, solid, transparent glass structures. This technique enables the mold-free formation of transparent glass structures previously inaccessible using conventional glass fabrication processes.

An investigation of hydrogenized amorphous Si structures with Doppler broadening positron annihilation techniques

NASA Astrophysics Data System (ADS)

Petkov, M. P.; Marek, T.; Asoka-Kumar, P.; Lynn, K. G.; Crandall, R. S.; Mahan, A. H.

1998-07-01

In this letter, we examine the feasibility of applying positron annihilation spectroscopy to the study of hydrogenized amorphous silicon (a-Si:H)-based structures produced by chemical vapor deposition techniques. The positron probe, sensitive to open volume formations, is used to characterize neutral and negatively charged silicon dangling bonds, typical for undoped and n-doped a-Si:H, respectively. Using depth profiling along the growth direction a difference was observed in the electronic environment of these defects, which enables their identification in a p-i-n device.

Distributions of Dusty Star Forming Region in Local Starburst Galaxies

NASA Astrophysics Data System (ADS)

Tateuchi, K.; Motohara, K.; Konishi, M.; Takahashi, H.; Kato, N.; Kitagawa, Y.; Yoshii, Y.; Doi, M.; Kohno, K.; Kawara, K.; Tanaka, M.; Miyata, T.; Tanabe, T.; Minezaki, T.; Sako, S.; Morokuma, T.; Tamura, Y.; Aoki, T.; Soyano, T.; Tarusawa, K.; Koshida, S.; Kamizuka, T.; Asano, K.; Uchiyama, M.; Okada, K.

2013-10-01

Since the first light observation of ANIR in June 2009, we have been carrying out a Paα narrow-band imaging survey of nearby luminous infrared galaxies (LIRGs). Because Paα is the strongest hydrogen recombination line in the infrared wavelength ranges, it is a good and direct tracer of dust-enshrouded star forming regions, and enables us to probe the star formation activities in LIRGs. We find that LIRGs have two star-forming modes. The origin of the two modes probably come from differences between merging stage and/or star-forming process.

Using IKAROS as a data transfer and management utility within the KM3NeT computing model

NASA Astrophysics Data System (ADS)

Filippidis, Christos; Cotronis, Yiannis; Markou, Christos

2016-04-01

KM3NeT is a future European deep-sea research infrastructure hosting a new generation neutrino detectors that - located at the bottom of the Mediterranean Sea - will open a new window on the universe and answer fundamental questions both in particle physics and astrophysics. IKAROS is a framework that enables creating scalable storage formations on-demand and helps addressing several limitations that the current file systems face when dealing with very large scale infrastructures. It enables creating ad-hoc nearby storage formations and can use a huge number of I/O nodes in order to increase the available bandwidth (I/O and network). IKAROS unifies remote and local access in the overall data flow, by permitting direct access to each I/O node. In this way we can handle the overall data flow at the network layer, limiting the interaction with the operating system. This approach allows virtually connecting, at the users level, the several different computing facilities used (Grids, Clouds, HPCs, Data Centers, Local computing Clusters and personal storage devices), on-demand, based on the needs, by using well known standards and protocols, like HTTP.

Real-time assays with molecular beacons and other fluorescent nucleic acid hybridization probes.

PubMed

Marras, Salvatore A E; Tyagi, Sanjay; Kramer, Fred Russell

2006-01-01

A number of formats for nucleic acid hybridization have been developed to identify DNA and RNA sequences that are involved in cellular processes and that aid in the diagnosis of genetic and infectious diseases. The introduction of hybridization probes with interactive fluorophore pairs has enabled the development of homogeneous hybridization assays for the direct identification of nucleic acids. A change in the fluorescence of these probes indicates the presence of a target nucleic acid, and there is no need to separate unbound probes from hybridized probes. The advantages of homogeneous hybridization assays are their speed and simplicity. In addition, homogeneous assays can be combined with nucleic acid amplification, enabling the detection of rare target nucleic acids. These assays can be followed in real time, providing quantitative determination of target nucleic acids over a broad range of concentrations.

Measuring the High-Mass IMF in Low-Metallicity Dwarf Galaxies

NASA Astrophysics Data System (ADS)

Weisz, Daniel

2017-08-01

We propose to measure the stellar initial mass function above >1-2 Msun in 46 nearby dwarf galaxies with archival HST observations. This novel approach leverages the redundant age information provided by the main sequence and blue core helium burning stars <500 years old to break the well-known degeneracy between the IMF and star formation history (SFH), enabling a direct measurement of the high-mass IMF in dwarf galaxies. We will be able to constrain the high-mass IMF slope to a precision better than 0.1 to 0.3 dex in each galaxy. Our sample spans a factor of 6 in metallicity ( 5-30% Zsun), 4 decades in star formation rate, and 3 decades in both stellar and gas mass, allowing us to explore the IMF over a wide range of extreme environments.Current observational evidence suggests that nearby dwarf galaxies are the most likely candidates to host significant and systematic variations in the high-mass IMF (e.g., Halpha/UV ratios). However, to date there have been no direct measurements of the high-mass IMF in environments with lower star formation rates and/or more metal poor than the Magellanic Clouds. Our program remedies this shortcoming allowing us to (1) make the first-ever measurement of the high-mass IMF in extremely metal-poor environments; (2) empirically quantify environmental the (lack of) variations in the high-mass IMF; (3) directly test the integrated galactic mass initial mass function (IGIMF), which predicts environmental sensitivity of the IMF in dwarf galaxies.

Development of a homogeneous assay format for p53 antibodies using fluorescence correlation spectroscopy

NASA Astrophysics Data System (ADS)

Neuweiler, Hannes; Scheffler, Silvia; Sauer, Markus

2005-08-01

The development of reliable methods for the detection of minute amounts of antibodies directly in homogeneous solution represents one of the major tasks in the current research field of molecular diagnostics. We demonstrate the potential of fluorescence correlation spectroscopy (FCS) in combination with quenched peptide-based fluorescence probes for sensitive detection of p53 antibodies directly in homogeneous solution. Single tryptophan (Trp) residues in the sequences of short, synthetic peptide epitopes of the human p53 protein efficiently quench the fluorescence of an oxazine fluorophore attached to the amino terminal ends of the peptides. The fluorescence quenching mechanism is thought to be a photoinduced electron transfer reaction from Trp to the dye enabled by the formation of intramolecular complexes between dye and Trp. Specific recognition of the epitope by the antibody confines the conformational flexibility of the peptide. Consequently, complex formation between dye and Trp is abolished and fluorescence is recovered. Using fluorescence correlation spectroscopy (FCS), antibody binding can be monitored observing two parameters simultaneously: the diffusional mobility of the peptide as well as the quenching amplitude induced by the conformational flexibility of the peptide change significantly upon antibody binding. Our data demonstrate that FCS in combination with fluorescence-quenched peptide epitopes opens new possibilities for the reliable detection of antibody binding events in homogeneous solution.

External Data and Attribute Hyperlink Programs for Promis*e(Registered Trademark)

NASA Technical Reports Server (NTRS)

Derengowski, Rich; Gruel, Andrew

2001-01-01

External Data and Attribute Hyperlink are computer programs that can be added to Promis*e(trademark) which is a commercial software system that automates routine tasks in the design (including drawing schematic diagrams) of electrical control systems. The programs were developed under the Stennis Space Center's (SSC) Dual Use Technology Development Program to provide capabilities for SSC's BMCS configuration management system which uses Promis*e(trademark). The External Data program enables the storage and management of information in an external database linked to a drawing. Changes can be made either in the database or on the drawing. Information that originates outside Promis*e(trademark) can be stored in custom fields that can be added to the database. Although this information is not available in Promis*e(trademark) printed drawings, it can be associated with symbols in the drawings, and can be retrieved through the drawings when the software is running. The Attribute Hyperlink program enables the addition of hyperlink information as attributes of symbols. This program enables the formation of a direct hyperlink between a schematic diagram and an Internet site or a file on a compact disk, on the user's hard drive, or on another computer on a network to which the user's computer is connected. The user can then obtain information directly related to the part (e.g., maintenance, or troubleshooting information) associated with the hyperlink.

proBAMconvert: A Conversion Tool for proBAM/proBed.

PubMed

Olexiouk, Volodimir; Menschaert, Gerben

2017-07-07

The introduction of new standard formats, proBAM and proBed, improves the integration of genomics and proteomics information, thus aiding proteogenomics applications. These novel formats enable peptide spectrum matches (PSM) to be stored, inspected, and analyzed within the context of the genome. However, an easy-to-use and transparent tool to convert mass spectrometry identification files to these new formats is indispensable. proBAMconvert enables the conversion of common identification file formats (mzIdentML, mzTab, and pepXML) to proBAM/proBed using an intuitive interface. Furthermore, ProBAMconvert enables information to be output both at the PSM and peptide levels and has a command line interface next to the graphical user interface. Detailed documentation and a completely worked-out tutorial is available at http://probam.biobix.be .

N-BODY SIMULATION OF PLANETESIMAL FORMATION THROUGH GRAVITATIONAL INSTABILITY AND COAGULATION. II. ACCRETION MODEL

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

Michikoshi, Shugo; Kokubo, Eiichiro; Inutsuka, Shu-ichiro, E-mail: michikoshi@cfca.j, E-mail: kokubo@th.nao.ac.j, E-mail: inutsuka@tap.scphys.kyoto-u.ac.j

2009-10-01

The gravitational instability of a dust layer is one of the scenarios for planetesimal formation. If the density of a dust layer becomes sufficiently high as a result of the sedimentation of dust grains toward the midplane of a protoplanetary disk, the layer becomes gravitationally unstable and spontaneously fragments into planetesimals. Using a shearing box method, we performed local N-body simulations of gravitational instability of a dust layer and subsequent coagulation without gas and investigated the basic formation process of planetesimals. In this paper, we adopted the accretion model as a collision model. A gravitationally bound pair of particles ismore » replaced by a single particle with the total mass of the pair. This accretion model enables us to perform long-term and large-scale calculations. We confirmed that the formation process of planetesimals is the same as that in the previous paper with the rubble pile models. The formation process is divided into three stages: the formation of nonaxisymmetric structures; the creation of planetesimal seeds; and their collisional growth. We investigated the dependence of the planetesimal mass on the simulation domain size. We found that the mean mass of planetesimals formed in simulations is proportional to L {sup 3/2} {sub y}, where L{sub y} is the size of the computational domain in the direction of rotation. However, the mean mass of planetesimals is independent of L{sub x} , where L{sub x} is the size of the computational domain in the radial direction if L{sub x} is sufficiently large. We presented the estimation formula of the planetesimal mass taking into account the simulation domain size.« less

An analytic resolution to the competition between Lyman-Werner radiation and metal winds in direct collapse black hole hosts

NASA Astrophysics Data System (ADS)

Agarwal, Bhaskar; Regan, John; Klessen, Ralf S.; Downes, Turlough P.; Zackrisson, Erik

2017-10-01

A near pristine atomic cooling halo close to a star forming galaxy offers a natural pathway for forming massive direct collapse black hole (DCBH) seeds, which could be the progenitors of the z > 6 redshift quasars. The close proximity of the haloes enables a sufficient Lyman-Werner flux to effectively dissociate H2 in the core of the atomic cooling halo. A mild background may also be required to delay star formation in the atomic cooling halo, often attributed to distant background galaxies. In this paper, we investigate the impact of metal pollution from both the background galaxies and the close star forming galaxy under extremely unfavourable conditions such as instantaneous metal mixing. We find that within the time window of DCBH formation, the level of pollution never exceeds the critical threshold (Zcr ˜ 1 × 10-5 Z⊙) and attains a maximum metallicity of Z ˜ 2 × 10- 6 Z⊙. As the system evolves, the metallicity eventually exceeds the critical threshold, long after the DCBH has formed.

Stabilization of the Peregrine soliton and Kuznetsov-Ma breathers by means of nonlinearity and dispersion management

NASA Astrophysics Data System (ADS)

Cuevas-Maraver, J.; Malomed, Boris A.; Kevrekidis, P. G.; Frantzeskakis, D. J.

2018-04-01

We demonstrate a possibility to make rogue waves (RWs) in the form of the Peregrine soliton (PS) and Kuznetsov-Ma breathers (KMBs) effectively stable objects, with the help of properly defined dispersion or nonlinearity management applied to the continuous-wave (CW) background supporting the RWs. In particular, it is found that either management scheme, if applied along the longitudinal coordinate, making the underlying nonlinear Schrödinger equation (NLSE) self-defocusing in the course of disappearance of the PS, indeed stabilizes the global solution with respect to the modulational instability of the background. In the process, additional excitations are generated, namely, dispersive shock waves and, in some cases, also a pair of slowly separating dark solitons. Further, the nonlinearity-management format, which makes the NLSE defocusing outside of a finite domain in the transverse direction, enables the stabilization of the KMBs, in the form of confined oscillating states. On the other hand, a nonlinearity-management format applied periodically along the propagation direction, creates expanding patterns featuring multiplication of KMBs through their cascading fission.

Bending nanofibers into nanospirals: coordination chemistry as a tool for shaping hydrophobic assemblies.

PubMed

Kossoy, Elizaveta; Weissman, Haim; Rybtchinski, Boris

2015-01-02

In the current work, we demonstrate how coordination chemistry can be employed to direct self-assembly based on strong hydrophobic interactions. To investigate the influence of coordination sphere geometry on aqueous self-assembly, we synthesized complexes of the amphiphilic perylene diimide terpyridine ligand with the first-row transition-metal centers (zinc, cobalt, and nickel). In aqueous medium, aggregation of these complexes is induced by hydrophobic interactions between the ligands. However, the final shapes of the resulting assemblies depend on the preferred geometry of the coordination spheres typical for the particular metal center. The self-assembly process was characterized by UV/Vis spectroscopy, zeta potential measurements, and cryogenic transmission electron microscopy (cryo-TEM). Coordination of zinc(II) and cobalt(II) leads to the formation of unique nanospiral assemblies, whereas complexation of nickel(II) leads to the formation of straight nanofibers. Notably, coordination bonds are utilized not as connectors between elementary building blocks, but as directing interactions, enabling control over supramolecular geometry. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Selective anaerobic oxidation of methane enables direct synthesis of methanol.

PubMed

Sushkevich, Vitaly L; Palagin, Dennis; Ranocchiari, Marco; van Bokhoven, Jeroen A

2017-05-05

Direct functionalization of methane in natural gas remains a key challenge. We present a direct stepwise method for converting methane into methanol with high selectivity (~97%) over a copper-containing zeolite, based on partial oxidation with water. The activation in helium at 673 kelvin (K), followed by consecutive catalyst exposures to 7 bars of methane and then water at 473 K, consistently produced 0.204 mole of CH 3 OH per mole of copper in zeolite. Isotopic labeling confirmed water as the source of oxygen to regenerate the zeolite active centers and renders methanol desorption energetically favorable. On the basis of in situ x-ray absorption spectroscopy, infrared spectroscopy, and density functional theory calculations, we propose a mechanism involving methane oxidation at Cu II oxide active centers, followed by Cu I reoxidation by water with concurrent formation of hydrogen. Copyright © 2017, American Association for the Advancement of Science.

Controlling the Localization of Liquid Droplets in Polymer Matrices by Evaporative Lithography.

PubMed

Zhao, Huaixia; Xu, Jiajia; Jing, Guangyin; Prieto-López, Lizbeth Ofelia; Deng, Xu; Cui, Jiaxi

2016-08-26

Localized inclusions of liquids provide solid materials with many functions, such as self-healing, secretion, and tunable mechanical properties, in a spatially controlled mode. However, a strategy to control the distribution of liquid droplets in solid matrices directly obtained from a homogeneous solution has not been reported thus far. Herein, we describe an approach to selectively localize liquid droplets in a supramolecular gel directly obtained from its solution by using evaporative lithography. In this process, the formation of droplet-embedded domains occurs in regions of free evaporation where the non-volatile liquid is concentrated and undergoes a phase separation to create liquid droplets prior to gelation, while a homogeneous gel matrix is formed in the regions of hindered evaporation. The different regions of a coating with droplet embedment patterns display different secretion abilities, enabling the control of the directional movement of water droplets. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Granules harboring translationally active mRNAs provide a platform for P-body formation following stress.

PubMed

Lui, Jennifer; Castelli, Lydia M; Pizzinga, Mariavittoria; Simpson, Clare E; Hoyle, Nathaniel P; Bailey, Kathryn L; Campbell, Susan G; Ashe, Mark P

2014-11-06

The localization of mRNA to defined cytoplasmic sites in eukaryotic cells not only allows localized protein production but also determines the fate of mRNAs. For instance, translationally repressed mRNAs localize to P-bodies and stress granules where their decay and storage, respectively, are directed. Here, we find that several mRNAs are localized to granules in unstressed, actively growing cells. These granules play a key role in the stress-dependent formation of P-bodies. Specific glycolytic mRNAs are colocalized in multiple granules per cell, which aggregate during P-body formation. Such aggregation is still observed under conditions or in mutants where P-bodies do not form. In unstressed cells, the mRNA granules appear associated with active translation; this might enable a coregulation of protein expression from the same pathways or complexes. Parallels can be drawn between this coregulation and the advantage of operons in prokaryotic systems. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

The force-sensing peptide VemP employs extreme compaction and secondary structure formation to induce ribosomal stalling

PubMed Central

Su, Ting; Cheng, Jingdong; Sohmen, Daniel; Hedman, Rickard; Berninghausen, Otto; von Heijne, Gunnar; Wilson, Daniel N; Beckmann, Roland

2017-01-01

Interaction between the nascent polypeptide chain and the ribosomal exit tunnel can modulate the rate of translation and induce translational arrest to regulate expression of downstream genes. The ribosomal tunnel also provides a protected environment for initial protein folding events. Here, we present a 2.9 Å cryo-electron microscopy structure of a ribosome stalled during translation of the extremely compacted VemP nascent chain. The nascent chain forms two α-helices connected by an α-turn and a loop, enabling a total of 37 amino acids to be observed within the first 50–55 Å of the exit tunnel. The structure reveals how α-helix formation directly within the peptidyltransferase center of the ribosome interferes with aminoacyl-tRNA accommodation, suggesting that during canonical translation, a major role of the exit tunnel is to prevent excessive secondary structure formation that can interfere with the peptidyltransferase activity of the ribosome. DOI: http://dx.doi.org/10.7554/eLife.25642.001 PMID:28556777

Analytical solution of perturbed relative motion: an application of satellite formations to geodesy

NASA Astrophysics Data System (ADS)

Wnuk, Edwin

In the upcoming years, several space missions will be operated using a number of spacecraft flying in formation. Clusters of spacecraft with a carefully designed orbits and optimal formation geometry enable a wide variety of applications ranging from remote sensing to astronomy, geodesy and basic physics. Many of the applications require precise relative navigation and autonomous orbit control of satellites moving in a formation. For many missions a centimeter level of orbit control accuracy is required. The GRACE mission, since its launch in 2002, has been improving the Earth's gravity field model to a very high level of accuracy. This mission is a formation flying one consisting of two satellites moving in coplanar orbits and provides range and range-rate measurements between the satellites in the along-track direction. Future geodetic missions probably will employ alternative architectures using additional satellites and/or performing out-of-plane motion, e.g cartwheel orbits. The paper presents an analytical model of a satellite formation motion that enables propagation of the relative spacecraft motion. The model is based on the analytical theory of satellite relative motion that was presented in the previous our papers (Wnuk and Golebiewska, 2005, 2006). This theory takes into account the influence of the following gravitational perturbation effects: 1) zonal and tesseral harmonic geopotential coefficients up to arbitrary degree and order, 2) Lunar gravity, 3) Sun gravity. Formulas for differential perturbations were derived with any restriction concerning a plane of satellite orbits. They can be applied in both: in plane and out of plane cases. Using this propagator we calculated relative orbits and future relative satellite positions for different types of formations: in plane, out of plane, cartwheel and others. We analyzed the influence of particular parts of perturbation effects and estimated the accuracy of predicted relative spacecrafts positions. References 1,Wnuk E., Golebiewska J.,2005, ,,The relative motion of Earth's orbiting satellites", Celestial Mechanics, 91, 373-389. 2.Wnuk E., Golebiewska J.,2006, "Differential Perturbations and Semimajor Axis Estimation for Satellite Formation Orbits", American Institute of Aeronautics and Astronautics, Electronic Library, 2006, 6018.

Enhanced DNA Sensing via Catalytic Aggregation of Gold Nanoparticles

PubMed Central

Huttanus, Herbert M.; Graugnard, Elton; Yurke, Bernard; Knowlton, William B.; Kuang, Wan; Hughes, William L.; Lee, Jeunghoon

2014-01-01

A catalytic colorimetric detection scheme that incorporates a DNA-based hybridization chain reaction into gold nanoparticles was designed and tested. While direct aggregation forms an inter-particle linkage from only ones target DNA strand, the catalytic aggregation forms multiple linkages from a single target DNA strand. Gold nanoparticles were functionalized with thiol-modified DNA strands capable of undergoing hybridization chain reactions. The changes in their absorption spectra were measured at different times and target concentrations and compared against direct aggregation. Catalytic aggregation showed a multifold increase in sensitivity at low target concentrations when compared to direct aggregation. Gel electrophoresis was performed to compare DNA hybridization reactions in catalytic and direct aggregation schemes, and the product formation was confirmed in the catalytic aggregation scheme at low levels of target concentrations. The catalytic aggregation scheme also showed high target specificity. This application of a DNA reaction network to gold nanoparticle-based colorimetric detection enables highly-sensitive, field-deployable, colorimetric readout systems capable of detecting a variety of biomolecules. PMID:23891867

How Elsevier's Article of the Future supports researchers in the digital era

NASA Astrophysics Data System (ADS)

Keall, B.

2012-04-01

The first phase of Elsevier's Article of the Future article format was released on SciVerse ScienceDirect in January 2012. While this new format for online scholarly articles brings a significantly improved online presentation, it also enables further enhancements in terms of domain-specific content and contextualization of research results. Of particular interest to the Earth Sciences research community are the seamless integration of an interactive map viewer that displays author-submitted KML files inside the article, and real-time links to leading research data portals like Pangaea and Earthchem. These enhancements allow for a richer form of communication between authors and readers, and present researchers with valuable additional information in the context of the article. In this presentaion I will review these ongoing efforts to enhance online articles in the digital era.

Time lapse microscopy of temperature control during self-assembly of 3D DNA crystals

NASA Astrophysics Data System (ADS)

Conn, Fiona W.; Jong, Michael Alexander; Tan, Andre; Tseng, Robert; Park, Eunice; Ohayon, Yoel P.; Sha, Ruojie; Mao, Chengde; Seeman, Nadrian C.

2017-10-01

DNA nanostructures are created by exploiting the high fidelity base-pairing interactions of double-stranded branched DNA molecules. These structures present a convenient medium for the self-assembly of macroscopic 3D crystals. In some self-assemblies in this system, crystals can be formed by lowering the temperature, and they can be dissolved by raising it. The ability to monitor the formation and melting of these crystals yields information that can be used to monitor crystal formation and growth. Here, we describe the development of an inexpensive tool that enables direct observation of the crystal growth process as a function of both time and temperature. Using the hanging-drop crystallization of the well-characterized 2-turn DNA tensegrity triangle motif for our model system, its response to temperature has been characterized visually.

Optical instrumentation for science and formation flying with a starshade observatory

NASA Astrophysics Data System (ADS)

Martin, Stefan; Scharf, Daniel; Cady, Eric; Liebe, Carl; Tang, Hong

2015-09-01

In conjunction with a space telescope of modest size, a starshade enables observation of small exoplanets close to the parent star by blocking the direct starlight while the planet light remains unobscured. The starshade is flown some tens of thousands of kilometers ahead of the telescope. Science instruments may include a wide field camera for imaging the target exoplanetary system as well as an integral field spectrometer for characterization of exoplanet atmospheres. We show the preliminary designs of the optical instruments for observatories such as Exo-S, discuss formation flying and control, retargeting maneuvers and other aspects of a starshade mission. The implementation of a starshade-ready WFIRST-AFTA is discussed and we show how a compact, standalone instrument package could be developed as an add-on to future space telescopes, requiring only minor additions to the telescope spacecraft.

Enabling Large Focal Plane Arrays Through Mosaic Hybridization

NASA Technical Reports Server (NTRS)

Miller, Timothy M.; Jhabvala, Christine A.; Leong, Edward; Costen, Nick P.; Sharp, Elmer; Adachi, Tomoko; Benford, Dominic J.

2012-01-01

We have demonstrated advances in mosaic hybridization that will enable very large format far-infrared detectors. Specifically we have produced electrical detector models via mosaic hybridization yielding superconducting circuit patbs by hybridizing separately fabricated sub-units onto a single detector unit. The detector model was made on a 100mm diameter wafer while four model readout quadrant chips were made from a separate 100mm wafer. The individually fabric.ted parts were hybridized using a Suss FCI50 flip chip bonder to assemble the detector-readout stack. Once all of the hybridized readouts were in place, a single, large and thick silicon substrate was placed on the stack and attached with permanent epoxy to provide strength and a Coefficient of Thermal Expansion match to the silicon components underneath. Wirebond pads on the readout chips connect circuits to warm readout electronics; and were used to validate the successful superconducting electrical interconnection of the model mosaic-hybrid detector. This demonstration is directly scalable to 150 mm diameter wafers, enabling pixel areas over ten times the area currently available.

CuInSe₂ thin-film solar cells with 7.72 % efficiency prepared via direct coating of a metal salts/alcohol-based precursor solution.

PubMed

Ahn, Sejin; Son, Tae Hwa; Cho, Ara; Gwak, Jihye; Yun, Jae Ho; Shin, Keeshik; Ahn, Seoung Kyu; Park, Sang Hyun; Yoon, Kyunghoon

2012-09-01

A simple direct solution coating process for forming CuInSe₂ (CIS) thin films was described, employing a low-cost and environmentally friendly precursor solution. The precursor solution was prepared by mixing metal acetates, ethanol, and ethanolamine. The facile formation of a precursor solution without the need to prefabricate nanoparticles enables a rapid and easy processing, and the high stability of the solution in air further ensures the precursor preparation and the film deposition in ambient conditions without a glove box. The thin film solar cell fabricated with the absorber film prepared by this route showed an initial conversion efficiency of as high as 7.72 %. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Microchannel gel electrophoretic separation systems and methods for preparing and using

DOEpatents

Herr, Amy E; Singh, Anup K; Throckmorton, Daniel J

2015-02-24

A micro-analytical platform for performing electrophoresis-based immunoassays was developed by integrating photopolymerized cross-linked polyacrylamide gels within a microfluidic device. The microfluidic immunoassays are performed by gel electrophoretic separation and quantifying analyte concentration based upon conventional polyacrylamide gel electrophoresis (PAGE). To retain biological activity of proteins and maintain intact immune complexes, native PAGE conditions were employed. Both direct (non-competitive) and competitive immunoassay formats are demonstrated in microchips for detecting toxins and biomarkers (cytokines, c-reactive protein) in bodily fluids (serum, saliva, oral fluids). Further, a description of gradient gels fabrication is included, in an effort to describe methods we have developed for further optimization of on-chip PAGE immunoassays. The described chip-based PAGE immunoassay method enables immunoassays that are fast (minutes) and require very small amounts of sample (less than a few microliters). Use of microfabricated chips as a platform enables integration, parallel assays, automation and development of portable devices.

Microchannel gel electrophoretic separation systems and methods for preparing and using

DOEpatents

Herr, Amy; Singh, Anup K; Throckmorton, Daniel J

2013-09-03

A micro-analytical platform for performing electrophoresis-based immunoassays was developed by integrating photopolymerized cross-linked polyacrylamide gels within a microfluidic device. The microfluidic immunoassays are performed by gel electrophoretic separation and quantifying analyte concentration based upon conventional polyacrylamide gel electrophoresis (PAGE). To retain biological activity of proteins and maintain intact immune complexes, native PAGE conditions were employed. Both direct (non-competitive) and competitive immunoassay formats are demonstrated in microchips for detecting toxins and biomarkers (cytokines, c-reactive protein) in bodily fluids (serum, saliva, oral fluids). Further, a description of gradient gels fabrication is included, in an effort to describe methods we have developed for further optimization of on-chip PAGE immunoassays. The described chip-based PAGE immunoassay method enables immunoassays that are fast (minutes) and require very small amounts of sample (less than a few microliters). Use of microfabricated chips as a platform enables integration, parallel assays, automation and development of portable devices.

Tailings Pond Characterization And Designing Through Geophysical Surveys In Dipping Sedimentary Formations

NASA Astrophysics Data System (ADS)

Muralidharan, D.; Andrade, R.; Anand, K.; Sathish, R.; Goud, K.

2009-12-01

Mining activities results into generation of disintegrated waste materials attaining increased mobilization status and requires a safe disposal mechanism through back filling process or secluded storage on surface with prevention of its interaction with environment cycle. The surface disposal of waste materials will become more critical in case of mined minerals having toxic or radioactive elements. In such cases, the surface disposal site is to be characterized for its sub-surface nature to understand its role in environmental impact due to the loading of waste materials. Near surface geophysics plays a major role in mapping the geophysical characters of the sub-surface formations in and around the disposal site and even to certain extent helps in designing of the storage structure. Integrated geophysical methods involving resistivity tomography, ground magnetic and shallow seismic studies were carried out over proposed tailings pond area of 0.3 sq. kms underlined by dipping sedimentary rocks consisting of ferruginous shales and dolomitic to siliceous limestone with varying thicknesses. The investigated site being located in tectonically disturbed area, geophysical investigations were carried out with number of profiles to visualize the sub-surface nature with clarity. The integration of results of twenty profiles of resistivity tomography with 2 m (shallow) and 10 m (moderate depth) electrode spacing’s enabled in preparing probable sub-surface geological section along the strike direction of the formation under the tailings pond with some geo-tectonic structure inferred to be a fault. Similarly, two resistivity tomography profiles perpendicular to the strike direction of the formations brought out the existence of buried basic intrusive body on the northern boundary of the proposed tailings pond. Two resistivity tomography profiles in criss-cross direction over the suspected fault zone confirmed fault existence on the north-eastern part of tailings pond. Thirty two magnetic profiles inside the tailings pond and surrounding areas on the southern part of the tailings pond enabled in identifying two parallel east-west intrusive bodies forming the impermeable boundary for the tailings pond. The shallow seismic refraction and the geophysical studies in and around the proposed tailings pond brought out the suitability of the site, even when the toxic elements percolates through the subsurface formations in to the groundwater system, the existence of dykes on either side of the proposed ponding area won’t allow the water to move across them thus by restricting the contamination within the tailings pond area. Similarly, the delineation of a fault zone within the tailings pond area helped in shifting the proposed dam axis of the pond to avoid leakage through the fault zone causing concern to environment pollution.

SOA formation from gasoline vehicles: from the tailpipe to the atmosphere

NASA Astrophysics Data System (ADS)

Robinson, A. L.; Zhao, Y.; Lambe, A. T.; Saleh, R.; Saliba, G.; Tkacik, D. S.

2017-12-01

Secondary organic aerosol (SOA) formation from gasoline vehicles has been indicated as an important source of atmospheric SOA, but its contribution to atmospheric SOA is loosely constrained due to the lack of measurements to link SOA formation from the tailpipe to atmospheric SOA. In this study, we determine the contribution of SOA formation based on measurements made with a Potential Aerosol Mass (PAM) oxidation flow reactor by oxidizing vehicular exhaust and ambient air. We first investigate SOA formation from dilute gasoline-vehicle exhaust during chassis dynamometer testing. The test fleet consists of both vehicles equipped with gasoline direct injection engines (GDI vehicles) and those equipped with port fuel injection engines (PFI vehicles). These vehicles span a wide range of emissions standards from Tier0 to Super Ultra-Low Emission Vehicles (SULEV). Then, we combine our measurements of SOA formation from gasoline vehicles during dynamometer testing with measurements of SOA formation using a PAM reactor conducted in a highway tunnel and in the unban atmosphere. Comparisons of SOA formation between these datasets enable us to quantitatively connect SOA formation from individual vehicles, to a large on-road fleet, and to the atmosphere. To facilitate the comparisons, we account for the effects of both the photochemical age and dilution on SOA formation. Our results show that SOA formation from gasoline vehicles can contribute over 50% of fossil fuel-related atmospheric SOA in the Los Angeles area. Furthermore, our results demonstrate that the tightening of emissions standards effectively reduces SOA formation from gasoline vehicles, including both PFI and GDI vehicles, if the atmospheric chemistry regime remains the same.

Google Glass-Directed Monitoring and Control of Microfluidic Biosensors and Actuators

PubMed Central

Zhang, Yu Shrike; Busignani, Fabio; Ribas, João; Aleman, Julio; Rodrigues, Talles Nascimento; Shaegh, Seyed Ali Mousavi; Massa, Solange; Rossi, Camilla Baj; Taurino, Irene; Shin, Su-Ryon; Calzone, Giovanni; Amaratunga, Givan Mark; Chambers, Douglas Leon; Jabari, Saman; Niu, Yuxi; Manoharan, Vijayan; Dokmeci, Mehmet Remzi; Carrara, Sandro; Demarchi, Danilo; Khademhosseini, Ali

2016-01-01

Google Glass is a recently designed wearable device capable of displaying information in a smartphone-like hands-free format by wireless communication. The Glass also provides convenient control over remote devices, primarily enabled by voice recognition commands. These unique features of the Google Glass make it useful for medical and biomedical applications where hands-free experiences are strongly preferred. Here, we report for the first time, an integral set of hardware, firmware, software, and Glassware that enabled wireless transmission of sensor data onto the Google Glass for on-demand data visualization and real-time analysis. Additionally, the platform allowed the user to control outputs entered through the Glass, therefore achieving bi-directional Glass-device interfacing. Using this versatile platform, we demonstrated its capability in monitoring physical and physiological parameters such as temperature, pH, and morphology of liver- and heart-on-chips. Furthermore, we showed the capability to remotely introduce pharmaceutical compounds into a microfluidic human primary liver bioreactor at desired time points while monitoring their effects through the Glass. We believe that such an innovative platform, along with its concept, has set up a premise in wearable monitoring and controlling technology for a wide variety of applications in biomedicine. PMID:26928456

Google Glass-Directed Monitoring and Control of Microfluidic Biosensors and Actuators

NASA Astrophysics Data System (ADS)

Zhang, Yu Shrike; Busignani, Fabio; Ribas, João; Aleman, Julio; Rodrigues, Talles Nascimento; Shaegh, Seyed Ali Mousavi; Massa, Solange; Rossi, Camilla Baj; Taurino, Irene; Shin, Su-Ryon; Calzone, Giovanni; Amaratunga, Givan Mark; Chambers, Douglas Leon; Jabari, Saman; Niu, Yuxi; Manoharan, Vijayan; Dokmeci, Mehmet Remzi; Carrara, Sandro; Demarchi, Danilo; Khademhosseini, Ali

2016-03-01

Google Glass is a recently designed wearable device capable of displaying information in a smartphone-like hands-free format by wireless communication. The Glass also provides convenient control over remote devices, primarily enabled by voice recognition commands. These unique features of the Google Glass make it useful for medical and biomedical applications where hands-free experiences are strongly preferred. Here, we report for the first time, an integral set of hardware, firmware, software, and Glassware that enabled wireless transmission of sensor data onto the Google Glass for on-demand data visualization and real-time analysis. Additionally, the platform allowed the user to control outputs entered through the Glass, therefore achieving bi-directional Glass-device interfacing. Using this versatile platform, we demonstrated its capability in monitoring physical and physiological parameters such as temperature, pH, and morphology of liver- and heart-on-chips. Furthermore, we showed the capability to remotely introduce pharmaceutical compounds into a microfluidic human primary liver bioreactor at desired time points while monitoring their effects through the Glass. We believe that such an innovative platform, along with its concept, has set up a premise in wearable monitoring and controlling technology for a wide variety of applications in biomedicine.

Google Glass-Directed Monitoring and Control of Microfluidic Biosensors and Actuators.

PubMed

Zhang, Yu Shrike; Busignani, Fabio; Ribas, João; Aleman, Julio; Rodrigues, Talles Nascimento; Shaegh, Seyed Ali Mousavi; Massa, Solange; Baj Rossi, Camilla; Taurino, Irene; Shin, Su-Ryon; Calzone, Giovanni; Amaratunga, Givan Mark; Chambers, Douglas Leon; Jabari, Saman; Niu, Yuxi; Manoharan, Vijayan; Dokmeci, Mehmet Remzi; Carrara, Sandro; Demarchi, Danilo; Khademhosseini, Ali

2016-03-01

Google Glass is a recently designed wearable device capable of displaying information in a smartphone-like hands-free format by wireless communication. The Glass also provides convenient control over remote devices, primarily enabled by voice recognition commands. These unique features of the Google Glass make it useful for medical and biomedical applications where hands-free experiences are strongly preferred. Here, we report for the first time, an integral set of hardware, firmware, software, and Glassware that enabled wireless transmission of sensor data onto the Google Glass for on-demand data visualization and real-time analysis. Additionally, the platform allowed the user to control outputs entered through the Glass, therefore achieving bi-directional Glass-device interfacing. Using this versatile platform, we demonstrated its capability in monitoring physical and physiological parameters such as temperature, pH, and morphology of liver- and heart-on-chips. Furthermore, we showed the capability to remotely introduce pharmaceutical compounds into a microfluidic human primary liver bioreactor at desired time points while monitoring their effects through the Glass. We believe that such an innovative platform, along with its concept, has set up a premise in wearable monitoring and controlling technology for a wide variety of applications in biomedicine.

Controlled 1.1-1.6 μm luminescence in gold-free multi-stacked InAs/InP heterostructure nanowires.

PubMed

Zhang, Guoqiang; Tateno, Kouta; Birowosuto, Muhammad Danang; Notomi, Masaya; Sogawa, Tetsuomi; Gotoh, Hideki

2015-03-20

We report controlled 1.1-1.6 μm luminescence in gold-free multi-stacked InAs/InP heterostructure nanowires (NWs). We realized the NWs by using an indium-particle-assisted vapor-liquid-solid synthesis approach. The growth temperature, as low as 320 °C, enables the formation of an atomically abrupt InP/InAs interface by supressing the diffusion and weakening the reservoir effect in the indium droplet. The low growth temperature also enables us to grow multi-stacked InAs/InP NWs in the axial direction without any growth on the NW side face. The high controllability of the growth technology ensures that the luminescence can be tailored by the thickness of InAs segment in InP NWs and cover the 1.3-1.5 μm telecommunication window range. By using the nanoscale-spatial-resolution technology combing cathodoluminescence with scanning electron microscopy, we directly correlated the site of different-thickness InAs segments with its luminescence property in a single NW and demonstrate the InAs-thickness-controlled energy of optical emission in 1.1-1.6 μm.

A Neurocomputational Model of Goal-Directed Navigation in Insect-Inspired Artificial Agents

PubMed Central

Goldschmidt, Dennis; Manoonpong, Poramate; Dasgupta, Sakyasingha

2017-01-01

Despite their small size, insect brains are able to produce robust and efficient navigation in complex environments. Specifically in social insects, such as ants and bees, these navigational capabilities are guided by orientation directing vectors generated by a process called path integration. During this process, they integrate compass and odometric cues to estimate their current location as a vector, called the home vector for guiding them back home on a straight path. They further acquire and retrieve path integration-based vector memories globally to the nest or based on visual landmarks. Although existing computational models reproduced similar behaviors, a neurocomputational model of vector navigation including the acquisition of vector representations has not been described before. Here we present a model of neural mechanisms in a modular closed-loop control—enabling vector navigation in artificial agents. The model consists of a path integration mechanism, reward-modulated global learning, random search, and action selection. The path integration mechanism integrates compass and odometric cues to compute a vectorial representation of the agent's current location as neural activity patterns in circular arrays. A reward-modulated learning rule enables the acquisition of vector memories by associating the local food reward with the path integration state. A motor output is computed based on the combination of vector memories and random exploration. In simulation, we show that the neural mechanisms enable robust homing and localization, even in the presence of external sensory noise. The proposed learning rules lead to goal-directed navigation and route formation performed under realistic conditions. Consequently, we provide a novel approach for vector learning and navigation in a simulated, situated agent linking behavioral observations to their possible underlying neural substrates. PMID:28446872

A Neurocomputational Model of Goal-Directed Navigation in Insect-Inspired Artificial Agents.

PubMed

Goldschmidt, Dennis; Manoonpong, Poramate; Dasgupta, Sakyasingha

2017-01-01

Despite their small size, insect brains are able to produce robust and efficient navigation in complex environments. Specifically in social insects, such as ants and bees, these navigational capabilities are guided by orientation directing vectors generated by a process called path integration. During this process, they integrate compass and odometric cues to estimate their current location as a vector, called the home vector for guiding them back home on a straight path. They further acquire and retrieve path integration-based vector memories globally to the nest or based on visual landmarks. Although existing computational models reproduced similar behaviors, a neurocomputational model of vector navigation including the acquisition of vector representations has not been described before. Here we present a model of neural mechanisms in a modular closed-loop control-enabling vector navigation in artificial agents. The model consists of a path integration mechanism, reward-modulated global learning, random search, and action selection. The path integration mechanism integrates compass and odometric cues to compute a vectorial representation of the agent's current location as neural activity patterns in circular arrays. A reward-modulated learning rule enables the acquisition of vector memories by associating the local food reward with the path integration state. A motor output is computed based on the combination of vector memories and random exploration. In simulation, we show that the neural mechanisms enable robust homing and localization, even in the presence of external sensory noise. The proposed learning rules lead to goal-directed navigation and route formation performed under realistic conditions. Consequently, we provide a novel approach for vector learning and navigation in a simulated, situated agent linking behavioral observations to their possible underlying neural substrates.

A photo-cross-linking approach to monitor folding and assembly of newly synthesized proteins in a living cell.

PubMed

Miyazaki, Ryoji; Myougo, Naomi; Mori, Hiroyuki; Akiyama, Yoshinori

2018-01-12

Many proteins form multimeric complexes that play crucial roles in various cellular processes. Studying how proteins are correctly folded and assembled into such complexes in a living cell is important for understanding the physiological roles and the qualitative and quantitative regulation of the complex. However, few methods are suitable for analyzing these rapidly occurring processes. Site-directed in vivo photo-cross-linking is an elegant technique that enables analysis of protein-protein interactions in living cells with high spatial resolution. However, the conventional site-directed in vivo photo-cross-linking method is unsuitable for analyzing dynamic processes. Here, by combining an improved site-directed in vivo photo-cross-linking technique with a pulse-chase approach, we developed a new method that can analyze the folding and assembly of a newly synthesized protein with high spatiotemporal resolution. We demonstrate that this method, named the pulse-chase and in vivo photo-cross-linking experiment (PiXie), enables the kinetic analysis of the formation of an Escherichia coli periplasmic (soluble) protein complex (PhoA). We also used our new technique to investigate assembly/folding processes of two membrane complexes (SecD-SecF in the inner membrane and LptD-LptE in the outer membrane), which provided new insights into the biogenesis of these complexes. Our PiXie method permits analysis of the dynamic behavior of various proteins and enables examination of protein-protein interactions at the level of individual amino acid residues. We anticipate that our new technique will have valuable utility for studies of protein dynamics in many organisms. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Overview and Status of the Laser Communication Relay Demonstration

NASA Technical Reports Server (NTRS)

Luzhanskiy, E.; Edwards, B.; Israel, D.; Cornwell, D.; Staren, J.; Cummings, N.; Roberts, T.; Patschke, R.

2016-01-01

NASA is presently developing first all optical high data rate satellite relay system, LCRD. To be flown on commercial geosynchronous satellite, it will communicate at DPSK and PPM modulation formats up to 1.244 Gbps. LCRD flight payload is being developed by NASA's Goddard Space Flight Center. The two ground stations, one on Table Mountain in CA, developed by NASA's Jet Propulsion Laboratory and another on Hawaiian island will enable bi-directional relay operation and ground sites diversity experiments. In this paper we will report on the current state of LCRD system development, planned operational scenarios and expected system performance.

Experimenter's Laboratory for Visualized Interactive Science

NASA Technical Reports Server (NTRS)

Hansen, Elaine R.; Rodier, Daniel R.; Klemp, Marjorie K.

1994-01-01

ELVIS (Experimenter's Laboratory for Visualized Interactive Science) is an interactive visualization environment that enables scientists, students, and educators to visualize and analyze large, complex, and diverse sets of scientific data. It accomplishes this by presenting the data sets as 2-D, 3-D, color, stereo, and graphic images with movable and multiple light sources combined with displays of solid-surface, contours, wire-frame, and transparency. By simultaneously rendering diverse data sets acquired from multiple sources, formats, and resolutions and by interacting with the data through an intuitive, direct-manipulation interface, ELVIS provides an interactive and responsive environment for exploratory data analysis.

Simulating Vibrations in a Complex Loaded Structure

NASA Technical Reports Server (NTRS)

Cao, Tim T.

2005-01-01

The Dynamic Response Computation (DIRECT) computer program simulates vibrations induced in a complex structure by applied dynamic loads. Developed to enable rapid analysis of launch- and landing- induced vibrations and stresses in a space shuttle, DIRECT also can be used to analyze dynamic responses of other structures - for example, the response of a building to an earthquake, or the response of an oil-drilling platform and attached tanks to large ocean waves. For a space-shuttle simulation, the required input to DIRECT includes mathematical models of the space shuttle and its payloads, and a set of forcing functions that simulates launch and landing loads. DIRECT can accommodate multiple levels of payload attachment and substructure as well as nonlinear dynamic responses of structural interfaces. DIRECT combines the shuttle and payload models into a single structural model, to which the forcing functions are then applied. The resulting equations of motion are reduced to an optimum set and decoupled into a unique format for simulating dynamics. During the simulation, maximum vibrations, loads, and stresses are monitored and recorded for subsequent analysis to identify structural deficiencies in the shuttle and/or payloads.

Auto Indexer Auto-Indexer for Percussive Hammers: Vane Motor Dynamometer Testing

DOE Data Explorer

Su, Jiann

2012-01-01

Objectives Options associated with geothermal drilling operations are generally limited by factors such as formation temperature and rock strength. The objective of the research is to expand the "tool box" available to the geothermal driller by furthering the development of a high-temperature drilling motor that can be used in directional drilling applications for drilling high temperature geothermal formations. The motor is specifically designed to operate in conjunction with a pneumatic down-the-hole-hammer. It provides a more compact design compared to traditional drilling motors such as PDMs (positive displacement motors). The packaging can help to enhance directional drilling capabilities. It uses no elastomeric components, which enables it to operate in higher temperatures ( >250 °F). Current work on the motor has shown that is a capable of operating under pneumatic power with a down-the-hole-hammer. Further development work will include continued testing and refining motor components and evaluating motor capabilities. Targets/Milestones Complete testing current motor - 12/31/2010 Make final material and design decisions - 01/31/2011 Build and test final prototype - 04/31/2011 Final demonstration - 07/31/2011 Impacts The development of the motor will help to achieve program technical objectives by improving well construction capabilities. This includes enabling high-temperature drilling as well as enhancing directional drilling. A key component in the auto indexer is the drive motor. It is an air-driven vane motor that converts the energy stored in the compressed air to mechanical energy. The motor is attached to hammer-like components which impart an impulsive load onto the drive shaft. The impulsive force on the drive shaft in turn creates an indexing action. A controlled test was performed to characterize the performance of the the vane motor for a given pressure. The Sandia dynamometer test station was used to determine the performance of the motor for a given input pressure.

Radio-frequency response of single pores and artificial ion channels

NASA Astrophysics Data System (ADS)

Kim, H. S.; Ramachandran, S.; Stava, E.; van der Weide, D. W.; Blick, R. H.

2011-09-01

Intercellular communication relies on ion channels and pores in cell membranes. These protein-formed channels enable the exchange of ions and small molecules to electrically and/or chemically interact with the cells. Traditionally, recordings on single-ion channels and pores are performed in the dc regime, due to the extremely high impedance of these molecular junctions. This paper is intended as an introduction to radio-frequency (RF) recordings of single-molecule junctions in bilipid membranes. First, we demonstrate how early approaches to using microwave circuitry as readout devices for ion channel formation were realized. The second step will then focus on how to engineer microwave coupling into the high-impedance channel by making use of bio-compatible micro-coaxial lines. We then demonstrate integration of an ultra-broadband microwave circuit for the direct sampling of single α-hemolysin pores in a suspended bilipid membrane. Simultaneous direct current recordings reveal that we can monitor and correlate the RF transmission signal. This enables us to relate the open-close states of the direct current to the RF signal. Altogether, our experiments lay the ground for an RF-readout technique to perform real-time in vitro recordings of pores. The technique thus holds great promise for research and drug screening applications. The possible enhancement of sampling rates of single channels and pores by the large recording bandwidth will allow us to track the passage of single ions.

EMERALD: Coping with the Explosion of Seismic Data

NASA Astrophysics Data System (ADS)

West, J. D.; Fouch, M. J.; Arrowsmith, R.

2009-12-01

The geosciences are currently generating an unparalleled quantity of new public broadband seismic data with the establishment of large-scale seismic arrays such as the EarthScope USArray, which are enabling new and transformative scientific discoveries of the structure and dynamics of the Earth’s interior. Much of this explosion of data is a direct result of the formation of the IRIS consortium, which has enabled an unparalleled level of open exchange of seismic instrumentation, data, and methods. The production of these massive volumes of data has generated new and serious data management challenges for the seismological community. A significant challenge is the maintenance and updating of seismic metadata, which includes information such as station location, sensor orientation, instrument response, and clock timing data. This key information changes at unknown intervals, and the changes are not generally communicated to data users who have already downloaded and processed data. Another basic challenge is the ability to handle massive seismic datasets when waveform file volumes exceed the fundamental limitations of a computer’s operating system. A third, long-standing challenge is the difficulty of exchanging seismic processing codes between researchers; each scientist typically develops his or her own unique directory structure and file naming convention, requiring that codes developed by another researcher be rewritten before they can be used. To address these challenges, we are developing EMERALD (Explore, Manage, Edit, Reduce, & Analyze Large Datasets). The overarching goal of the EMERALD project is to enable more efficient and effective use of seismic datasets ranging from just a few hundred to millions of waveforms with a complete database-driven system, leading to higher quality seismic datasets for scientific analysis and enabling faster, more efficient scientific research. We will present a preliminary (beta) version of EMERALD, an integrated, extensible, standalone database server system based on the open-source PostgreSQL database engine. The system is designed for fast and easy processing of seismic datasets, and provides the necessary tools to manage very large datasets and all associated metadata. EMERALD provides methods for efficient preprocessing of seismic records; large record sets can be easily and quickly searched, reviewed, revised, reprocessed, and exported. EMERALD can retrieve and store station metadata and alert the user to metadata changes. The system provides many methods for visualizing data, analyzing dataset statistics, and tracking the processing history of individual datasets. EMERALD allows development and sharing of visualization and processing methods using any of 12 programming languages. EMERALD is designed to integrate existing software tools; the system provides wrapper functionality for existing widely-used programs such as GMT, SOD, and TauP. Users can interact with EMERALD via a web browser interface, or they can directly access their data from a variety of database-enabled external tools. Data can be imported and exported from the system in a variety of file formats, or can be directly requested and downloaded from the IRIS DMC from within EMERALD.

Heterologous Expression of sahH Reveals That Biofilm Formation Is Autoinducer-2-independent in Streptococcus sanguinis but Is Associated with an Intact Activated Methionine Cycle*

PubMed Central

Redanz, Sylvio; Standar, Kerstin; Podbielski, Andreas; Kreikemeyer, Bernd

2012-01-01

Numerous studies have claimed deleterious effects of LuxS mutation on many bacterial phenotypes, including bacterial biofilm formation. Genetic complementation mostly restored the observed mutant phenotypes to WT levels, leading to the postulation that quorum sensing via a family of molecules generically termed autoinducer-2 (AI-2) is essential for many phenotypes. Because LuxS mutation has dual effects, this hypothesis needs to be investigated into the details for each bacterial species. In this study we used S. sanguinis SK36 as a model biofilm bacterium and employed physiological characterization and transcriptome approaches on WT and luxS-deficient strains, in combination with chemical, luxS, and sahH complementation experiments. SahH enables a direct conversion of SAH to homocysteine and thereby restores the activated methionine cycle in a luxS-negative background without formation of the AI-2 precursor 4,5-dihydroxy-2,3-pentanedione. With this strategy we were able to dissect the individual contribution of LuxS and AI-2 activity in detail. Our data revealed that S. sanguinis biofilm formation is independent from AI-2 substance pools and is rather supported by an intact activated methyl cycle. Of 216 differentially transcribed genes in the luxS mutant, 209 were restored by complementation with a gene encoding the S-adenosylhomocysteine hydrolase. Only nine genes, mainly involved in natural competence, were directly affected by the AI-2 quorum-sensing substance pool. Cumulatively, this suggested that biofilm formation in S. sanguinis is not under control of AI-2. Our study suggests that previously evaluated LuxS mutants in other species need to be revisited to resolve the precise contribution of AI-2 substance pools and the methionine pathways. PMID:22942290

Optical resonance-enhanced absorption-based near-field immunochip biosensor for allergen detection.

PubMed

Maier, Irene; Morgan, Michael R A; Lindner, Wolfgang; Pittner, Fritz

2008-04-15

An optical immunochip biosensor has been developed as a rapid method for allergen detection in complex food matrixes, and its application evaluated for the detection of the egg white allergens, ovalbumin and ovomucoid. The optical near-field phenomenon underlying the basic principle of the sensor design is called resonance-enhanced absorption (REA), which utilizes gold nanoparticles (Au NPs) as signal transducers in a highly sensitive interferometric setup. Using this approach, a novel, simple, and rapid colorimetric solid-phase immunoassay on a planar chip substrate was realized in direct and sandwich assay formats, with a detection system that does not require any instrumentation for readout. Semiquantitative immunochemical responses are directly visible to the naked eye of the analyst. The biosensor shows concentration-dependent color development by capturing antibody-functionalized Au NPs on allergen-coated chips and has a detection limit of 1 ng/mL. To establish a rapid method, we took advantage of the physicochemical microenvironment of the Au NP-antibody bioconjugate to be bound directly over an interacting poly(styrene-methyl methacrylate) interlayer by an immobilized antigen. In the direct assay format, a coating time with allergen of only 5 min under "soft" nondenaturing conditions was sufficient for accurate reproducibility and sensitivity. In conclusion, the REA-based immunochip sensor is easy to fabricate, is reproducible and selective in its performance, has minimal technical requirements, and will enable high-throughput screening of affinity binding interactions in technological and medical applications.

Protein Oxidation in Aging: Does It Play a Role in Aging Progression?

PubMed Central

Reeg, Sandra

2015-01-01

Abstract Significance: A constant accumulation of oxidized proteins takes place during aging. Oxidation of proteins leads to a partial unfolding and, therefore, to aggregation. Protein aggregates impair the activity of cellular proteolytic systems (proteasomes, lysosomes), resulting in further accumulation of oxidized proteins. In addition, the accumulation of highly crosslinked protein aggregates leads to further oxidant formation, damage to macromolecules, and, finally, to apoptotic cell death. Furthermore, protein oxidation seems to play a role in the development of various age-related diseases, for example, neurodegenerative diseases. Recent Advances: The highly oxidized lipofuscin accumulates during aging. Lipofuscin formation might cause impaired lysosomal and proteasomal degradation, metal ion accumulation, increased reactive oxygen species formation, and apoptosis. Critical Issues: It is still unclear to which extent protein oxidation is involved in the progression of aging and in the development of some age-related diseases. Future Directions: An extensive knowledge of the effects of protein oxidation on the aging process and its contribution to the development of age-related diseases could enable further strategies to reduce age-related impairments. Strategies aimed at lowering aggregate formation might be a straightforward intervention to reduce age-related malfunctions of organs. Antioxid. Redox Signal. 23, 239–255. PMID:25178482

Mushroom bodies regulate habit formation in Drosophila.

PubMed

Brembs, Björn

2009-08-25

To make good decisions, we evaluate past choices to guide later decisions. In most situations, we have the opportunity to simultaneously learn about both the consequences of our choice (i.e., operantly) and the stimuli associated with correct or incorrect choices (i.e., classically). Interestingly, in many species, including humans, these learning processes occasionally lead to irrational decisions. An extreme case is the habitual drug user consistently administering the drug despite the negative consequences, but we all have experience with our own, less severe habits. The standard animal model employs a combination of operant and classical learning components to bring about habit formation in rodents. After extended training, these animals will press a lever even if the outcome associated with lever-pressing is no longer desired. In this study, experiments with wild-type and transgenic flies revealed that a prominent insect neuropil, the mushroom bodies (MBs), regulates habit formation in flies by inhibiting the operant learning system when a predictive stimulus is present. This inhibition enables generalization of the classical memory and prevents premature habit formation. Extended training in wild-type flies produced a phenocopy of MB-impaired flies, such that generalization was abolished and goal-directed actions were transformed into habitual responses.

Preschool Children's Explanations of Plant Growth and Rain Formation: A Comparative Analysis

NASA Astrophysics Data System (ADS)

Christidou, Vasilia; Hatzinikita, Vassilia

2006-09-01

This paper explores the different types and characteristics of preschool children's explanations of plant growth and rain formation. The children's explanations were categorized as naturalistic, non-naturalistic, or synthetic, i.e., explanations containing both naturalistic and non-naturalistic parts. In regards to plant growth the children tended to rely on synthetic or on naturalistic explanations, which involved direct and indirect agents (such as water, a person, fertilizers, roots) enabling the plant to grow. Non-naturalistic explanations of plant growth, or the non-naturalistic parts of synthetic explanations, were mainly animistic (anthropomorphic). In the case of rain formation the children most frequently used non-naturalistic explanations, which were mainly teleological or metaphysical. The naturalistic explanations recorded on rain formation, as well as the naturalistic parts of synthetic explanations tended to have a non-agentive character, i.e., children considered rainwater as preexisting in containers such as the clouds. Overall, the explanations recorded about plant growth tended to be more complex than the ones for rain formation. It is suggested that science activities designed for preschool children should take into account the types and characteristics of their explanations in order to select which phenomena are appropriate for this age group, and aim at fostering the children's ability at formulating naturalistic explanations.

A visual identification key utilizing both gestalt and analytic approaches to identification of Carices present in North America (Plantae, Cyperaceae)

PubMed Central

2013-01-01

Abstract Images are a critical part of the identification process because they enable direct, immediate and relatively unmediated comparisons between a specimen being identified and one or more reference specimens. The Carices Interactive Visual Identification Key (CIVIK) is a novel tool for identification of North American Carex species, the largest vascular plant genus in North America, and two less numerous closely-related genera, Cymophyllus and Kobresia. CIVIK incorporates 1288 high-resolution tiled image sets that allow users to zoom in to view minute structures that are crucial at times for identification in these genera. Morphological data are derived from the earlier Carex Interactive Identification Key (CIIK) which in turn used data from the Flora of North America treatments. In this new iteration, images can be viewed in a grid or histogram format, allowing multiple representations of data. In both formats the images are fully zoomable. PMID:24723777

Interfacial complexation in microfluidic droplets for single-step fabrication of microcapsule

NASA Astrophysics Data System (ADS)

Kaufman, Gilad; Nejati, Siamak; Sarfati, Raphael; Boltyanskiy, Rostislav; Williams, Danielle; Liu, Wei; Schloss, Ashley; Regan, Lynn; Yan, Elsa; Dufrense, Eric; Loewenberg, Michael; Osuji, Chinedum

We present microfluidic interfacial complexation in emulsion droplets as a simple single-step approach for fabricating a large variety of stable monodisperse microcapsules with tailored mechanical properties, protein binding and controlled release behavior. We rely on electrostatic interactions and hydrogen bonding to direct the assembly of complementary species at oil-water droplet interfaces to form microcapsules with polyelectrolyte shells, composite polyelectrolyte-nanoparticle shells, and copolymer-nanofiber shells. Additionally, we demonstrate the formation of microcapsules by adsorption of an amphiphilic bacterial hydrophobin, BslA, at oil-in-water and water-in-oil droplets, and protein capture on these capsules using engineered variants of the hydrophobin. We discuss the composition dependence of mechanical properties, shell thickness and release behavior, and regimes of stability for microcapsule fabrication. Nanoparticle based microcapsules display an intriguing plastic deformation response which enables the formation of large aspect ratio asperities by pipette aspiration of the shell.

Conclusive evidence of abrupt coagulation inside the void during cyclic nanoparticle formation in reactive plasma

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

Wetering, F. M. J. H. van de; Nijdam, S.; Beckers, J.

2016-07-25

In this letter, we present scanning electron microscopy (SEM) results that confirm in a direct way our earlier explanation of an abrupt coagulation event as the cause for the void hiccup. In a recent paper, we reported on the fast and interrupted expansion of voids in a reactive dusty argon–acetylene plasma. The voids appeared one after the other, each showing a peculiar, though reproducible, behavior of successive periods of fast expansion, abrupt contraction, and continued expansion. The abrupt contraction was termed “hiccup” and was related to collective coagulation of a new generation of nanoparticles growing in the void using relativelymore » indirect methods: electron density measurements and optical emission spectroscopy. In this letter, we present conclusive evidence using SEM of particles collected at different moments in time spanning several growth cycles, which enables us to follow the nanoparticle formation process in great detail.« less

In vivo assimilation of one-carbon via a synthetic reductive glycine pathway in Escherichia coli.

PubMed

Yishai, Oren; Bouzon, Madeleine; Döring, Volker; Bar-Even, Arren

2018-05-15

Assimilation of one-carbon compounds presents a key biochemical challenge, which limits their use as sustainable feedstocks for microbial growth and production. The reductive glycine pathway is a synthetic metabolic route that could provide an optimal way for the aerobic assimilation of reduced C1 compounds. Here, we show that a rational integration of native and foreign enzymes enables the tetrahydrofolate and glycine cleavage/synthase systems to operate in the reductive direction, such that Escherichia coli satisfies all of its glycine and serine requirements from the assimilation of formate and CO2. Importantly, the biosynthesis of serine from formate and CO2 does not lower the growth rate, indicating high flux that is able to provide 10% of cellular carbon. Our findings assert that the reductive glycine pathway could support highly efficient aerobic assimilation of C1-feedstocks.

Dopaminergic inputs in the dentate gyrus direct the choice of memory encoding.

PubMed

Du, Huiyun; Deng, Wei; Aimone, James B; Ge, Minyan; Parylak, Sarah; Walch, Keenan; Zhang, Wei; Cook, Jonathan; Song, Huina; Wang, Liping; Gage, Fred H; Mu, Yangling

2016-09-13

Rewarding experiences are often well remembered, and such memory formation is known to be dependent on dopamine modulation of the neural substrates engaged in learning and memory; however, it is unknown how and where in the brain dopamine signals bias episodic memory toward preceding rather than subsequent events. Here we found that photostimulation of channelrhodopsin-2-expressing dopaminergic fibers in the dentate gyrus induced a long-term depression of cortical inputs, diminished theta oscillations, and impaired subsequent contextual learning. Computational modeling based on this dopamine modulation indicated an asymmetric association of events occurring before and after reward in memory tasks. In subsequent behavioral experiments, preexposure to a natural reward suppressed hippocampus-dependent memory formation, with an effective time window consistent with the duration of dopamine-induced changes of dentate activity. Overall, our results suggest a mechanism by which dopamine enables the hippocampus to encode memory with reduced interference from subsequent experience.

Dopaminergic inputs in the dentate gyrus direct the choice of memory encoding

PubMed Central

Du, Huiyun; Deng, Wei; Aimone, James B.; Ge, Minyan; Parylak, Sarah; Walch, Keenan; Zhang, Wei; Cook, Jonathan; Song, Huina; Wang, Liping; Gage, Fred H.; Mu, Yangling

2016-01-01

Rewarding experiences are often well remembered, and such memory formation is known to be dependent on dopamine modulation of the neural substrates engaged in learning and memory; however, it is unknown how and where in the brain dopamine signals bias episodic memory toward preceding rather than subsequent events. Here we found that photostimulation of channelrhodopsin-2–expressing dopaminergic fibers in the dentate gyrus induced a long-term depression of cortical inputs, diminished theta oscillations, and impaired subsequent contextual learning. Computational modeling based on this dopamine modulation indicated an asymmetric association of events occurring before and after reward in memory tasks. In subsequent behavioral experiments, preexposure to a natural reward suppressed hippocampus-dependent memory formation, with an effective time window consistent with the duration of dopamine-induced changes of dentate activity. Overall, our results suggest a mechanism by which dopamine enables the hippocampus to encode memory with reduced interference from subsequent experience. PMID:27573822

Technology gap assessment for a future large-aperture ultraviolet-optical-infrared space telescope

NASA Astrophysics Data System (ADS)

Bolcar, Matthew R.; Balasubramanian, Kunjithapatham; Crooke, Julie; Feinberg, Lee; Quijada, Manuel; Rauscher, Bernard J.; Redding, David; Rioux, Norman; Shaklan, Stuart; Stahl, H. Philip; Stahle, Carl M.; Thronson, Harley

2016-10-01

The Advanced Technology Large Aperture Space Telescope (ATLAST) team identified five key technology areas to enable candidate architectures for a future large-aperture ultraviolet/optical/infrared (LUVOIR) space observatory envisioned by the NASA Astrophysics 30-year roadmap, "Enduring Quests, Daring Visions." The science goals of ATLAST address a broad range of astrophysical questions from early galaxy and star formation to the processes that contributed to the formation of life on Earth, combining general astrophysics with direct-imaging and spectroscopy of habitable exoplanets. The key technology areas are internal coronagraphs, starshades (or external occulters), ultra-stable large-aperture telescope systems, detectors, and mirror coatings. For each technology area, we define best estimates of required capabilities, current state-of-the-art performance, and current technology readiness level (TRL), thus identifying the current technology gap. We also report on current, planned, or recommended efforts to develop each technology to TRL 5.

Spatial and Temporal Control of T Cell Activation Using a Photoactivatable Agonist.

PubMed

Sanchez, Elisa; Huse, Morgan

2018-04-25

T lymphocytes engage in rapid, polarized signaling, occurring within minutes following TCR activation. This induces formation of the immunological synapse, a stereotyped cell-cell junction that regulates T cell activation and directionally targets effector responses. To study these processes effectively, an imaging approach that is tailored to capturing fast, polarized responses is necessary. This protocol describes such a system, which is based on a photoactivatable peptide-major histocompatibility complex (pMHC) that is non-stimulatory until it is exposed to ultraviolet light. Targeted decaging of this reagent during videomicroscopy experiments enables precise spatiotemporal control of TCR activation and high-resolution monitoring of subsequent cellular responses by total internal reflection (TIRF) imaging. This approach is also compatible with genetic and pharmacological perturbation strategies. This allows for the assembly of well-defined molecular pathways that link TCR signaling to the formation of the polarized cytoskeletal structures that underlie the immunological synapse.

Direct fabrication of gas diffusion cathode by pulse electrodeposition for proton exchange membrane water electrolysis

NASA Astrophysics Data System (ADS)

Park, Hyanjoo; Choe, Seunghoe; Kim, Hoyoung; Kim, Dong-Kwon; Cho, GeonHee; Park, YoonSu; Jang, Jong Hyun; Ha, Don-Hyung; Ahn, Sang Hyun; Kim, Soo-Kil

2018-06-01

Pt catalysts for water electrolysis were prepared on carbon paper by using both direct current and pulse electrodeposition. Controlling the mass transfer of Pt precursor in the electrolyte by varying the deposition potential enables the formation of various Pt particle shapes such as flower-like and polyhedral particles. Further control of the deposition parameters for pulse electrodeposition resulted in changes to the particle size and density. In particular, the upper potential of pulse was found to be the critical parameter controlling the morphology of the particles and their catalytic activity. In addition to the typical electrochemical measurements, Pt samples deposited on carbon paper were used as cathodes for a proton exchange membrane water electrolyser. This single cell test revealed that our Pt particle samples have exceptional mass activity while being cost effective.

DNA Origami: Folded DNA-Nanodevices That Can Direct and Interpret Cell Behavior

PubMed Central

Kearney, Cathal J.; Lucas, Christopher R.; O'Brien, Fergal J.; Castro, Carlos E.

2016-01-01

DNA origami is a DNA-based nanotechnology that utilizes programmed combinations of short complementary oligonucleotides to fold a large single strand of DNA into precise 2-D and 3-D shapes. The exquisite nanoscale shape control of this inherently biocompatible material is combined with the potential to spatially address the origami structures with diverse cargos including drugs, antibodies, nucleic acid sequences, small molecules and inorganic particles. This programmable flexibility enables the fabrication of precise nanoscale devices that have already shown great potential for biomedical applications such as: drug delivery, biosensing and synthetic nanopore formation. In this Progress Report, we will review the advances in the DNA origami field since its inception several years ago and then focus on how these DNA-nanodevices can be designed to interact with cells to direct or probe their behavior. PMID:26840503

Direct Determination of the Base-Pair Force Constant of DNA from the Acoustic Phonon Dispersion of the Double Helix

NASA Astrophysics Data System (ADS)

van Eijck, L.; Merzel, F.; Rols, S.; Ollivier, J.; Forsyth, V. T.; Johnson, M. R.

2011-08-01

Quantifying the molecular elasticity of DNA is fundamental to our understanding of its biological functions. Recently different groups, through experiments on tailored DNA samples and numerical models, have reported a range of stretching force constants (0.3 to 3N/m). However, the most direct, microscopic measurement of DNA stiffness is obtained from the dispersion of its vibrations. A new neutron scattering spectrometer and aligned, wet spun samples have enabled such measurements, which provide the first data of collective excitations of DNA and yield a force constant of 83N/m. Structural and dynamic order persists unchanged to within 15 K of the melting point of the sample, precluding the formation of bubbles. These findings are supported by large scale phonon and molecular dynamics calculations, which reconcile hard and soft force constants.

Optimization of the biotechnological production of a novel class of anti-MRSA antibiotics from Chitinophaga sancti.

PubMed

Beckmann, Amelie; Hüttel, Stephan; Schmitt, Viktoria; Müller, Rolf; Stadler, Marc

2017-08-17

Recently, the discovery of the elansolids, a group of macrolides, was reported. The molecules show activity against methicillin-resistant Staphylococcus aureus as well as other gram-positive organisms. This fact renders those substances a promising starting point for future chemical development. The active atropisomers A1/A2 are formed by macrolactonization of the biosynthesis product A3 but are prone to ring opening and subsequent formation of several unwanted side products. Recently it could be shown that addition of different nucleophiles to culture extracts of Chitinophaga sancti enable the formation of new stable elansolid derivatives. Furthermore, addition of such a nucleophile directly into the culture led exclusively to formation of a single active elansolid derivative. Due to low product yields, methods for production of gram amounts of these molecules have to be established to enable further development of this promising compound class. Production of elansolid A2 by C. sancti was enabled using a synthetic medium with sucrose as carbon source to a final concentration of 18.9 mg L -1 . A fed-batch fermentation was ensued that resulted in an elansolid A2 concentration of 55.3 mg L -1 . When using glucose as carbon source in a fed-batch fermentation only 34.4 mg L -1 elansolid A2 but 223.1 mg L -1 elansolid C1 were produced. This finding was not unexpected since elansolids A1/A2 and A3 have been reported to easily react with nucleophiles like anthranilic acid, a precursor of tryptophan biosynthesis. Due to the fact that nucleophiles can be incorporated in vivo, a fed-batch cultivation under identical conditions, with addition of anthranilic acid was carried out and lead to almost exclusive formation of elansolid C1 (257.5 mg L -1 ). Reproducible elansolid A2 and C1 production is feasible in different synthetic media at relatively high concentrations that will allow further investigation and semi-synthetic optimization. The feeding of anthranilic acid enables the exclusive production of the stable elansolid derivative C1, which reduces product loss by unspecific reactions and eases downstream processing. This derivative shows activity in the same range as the elansolids A1/A2. Hence, the method can possibly serve as a model-process for incorporation of other nucleophiles and biotechnological production of specifically designed molecules.

Interaction mining and skill-dependent recommendations for multi-objective team composition

PubMed Central

Dorn, Christoph; Skopik, Florian; Schall, Daniel; Dustdar, Schahram

2011-01-01

Web-based collaboration and virtual environments supported by various Web 2.0 concepts enable the application of numerous monitoring, mining and analysis tools to study human interactions and team formation processes. The composition of an effective team requires a balance between adequate skill fulfillment and sufficient team connectivity. The underlying interaction structure reflects social behavior and relations of individuals and determines to a large degree how well people can be expected to collaborate. In this paper we address an extended team formation problem that does not only require direct interactions to determine team connectivity but additionally uses implicit recommendations of collaboration partners to support even sparsely connected networks. We provide two heuristics based on Genetic Algorithms and Simulated Annealing for discovering efficient team configurations that yield the best trade-off between skill coverage and team connectivity. Our self-adjusting mechanism aims to discover the best combination of direct interactions and recommendations when deriving connectivity. We evaluate our approach based on multiple configurations of a simulated collaboration network that features close resemblance to real world expert networks. We demonstrate that our algorithm successfully identifies efficient team configurations even when removing up to 40% of experts from various social network configurations. PMID:22298939

Fastest Formation Routes of Nanocarbons in Solution Plasma Processes.

PubMed

Morishita, Tetsunori; Ueno, Tomonaga; Panomsuwan, Gasidit; Hieda, Junko; Yoshida, Akihito; Bratescu, Maria Antoaneta; Saito, Nagahiro

2016-11-14

Although solution-plasma processing enables room-temperature synthesis of nanocarbons, the underlying mechanisms are not well understood. We investigated the routes of solution-plasma-induced nanocarbon formation from hexane, hexadecane, cyclohexane, and benzene. The synthesis rate from benzene was the highest. However, the nanocarbons from linear molecules were more crystalline than those from ring molecules. Linear molecules decomposed into shorter olefins, whereas ring molecules were reconstructed in the plasma. In the saturated ring molecules, C-H dissociation proceeded, followed by conversion into unsaturated ring molecules. However, unsaturated ring molecules were directly polymerized through cation radicals, such as benzene radical cation, and were converted into two- and three-ring molecules at the plasma-solution interface. The nanocarbons from linear molecules were synthesized in plasma from small molecules such as C 2 under heat; the obtained products were the same as those obtained via pyrolysis synthesis. Conversely, the nanocarbons obtained from ring molecules were directly synthesized through an intermediate, such as benzene radical cation, at the interface between plasma and solution, resulting in the same products as those obtained via polymerization. These two different reaction fields provide a reasonable explanation for the fastest synthesis rate observed in the case of benzene.

Fastest Formation Routes of Nanocarbons in Solution Plasma Processes

PubMed Central

Morishita, Tetsunori; Ueno, Tomonaga; Panomsuwan, Gasidit; Hieda, Junko; Yoshida, Akihito; Bratescu, Maria Antoaneta; Saito, Nagahiro

2016-01-01

Although solution-plasma processing enables room-temperature synthesis of nanocarbons, the underlying mechanisms are not well understood. We investigated the routes of solution-plasma-induced nanocarbon formation from hexane, hexadecane, cyclohexane, and benzene. The synthesis rate from benzene was the highest. However, the nanocarbons from linear molecules were more crystalline than those from ring molecules. Linear molecules decomposed into shorter olefins, whereas ring molecules were reconstructed in the plasma. In the saturated ring molecules, C–H dissociation proceeded, followed by conversion into unsaturated ring molecules. However, unsaturated ring molecules were directly polymerized through cation radicals, such as benzene radical cation, and were converted into two- and three-ring molecules at the plasma–solution interface. The nanocarbons from linear molecules were synthesized in plasma from small molecules such as C2 under heat; the obtained products were the same as those obtained via pyrolysis synthesis. Conversely, the nanocarbons obtained from ring molecules were directly synthesized through an intermediate, such as benzene radical cation, at the interface between plasma and solution, resulting in the same products as those obtained via polymerization. These two different reaction fields provide a reasonable explanation for the fastest synthesis rate observed in the case of benzene. PMID:27841288

DETECTION OF SHARP SYMMETRIC FEATURES IN THE CIRCUMBINARY DISK AROUND AK Sco

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

Janson, Markus; Asensio-Torres, Ruben; Thalmann, Christian

The Search for Planets Orbiting Two Stars survey aims to study the formation and distribution of planets in binary systems by detecting and characterizing circumbinary planets and their formation environments through direct imaging. With the SPHERE Extreme Adaptive Optics instrument, a good contrast can be achieved even at small (<300 mas) separations from bright stars, which enables studies of planets and disks in a separation range that was previously inaccessible. Here, we report the discovery of resolved scattered light emission from the circumbinary disk around the well-studied young double star AK Sco, at projected separations in the ∼13–40 AU range. Themore » sharp morphology of the imaged feature is surprising, given the smooth appearance of the disk in its spectral energy distribution. We show that the observed morphology can be represented either as a highly eccentric ring around AK Sco, or as two separate spiral arms in the disk, wound in opposite directions. The relative merits of these interpretations are discussed, as well as whether these features may have been caused by one or several circumbinary planets interacting with the disk.« less

Use of Mutated Self-Cleaving 2A Peptides as a Molecular Rheostat to Direct Simultaneous Formation of Membrane and Secreted Anti-HIV Immunoglobulins

PubMed Central

Yu, Kenneth K.; Aguilar, Kiefer; Tsai, Jonathan; Galimidi, Rachel; Gnanapragasam, Priyanthi; Yang, Lili; Baltimore, David

2012-01-01

In nature, B cells produce surface immunoglobulin and secreted antibody from the same immunoglobulin gene via alternative splicing of the pre-messenger RNA. Here we present a novel system for genetically programming B cells to direct the simultaneous formation of membrane-bound and secreted immunoglobulins that we term a “Molecular Rheostat”, based on the use of mutated “self-cleaving” 2A peptides. The Molecular Rheostat is designed so that the ratio of secreted to membrane-bound immunoglobulins can be controlled by selecting appropriate mutations in the 2A peptide. Lentiviral transgenesis of Molecular Rheostat constructs into B cell lines enables the simultaneous expression of functional b12-based IgM-like BCRs that signal to the cells and mediate the secretion of b12 IgG broadly neutralizing antibodies that can bind and neutralize HIV-1 pseudovirus. We show that these b12-based Molecular Rheostat constructs promote the maturation of EU12 B cells in an in vitro model of B lymphopoiesis. The Molecular Rheostat offers a novel tool for genetically manipulating B cell specificity for B-cell based gene therapy. PMID:23209743

Study of Direct-Contact HfO2/Si Interfaces

PubMed Central

Miyata, Noriyuki

2012-01-01

Controlling monolayer Si oxide at the HfO2/Si interface is a challenging issue in scaling the equivalent oxide thickness of HfO2/Si gate stack structures. A concept that the author proposes to control the Si oxide interface by using ultra-high vacuum electron-beam HfO2 deposition is described in this review paper, which enables the so-called direct-contact HfO2/Si structures to be prepared. The electrical characteristics of the HfO2/Si metal-oxide-semiconductor capacitors are reviewed, which suggest a sufficiently low interface state density for the operation of metal-oxide-semiconductor field-effect-transistors (MOSFETs) but reveal the formation of an unexpected strong interface dipole. Kelvin probe measurements of the HfO2/Si structures provide obvious evidence for the formation of dipoles at the HfO2/Si interfaces. The author proposes that one-monolayer Si-O bonds at the HfO2/Si interface naturally lead to a large potential difference, mainly due to the large dielectric constant of the HfO2. Dipole scattering is demonstrated to not be a major concern in the channel mobility of MOSFETs. PMID:28817060

Exchanging the Context between OGC Geospatial Web clients and GIS applications using Atom

NASA Astrophysics Data System (ADS)

Maso, Joan; Díaz, Paula; Riverola, Anna; Pons, Xavier

2013-04-01

Currently, the discovery and sharing of geospatial information over the web still presents difficulties. News distribution through website content was simplified by the use of Really Simple Syndication (RSS) and Atom syndication formats. This communication exposes an extension of Atom to redistribute references to geospatial information in a Spatial Data Infrastructure distributed environment. A geospatial client can save the status of an application that involves several OGC services of different kind and direct data and share this status with other users that need the same information and use different client vendor products in an interoperable way. The extensibility of the Atom format was essential to define a format that could be used in RSS enabled web browser, Mass Market map viewers and emerging geospatial enable integrated clients that support Open Geospatial Consortium (OGC) services. Since OWS Context has been designed as an Atom extension, it is possible to see the document in common places where Atom documents are valid. Internet web browsers are able to present the document as a list of items with title, abstract, time, description and downloading features. OWS Context uses GeoRSS so that, the document can be to be interpreted by both Google maps and Bing Maps as items that have the extent represented in a dynamic map. Another way to explode a OWS Context is to develop an XSLT to transform the Atom feed into an HTML5 document that shows the exact status of the client view window that saved the context document. To accomplish so, we use the width and height of the client window, and the extent of the view in world (geographic) coordinates in order to calculate the scale of the map. Then, we can mix elements in world coordinates (such as CF-NetCDF files or GML) with elements in pixel coordinates (such as WMS maps, WMTS tiles and direct SVG content). A smarter map browser application called MiraMon Map Browser is able to write a context document and read it again to recover the context of the previous view or load a context generated by another application. The possibility to store direct links to direct files in OWS Context is particularly interesting for GIS desktop solutions. This communication also presents the development made in the MiraMon desktop GIS solution to include OWS Context. MiraMon software is able to deal either with local files, web services and database connections. As in any other GIS solution, MiraMon team designed its own file (MiraMon Map MMM) for storing and sharing the status of a GIS session. The new OWS Context format is now adopted as an interoperable substitution of the MMM. The extensibility of the format makes it possible to map concepts in the MMM to current OWS Context elements (such as titles, data links, extent, etc) and to generate new elements that are able to include all extra metadata not currently covered by OWS Context. These developments were done in the nine edition of the OpenGIS Web Services Interoperability Experiment (OWS-9) and are demonstrated in this communication.

A sensor data format incorporating battery charge information for smartphone-based mHealth applications

NASA Astrophysics Data System (ADS)

Escobar, Rodrigo; Akopian, David; Boppana, Rajendra

2015-03-01

Remote health monitoring systems involve energy-constrained devices, such as sensors and mobile gateways. Current data formats for communication of health data, such as DICOM and HL7, were not designed for multi-sensor applications or to enable the management of power-constrained devices in health monitoring processes. In this paper, a data format suitable for collection of multiple sensor data, including readings and other operational parameters is presented. By using the data format, the system management can assess energy consumptions and plan realistic monitoring scenarios. The proposed data format not only outperforms other known data formats in terms of readability, flexibility, interoperability and validation of compliant documents, but also enables energy assessment capability for realistic data collection scenarios and maintains or even reduces the overhead introduced due to formatting. Additionally, we provide analytical methods to estimate incremental energy consumption by various sensors and experiments to measure the actual battery drain on smartphones.

Psyplot: Visualizing rectangular and triangular Climate Model Data with Python

NASA Astrophysics Data System (ADS)

Sommer, Philipp

2016-04-01

The development and use of climate models often requires the visualization of geo-referenced data. Creating visualizations should be fast, attractive, flexible, easily applicable and easily reproducible. There is a wide range of software tools available for visualizing raster data, but they often are inaccessible to many users (e.g. because they are difficult to use in a script or have low flexibility). In order to facilitate easy visualization of geo-referenced data, we developed a new framework called "psyplot," which can aid earth system scientists with their daily work. It is purely written in the programming language Python and primarily built upon the python packages matplotlib, cartopy and xray. The package can visualize data stored on the hard disk (e.g. NetCDF, GeoTIFF, any other file format supported by the xray package), or directly from the memory or Climate Data Operators (CDOs). Furthermore, data can be visualized on a rectangular grid (following or not following the CF Conventions) and on a triangular grid (following the CF or UGRID Conventions). Psyplot visualizes 2D scalar and vector fields, enabling the user to easily manage and format multiple plots at the same time, and to export the plots into all common picture formats and movies covered by the matplotlib package. The package can currently be used in an interactive python session or in python scripts, and will soon be developed for use with a graphical user interface (GUI). Finally, the psyplot framework enables flexible configuration, allows easy integration into other scripts that uses matplotlib, and provides a flexible foundation for further development.

Synergism of Dewetting and Self-Wrinkling To Create Two-Dimensional Ordered Arrays of Functional Microspheres.

PubMed

Han, Xue; Hou, Jing; Xie, Jixun; Yin, Jian; Tong, Yi; Lu, Conghua; Möhwald, Helmuth

2016-06-29

Here we report a simple, novel, yet robust nonlithographic method for the controlled fabrication of two-dimensional (2-D) ordered arrays of polyethylene glycol (PEG) microspheres. It is based on the synergistic combination of two bottom-up processes enabling periodic structure formation for the first time: dewetting and the mechanical wrinkle formation. The deterministic dewetting results from the hydrophilic polymer PEG on an incompatible polystyrene (PS) film bound to a polydimethylsiloxane (PDMS) substrate, which is directed both by a wrinkled template and by the template-directed in-situ self-wrinkling PS/PDMS substrate. Two strategies have been introduced to achieve synergism to enhance the 2-D ordering, i.e., employing 2-D in-situ self-wrinkling substrates and boundary conditions. As a result, we achieve highly ordered 2-D arrays of PEG microspheres with desired self-organized microstructures, such as the array location (e.g., selectively on the crest/in the valley of the wrinkles), diameter, spacing of the microspheres, and array direction. Additionally, the coordination of PEG with HAuCl4 is utilized to fabricate 2-D ordered arrays of functional PEG-HAuCl4 composite microspheres, which are further converted into different Au nanoparticle arrays. This simple versatile combined strategy could be extended to fabricate highly ordered 2-D arrays of other functional materials and achieve desirable properties and functionalities.

Imaging initial formation processes of nanobubbles at the graphite-water interface through high-speed atomic force microscopy

NASA Astrophysics Data System (ADS)

Liao, Hsien-Shun; Yang, Chih-Wen; Ko, Hsien-Chen; Hwu, En-Te; Hwang, Ing-Shouh

2018-03-01

The initial formation process of nanobubbles at solid-water interfaces remains unclear because of the limitations of current imaging techniques. To directly observe the formation process, an astigmatic high-speed atomic force microscope (AFM) was modified to enable imaging in the liquid environment. By using a customized cantilever holder, the resonance of small cantilevers was effectively enhanced in water. The proposed high-speed imaging technique yielded highly dynamic quasi-two-dimensional (2D) gas structures (thickness: 20-30 nm) initially at the graphite-water interface. The 2D structures were laterally mobile mainly within certain areas, but occasionally a gas structure might extensively migrate and settle in a new area. The 2D structures were often confined by substrate step edges in one lateral dimension. Eventually, all quasi-2D gas structures were transformed into cap-shaped nanobubbles of higher heights and reduced lateral dimensions. These nanobubbles were immobile and remained stable under continuous AFM imaging. This study demonstrated that nanobubbles could be stably imaged at a scan rate of 100 lines per second (640 μm/s).

Opacplot2: Enabling tabulated EoS and opacity compatibility for HEDLP simulations with the FLASH code

NASA Astrophysics Data System (ADS)

Laune, Jordan; Tzeferacos, Petros; Feister, Scott; Fatenejad, Milad; Yurchak, Roman; Flocke, Norbert; Weide, Klaus; Lamb, Donald

2017-10-01

Thermodynamic and opacity properties of materials are necessary to accurately simulate laser-driven laboratory experiments. Such data are compiled in tabular format since the thermodynamic range that needs to be covered cannot be described with one single theoretical model. Moreover, tabulated data can be made available prior to runtime, reducing both compute cost and code complexity. This approach is employed by the FLASH code. Equation of state (EoS) and opacity data comes in various formats, matrix-layouts, and file-structures. We discuss recent developments on opacplot2, an open-source Python module that manipulates tabulated EoS and opacity data. We present software that builds upon opacplot2 and enables easy-to-use conversion of different table formats into the IONMIX format, the native tabular input used by FLASH. Our work enables FLASH users to take advantage of a wider range of accurate EoS and opacity tables in simulating HELP experiments at the National Laser User Facilities.

Experimental observation of the stratified electrothermal instability on aluminum with thickness greater than a skin depth

NASA Astrophysics Data System (ADS)

Hutchinson, T. M.; Awe, T. J.; Bauer, B. S.; Yates, K. C.; Yu, E. P.; Yelton, W. G.; Fuelling, S.

2018-05-01

A direct observation of the stratified electrothermal instability on the surface of thick metal is reported. Aluminum rods coated with 70 μ m Parylene-N were driven to 1 MA in 100 ns , with the metal thicker than the skin depth. The dielectric coating suppressed plasma formation, enabling persistent observation of discrete azimuthally correlated stratified thermal perturbations perpendicular to the current whose wave numbers, k , grew exponentially with rate γ (k ) =0.06 n s-1-(0.4 n s-1μ m2ra d-2 ) k2 in ˜1 g /c m3 , ˜7000 K aluminum.

Magnetic-field-induced delocalized to localized transformation in GaAs:N.

PubMed

Alberi, K; Crooker, S A; Fluegel, B; Beaton, D A; Ptak, A J; Mascarenhas, A

2013-04-12

The use of a high magnetic field (57 T) to study the formation and evolution of nitrogen (N) cluster and supercluster states in GaAs:N is demonstrated. A magnetic field is used to lift the conduction band edge and expose resonant N cluster states so that they can be directly experimentally investigated. The reduction of the exciton Bohr radius also results in the fragmentation of N supercluster states, enabling a magnetic field induced delocalized to localized transition. The application of very high magnetic fields thus presents a powerful way to probe percolation phenomena in semiconductors with bound and resonant isoelectronic cluster states.

The SEEDS of Planet Formation: Indirect Signatures of Giant Planets in Transitional Disks

NASA Technical Reports Server (NTRS)

Grady, Carol

2012-01-01

Circumstellar disks associated with PMS stars are the site where planetesimals form and grow, and ultimately where planets are produced. A key phase in the evolution of such disks is the phase where clearing of the disk has begun, potentially enabling direct detection of giant planets, but the disk retains sufficient material that indirect signatures that these are young planetary systems are also present. After reviewing what has been learned from studies of the IR spectral energy distribution and (sub )mm-interferometry, I will discuss recent results obtained as part of the Strategic Exploration of Exoplanets and Disks with Subaru (SEEDS).

Experimental Observation of the Stratified Electrothermal Instability on Aluminum with Thickness Greater than a Skin Depth

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

Hutchinson, Trevor M.; Hutchinson, Trevor M.; Awe, Thomas James

The first direct observation of the stratified electrothermal instability on the surface of thick metal is reported. Aluminum rods coated with 70 μm Parylene-N were driven to 1 MA in approximately 100 ns, with the metal thicker than the skin depth. The dielectric coating suppressed plasma formation, enabling persistent observation of discrete azimuthally-correlated stratified structures perpendicular to the current. Strata amplitudes grow rapidly, while their Fourier spectrum shifts toward longer wavelength. Assuming blackbody emission, radiometric calculations indicate strata are temperature perturbations that grow exponentially with rate γ = 0.04 ns -1 in 3000- 10,000 K aluminum.

Re–Os geochronology of the lacustrine Green River Formation: Insights into direct depositional dating of lacustrine successions, Re–Os systematics and paleocontinental weathering

USGS Publications Warehouse

Cumming, Vivien M.; Selby, David; Lillis, Paul G.

2012-01-01

Lacustrine sedimentary successions provide exceptionally high-resolution records of continental geological processes, responding to tectonic, climatic and magmatic influences. These successions are therefore essential for correlating geological and climatic phenomena across continents and furthermore the globe. Producing accurate geochronological frameworks within lacustrine strata is challenging because the stratigraphy is often bereft of biostratigraphy and directly dateable tuff horizons. The rhenium–osmium (Re–Os) geochronometer is a well-established tool for determining precise and accurate depositional ages of marine organic-rich rocks. Lake systems with stratified water columns are predisposed to the preservation of organic-rich rocks and thus should permit direct Re–Os geochronology of lacustrine strata. We present Re–Os systematics from one of the world's best documented lacustrine systems, the Eocene Green River Formation, providing accurate Re–Os depositional dates that are supported by Ar–Ar and U–Pb ages of intercalated tuff horizons. Precision of the Green River Formation Re–Os dates is controlled by the variation in initial 187Os/188Os and the range of 187Re/188Os ratios, as also documented in marine systems. Controls on uptake and fractionation of Re and Os are considered to relate mainly to depositional setting and the type of organic matter deposited, with the need to further understand the chelating precursors of Re and Os in organic matter highlighted. In addition to geochronology, the Re–Os data records the 187Os/188Os composition of lake water (1.41–1.54) at the time of deposition, giving an insight into continental runoff derived from weathering of the geological hinterland of the Green River Formation. Such insights enable us to evaluate fluctuations in continental climatic, tectonic and magmatic processes and provide the ability for chemostratigraphic correlation combined with direct depositional dates. Furthermore, initial 187Os/188Os values can be used as a diagnostic tool to distinguish between lacustrine and marine depositional settings when compared to known oceanic 187Os/188Os values.

Surface-tension driven open microfluidic platform for hanging droplet culture

PubMed Central

de Groot, T. E.; Veserat, K. S.; Berthier, E.; Beebe, D. J.; Theberge, A. B.

2015-01-01

The hanging droplet technique for three-dimensional tissue culture has been used for decades in biology labs, with the core technology remaining relatively unchanged. Recently microscale approaches have expanded the capabilities of the hanging droplet method, making it more user-friendly. We present a spontaneously driven, open hanging droplet culture platform to address many limitations of current platforms. Our platform makes use of two interconnected hanging droplet wells, a larger well where cells are cultured and a smaller well for user interface via a pipette. The two-well system results in lower shear stress in the culture well during fluid exchange, enabling shear sensitive or non-adherent cells to be cultured in a droplet. The ability to perform fluid exchanges in-droplet enables long-term culture, treatment, and characterization without disruption of the culture. The open well format of the platform was utilized to perform time-dependent coculture, enabling culture configurations with bone tissue scaffolds and cells grown in suspension. The open nature of the system allowed the direct addition or removal of tissue over the course of an experiment, manipulations that would be impractical in other microfluidic or hanging droplet culture platforms. PMID:26660268

Direct UV/Optical Imaging of Stellar Surfaces: The Stellar Imager (SI) Vision Mission

NASA Technical Reports Server (NTRS)

Carpenter, Kenneth G.; Lyon, Richard G.; Schrijver, Carolus; Karovska, Margarita; Mozurkewich, David

2007-01-01

The Stellar Imager (SI) is a UV/optical, space-based interferometer designed to enable 0.1 milli-arcsecond (mas) spectral imaging of stellar surfaces and, via asteroseismology, stellar interiors and of the Universe in general. SI's science focuses on the role of magnetism in the Universe, particularly on magnetic activity on the surfaces of stars like the Sun. SI's prime goal is to enable long-term forecasting of solar activity and the space weather that it drives, in support of the Living with a Star program in the Exploration Era. SI will also revolutionize our understanding of the formation of planetary systems, of the habitability and climatology of distant planets, and of many magneto-hydrodynamically controlled processes in thc Universe. SI is a "Flagship and Landmark Discovery Mission" in the 2005 Sun Solar System Connection (SSSC) Roadmap and a candidate for a "Pathways to Life Observatory" in the Exploration of the Universe Division (EUD) Roadmap. We discuss herein the science goals of the SI Mission, a mission architecture that could meet those goals, and the technologies needed to enable this mission. Additional information on SI can be found at: http://hires.gsfc.nasa.gov/si/.

Deciphering protein signatures using color, morphological, and topological analysis of immunohistochemically stained human tissues

NASA Astrophysics Data System (ADS)

Zerhouni, Erwan; Prisacari, Bogdan; Zhong, Qing; Wild, Peter; Gabrani, Maria

2016-03-01

Images of tissue specimens enable evidence-based study of disease susceptibility and stratification. Moreover, staining technologies empower the evidencing of molecular expression patterns by multicolor visualization, thus enabling personalized disease treatment and prevention. However, translating molecular expression imaging into direct health benefits has been slow. Two major factors contribute to that. On the one hand, disease susceptibility and progression is a complex, multifactorial molecular process. Diseases, such as cancer, exhibit cellular heterogeneity, impeding the differentiation between diverse grades or types of cell formations. On the other hand, the relative quantification of the stained tissue selected features is ambiguous, tedious and time consuming, prone to clerical error, leading to intra- and inter-observer variability and low throughput. Image analysis of digital histopathology images is a fast-developing and exciting area of disease research that aims to address the above limitations. We have developed a computational framework that extracts unique signatures using color, morphological and topological information and allows the combination thereof. The integration of the above information enables diagnosis of disease with AUC as high as 0.97. Multiple staining show significant improvement with respect to most proteins, and an AUC as high as 0.99.

Exoplanet Community Report on Direct Infrared Imaging of Exoplanets

NASA Technical Reports Server (NTRS)

Danchi, William C.; Lawson, Peter R.

2009-01-01

Direct infrared imaging and spectroscopy of exoplanets will allow for detailed characterization of the atmospheric constituents of more than 200 nearby Earth-like planets, more than is possible with any other method under consideration. A flagship mission based on larger passively cooled infrared telescopes and formation flying technologies would have the highest angular resolution of any concept under consideration. The 2008 Exoplanet Forum committee on Direct Infrared Imaging of Exoplanets recommends: (1) a vigorous technology program including component development, integrated testbeds, and end-to-end modeling in the areas of formation flying and mid-infrared nulling; (2) a probe-scale mission based on a passively cooled structurally connected interferometer to be started within the next two to five years, for exoplanetary system characterization that is not accessible from the ground, and which would provide transformative science and lay the engineering groundwork for the flagship mission with formation flying elements. Such a mission would enable a complete exozodiacal dust survey (<1 solar system zodi) in the habitable zone of all nearby stars. This information will allow for a more efficient strategy of spectral characterization of Earth-sized planets for the flagship missions, and also will allow for optimization of the search strategy of an astrometric mission if such a mission were delayed due to cost or technology reasons. (3) Both the flagship and probe missions should be pursued with international partners if possible. Fruitful collaboration with international partners on mission concepts and relevant technology should be continued. (4) Research and Analysis (R&A) should be supported for the development of preliminary science and mission designs. Ongoing efforts to characterize the the typical level of exozodiacal light around Sun-like stars with ground-based nulling technology should be continued.

A Tiered Mentoring Model of Exposing and Engaging Students with Research Throughout the Undergraduate Curriculum

NASA Astrophysics Data System (ADS)

Guerard, J.; Hayes, S. M.

2015-12-01

Incorporating research into undergraduate curricula has been linked to improved critical thinking, intellectual independence, and student retention, resulting in a graduating population more ready for the workforce or graduate school. We have designed a three-tier model of undergraduate chemistry courses that enable first-year students with no previous research experience to gain the skills needed to develop, fund and execute independent research projects by the close of their undergraduate studies. First-year students are provided with context through a broadly focused introductory class that exposes them to current faculty research activities, and also gives them direct experience with the research process through peer mentored research teams as they participate in faculty-directed projects. Mid-career undergraduate students receive exposure and support in two formats: illustrative examples from current faculty research are incorporated into lessons in core classes, and courses specially designed to foster research independence. This is done by providing content and process mentoring as students develop independent projects, write proposals, and build relationships with faculty and graduate students in research groups. Advanced undergraduates further develop their research independence performing student-designed projects with faculty collaboration that frequently result in tangible research products. Further, graduate students gain experience in mentoring though formal training, as well as through actively mentoring mid-career undergraduates. This novel, integrated approach enables faculty to directly incorporate their research into all levels of the undergraduate curriculum while fostering undergraduates in developing and executing independent projects and empowering mentoring relationships.

Concise Synthesis of (-)-Hodgkinsine, (-)-Calycosidine, (-)-Hodgkinsine B, (-)-Quadrigemine C, and (-)-Psycholeine via Convergent and Directed Modular Assembly of Cyclotryptamines.

PubMed

Lindovska, Petra; Movassaghi, Mohammad

2017-12-06

The enantioselective total synthesis of (-)-hodgkinsine, (-)-calycosidine, (-)-hodgkinsine B, (-)-quadrigemine C, and (-)-psycholeine through a diazene-directed assembly of cyclotryptamine fragments is described. Our synthetic strategy enables multiple and directed assembly of intact cyclotryptamine subunits for convergent synthesis of highly complex bis- and tris-diazene intermediates. Photoextrusion of dinitrogen from these intermediates enables completely stereoselective formation of all C3a-C3a' and C3a-C7' carbon-carbon bonds and all the associated quaternary stereogenic centers. In a representative example, photoextrusion of three dinitrogen molecules from an advanced intermediate in a single-step led to completely controlled introduction of four quaternary stereogenic centers and guided the assembly of four cyclotryptamine monomers en route to (-)-quadrigemine C. The synthesis of these complex diazenes was made possible through a new methodology for synthesis of aryl-alkyl diazenes using electronically attenuated hydrazine-nucleophiles for a silver-promoted addition to C3a-bromocyclotryptamines. The application of Rh- and Ir-catalyzed C-H amination reactions in complex settings were used to gain rapid access to C3a- and C7-functionalized cyclotryptamine monomers, respectively, used for diazene synthesis. This convergent and modular assembly of intact cyclotryptamines offers the first solution to access these alkaloids through completely stereoselective union of monomers at challenging linkages and the associated quaternary stereocenters as illustrated in our synthesis of five members of the oligocyclotryptamine family of alkaloids.

Three-dimensional controlled growth of monodisperse sub-50 nm heterogeneous nanocrystals

PubMed Central

Liu, Deming; Xu, Xiaoxue; Du, Yi; Qin, Xian; Zhang, Yuhai; Ma, Chenshuo; Wen, Shihui; Ren, Wei; Goldys, Ewa M.; Piper, James A.; Dou, Shixue; Liu, Xiaogang; Jin, Dayong

2016-01-01

The ultimate frontier in nanomaterials engineering is to realize their composition control with atomic scale precision to enable fabrication of nanoparticles with desirable size, shape and surface properties. Such control becomes even more useful when growing hybrid nanocrystals designed to integrate multiple functionalities. Here we report achieving such degree of control in a family of rare-earth-doped nanomaterials. We experimentally verify the co-existence and different roles of oleate anions (OA−) and molecules (OAH) in the crystal formation. We identify that the control over the ratio of OA− to OAH can be used to directionally inhibit, promote or etch the crystallographic facets of the nanoparticles. This control enables selective grafting of shells with complex morphologies grown over nanocrystal cores, thus allowing the fabrication of a diverse library of monodisperse sub-50 nm nanoparticles. With such programmable additive and subtractive engineering a variety of three-dimensional shapes can be implemented using a bottom–up scalable approach. PMID:26743184

Thiol-ene immobilisation of carbohydrates onto glass slides as a simple alternative to gold-thiol monolayers, amines or lipid binding.

PubMed

Biggs, Caroline I; Edmondson, Steve; Gibson, Matthew I

2015-01-01

Carbohydrate arrays are a vital tool in studying infection, probing the mechanisms of bacterial, viral and toxin adhesion and the development of new treatments, by mimicking the structure of the glycocalyx. Current methods rely on the formation of monolayers of carbohydrates that have been chemically modified with a linker to enable interaction with a functionalised surface. This includes amines, biotin, lipids or thiols. Thiol-addition to gold to form self-assembled monolayers is perhaps the simplest method for immobilisation as thiolated glycans are readily accessible from reducing carbohydrates in a single step, but are limited to gold surfaces. Here we have developed a quick and versatile methodology which enables the use of thiolated carbohydrates to be immobilised as monolayers directly onto acrylate-functional glass slides via a 'thiol-ene'/Michael-type reaction. By combining the ease of thiol chemistry with glass slides, which are compatible with microarray scanners this offers a cost effective, but also useful method to assemble arrays.

Phenotypic diversification by enhanced genome restructuring after induction of multiple DNA double-strand breaks.

PubMed

Muramoto, Nobuhiko; Oda, Arisa; Tanaka, Hidenori; Nakamura, Takahiro; Kugou, Kazuto; Suda, Kazuki; Kobayashi, Aki; Yoneda, Shiori; Ikeuchi, Akinori; Sugimoto, Hiroki; Kondo, Satoshi; Ohto, Chikara; Shibata, Takehiko; Mitsukawa, Norihiro; Ohta, Kunihiro

2018-05-18

DNA double-strand break (DSB)-mediated genome rearrangements are assumed to provide diverse raw genetic materials enabling accelerated adaptive evolution; however, it remains unclear about the consequences of massive simultaneous DSB formation in cells and their resulting phenotypic impact. Here, we establish an artificial genome-restructuring technology by conditionally introducing multiple genomic DSBs in vivo using a temperature-dependent endonuclease TaqI. Application in yeast and Arabidopsis thaliana generates strains with phenotypes, including improved ethanol production from xylose at higher temperature and increased plant biomass, that are stably inherited to offspring after multiple passages. High-throughput genome resequencing revealed that these strains harbor diverse rearrangements, including copy number variations, translocations in retrotransposons, and direct end-joinings at TaqI-cleavage sites. Furthermore, large-scale rearrangements occur frequently in diploid yeasts (28.1%) and tetraploid plants (46.3%), whereas haploid yeasts and diploid plants undergo minimal rearrangement. This genome-restructuring system (TAQing system) will enable rapid genome breeding and aid genome-evolution studies.

MyChemise: A 2D drawing program that uses morphing for visualisation purposes

PubMed Central

2011-01-01

MyChemise (My Chemical Structure Editor) is a new 2D structure editor. It is designed as a Java applet that enables the direct creation of structures in the Internet using a web browser. MyChemise saves files in a digital format (.cse) and the import and export of .mol files using the appropriate connection tables is also possible. MyChemise is available as a free online version in English and German. The MyChemise GUI is designed to be user friendly and can be used intuitively. There is also an English and German program description available as a PDF file. In addition to the known ways of drawing chemical structure formulas, there are also parts implemented in the program that allow the creation of different types of presentation. The morphing module uses this technology as a component for dynamic visualisation. For example, it enables a clear and simple illustration of molecule vibrations and reaction sequences. PMID:22152022

Electromagnetic Design of Feedhorn-Coupled Transition-Edge Sensors for Cosmic Microwave Background Polarimetery

NASA Technical Reports Server (NTRS)

Chuss, David T.

2011-01-01

Observations of the cosmic microwave background (CMB) provide a powerful tool for probing the evolution of the early universe. Specifically, precision measurement of the polarization of the CMB enables a direct test for cosmic inflation. A key technological element on the path to the measurement of this faint signal is the capability to produce large format arrays of background-limited detectors. We describe the electromagnetic design of feedhorn-coupled, TES-based sensors. Each linear orthogonal polarization from the feed horn is coupled to a superconducting microstrip line via a symmetric planar orthomode transducer (OMT). The symmetric OMT design allows for highly-symmetric beams with low cross-polarization over a wide bandwidth. In addition, this architecture enables a single microstrip filter to define the passband for each polarization. Care has been taken in the design to eliminate stray coupling paths to the absorbers. These detectors will be fielded in the Cosmology Large Angular Scale Surveyor (CLASS).

Patterning of ultrathin polymethylmethacrylate films by in-situ photodirecting of the Marangoni flow

NASA Astrophysics Data System (ADS)

Elashnikov, Roman; Fitl, Premysl; Svorcik, Vaclav; Lyutakov, Oleksiy

2017-02-01

Laser heating and Marangoni flow result in the formation of surface structures with different geometries and shape on thin polymer films. By laser beam irradiation combined with a sample movement the solid polymethylmethacrylate (PMMA) films are heated and undergo phase transition which leads to a material flow. Since the laser beam has a non-linear distribution of energy, the PMMA film is heated inhomogeneously and a surface tension gradient in a lateral direction is introduced. During this procedure additional phenomena such as "reversible" or cyclic polymer flow also take place. The careful choice of experimental conditions enables the preparation of patterns with sophisticated geometries and with hierarchical pattern organization. Depending on initial PMMA film thickness and speed of the sample movement line arrays are created, which can subsequently be transformed into the crimped lines or system of circular holes. In addition, the introduction of a constant acceleration in the sample movement or a laser beam distortion enables the preparation of regularly crimped lines, ordered hexagonal holes or overlapped plates.

A sliding technique to load thin endothelial donor lamella onto Busin glide for Descemet-stripping automated endothelial keratoplasty

PubMed Central

Kobayashi, Akira; Yokogawa, Hideaki; Sugiyama, Kazuhisa

2012-01-01

We describe a modified technique for loading donor corneal endothelial lamella onto a Busin glide® without causing wrinkles, as part of the procedure of Descemet-stripping automated endothelial keratoplasty. Briefly, after punching out a composite of the donor-endothelial lamella and a microkeratome-dissected cap, several drops of dispersive ophthalmic viscosurgical device are placed onto the endothelial surface. The Busin glide surface is then wetted with several drops of balanced salt solution. After the composite is transferred onto the Busin glide, hydrodissection of the potential space between the donor-endothelial lamella and the microkeratome-dissected cap is carefully performed to enable smooth detachment of these two lamellae. Whereas simply dragging the donor-endothelial lamella directly onto the glide can cause wrinkling or folding of the donor lamella, this technique enables smooth detachment of the composite without wrinkle or fold formation, and results in less endothelial cell damage. PMID:22927732

Colloidal Random Terpolymers: Controlling Reactivity Ratios of Colloidal Comonomers via Metal Tipping

DOE PAGES

Pavlopoulos, Nicholas G.; Dubose, Jeffrey T.; Hartnett, Erin D.; ...

2016-07-26

We report on a versatile synthetic m-shell nanoparticles (NPs) in the backbone, along with semiconductor CdSe@CdS nanorod (NR), or tetrapod (TP) side chain groups. A seven-step colloidal total synthesis enabled the synthesis of well-defined colloidal comonomers composed of a dipolar Au@CoNP attached to a single CdSe@CdS NR, or TP, where magnetic dipolar associations between Au@CoNP units promoted the formation of colloidal co- or terpolymers. The key step in this synthesis was the ability to photodeposit a single AuNP tip onto CdSe@CdS NR or TP that enables selective seeding of a dipolar CoNP onto the AuNP seed. In conclusion, we showmore » that the variation of the AuNP size directly controlled the size and dipolar character of the CoNP tip, where the size modulation of the Au and Au@CoNP tips is analogous to control of comonomer reactivity ratios in classical copolymerization processes.« less

Alkyne–Aldehyde Reductive C–C Coupling through Ruthenium-Catalyzed Transfer Hydrogenation: Direct Regio- and Stereoselective Carbonyl Vinylation to Form Trisubstituted Allylic Alcohols in the Absence of Premetallated Reagents

PubMed Central

Leung, Joyce C.; Patman, Ryan L.; Sam, Brannon

2011-01-01

Nonsymmetric 1,2-disubstituted alkynes engage in reductive coupling to a variety of aldehydes under the conditions of ruthenium-catalyzed transfer hydrogenation by employing formic acid as the terminal reductant and delivering the products of carbonyl vinylation with good to excellent levels of regioselectivity and with complete control of olefin stereochemistry. As revealed in an assessment of the ruthenium counterion, iodide plays an essential role in directing the regioselectivity of C–C bond formation. Isotopic labeling studies corroborate reversible catalytic propargyl C–H oxidative addition in advance of the C–C coupling, and demonstrate that the C–C coupling products do not experience reversible dehydrogenation by way of enone intermediates. This transfer hydrogenation protocol enables carbonyl vinylation in the absence of stoichiometric metallic reagents. PMID:21953608

Turbine airfoil with dual wall formed from inner and outer layers separated by a compliant structure

DOEpatents

Campbell,; Christian X. , Morrison; Jay, A [Oviedo, FL

2011-12-20

A turbine airfoil usable in a turbine engine with a cooling system and a compliant dual wall configuration configured to enable thermal expansion between inner and outer layers while eliminating stress formation is disclosed. The compliant dual wall configuration may be formed a dual wall formed from inner and outer layers separated by a compliant structure. The compliant structure may be configured such that the outer layer may thermally expand without limitation by the inner layer. The compliant structure may be formed from a plurality of pedestals positioned generally parallel with each other. The pedestals may include a first foot attached to a first end of the pedestal and extending in a first direction aligned with the outer layer, and may include a second foot attached to a second end of the pedestal and extending in a second direction aligned with the inner layer.

Influence of firebed temperature on inorganic particle emissions in a residential wood pellet boiler

NASA Astrophysics Data System (ADS)

Gehrig, Matthias; Jaeger, Dirk; Pelz, Stefan K.; Weissinger, Alexander; Groll, Andreas; Thorwarth, Harald; Haslinger, Walter

2016-07-01

The temperature-dependent release of inorganic elements is the first step of the main formation pathway of particle emissions in automatically fired biomass burners. To investigate this step, a residential pellet boiler with an underfeed-burner was equipped with a direct firebed cooling. This test setup enabled decreased firebed temperatures without affecting further parameters like air flow rates or oxygen content in the firebed. A reduction of particle emissions in PM1-fraction at activated firebed cooling was found by impactor measurement and by optical particle counter. The affected particles were found in the size range <0.3 μm and have been composed mainly of potassium chloride (KCl). The chemical analysis of PM1 and boiler ash showed no statistically significant differences due to the firebed cooling. Therefore, our results indicate that the direct firebed cooling influenced the release of potassium (K) without affecting other chemical reactions.

Femtosecond laser patterning, synthesis, defect formation, and structural modification of atomic layered materials

DOE PAGES

Yoo, Jae-Hyuck; Kim, Eunpa; Hwang, David J.

2016-12-06

This article summarizes recent research on laser-based processing of twodimensional (2D) atomic layered materials, including graphene and transition metal dichalcogenides (TMDCs). Ultrafast lasers offer unique processing routes that take advantage of distinct interaction mechanisms with 2D materials to enable extremely localized energy deposition. Experiments have shown that ablative direct patterning of graphene by ultrafast lasers can achieve resolutions of tens of nanometers, as well as single-step pattern transfer. Ultrafast lasers also induce non-thermal excitation mechanisms that are useful for the thinning of TMDCs to tune the 2D material bandgap. Laser-assisted site-specific doping was recently demonstrated where ultrafast laser radiation undermore » ambient air environment could be used for the direct writing of high-quality graphene patterns on insulating substrates. This article concludes with an outlook towards developing further advanced laser processing with scalability, in situ monitoring strategies and potential applications.« less

Direct Synthesis of Polymer Nanotubes by Aqueous Dispersion Polymerization of a Cyclodextrin/Styrene Complex.

PubMed

Chen, Xi; Liu, Lei; Huo, Meng; Zeng, Min; Peng, Liao; Feng, Anchao; Wang, Xiaosong; Yuan, Jinying

2017-12-22

A one-step synthesis of nanotubes by RAFT dispersion polymerization of cyclodextrin/styrene (CD/St) complexes directly in water is presented. The resulted amphiphilic PEG-b-PS diblock copolymers self-assemble in situ into nanoparticles with various morphologies. Spheres, worms, lamellae, and nanotubes were controllably obtained. Because of the complexation, the swelling degree of polystyrene (PS) blocks by free St is limited, resulting in limited mobility of PS chains. Consequently, kinetically trapped lamellae and nanotubes were obtained instead of spherical vesicles. During the formation of nanotubes, small vesicles first formed at the ends of the tape-like lamellae, then grew and fused into nanotubes with a limited chain rearrangement. The introduction of a host-guest interaction based on CDs enables the aqueous dispersion polymerization of water-immiscible monomers, and produces kinetically trapped nanostructures, which could be a powerful technique for nanomaterials synthesis. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

The elusive abnormal CO2 insertion enabled by metal-ligand cooperative photochemical selectivity inversion.

PubMed

Schneck, Felix; Ahrens, Jennifer; Finger, Markus; Stückl, A Claudia; Würtele, Christian; Schwarzer, Dirk; Schneider, Sven

2018-03-21

Direct hydrogenation of CO 2 to CO, the reverse water-gas shift reaction, is an attractive route to CO 2 utilization. However, the use of molecular catalysts is impeded by the general reactivity of metal hydrides with CO 2 . Insertion into M-H bonds results in formates (MO(O)CH), whereas the abnormal insertion to the hydroxycarbonyl isomer (MC(O)OH), which is the key intermediate for CO-selective catalysis, has never been directly observed. We here report that the selectivity of CO 2 insertion into a Ni-H bond can be inverted from normal to abnormal insertion upon switching from thermal to photochemical conditions. Mechanistic examination for abnormal insertion indicates photochemical N-H reductive elimination as the pivotal step that leads to an umpolung of the hydride ligand. This study conceptually introduces metal-ligand cooperation for selectivity control in photochemical transformations.

A solid state source of photon triplets based on quantum dot molecules

PubMed Central

Khoshnegar, Milad; Huber, Tobias; Predojević, Ana; Dalacu, Dan; Prilmüller, Maximilian; Lapointe, Jean; Wu, Xiaohua; Tamarat, Philippe; Lounis, Brahim; Poole, Philip; Weihs, Gregor; Majedi, Hamed

2017-01-01

Producing advanced quantum states of light is a priority in quantum information technologies. In this context, experimental realizations of multipartite photon states would enable improved tests of the foundations of quantum mechanics as well as implementations of complex quantum optical networks and protocols. It is favourable to directly generate these states using solid state systems, for simpler handling and the promise of reversible transfer of quantum information between stationary and flying qubits. Here we use the ground states of two optically active coupled quantum dots to directly produce photon triplets. The formation of a triexciton in these ground states leads to a triple cascade recombination and sequential emission of three photons with strong correlations. We record 65.62 photon triplets per minute under continuous-wave pumping, surpassing rates of earlier reported sources. Our structure and data pave the way towards implementing multipartite photon entanglement and multi-qubit readout schemes in solid state devices. PMID:28604705

Metal hierarchical patterning by direct nanoimprint lithography

PubMed Central

Radha, Boya; Lim, Su Hui; Saifullah, Mohammad S. M.; Kulkarni, Giridhar U.

2013-01-01

Three-dimensional hierarchical patterning of metals is of paramount importance in diverse fields involving photonics, controlling surface wettability and wearable electronics. Conventionally, this type of structuring is tedious and usually involves layer-by-layer lithographic patterning. Here, we describe a simple process of direct nanoimprint lithography using palladium benzylthiolate, a versatile metal-organic ink, which not only leads to the formation of hierarchical patterns but also is amenable to layer-by-layer stacking of the metal over large areas. The key to achieving such multi-faceted patterning is hysteretic melting of ink, enabling its shaping. It undergoes transformation to metallic palladium under gentle thermal conditions without affecting the integrity of the hierarchical patterns on micro- as well as nanoscale. A metallic rice leaf structure showing anisotropic wetting behavior and woodpile-like structures were thus fabricated. Furthermore, this method is extendable for transferring imprinted structures to a flexible substrate to make them robust enough to sustain numerous bending cycles. PMID:23446801

The role of Myc-induced protein synthesis in cancer

PubMed Central

Ruggero, Davide

2009-01-01

Deregulation in different steps of translational control is an emerging mechanism for cancer formation. One example of an oncogene with a direct role in control of translation is the Myc transcription factor. Myc directly increases protein synthesis rates by controlling the expression of multiple components of the protein synthetic machinery, including ribosomal proteins, initiation factors of translation, Pol III and rDNA. However, the contribution of Myc-dependent increases in protein synthesis towards the multi-step process leading to cancer has remained unknown. Recent evidence strongly suggests that Myc oncogenic signaling may monopolize the translational machinery to elicit cooperative effects on cell growth, cell cycle progression, and genome instability as a mechanism for cancer initiation. Moreover, new genetic tools to restore aberrant increases in protein synthesis control are now available, which should enable the dissection of important mechanisms in cancer that rely on the translational machinery. PMID:19934336

Phage-Enabled Nanomedicine: From Probes to Therapeutics in Precision Medicine.

PubMed

Sunderland, Kegan S; Yang, Mingying; Mao, Chuanbin

2017-02-13

Both lytic and temperate bacteriophages (phages) can be applied in nanomedicine, in particular, as nanoprobes for precise disease diagnosis and nanotherapeutics for targeted disease treatment. Since phages are bacteria-specific viruses, they do not naturally infect eukaryotic cells and are not toxic to them. They can be genetically engineered to target nanoparticles, cells, tissues, and organs, and can also be modified with functional abiotic nanomaterials for disease diagnosis and treatment. This Review will summarize the current use of phage structures in many aspects of precision nanomedicine, including ultrasensitive biomarker detection, enhanced bioimaging for disease diagnosis, targeted drug and gene delivery, directed stem cell differentiation, accelerated tissue formation, effective vaccination, and nanotherapeutics for targeted disease treatment. We will also propose future directions in the area of phage-based nanomedicines, and discuss the state of phage-based clinical trials. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Light as a central modulator of circadian rhythms, sleep and affect.

PubMed

LeGates, Tara A; Fernandez, Diego C; Hattar, Samer

2014-07-01

Light has profoundly influenced the evolution of life on earth. As widely appreciated, light enables us to generate images of our environment. However, light - through intrinsically photosensitive retinal ganglion cells (ipRGCs) - also influences behaviours that are essential for our health and quality of life but are independent of image formation. These include the synchronization of the circadian clock to the solar day, tracking of seasonal changes and the regulation of sleep. Irregular light environments lead to problems in circadian rhythms and sleep, which eventually cause mood and learning deficits. Recently, it was found that irregular light can also directly affect mood and learning without producing major disruptions in circadian rhythms and sleep. In this Review, we discuss the indirect and direct influence of light on mood and learning, and provide a model for how light, the circadian clock and sleep interact to influence mood and cognitive functions.

Generation of binary holograms with a Kinect sensor for a high speed color holographic display

NASA Astrophysics Data System (ADS)

Leportier, Thibault; Park, Min-Chul; Yano, Sumio; Son, Jung-Young

2017-05-01

The Kinect sensor is a device that enables to capture a real scene with a camera and a depth sensor. A virtual model of the scene can then be obtained with a point cloud representation. A complex hologram can then be computed. However, complex data cannot be used directly because display devices cannot handle amplitude and phase modulation at the same time. Binary holograms are commonly used since they present several advantages. Among the methods that were proposed to convert holograms into a binary format, the direct-binary search (DBS) not only gives the best performance, it also offers the possibility to choose the display parameters of the binary hologram differently than the original complex hologram. Since wavelength and reconstruction distance can be modified, compensation of chromatic aberrations can be handled. In this study, we examine the potential of DBS for RGB holographic display.

Carbon nanotube-templated assembly of regioregular poly(3-alkylthiophene) in solution

NASA Astrophysics Data System (ADS)

Zhu, Jiahua; Stevens, Eric; He, Youjun; Hong, Kunlun; Ivanov, Ilia

2016-09-01

Control of structural heterogeneity by rationally encoding of the molecular assemblies is a key enabling design of hierarchical, multifunctional materials of the future. Here we report the strategies to gain such control using solution- based assembly to construct a hybrid nano-assembly and a network hybrid structure of regioregular poly(3- alkylthiophene) - carbon nanotube (P3AT-CNT). The opto-electronic performance of conjugated polymer (P3AT) is defined by the structure of the aggregate in solution and in the solid film. Control of P3AT aggregation would allow formation of broad range of morphologies with very distinct electro-optical. We utilize interactive templating to confine the assembly behavior of conjugated polymers, replacing poorly controlled solution processing approach. Perfect crystalline surface of the single-walled and multi-walled carbon nanotube (SWCNT/MWCNT) acts as a template, seeding P3AT aggregation of the surface of the nanotube. The seed continues directional growth through pi-pi stacking leading to the formation of to well-defined P3AT-CNT morphologies, including comb-like nano-assemblies, super- structures and gel networks. Interconnected, highly-branched network structure of P3AT-CNT hybrids is of particular interest to enable efficient, long-range, balanced charge carrier transport. The structure and opto-electionic function of the intermediate assemblies and networks of P3AT/CNT hybrids are characterized by transmission election microscopy and UV-vis absorption.

Ion-gel-gating-induced oxygen vacancy formation in epitaxial L a0.5S r0.5Co O3 -δ films from in operando x-ray and neutron scattering

NASA Astrophysics Data System (ADS)

Walter, Jeff; Yu, Guichuan; Yu, Biqiong; Grutter, Alexander; Kirby, Brian; Borchers, Julie; Zhang, Zhan; Zhou, Hua; Birol, Turan; Greven, Martin; Leighton, Chris

2017-12-01

Ionic-liquid/gel-based transistors have emerged as a potentially ideal means to accumulate high charge-carrier densities at the surfaces of materials such as oxides, enabling control over electronic phase transitions. Substantial gaps remain in the understanding of gating mechanisms, however, particularly with respect to charge carrier vs oxygen defect creation, one contributing factor being the dearth of experimental probes beyond electronic transport. Here we demonstrate the use of synchrotron hard x-ray diffraction and polarized neutron reflectometry as in operando probes of ion-gel transistors based on ferromagnetic L a0.5S r0.5Co O3 -δ . An asymmetric gate-bias response is confirmed to derive from electrostatic hole accumulation at negative gate bias vs oxygen vacancy formation at positive bias. The latter is detected via a large gate-induced lattice expansion (up to 1%), complementary bulk measurements and density functional calculations enabling quantification of the bias-dependent oxygen vacancy density. Remarkably, the gate-induced oxygen vacancies proliferate through the entire thickness of 30-40-unit-cell-thick films, quantitatively accounting for changes in the magnetization depth profile. These results directly elucidate the issue of electrostatic vs redox-based response in electrolyte-gated oxides, also demonstrating powerful approaches to their in operando investigation.

Consolidated bioprocessing of lignocellulosic biomass to lactic acid by a synthetic fungal-bacterial consortium.

PubMed

Shahab, Robert L; Luterbacher, Jeremy S; Brethauer, Simone; Studer, Michael H

2018-05-01

Consolidated bioprocessing (CBP) of lignocellulosic feedstocks to platform chemicals requires complex metabolic processes, which are commonly executed by single genetically engineered microorganisms. Alternatively, synthetic consortia can be employed to compartmentalize the required metabolic functions among different specialized microorganisms as demonstrated in this work for the direct production of lactic acid from lignocellulosic biomass. We composed an artificial cross-kingdom consortium and co-cultivated the aerobic fungus Trichoderma reesei for the secretion of cellulolytic enzymes with facultative anaerobic lactic acid bacteria. We engineered ecological niches to enable the formation of a spatially structured biofilm. Up to 34.7 gL -1 lactic acid could be produced from 5% (w/w) microcrystalline cellulose. Challenges in converting pretreated lignocellulosic biomass include the presence of inhibitors, the formation of acetic acid and carbon catabolite repression. In the CBP consortium hexoses and pentoses were simultaneously consumed and metabolic cross-feeding enabled the in situ degradation of acetic acid. As a result, superior product purities were achieved and 19.8 gL -1 (85.2% of the theoretical maximum) of lactic acid could be produced from non-detoxified steam-pretreated beech wood. These results demonstrate the potential of consortium-based CBP technologies for the production of high value chemicals from pretreated lignocellulosic biomass in a single step. © 2018 Wiley Periodicals, Inc.

Formation Flying Design and Applications in Weak Stability Boundary Regions

NASA Technical Reports Server (NTRS)

Folta, David

2003-01-01

Weak Stability regions serve as superior locations for interferometric scientific investigations. These regions are often selected to minimize environmental disturbances and maximize observing efficiency. Design of formations in these regions are becoming ever more challenging as more complex missions are envisioned. The development of algorithms to enable the capability for formation design must be further enabled to incorporate better understanding of WSB solution space. This development will improve the efficiency and expand the capabilities of current approaches. The Goddard Space Flight Center (GSFC) is currently supporting multiple formation missions in WSB regions. This end-to-end support consists of mission operations, trajectory design, and control. It also includes both algorithm and software development. The Constellation-X, Maxim, and Stellar Imager missions are examples of the use of improved numerical methods for attaining constrained formation geometries and controlling their dynamical evolution. This paper presents a survey of formation missions in the WSB regions and a brief description of the formation design using numerical and dynamical techniques.

Formation flying design and applications in weak stability boundary regions.

PubMed

Folta, David

2004-05-01

Weak stability regions serve as superior locations for interferomertric scientific investigations. These regions are often selected to minimize environmental disturbances and maximize observation efficiency. Designs of formations in these regions are becoming ever more challenging as more complex missions are envisioned. The development of algorithms to enable the capability for formation design must be further enabled to incorporate better understanding of weak stability boundary solution space. This development will improve the efficiency and expand the capabilities of current approaches. The Goddard Space Flight Center (GSFC) is currently supporting multiple formation missions in weak stability boundary regions. This end-to-end support consists of mission operations, trajectory design, and control. It also includes both algorithm and software development. The Constellation-X, Maxim, and Stellar Imager missions are examples of the use of improved numeric methods to attain constrained formation geometries and control their dynamical evolution. This paper presents a survey of formation missions in the weak stability boundary regions and a brief description of formation design using numerical and dynamical techniques.

Construction of three-dimensional tooth model by micro-computed tomography and application for data sharing.

PubMed

Kato, A; Ohno, N

2009-03-01

The study of dental morphology is essential in terms of phylogeny. Advances in three-dimensional (3D) measurement devices have enabled us to make 3D images of teeth without destruction of samples. However, raw fundamental data on tooth shape requires complex equipment and techniques. An online database of 3D teeth models is therefore indispensable. We aimed to explore the basic methodology for constructing 3D teeth models, with application for data sharing. Geometric information on the human permanent upper left incisor was obtained using micro-computed tomography (micro-CT). Enamel, dentine, and pulp were segmented by thresholding of different gray-scale intensities. Segmented data were separately exported in STereo-Lithography Interface Format (STL). STL data were converted to Wavefront OBJ (OBJect), as many 3D computer graphics programs support the Wavefront OBJ format. Data were also applied to Quick Time Virtual Reality (QTVR) format, which allows the image to be viewed from any direction. In addition to Wavefront OBJ and QTVR data, the original CT series were provided as 16-bit Tag Image File Format (TIFF) images on the website. In conclusion, 3D teeth models were constructed in general-purpose data formats, using micro-CT and commercially available programs. Teeth models that can be used widely would benefit all those who study dental morphology.

Percolation blockage: A process that enables melt pond formation on first year Arctic sea ice

NASA Astrophysics Data System (ADS)

Polashenski, Chris; Golden, Kenneth M.; Perovich, Donald K.; Skyllingstad, Eric; Arnsten, Alexandra; Stwertka, Carolyn; Wright, Nicholas

2017-01-01

Melt pond formation atop Arctic sea ice is a primary control of shortwave energy balance in the Arctic Ocean. During late spring and summer, the ponds determine sea ice albedo and how much solar radiation is transmitted into the upper ocean through the sea ice. The initial formation of ponds requires that melt water be retained above sea level on the ice surface. Both theory and observations, however, show that first year sea ice is so highly porous prior to the formation of melt ponds that multiday retention of water above hydraulic equilibrium should not be possible. Here we present results of percolation experiments that identify and directly demonstrate a mechanism allowing melt pond formation. The infiltration of fresh water into the pore structure of sea ice is responsible for blocking percolation pathways with ice, sealing the ice against water percolation, and allowing water to pool above sea level. We demonstrate that this mechanism is dependent on fresh water availability, known to be predominantly from snowmelt, and ice temperature at melt onset. We argue that the blockage process has the potential to exert significant control over interannual variability in ice albedo. Finally, we suggest that incorporating the mechanism into models would enhance their physical realism. Full treatment would be complex. We provide a simple temperature threshold-based scheme that may be used to incorporate percolation blockage behavior into existing model frameworks.

A Columnar Storage Strategy with Spatiotemporal Index for Big Climate Data

NASA Astrophysics Data System (ADS)

Hu, F.; Bowen, M. K.; Li, Z.; Schnase, J. L.; Duffy, D.; Lee, T. J.; Yang, C. P.

2015-12-01

Large collections of observational, reanalysis, and climate model output data may grow to as large as a 100 PB in the coming years, so climate dataset is in the Big Data domain, and various distributed computing frameworks have been utilized to address the challenges by big climate data analysis. However, due to the binary data format (NetCDF, HDF) with high spatial and temporal dimensions, the computing frameworks in Apache Hadoop ecosystem are not originally suited for big climate data. In order to make the computing frameworks in Hadoop ecosystem directly support big climate data, we propose a columnar storage format with spatiotemporal index to store climate data, which will support any project in the Apache Hadoop ecosystem (e.g. MapReduce, Spark, Hive, Impala). With this approach, the climate data will be transferred into binary Parquet data format, a columnar storage format, and spatial and temporal index will be built and attached into the end of Parquet files to enable real-time data query. Then such climate data in Parquet data format could be available to any computing frameworks in Hadoop ecosystem. The proposed approach is evaluated using the NASA Modern-Era Retrospective Analysis for Research and Applications (MERRA) climate reanalysis dataset. Experimental results show that this approach could efficiently overcome the gap between the big climate data and the distributed computing frameworks, and the spatiotemporal index could significantly accelerate data querying and processing.

Origin and effective reduction of inversion domains in aluminum nitride grown by a sublimation method

NASA Astrophysics Data System (ADS)

Shigetoh, Keisuke; Horibuchi, Kayo; Nakamura, Daisuke

2017-11-01

Owing to the large differences in the chemical properties between Al and N polarities in aluminum nitride (AlN), the choice of the polar direction for crystal growth strongly affects not only the quality but also the shape (facet formation) of the grown crystal. In particular, N-polar (0 0 0 -1) has been considered to be a more preferable direction than Al-polar (0 0 0 1) for sublimation growth because compared to Al-polar (0 0 0 1), N-polar (0 0 0 -1) exhibits better stability at high growth rate (high supersaturation) conditions and enables easier lateral enlargement of the crystal. However, some critical growth conditions induce polarity inversion and hinder stable N-polar growth. Furthermore, the origin of the polarity inversion in AlN growth by the sublimation method is still unclear. To ensure stable N-polar growth without polarity inversion, the formation mechanism of the inversion domain during AlN sublimation growth must be elucidated. Therefore, herein, we demonstrate homoepitaxial growth on an N-polar seed and carefully investigate the obtained crystal that shows polarity inversion. Annular bright-field scanning transmission electron microscopy reveals that polarity is completely converted to the Al polarity via the formation of a 30 nm thick mixed polar layer (MPL) just above the seed. Moreover, three-dimensional atom probe tomography shows the segregation of the oxygen impurities in the MPL with a high concentration of about 3 atom%. Finally, by avoiding the incorporation of oxygen impurity into the crystal at the initial stage of the growth, we demonstrate an effective reduction (seven orders of magnitude) of the inversion domain boundary formation.

Effects of Propylene Carbonate Content in CsPF6-Containing Electrolytes on the Enhanced Performances of Graphite Electrode for Lithium-Ion Batteries

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

Zheng, Jianming; Yan, Pengfei; Cao, Ruiguo

2016-02-10

Cesium salt has been demonstrated as an efficient electrolyte additive in suppressing the lithium (Li) dendrite formation and directing the formation of an ultrathin and stable solid electrolyte interphase (SEI) even in propylene carbonate (PC)-ethylene carbonate (EC)-based electrolytes. Here, we further investigate the effect of PC content in the presence of CsPF6 additive (0.05 M) on the performances of graphite electrode in Li||graphite half cells and in graphite||LiNi0.80Co0.15Al0.05O2 (NCA) full cells. It is found that the performance of graphite electrode is also affected by PC content even though CsPF6 additive is present in the electrolytes. An optimal PC content ofmore » 20% by weight in the solvent mixtures is identified. The enhanced electrochemical performance of graphite electrode is attributed to the synergistic effects of the Cs+ additive and the PC solvent. The formation of a robust, ultrathin and compact SEI layer containing lithium-enriched species on the graphite electrode, directed by Cs+, effectively suppresses the PC co-intercalation and thus prevents the graphite exfoliation. This SEI layer is only permeable for de-solvated Li+ ions and allows fast Li+ ion transport through it, which therefore largely alleviates the Li dendrite formation on graphite electrode during lithiation even at high current densities. The presence of low-melting-point PC solvent also enables the sustainable operation of the graphite||NCA full cells under a wide spectrum of temperatures. The fundamental findings of this work shed light on the importance of manipulating/maintaining the electrode/electrolyte interphasial stability in a variety of energy storage devices.« less

Necrotic platelets provide a procoagulant surface during thrombosis

PubMed Central

Hua, Vu Minh; Abeynaike, Latasha; Glaros, Elias; Campbell, Heather; Pasalic, Leonardo; Chen, Vivien M. Y.

2015-01-01

A subpopulation of platelets fulfills a procoagulant role in hemostasis and thrombosis by enabling the thrombin burst required for fibrin formation and clot stability at the site of vascular injury. Excess procoagulant activity is linked with pathological thrombosis. The identity of the procoagulant platelet has been elusive. The cell death marker 4-[N-(S-glutathionylacetyl)amino]phenylarsonous acid (GSAO) rapidly enters a subpopulation of agonist-stimulated platelets via an organic anion-transporting polypeptide and is retained in the cytosol through covalent reaction with protein dithiols. Labeling with GSAO, together with exposure of P-selectin, distinguishes necrotic from apoptotic platelets and correlates with procoagulant potential. GSAO+ platelets form in occluding murine thrombi after ferric chloride injury and are attenuated with megakaryocyte-directed deletion of the cyclophilin D gene. These platelets form a procoagulant surface, supporting fibrin formation, and reduction in GSAO+ platelets is associated with reduction in platelet thrombus size and fibrin formation. Analysis of platelets from human subjects receiving aspirin therapy indicates that these procoagulant platelets form despite aspirin therapy, but are attenuated by inhibition of the necrosis pathway. These findings indicate that the major subpopulation of platelets involved in fibrin formation are formed via regulated necrosis involving cyclophilin D, and that they may be targeted independent of platelet activation. PMID:26474813

Reaction of methyl formate with VC(1 0 0) and TiC(1 0 0) surfaces

NASA Astrophysics Data System (ADS)

Frantz, Peter; Kim, Hyun I.; Didziulis, Stephen V.; Li, Shuang; Chen, Zhiying; Perry, Scott S.

2005-12-01

The chemistry of the (1 0 0) surface of the tribologically important materials vanadium carbide (VC) and titanium carbide (TiC) with methyl formate (CH 3OCHO) has been studied with X-ray photoelectron spectroscopy (XPS), high resolution electron energy loss spectroscopy (HREELS), and temperature programmed desorption (TPD). The molecule reacts with each surface at temperatures below 150 K, although the extent of reaction is greater on the TiC surface. XPS and HREELS results indicate that the first step in this chemistry is the cleavage of the CH 3O-CHO bond, generating surface methoxy groups (CH 3O-) and either carbon monoxide on VC or a formyl (CHO) group on TiC. The methoxy group reacts further on both surfaces via pathways expected based on previous methanol adsorption studies, primarily decomposing through a formyl intermediate on VC to generate formaldehyde and evolving methanol on TiC. The formyl group formed directly from methyl formate on TiC enables the production and evolution of formaldehyde, and also appears to break down further to the elements. These results indicate a propensity for these carbides to react with esters, leading potentially to the beneficial formation of friction lowering surface films or the deleterious degradation of ester-based lubricants.

Directional reversals enable Myxococcus xanthus cells to produce collective one-dimensional streams during fruiting-body formation

PubMed Central

Thutupalli, Shashi; Sun, Mingzhai; Bunyak, Filiz; Palaniappan, Kannappan; Shaevitz, Joshua W.

2015-01-01

The formation of a collectively moving group benefits individuals within a population in a variety of ways. The surface-dwelling bacterium Myxococcus xanthus forms dynamic collective groups both to feed on prey and to aggregate during times of starvation. The latter behaviour, termed fruiting-body formation, involves a complex, coordinated series of density changes that ultimately lead to three-dimensional aggregates comprising hundreds of thousands of cells and spores. How a loose, two-dimensional sheet of motile cells produces a fixed aggregate has remained a mystery as current models of aggregation are either inconsistent with experimental data or ultimately predict unstable structures that do not remain fixed in space. Here, we use high-resolution microscopy and computer vision software to spatio-temporally track the motion of thousands of individuals during the initial stages of fruiting-body formation. We find that cells undergo a phase transition from exploratory flocking, in which unstable cell groups move rapidly and coherently over long distances, to a reversal-mediated localization into one-dimensional growing streams that are inherently stable in space. These observations identify a new phase of active collective behaviour and answer a long-standing open question in Myxococcus development by describing how motile cell groups can remain statistically fixed in a spatial location. PMID:26246416

Toward Molecular Engineering of Polymer Glasses

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

Freed, Karl F.; Xu, Wen-Sheng; Dudowicz, Jacek B.

Glass formation has been central to fabrication technologies since the dawn of civilization. Glasses not only encompass window panes, the insulation in our homes, the optical fibers supplying our cable TV, and vessels for eating and drinking, but they also include a vast array of ‘‘plastic’’ polymeric materials. Glasses find applications in high technology (e.g., producing microelectronic materials, etc., amorphous semiconductors), and recent advances have created ‘‘plastic metallic glasses’’ that are promising for fabricating everyday structural materials. Many commercially relevant systems, such as microemulsions and colloidal suspensions, have complex molecular structures and thus solidify by glass formation. Despite the importancemore » of understanding the fundamental nature of glass formation for the synthesis of new materials, a predictive molecular theory has been lacking. Much of our understanding of glass formation derives from the analysis of experimental data, a process that has uncovered a number of interesting universal behaviors, namely, relations between properties that are independent of molecular details. However, these empirically derived relations and their limitations remain to be understood on the basis of theories, and, more importantly, there is strong need for theories of the explicit variation with molecular system to enable the rational design and tailoring of new materials. We have recently developed the generalized entropy theory, the only analytic, theory that enables describing the dependence of the properties of glass-formation on monomer molecular structures. These properties include the two central quantities of glass formation, the glass transition temperature and the glass fragility parameter, material dependent properties that govern how a material may be processed (e.g., by extrusion, ink jet, molding, etc.) Our recent works, which are further described below, extend the studies of glass formation in polymer systems to test the theory by directly comparing between the predictions of our generalized entropy theory with experiment and with simulations and to expand the vistas of the theory to describe a wider range of important systems (e.g. glass formation in binary blends and systems with specific interactions) and phenomena that are describable by the generalized entropy theory. In addition, we have addressed longstanding fundamental problems associated with the validity of the Adam-Gibbs theory, one of the underpinnings of the general entropy theory. Theoretical advances to enable describing the properties of glass-formation over a wider class of important polymeric systems, included semi-flexible systems, the more general situation of specific interactions, and more. Our recent work removes the simplest approximation uses the simplest model in which the interaction is approximated by a single, monomer average. Thus, the theory has been extended to allow some variations of the energy parameters between the atoms within the monomers. The theory has also been extended to include all the contributions from chain semi-flexibility. Both projects are extremely difficult, but the payback is that the process of solving the problems developed strong theoretical skills in Dr. Xu, who has recently begun a postdoc position at ORNL. The theory has also been extended to describe glass formation in partially miscible blends, with good general agreement with experiment. Again, the development of the theory presented an extremely difficult problem, but the payback is the development of a theory for a very important class of systems. Another project provides an extremely simple approximation for certain properties of glass formation in polymer melts and should make the theory more accessible to everyone.« less

Bartonella henselae engages inside-out and outside-in signaling by integrin β1 and talin1 during invasome-mediated bacterial uptake.

PubMed

Truttmann, Matthias C; Misselwitz, Benjamin; Huser, Sonja; Hardt, Wolf-Dietrich; Critchley, David R; Dehio, Christoph

2011-11-01

The VirB/D4 type IV secretion system (T4SS) of the bacterial pathogen Bartonella henselae (Bhe) translocates seven effector proteins (BepA-BepG) into human cells that subvert host cellular functions. Two redundant pathways dependent on BepG or the combination of BepC and BepF trigger the formation of a bacterial uptake structure termed the invasome. Invasome formation is a multi-step process consisting of bacterial adherence, effector translocation, aggregation of bacteria on the cell surface and engulfment, and eventually, complete internalization of the bacterial aggregate occurs in an F-actin-dependent manner. In the present study, we show that Bhe-triggered invasome formation depends on integrin-β1-mediated signaling cascades that enable assembly of the F-actin invasome structure. We demonstrate that Bhe interacts with integrin β1 in a fibronectin- and VirB/D4 T4SS-independent manner and that activated integrin β1 is essential for both effector translocation and the actin rearrangements leading to invasome formation. Furthermore, we show that talin1, but not talin2, is required for inside-out activation of integrin β1 during invasome formation. Finally, integrin-β1-mediated outside-in signaling by FAK, Src, paxillin and vinculin is necessary for invasome formation. This is the first example of a bacterial entry process that fully exploits the bi-directional signaling capacity of integrin receptors in a talin1-specific manner.

Development of fusogenic glass surfaces that impart spatiotemporal control over macrophage fusion: Direct visualization of multinucleated giant cell formation

PubMed Central

Faust, James J.; Christenson, Wayne; Doudrick, Kyle; Ros, Robert

2017-01-01

Implantation of synthetic material, including vascular grafts, pacemakers, etc. results in the foreign body reaction and the formation of multinucleated giant cells (MGCs) at the exterior surface of the implant. Despite the long-standing premise that fusion of mononucleated macrophages results in the formation of MGCs, to date, no published study has shown fusion in context with living specimens. This is due to the fact that optical-quality glass, which is required for the majority of live imaging techniques, does not promote macrophage fusion. Consequently, the morphological changes that macrophages undergo during fusion as well as the mechanisms that govern this process remain ill-defined. In this study, we serendipitously identified a highly fusogenic glass surface and discovered that the capacity to promote fusion was due to oleamide contamination. When adsorbed on glass, oleamide and other molecules that contain long-chain hydrocarbons promoted high levels of macrophage fusion. Adhesion, an essential step for macrophage fusion, was apparently mediated by Mac-1 integrin (CD11b/CD18, αMβ2) as determined by single cell force spectroscopy and adhesion assays. Micropatterned glass further increased fusion and enabled a remarkable degree of spatiotemporal control over MGC formation. Using these surfaces, we reveal the kinetics that govern MGC formation in vitro. We anticipate that the spatiotemporal control afforded by these surfaces will expedite studies designed to identify the mechanism(s) of macrophage fusion and MGC formation with implication for the design of novel biomaterials. PMID:28340410

Application of the unified mask data format based on OASIS for VSB EB writers

NASA Astrophysics Data System (ADS)

Suzuki, Toshio; Hirumi, Junji; Suga, Osamu

2005-11-01

Mask data preparation (MDP) for modern mask manufacturing becomes a complex process because many kinds of EB data formats are used in mask makers and EB data files continue to become bigger by the application of RET. Therefore we developed a unified mask pattern data format named "OASIS.VSB1" and a job deck format named "MALY2" for Variable-Shaped-Beam (VSB) EB writers. OASIS.VSB is the mask pattern data format based on OASISTM 3 (Open Artwork System Interchange Standard) released as a successive format to GDSII by SEMI. We defined restrictions on OASIS for VSB EB writers to input OASIS.VSB data directly to VSB EB writers just like the native EB data. OASIS.VSB specification and MALY specification have been disclosed to the public and will become a SEMI standard in the near future. We started to promote the spread activities of OASIS.VSB and MALY. For practical use of OASIS.VSB and MALY, we are discussing the infrastructure system of MDP processing using OASIS.VSB and MALY with mask makers, VSB EB makers, and device makers. We are also discussing the tools for the infrastructure system with EDA vendors. The infrastructure system will enable TAT, the man-hour, and the cost in MDP to be reduced. In this paper, we propose the plan of the infrastructure system of MDP processing using OASIS.VSB and MALY as an application of OASIS.VSB and MALY.

‘In-Format’ screening of a novel bispecific antibody format reveals significant potency improvements relative to unformatted molecules

PubMed Central

Scott, Martin J.; Lee, Jennifer A.; Wake, Matthew S.; Batt, Kelly V.; Wattam, Trevor A.; Hiles, Ian D.; Batuwangala, Thil D.; Ashman, Claire I.; Steward, Michael

2017-01-01

ABSTRACT Bispecific antibodies (BsAbs) are emerging as an important class of biopharmaceutical. The majority of BsAbs are created from conventional antibodies or fragments engineered into more complex configurations. A recurring challenge in their development, however, is the identification of components that are optimised for inclusion in the final format in order to deliver both efficacy and robust biophysical properties. Using a modular BsAb format, the mAb-dAb, we assessed whether an ‘in-format’ screening approach, designed to select format-compatible domain antibodies, could expedite lead discovery. Human nerve growth factor (NGF) was selected as an antigen to validate the approach; domain antibody (dAb) libraries were screened, panels of binders identified, and binding affinities and potencies compared for selected dAbs and corresponding mAb-dAbs. A number of dAbs that exhibited high potency (IC50) when assessed in-format were identified. In contrast, the corresponding dAb monomers had ∼1000-fold lower potency than the formatted dAbs; such dAb monomers would therefore have been omitted from further characterization. Subsequent stoichiometric analyses of mAb-dAbs bound to NGF, or an additional target antigen (vascular endothelial growth factor), suggested different target binding modes; this indicates that the observed potency improvements cannot be attributed simply to an avidity effect offered by the mAb-dAb format. We conclude that, for certain antigens, screening naïve selection outputs directly in-format enables the identification of a subset of format-compatible dAbs, and that this offers substantial benefits in terms of molecular properties and development time. PMID:27786601

Effective Light Directed Assembly of Building Blocks with Microscale Control.

PubMed

Dinh, Ngoc-Duy; Luo, Rongcong; Christine, Maria Tankeh Asuncion; Lin, Weikang Nicholas; Shih, Wei-Chuan; Goh, James Cho-Hong; Chen, Chia-Hung

2017-06-01

Light-directed forces have been widely used to pattern micro/nanoscale objects with precise control, forming functional assemblies. However, a substantial laser intensity is required to generate sufficient optical gradient forces to move a small object in a certain direction, causing limited throughput for applications. A high-throughput light-directed assembly is demonstrated as a printing technology by introducing gold nanorods to induce thermal convection flows that move microparticles (diameter = 40 µm to several hundreds of micrometers) to specific light-guided locations, forming desired patterns. With the advantage of effective light-directed assembly, the microfluidic-fabricated monodispersed biocompatible microparticles are used as building blocks to construct a structured assembly (≈10 cm scale) in ≈2 min. The control with microscale precision is approached by changing the size of the laser light spot. After crosslinking assembly of building blocks, a novel soft material with wanted pattern is approached. To demonstrate its application, the mesenchymal stem-cell-seeded hydrogel microparticles are prepared as functional building blocks to construct scaffold-free tissues with desired structures. This light-directed fabrication method can be applied to integrate different building units, enabling the bottom-up formation of materials with precise control over their internal structure for bioprinting, tissue engineering, and advanced manufacturing. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Miocene Roof Mapping Using Microtremor Recording and Electrical Survey Method in Blida City, Algeria

NASA Astrophysics Data System (ADS)

Bouchelouh, Assia; Bensalem, Rabah; Zaourar, Naima; Machane, Djamel; Moulouel, Hakim; Oubaiche, El Hadi

2018-01-01

Bedrock depths in the Mitidja basin in general and in the Blida region in particular are still poorly known despite, the existence of some relatively deep hydraulic boreholes that intersect only superficial alluvial formations. To assess the seismic risk of Blida town, knowledge of soil amplification requires the thickness and properties of sedimentary formations that cover the substratum. For the purposes of our study, the thicknesses obtained by the vertical electric soundings, carried out in the hydrogeological study of the basin, were combined with horizontal-to-vertical spectral ratio (HVSR) microtremor recordings. This combination made it possible to determine an empirical relationship between frequency and thickness specific to the Blida site area, which enabled the roof of the Miocene to be mapped and shows slight undulations with directions compatible with the tectonic constraints of the region. The boundaries between the low and high frequencies obtained by HVSR are well materialized, at south by Sidi El Kebir river, at west by Chiffa river and in the central part by a line of direction SE-NW corresponding to the old passage of Sidi El Kebir river. The presence of low frequencies attributed to the old alluvial deposits with significant thicknesses that originate just after Sidi El Kebir river confirms that the South Mitidjian contact is subvertical.

Observing the formation of ice and organic crystals in active sites

PubMed Central

Campbell, James M.; Meldrum, Fiona C.; Christenson, Hugo K.

2017-01-01

Heterogeneous nucleation is vital to a wide range of areas as diverse as ice nucleation on atmospheric aerosols and the fabrication of high-performance thin films. There is excellent evidence that surface topography is a key factor in directing crystallization in real systems; however, the mechanisms by which nanoscale pits and pores promote nucleation remain unclear. Here, we use natural cleavage defects on Muscovite mica to investigate the activity of topographical features in the nucleation from vapor of ice and various organic crystals. Direct observation of crystallization within surface pockets using optical microscopy and also interferometry demonstrates that these sharply acute features provide extremely effective nucleation sites and allows us to determine the mechanism by which this occurs. A confined phase is first seen to form along the apex of the wedge and then grows out of the pocket opening to generate a bulk crystal after a threshold saturation has been achieved. Ice nucleation proceeds in a comparable manner, although our resolution is insufficient to directly observe a condensate before the growth of a bulk crystal. These results provide insight into the mechanism of crystal deposition from vapor on real surfaces, where this will ultimately enable us to use topography to control crystal deposition on surfaces. They are also particularly relevant to our understanding of processes such as cirrus cloud formation, where such topographical features are likely candidates for the “active sites” that make clay particles effective nucleants for ice in the atmosphere. PMID:27994140

Membrane Tension Acts Through PLD2 and mTORC2 to Limit Actin Network Assembly During Neutrophil Migration

PubMed Central

Diz-Muñoz, Alba; Thurley, Kevin; Chintamen, Sana; Altschuler, Steven J.; Fletcher, Daniel A.; Weiner, Orion D.

2016-01-01

For efficient polarity and migration, cells need to regulate the magnitude and spatial distribution of actin assembly. This process is coordinated by reciprocal interactions between the actin cytoskeleton and mechanical forces. Actin polymerization-based protrusion increases tension in the plasma membrane, which in turn acts as a long-range inhibitor of actin assembly. These interactions form a negative feedback circuit that limits the magnitude of membrane tension in neutrophils and prevents expansion of the existing front and the formation of secondary fronts. It has been suggested that the plasma membrane directly inhibits actin assembly by serving as a physical barrier that opposes protrusion. Here we show that efficient control of actin polymerization-based protrusion requires an additional mechanosensory feedback cascade that indirectly links membrane tension with actin assembly. Specifically, elevated membrane tension acts through phospholipase D2 (PLD2) and the mammalian target of rapamycin complex 2 (mTORC2) to limit actin nucleation. In the absence of this pathway, neutrophils exhibit larger leading edges, higher membrane tension, and profoundly defective chemotaxis. Mathematical modeling suggests roles for both the direct (mechanical) and indirect (biochemical via PLD2 and mTORC2) feedback loops in organizing cell polarity and motility—the indirect loop is better suited to enable competition between fronts, whereas the direct loop helps spatially organize actin nucleation for efficient leading edge formation and cell movement. This circuit is essential for polarity, motility, and the control of membrane tension. PMID:27280401

10.7 Gb/s uncompensated transmission over a 470 km hybrid fiber link with in-line SOAs using MLSE and duobinary signals.

PubMed

Downie, John D; Hurley, Jason; Mauro, Yihong

2008-09-29

We experimentally demonstrate uncompensated 8-channel wavelength division multiplexing (WDM) and single channel transmission at 10.7 Gb/s over a 470 km hybrid fiber link with in-line semiconductor optical amplifiers (SOAs). Two different forms of the duobinary modulation format are investigated and compared. Maximum Likelihood Sequence Estimation (MLSE) receiver technology is found to significantly mitigate nonlinear effects from the SOAs and to enable the long transmission, especially for optical duobinary signals derived from differential phase shift keying (DPSK) signals directly detected after narrowband optical filter demodulation. The MLSE also helps to compensate for a non-optimal Fabry-Perot optical filter demodulator.

Graphene-Based Three-Dimensional Capacitive Touch Sensor for Wearable Electronics.

PubMed

Kang, Minpyo; Kim, Jejung; Jang, Bongkyun; Chae, Youngcheol; Kim, Jae-Hyun; Ahn, Jong-Hyun

2017-08-22

The development of input device technology in a conformal and stretchable format is important for the advancement of various wearable electronics. Herein, we report a capacitive touch sensor with good sensing capabilities in both contact and noncontact modes, enabled by the use of graphene and a thin device geometry. This device can be integrated with highly deformable areas of the human body, such as the forearms and palms. This touch sensor detects multiple touch signals in acute recordings and recognizes the distance and shape of the approaching objects before direct contact is made. This technology offers a convenient and immersive human-machine interface and additional potential utility as a multifunctional sensor for emerging wearable electronics and robotics.

Low-cost synthesis and physical characterization of thieno[3,4-c]pyrrole-4,6-dione-based polymers.

PubMed

Berrouard, Philippe; Dufresne, Stéphane; Pron, Agnieszka; Veilleux, Justine; Leclerc, Mario

2012-09-21

The improved synthesis of thieno[3,4-c]pyrrole-4,6-dione (TPD) monomers, including Gewald thiophene ring formation, a Sandmeyer-type reaction, and neat condensation with an amine, is presented. This protocol enables faster, cheaper, and more efficient preparation of TPD units in comparison to traditional methods. Furthermore, a series of TPD homo- and pseudohomopolymers bearing various alkyl chains was synthesized via a direct heteroarylation polymerization (DHAP) procedure. UV-visible absorption and powder X-ray diffraction measurements revealed the relationship between the ratio of branched to linear alkyl chains and the optoelectronic properties of the polymers as well as their packing in the solid state.

Industrially Feasible Approach to Transparent, Flexible, and Conductive Carbon Nanotube Films: Cellulose-Assisted Film Deposition Followed by Solution and Photonic Processing

NASA Astrophysics Data System (ADS)

Kim, Yeji; Chikamatsu, Masayuki; Azumi, Reiko; Saito, Takeshi; Minami, Nobutsugu

2013-02-01

We report that single-walled nanotube (SWNT) films with precisely controlled thicknesses and transmittances can be produced through the doctor-blade method using SWNT-polymer inks. The matrix polymer around SWNTs were successfully removed by either solution curing or photonic curing at room temperature, which are advantageous processes enabling direct film formation on plastic substrates. Sheet resistances as low as 68-240 Ω/sq at T=89-98% were obtained. Furthermore, the SWNT film on poly(ethylene naphthalate) exhibited superior flexibility and stability in a flexure endurance test. The method may open a wide range of opportunities for flexible electrical devices.

Stop-Frame Filming and Discovery of Reactions at the Single-Molecule Level by Transmission Electron Microscopy

PubMed Central

2017-01-01

We report an approach, named chemTEM, to follow chemical transformations at the single-molecule level with the electron beam of a transmission electron microscope (TEM) applied as both a tunable source of energy and a sub-angstrom imaging probe. Deposited on graphene, disk-shaped perchlorocoronene molecules are precluded from intermolecular interactions. This allows monomolecular transformations to be studied at the single-molecule level in real time and reveals chlorine elimination and reactive aryne formation as a key initial stage of multistep reactions initiated by the 80 keV e-beam. Under the same conditions, perchlorocoronene confined within a nanotube cavity, where the molecules are situated in very close proximity to each other, enables imaging of intermolecular reactions, starting with the Diels–Alder cycloaddition of a generated aryne, followed by rearrangement of the angular adduct to a planar polyaromatic structure and the formation of a perchlorinated zigzag nanoribbon of graphene as the final product. ChemTEM enables the entire process of polycondensation, including the formation of metastable intermediates, to be captured in a one-shot “movie”. A molecule with a similar size and shape but with a different chemical composition, octathio[8]circulene, under the same conditions undergoes another type of polycondensation via thiyl biradical generation and subsequent reaction leading to polythiophene nanoribbons with irregular edges incorporating bridging sulfur atoms. Graphene or carbon nanotubes supporting the individual molecules during chemTEM studies ensure that the elastic interactions of the molecules with the e-beam are the dominant forces that initiate and drive the reactions we image. Our ab initio DFT calculations explicitly incorporating the e-beam in the theoretical model correlate with the chemTEM observations and give a mechanism for direct control not only of the type of the reaction but also of the reaction rate. Selection of the appropriate e-beam energy and control of the dose rate in chemTEM enabled imaging of reactions on a time frame commensurate with TEM image capture rates, revealing atomistic mechanisms of previously unknown processes. PMID:28191929

Physics and Chemistry of Star and Planet Formation in the Alma ERA

NASA Astrophysics Data System (ADS)

Bergin, Edwin

2014-06-01

ALMA will open up new avenues of exploration encompassing the wide range of star formation in our galaxy and peering into the central heart of planet-forming circumstellar disks. As we seek to explore the origins of stars and planets molecular emission will be at the front and center of many studies probing gas physics and chemistry. In this talk I will discus some of the areas where we can expect significant advances due to the increased sensitivity and superb spatial resolution of ALMA. In star-forming cores, a rich chemistry is revealed that may be the simpler molecular precursors to more complex organics, such as amino acids, seen within primitive rocks in our own solar system. ALMA will provide new information regarding the relative spatial distribution within a given source for a host of organics, sampling tens to hundreds of transitions of a variety of molecules, including presumably new ones. In this area there is a rich synergy with existing ground and space-based data, including Herschel/Spitzer. Here the increased sampling of sources to be enabled by ALMA should bring greater clarity toward the key products of interstellar chemistry and further constrain processes. On smaller Solar System scales, for over a decade most observations of planet-forming disks focused on the dust thermal continuum emission as a probe of the gas content and structure. ALMA will enable reliable and direct studies of gas to explore the evolving physics of planet-formation, the gas dissipation timescales (i.e. the upper limit to the timescale for giant planet birth), and also the chemistry. It is this chemistry that sets the composition of gas giants and also influences the ultimate composition of water and organic materials that are delivered to terrestrial worlds. Here I will show how we can use molecular emission to determine the gas thermal structure of a disk system and the total gas content - key astrophysical quantities. This will also enable more constrained chemical studies that will seek to determine whether the chemistry of planetary birth is universal and similar to our own.

High-yield cell-free synthesis of human EGFR by IRES-mediated protein translation in a continuous exchange cell-free reaction format

PubMed Central

Quast, Robert B.; Sonnabend, Andrei; Stech, Marlitt; Wüstenhagen, Doreen A.; Kubick, Stefan

2016-01-01

Cell-free protein synthesis systems derived from eukaryotic sources often provide comparatively low amounts of several μg per ml of de novo synthesized membrane protein. In order to overcome this, we herein demonstrate the high-yield cell-free synthesis of the human EGFR in a microsome-containing system derived from cultured Sf21 cells. Yields were increased more than 100-fold to more than 285 μg/ml by combination of IRES-mediated protein translation with a continuous exchange cell-free reaction format that allowed for prolonged reaction lifetimes exceeding 24 hours. In addition, an orthogonal cell-free translation system is presented that enabled the site-directed incorporation of p-Azido-L-phenylalanine by amber suppression. Functionality of cell-free synthesized receptor molecules is demonstrated by investigation of autophosphorylation activity in the absence of ligand and interaction with the cell-free synthesized adapter molecule Grb2. PMID:27456041

Elongation Factor Ts Directly Facilitates the Formation and Disassembly of the Escherichia coli Elongation Factor Tu·GTP·Aminoacyl-tRNA Ternary Complex*

PubMed Central

Burnett, Benjamin J.; Altman, Roger B.; Ferrao, Ryan; Alejo, Jose L.; Kaur, Navdep; Kanji, Joshua; Blanchard, Scott C.

2013-01-01

Aminoacyl-tRNA enters the translating ribosome in a ternary complex with elongation factor Tu (EF-Tu) and GTP. Here, we describe bulk steady state and pre-steady state fluorescence methods that enabled us to quantitatively explore the kinetic features of Escherichia coli ternary complex formation and decay. The data obtained suggest that both processes are controlled by a nucleotide-dependent, rate-determining conformational change in EF-Tu. Unexpectedly, we found that this conformational change is accelerated by elongation factor Ts (EF-Ts), the guanosine nucleotide exchange factor for EF-Tu. Notably, EF-Ts attenuates the affinity of EF-Tu for GTP and destabilizes ternary complex in the presence of non-hydrolyzable GTP analogs. These results suggest that EF-Ts serves an unanticipated role in the cell of actively regulating the abundance and stability of ternary complex in a manner that contributes to rapid and faithful protein synthesis. PMID:23539628

Supramolecular assemblies of a nitrogen-embedded buckybowl dimer with C60† †Electronic supplementary information (ESI) available. CCDC 1579079 and 1579080. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c7sc04453d

PubMed Central

Yokoi, Hiroki; Sakamaki, Daisuke; Seki, Shu

2017-01-01

A directly connected azabuckybowl dimer was synthesized via a palladium-catalysed C–H/C–Br coupling. The electron-donating nature of the pyrrolic nitrogen atoms of the azabuckybowl enabled a strong complexation with pristine C60. In the presence of two equivalents of C60, the azabuckybowl dimer formed crystals with a 1 : 2 stoichiometry. Conversely, in diluted solution, complexes with a 1 : 1 stoichiometry of the dimer and C60 were detected predominantly, and these precipitated upon increasing the concentration of C60. Scanning electron microscopy images of the precipitate showed fibre-like aggregates, indicating the formation of supramolecular assemblies with 1D chain structures. A variable-temperature 1H NMR analysis revealed that the precipitate consists of the dimer and C60 in a 1 : 1 ratio. PMID:29629149

Functional Hydrogel Materials Inspired by Amyloid

NASA Astrophysics Data System (ADS)

Schneider, Joel

2012-02-01

Protein assembly resulting in the formation of amyloid fibrils, assemblies rich in cross beta-sheet structure, is normally thought of as a deleterious event associated with disease. However, amyloid formation is also involved in a diverse array of normal biological functions such as cell adhesion, melanin synthesis, insect defense mechanism and modulation of water surface tension by fungi and bacteria. These findings indicate that Nature has evolved to take advantage of large, proteinaceous fibrillar assemblies to elicit function. We are designing functional materials, namely hydrogels, from peptides that self-assembled into fibrillar networks, rich in cross beta-sheet structure. These gels can be used for the direct encapsulation and delivery of small molecule-, protein- and cell-based therapeutics. Loaded gels exhibit shear-thinning/self-healing mechanical properties enabling their delivery via syringe. In addition to their use for delivery, we have found that some of these gels display antibacterial activity. Although cytocompatible towards mammalian cells, the hydrogels can kill a broad spectrum of bacteria on contact.

In situ real-time imaging of self-sorted supramolecular nanofibres

NASA Astrophysics Data System (ADS)

Onogi, Shoji; Shigemitsu, Hajime; Yoshii, Tatsuyuki; Tanida, Tatsuya; Ikeda, Masato; Kubota, Ryou; Hamachi, Itaru

2016-08-01

Self-sorted supramolecular nanofibres—a multicomponent system that consists of several types of fibre, each composed of distinct building units—play a crucial role in complex, well-organized systems with sophisticated functions, such as living cells. Designing and controlling self-sorting events in synthetic materials and understanding their structures and dynamics in detail are important elements in developing functional artificial systems. Here, we describe the in situ real-time imaging of self-sorted supramolecular nanofibre hydrogels consisting of a peptide gelator and an amphiphilic phosphate. The use of appropriate fluorescent probes enabled the visualization of self-sorted fibres entangled in two and three dimensions through confocal laser scanning microscopy and super-resolution imaging, with 80 nm resolution. In situ time-lapse imaging showed that the two types of fibre have different formation rates and that their respective physicochemical properties remain intact in the gel. Moreover, we directly visualized stochastic non-synchronous fibre formation and observed a cooperative mechanism.

Application of Fusion Gyrotrons to Enhanced Geothermal Systems (EGS)

NASA Astrophysics Data System (ADS)

Woskov, P.; Einstein, H.; Oglesby, K.

2013-10-01

The potential size of geothermal energy resources is second only to fusion energy. Advances are needed in drilling technology and heat reservoir formation to realize this potential. Millimeter-wave (MMW) gyrotrons and related technologies developed for fusion energy research could contribute to enabling EGS. Directed MMW energy can be used to advance rock penetration capabilities, borehole casing, and fracking. MMWs are ideally suited because they can penetrate through small particulate extraction plumes, can be efficiently guided long distances in borehole dimensions, and continuous megawatt sources are commercially available. Laboratory experiments with a 10 kW, 28 GHz CPI gyrotron have shown that granite rock can be fractured and melted with power intensities of about 1 kW/cm2 and minute exposure times. Observed melted rock MMW emissivity and estimated thermodynamics suggest that penetrating hot, hard crystalline rock formations may be economic with fusion research developed MMW sources. Supported by USDOE, Office of Energy Efficiency and Renewable Energy and Impact Technologies, LLC.

Self-cleaning and surface chemical reactions during hafnium dioxide atomic layer deposition on indium arsenide.

PubMed

Timm, Rainer; Head, Ashley R; Yngman, Sofie; Knutsson, Johan V; Hjort, Martin; McKibbin, Sarah R; Troian, Andrea; Persson, Olof; Urpelainen, Samuli; Knudsen, Jan; Schnadt, Joachim; Mikkelsen, Anders

2018-04-12

Atomic layer deposition (ALD) enables the ultrathin high-quality oxide layers that are central to all modern metal-oxide-semiconductor circuits. Crucial to achieving superior device performance are the chemical reactions during the first deposition cycle, which could ultimately result in atomic-scale perfection of the semiconductor-oxide interface. Here, we directly observe the chemical reactions at the surface during the first cycle of hafnium dioxide deposition on indium arsenide under realistic synthesis conditions using photoelectron spectroscopy. We find that the widely used ligand exchange model of the ALD process for the removal of native oxide on the semiconductor and the simultaneous formation of the first hafnium dioxide layer must be significantly revised. Our study provides substantial evidence that the efficiency of the self-cleaning process and the quality of the resulting semiconductor-oxide interface can be controlled by the molecular adsorption process of the ALD precursors, rather than the subsequent oxide formation.

Dopaminergic inputs in the dentate gyrus direct the choice of memory encoding

DOE PAGES

Du, Huiyun; Deng, Wei; Aimone, James B.; ...

2016-09-13

Rewarding experiences are often well remembered, and such memory formation is known to be dependent on dopamine modulation of the neural substrates engaged in learning and memory; however, it is unknown how and where in the brain dopamine signals bias episodic memory toward preceding rather than subsequent events. Here we found that photostimulation of channelrhodopsin-2–expressing dopaminergic fibers in the dentate gyrus induced a long-term depression of cortical inputs, diminished theta oscillations, and impaired subsequent contextual learning. Computational modeling based on this dopamine modulation indicated an asymmetric association of events occurring before and after reward in memory tasks. In subsequent behavioralmore » experiments, preexposure to a natural reward suppressed hippocampus-dependent memory formation, with an effective time window consistent with the duration of dopamine-induced changes of dentate activity. Altogether, our results suggest a mechanism by which dopamine enables the hippocampus to encode memory with reduced interference from subsequent experience.« less

Dopaminergic inputs in the dentate gyrus direct the choice of memory encoding

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

Du, Huiyun; Deng, Wei; Aimone, James B.

Rewarding experiences are often well remembered, and such memory formation is known to be dependent on dopamine modulation of the neural substrates engaged in learning and memory; however, it is unknown how and where in the brain dopamine signals bias episodic memory toward preceding rather than subsequent events. Here we found that photostimulation of channelrhodopsin-2–expressing dopaminergic fibers in the dentate gyrus induced a long-term depression of cortical inputs, diminished theta oscillations, and impaired subsequent contextual learning. Computational modeling based on this dopamine modulation indicated an asymmetric association of events occurring before and after reward in memory tasks. In subsequent behavioralmore » experiments, preexposure to a natural reward suppressed hippocampus-dependent memory formation, with an effective time window consistent with the duration of dopamine-induced changes of dentate activity. Altogether, our results suggest a mechanism by which dopamine enables the hippocampus to encode memory with reduced interference from subsequent experience.« less

The birth of embryonic pluripotency

PubMed Central

Boroviak, Thorsten; Nichols, Jennifer

2014-01-01

Formation of a eutherian mammal requires concurrent establishment of embryonic and extraembryonic lineages. The functions of the trophectoderm and primitive endoderm are to enable implantation in the maternal uterus, axis specification and delivery of nutrients. The pluripotent epiblast represents the founding cell population of the embryo proper, which is protected from ectopic and premature differentiation until it is required to respond to inductive cues to form the fetus. While positional information plays a major role in specifying the trophoblast lineage, segregation of primitive endoderm from epiblast depends upon gradual acquisition of transcriptional identity, directed but not initiated by fibroblast growth factor (FGF) signalling. Following early cleavage divisions and formation of the blastocyst, cells of the inner cell mass lose totipotency. Developing epiblast cells transiently attain the state of naive pluripotency and competence to self-renew in vitro as embryonic stem cells and in vivo by means of diapause. This property is lost after implantation as the epiblast epithelializes and becomes primed in preparation for gastrulation and subsequent organogenesis. PMID:25349450

A Survey of Geologic Resources. Chapter 11

NASA Technical Reports Server (NTRS)

Edmonson, Jennifer; Rickman, Doug

2012-01-01

This chapter focuses on the resources available from the Moon itself: regolith, geologically concentrated materials, and lunar physical features that will enable habitation and generation of power on the surface. This chapter briefly covers the formation of the Moon and thus the formation of the crust of the Moon, as well as the evolution of the regolith. The characteristics of the regolith are provided in some detail, including its mineralogy and lithology. The location of high concentrations of specific minerals or rocks is noted. Other ideal locations for in situ resource utilization technology and lunar habitation are presented. This chapter is intended to be a brief review of current knowledge, and to serve as a foundational source for further study. Each concept presented here has a wealth of literature associated with it; the reader is therefore directed to that literature with each discussion. With great interest in possible manned lunar landings and continued study of the Moon by multiple satellites, the available information changes regularly.

Galaxy Interactions, Tidal Debris, and the Origin of Intracluster Light in the Coma Cluster

NASA Astrophysics Data System (ADS)

Gregg, Michael

1999-07-01

We propose to obtain deep WFPC2 and parallel STIS images of low surface brightness tidal debris that we have recently discovered in the Coma cluster; the material is being stripped from its parent galaxy and added to the general cluster background. These images will enable direct study of the brightest blue and red supergiants, globular clusters, and star forming regions which may be present, or will place strong limits on the numbers of such objects and any recent star formation. We also propose similar observations of the parent spiral, NGC4911, in the core of Coma; it is losing its ISM to the hot cluster gas and as well as the low surface brightness tidal debris. By imaging this galaxy, we will get a high resolution look at the interaction between the galaxy and interstellar medium, as well as any ram-pressure induced star formation. The tidal features in Coma appear to be adding material to the background light and cD galaxy envelopes at a significant rate; determining the nature of the added stellar population and the interactions which produce it are critical to understanding the formation and evolution of cD galaxies and clusters.

Remote catalyzation for direct formation of graphene layers on oxides.

PubMed

Teng, Po-Yuan; Lu, Chun-Chieh; Akiyama-Hasegawa, Kotone; Lin, Yung-Chang; Yeh, Chao-Hui; Suenaga, Kazu; Chiu, Po-Wen

2012-03-14

Direct deposition of high-quality graphene layers on insulating substrates such as SiO(2) paves the way toward the development of graphene-based high-speed electronics. Here, we describe a novel growth technique that enables the direct deposition of graphene layers on SiO(2) with crystalline quality potentially comparable to graphene grown on Cu foils using chemical vapor deposition (CVD). Rather than using Cu foils as substrates, our approach uses them to provide subliming Cu atoms in the CVD process. The prime feature of the proposed technique is remote catalyzation using floating Cu and H atoms for the decomposition of hydrocarbons. This allows for the direct graphitization of carbon radicals on oxide surfaces, forming isolated low-defect graphene layers without the need for postgrowth etching or evaporation of the metal catalyst. The defect density of the resulting graphene layers can be significantly reduced by tuning growth parameters such as the gas ratios, Cu surface areas, and substrate-to-Cu distance. Under optimized conditions, graphene layers with nondiscernible Raman D peaks can be obtained when predeposited graphite flakes are used as seeds for extended growth. © 2012 American Chemical Society

Enabling Spacecraft Formation Flying in Any Earth Orbit Through Spaceborne GPS and Enhanced Autonomy Technologies

NASA Technical Reports Server (NTRS)

Bauer, F. H.; Bristow, J. O.; Carpenter, J. R.; Garrison, J. L.; Hartman, K. R.; Lee, T.; Long, A. C.; Kelbel, D.; Lu, V.; How, J. P.;

Electrophoresis for genotyping: microtiter array diagonal gel electrophoresis on horizontal polyacrylamide gels, hydrolink, or agarose.

PubMed

Day, I N; Humphries, S E

1994-11-01

Electrophoresis of DNA has been performed traditionally in either an agarose or acrylamide gel matrix. Considerable effort has been directed to improved quality agaroses capable of high resolution, but for small fragments, such as those from polymerase chain reaction (PCR) and post-PCR digests, acrylamide still offers the highest resolution. Although agarose gels can easily be prepared in an open-faced format to gain the conveniences of horizontal electrophoresis, acrylamide does not polymerize in the presence of air and the usual configurations for gel preparation lead to electrophoresis in the vertical dimension. We describe here a very simple device and method to prepare and manipulate horizontal polyacrylamide gels (H-PAGE). In addition, the open-faced horizontal arrangement enables loading of arrays of wells. Since many procedures are undertaken in standard 96-well microtiter plates, we have also designed a device which preserves the exact configuration of the 8 x 12 array and enables electrophoresis in tracks following a 71.6 degrees diagonal between wells (MADGE, microtiter array diagonal gel electrophoresis), using either acrylamide or agarose. This eliminates almost all of the staff time taken in setup, loading, and recordkeeping and offers high resolution for genotyping pattern recognition. The nature and size of the gels allow direct stacking of gels in one tank, so that a tank used typically to analyze 30-60 samples can readily be used to analyze 1000-2000 samples. The gels would also enable robotic loading. Electrophoresis allows analysis of size and charge, parameters inaccessible to liquid-phase methods: thus, genotyping size patterns, variable length repeats, and haplotypes is possible, as well as adaptability to typing of point variations using protocols which create a difference detectable by electrophoresis.

Characterization of graded TiC layers deposited by HiPIMS method

NASA Astrophysics Data System (ADS)

Bohovicova, Jana; Bonova, Lucia; Halanda, Juraj; Ivan, Jozef; Mesko, Marcel; Advanced Technologies Research Institute Team; Institute of Electronic; Photonic Team

2016-09-01

An advanced yet recent development of sputter technique is high power impulse magnetron sputtering (HiPIMS), in which short, energetic pulses are applied to the target, leading to a formation of an ultra-dense plasma in front of the cathode, that provide a high degree of ionization of sputtered material, and consequently enable to control the energy and the direction of the deposition flux. This gives a possibility to alter composition and microstructure in a controlled manner, enables the optimization of TiC for tribological applications. The aim of this work is to link physical phenomena in transient HiPIMS discharges to microstructural and compositional properties of graded TiC thin films. It was found that Ti bottom layer is contamination free. Compared to the direct current magnetron sputtering films, we observed an element specific reduction of impurities measured by ERDA by a factor 3 for N, 4 for H and by a factor of 20 for O. The high purity of Ti layer is partly explained by gas rarefaction and the cleaning effect of the bombarding ions. Graphitization degree of carbon top layer was elucidated by Raman spectroscopy. The compositional effects are correlated with differences in the film microstructure revealed by SEM, XRD and TEM analysis. This work was supported by VEGA, Project No. 1/0503/15 and APVV, Project No. 15-0168.

Conductive carbon tape used for support and mounting of both whole animal and fragile heat-treated tissue sections for MALDI MS imaging and quantitation.

PubMed

Goodwin, Richard J A; Nilsson, Anna; Borg, Daniel; Langridge-Smith, Pat R R; Harrison, David J; Mackay, C Logan; Iverson, Suzanne L; Andrén, Per E

2012-08-30

Analysis of whole animal tissue sections by MALDI MS imaging (MSI) requires effective sample collection and transfer methods to allow the highest quality of in situ analysis of small or hard to dissect tissues. We report on the use of double-sided adhesive conductive carbon tape during whole adult rat tissue sectioning of carboxymethyl cellulose (CMC) embedded animals, with samples mounted onto large format conductive glass and conductive plastic MALDI targets, enabling MSI analysis to be performed on both TOF and FT-ICR MALDI mass spectrometers. We show that mounting does not unduly affect small molecule MSI detection by analyzing tiotropium abundance and distribution in rat lung tissues, with direct on-tissue quantitation achieved. Significantly, we use the adhesive tape to provide support to embedded delicate heat-stabilized tissues, enabling sectioning and mounting to be performed that maintained tissue integrity on samples that had previously been impossible to adequately prepare section for MSI analysis. The mapping of larger peptidomic molecules was not hindered by tape mounting samples and we demonstrate this by mapping the distribution of PEP-19 in both native and heat-stabilized rat brains. Furthermore, we show that without heat stabilization PEP-19 degradation fragments can detected and identified directly by MALDI MSI analysis. Copyright © 2012 Elsevier B.V. All rights reserved.

Solar neutrino detection in a large volume double-phase liquid argon experiment

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

Franco, D.; Agnes, P.; Giganti, C.

2016-08-01

Precision measurements of solar neutrinos emitted by specific nuclear reaction chains in the Sun are of great interest for developing an improved understanding of star formation and evolution. Given the expected neutrino fluxes and known detection reactions, such measurements require detectors capable of collecting neutrino-electron scattering data in exposures on the order of 1 ktonne-yr, with good energy resolution and extremely low background. Two-phase liquid argon time projection chambers (LAr TPCs) are under development for direct Dark Matter WIMP searches, which possess very large sensitive mass, high scintillation light yield, good energy resolution, and good spatial resolution in all threemore » cartesian directions. While enabling Dark Matter searches with sensitivity extending to the ''neutrino floor'' (given by the rate of nuclear recoil events from solar neutrino coherent scattering), such detectors could also enable precision measurements of solar neutrino fluxes using the neutrino-electron elastic scattering events. Modeling results are presented for the cosmogenic and radiogenic backgrounds affecting solar neutrino detection in a 300 tonne (100 tonne fiducial) LAr TPC operating at LNGS depth (3,800 meters of water equivalent). The results show that such a detector could measure the CNO neutrino rate with ∼15% precision, and significantly improve the precision of the {sup 7}Be and pep neutrino rates compared to the currently available results from the Borexino organic liquid scintillator detector.« less

ascii2gdocs

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

Nightingale, Trever

2011-11-30

Enables UNIX and Mac OS X command line users to put (individually or batch mode) local ascii files into Google Documents, where the ascii is converted to Google Document format using formatting the user can specify.

Ground Operations Aerospace Language (GOAL). Volume 4: Interpretive code translator

NASA Technical Reports Server (NTRS)

1973-01-01

This specification identifies and describes the principal functions and elements of the Interpretive Code Translator which has been developed for use with the GOAL Compiler. This translator enables the user to convert a compliled GOAL program to a highly general binary format which is designed to enable interpretive execution. The translator program provides user controls which are designed to enable the selection of various output types and formats. These controls provide a means for accommodating many of the implementation options which are discussed in the Interpretive Code Guideline document. The technical design approach is given. The relationship between the translator and the GOAL compiler is explained and the principal functions performed by the Translator are described. Specific constraints regarding the use of the Translator are discussed. The control options are described. These options enable the user to select outputs to be generated by the translator and to control vrious aspects of the translation processing.

SAGE - MULTIDIMENSIONAL SELF-ADAPTIVE GRID CODE

NASA Technical Reports Server (NTRS)

Davies, C. B.

1994-01-01

SAGE, Self Adaptive Grid codE, is a flexible tool for adapting and restructuring both 2D and 3D grids. Solution-adaptive grid methods are useful tools for efficient and accurate flow predictions. In supersonic and hypersonic flows, strong gradient regions such as shocks, contact discontinuities, shear layers, etc., require careful distribution of grid points to minimize grid error and produce accurate flow-field predictions. SAGE helps the user obtain more accurate solutions by intelligently redistributing (i.e. adapting) the original grid points based on an initial or interim flow-field solution. The user then computes a new solution using the adapted grid as input to the flow solver. The adaptive-grid methodology poses the problem in an algebraic, unidirectional manner for multi-dimensional adaptations. The procedure is analogous to applying tension and torsion spring forces proportional to the local flow gradient at every grid point and finding the equilibrium position of the resulting system of grid points. The multi-dimensional problem of grid adaption is split into a series of one-dimensional problems along the computational coordinate lines. The reduced one dimensional problem then requires a tridiagonal solver to find the location of grid points along a coordinate line. Multi-directional adaption is achieved by the sequential application of the method in each coordinate direction. The tension forces direct the redistribution of points to the strong gradient region. To maintain smoothness and a measure of orthogonality of grid lines, torsional forces are introduced that relate information between the family of lines adjacent to one another. The smoothness and orthogonality constraints are direction-dependent, since they relate only the coordinate lines that are being adapted to the neighboring lines that have already been adapted. Therefore the solutions are non-unique and depend on the order and direction of adaption. Non-uniqueness of the adapted grid is acceptable since it makes possible an overall and local error reduction through grid redistribution. SAGE includes the ability to modify the adaption techniques in boundary regions, which substantially improves the flexibility of the adaptive scheme. The vectorial approach used in the analysis also provides flexibility. The user has complete choice of adaption direction and order of sequential adaptions without concern for the computational data structure. Multiple passes are available with no restraint on stepping directions; for each adaptive pass the user can choose a completely new set of adaptive parameters. This facility, combined with the capability of edge boundary control, enables the code to individually adapt multi-dimensional multiple grids. Zonal grids can be adapted while maintaining continuity along the common boundaries. For patched grids, the multiple-pass capability enables complete adaption. SAGE is written in FORTRAN 77 and is intended to be machine independent; however, it requires a FORTRAN compiler which supports NAMELIST input. It has been successfully implemented on Sun series computers, SGI IRIS's, DEC MicroVAX computers, HP series computers, the Cray YMP, and IBM PC compatibles. Source code is provided, but no sample input and output files are provided. The code reads three datafiles: one that contains the initial grid coordinates (x,y,z), one that contains corresponding flow-field variables, and one that contains the user control parameters. It is assumed that the first two datasets are formatted as defined in the plotting software package PLOT3D. Several machine versions of PLOT3D are available from COSMIC. The amount of main memory is dependent on the size of the matrix. The standard distribution medium for SAGE is a 5.25 inch 360K MS-DOS format diskette. It is also available on a .25 inch streaming magnetic tape cartridge in UNIX tar format or on a 9-track 1600 BPI ASCII CARD IMAGE format magnetic tape. SAGE was developed in 1989, first released as a 2D version in 1991 and updated to 3D in 1993.

DOES MAGNETIC-FIELD-ROTATION MISALIGNMENT SOLVE THE MAGNETIC BRAKING CATASTROPHE IN PROTOSTELLAR DISK FORMATION?

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

Li Zhiyun; Krasnopolsky, Ruben; Shang, Hsien

2013-09-01

Stars form in dense cores of molecular clouds that are observed to be significantly magnetized. In the simplest case of a laminar (non-turbulent) core with the magnetic field aligned with the rotation axis, both analytic considerations and numerical simulations have shown that the formation of a large, 10{sup 2} AU scale, rotationally supported protostellar disk is suppressed by magnetic braking in the ideal MHD limit for a realistic level of core magnetization. This theoretical difficulty in forming protostellar disks is termed the ''magnetic braking catastrophe''. A possible resolution to this problem, proposed by Hennebelle and Ciardi and Joos et al.,more » is that misalignment between the magnetic field and rotation axis may weaken the magnetic braking enough to enable disk formation. We evaluate this possibility quantitatively through numerical simulations. We confirm the basic result of Joos et al. that the misalignment is indeed conducive to disk formation. In relatively weakly magnetized cores with dimensionless mass-to-flux ratio {approx}> 4, it enabled the formation of rotationally supported disks that would otherwise be suppressed if the magnetic field and rotation axis are aligned. For more strongly magnetized cores, disk formation remains suppressed, however, even for the maximum tilt angle of 90 Degree-Sign . If dense cores are as strongly magnetized as indicated by OH Zeeman observations (with a mean dimensionless mass-to-flux ratio {approx}2), it would be difficult for the misalignment alone to enable disk formation in the majority of them. We conclude that, while beneficial to disk formation, especially for the relatively weak field case, misalignment does not completely solve the problem of catastrophic magnetic braking in general.« less

Decoupling of magnetic fields in collapsing protostellar envelopes and disc formation and fragmentation

NASA Astrophysics Data System (ADS)

Zhao, Bo; Caselli, Paola; Li, Zhi-Yun; Krasnopolsky, Ruben

2018-02-01

Efficient magnetic braking is a formidable obstacle to the formation of rotationally supported discs (RSDs) around protostars in magnetized dense cores. We have previously shown, through 2D (axisymmetric) non-ideal magnetohydrodynamic simulations, that removing very small grains (VSGs: ∼10 Å to few 100 Å) can greatly enhance ambipolar diffusion and enable the formation of RSDs. Here, we extend the simulations of disc formation enabled by VSG removal to 3D. We find that the key to this scenario of disc formation is that the drift velocity of the magnetic field almost cancels out the infall velocity of the neutrals in the 102-103 au scale 'pseudo-disc' where the field lines are most severely pinched and most of protostellar envelope mass infall occurs. As a result, the bulk neutral envelope matter can collapse without dragging much magnetic flux into the disc-forming region, which lowers the magnetic braking efficiency. We find that the initial discs enabled by VSG removal tend to be Toomre-unstable, which leads to the formation of prominent spiral structures that function as centrifugal barriers. The piling-up of infall material near the centrifugal barrier often produces dense fragments of tens of Jupiter masses, especially in cores that are not too strongly magnetized. Some fragments accrete on to the central stellar object, producing bursts in mass accretion rate. Others are longer lived, although whether they can survive for a long term to produce multiple systems remains to be ascertained. Our results highlight the importance of dust grain evolution in determining the formation and properties of protostellar discs and potentially multiple systems.

Interpretation of deep directional resistivity measurements acquired in high-angle and horizontal wells using 3-D inversion

NASA Astrophysics Data System (ADS)

Puzyrev, Vladimir; Torres-Verdín, Carlos; Calo, Victor

2018-05-01

The interpretation of resistivity measurements acquired in high-angle and horizontal wells is a critical technical problem in formation evaluation. We develop an efficient parallel 3-D inversion method to estimate the spatial distribution of electrical resistivity in the neighbourhood of a well from deep directional electromagnetic induction measurements. The methodology places no restriction on the spatial distribution of the electrical resistivity around arbitrary well trajectories. The fast forward modelling of triaxial induction measurements performed with multiple transmitter-receiver configurations employs a parallel direct solver. The inversion uses a pre-conditioned gradient-based method whose accuracy is improved using the Wolfe conditions to estimate optimal step lengths at each iteration. The large transmitter-receiver offsets, used in the latest generation of commercial directional resistivity tools, improve the depth of investigation to over 30 m from the wellbore. Several challenging synthetic examples confirm the feasibility of the full 3-D inversion-based interpretations for these distances, hence enabling the integration of resistivity measurements with seismic amplitude data to improve the forecast of the petrophysical and fluid properties. Employing parallel direct solvers for the triaxial induction problems allows for large reductions in computational effort, thereby opening the possibility to invert multiposition 3-D data in practical CPU times.

Femtosecond laser inscription of optical circuits in the cladding of optical fibers

NASA Astrophysics Data System (ADS)

Grenier, Jason R.

The aim of this dissertation was to address the question of whether the cladding of single-mode fibers (SMFs) could be modified to enable optical fibers to serve as a more integrated, highly functional platform for optical circuit devices that can efficiently interconnect with the pre-existing fiber core waveguide. The approach adopted in this dissertation was to employ femtosecond laser direct writing (FLDW), an inherently 3D fabrication technique that harnesses non-linear laser-material interactions to modify the fused silica fiber cladding. A fiber mounting and alignment technique was developed along with oil-immersion focusing to address the strong aberrations caused by the cylindrical fiber shape. The development of real-time device monitoring during the FLDW was instrumental to overcome the acute coupling sensitivity to laser alignment errors of +/-1 ?m positional uncertainty, and thereby opened a new practical direction for the precise fabrication of optical devices inside optical fibers. These powerful and flexible laser fabrication and characterization techniques were successfully employed to optimize optical waveguiding devices positioned within the core and cladding of optical fibers. X-, S-Bend, and directional couplers were developed to enable efficient coupling between the laser-formed cladding devices and the pre-existing core waveguide, enabling up to 62% power transfer over bandwidths up to 300 nm at telecommunication wavelengths. Precise alignment of femtosecond laser modification tracks were positioned inside or near the core waveguide of SMFs was further shown to enable a flexible reshaping of the optical properties to create multimode guiding sections arbitrarily along the fiber length. This core waveguide modification facilitated the precise formation of multimode interferometers along the core waveguide to precisely tailor the modal profiles, and control the spectral and polarization response. In-fiber multimode interference (MMI) splitters and couplers were fabricated with coupling ratios from 2% to 50% over a broad 350 nm bandwidth across the telecommunication band. Laser-induced birefringence was harnessed to generate polarization dependent MMI devices for strong polarization filtering (24 dB isolation), or polarization selective taps with up to 50% tapping efficiency over a 25 nm bandwidth. This dissertation is therefore the first demonstration of femtosecond laser direct writing as a flexible and monolithic means of embedding and integrating highly functional optical circuit devices within the cladding of optical fibers that can interconnect efficiently with the pre-existing fiber core waveguide. These developments represent a significant technological advancement for creating new 3D photonic integrated microsystems within the cladding of optical fibers and underpins a new technological platform of fiber cladding photonics.

The Confluence of GIS, Cloud and Open Source, Enabling Big Raster Data Applications

NASA Astrophysics Data System (ADS)

Plesea, L.; Emmart, C. B.; Boller, R. A.; Becker, P.; Baynes, K.

2016-12-01

The rapid evolution of available cloud services is profoundly changing the way applications are being developed and used. Massive object stores, service scalability, continuous integration are some of the most important cloud technology advances that directly influence science applications and GIS. At the same time, more and more scientists are using GIS platforms in their day to day research. Yet with new opportunities there are always some challenges. Given the large amount of data commonly required in science applications, usually large raster datasets, connectivity is one of the biggest problems. Connectivity has two aspects, one being the limited bandwidth and latency of the communication link due to the geographical location of the resources, the other one being the interoperability and intrinsic efficiency of the interface protocol used to connect. NASA and Esri are actively helping each other and collaborating on a few open source projects, aiming to provide some of the core technology components to directly address the GIS enabled data connectivity problems. Last year Esri contributed LERC, a very fast and efficient compression algorithm to the GDAL/MRF format, which itself is a NASA/Esri collaboration project. The MRF raster format has some cloud aware features that make it possible to build high performance web services on cloud platforms, as some of the Esri projects demonstrate. Currently, another NASA open source project, the high performance OnEarth WMTS server is being refactored and enhanced to better integrate with MRF, GDAL and Esri software. Taken together, the GDAL, MRF and OnEarth form the core of an open source CloudGIS toolkit that is already showing results. Since it is well integrated with GDAL, which is the most common interoperability component of GIS applications, this approach should improve the connectivity and performance of many science and GIS applications in the cloud.

Information management and analysis system for groundwater data in Thailand

NASA Astrophysics Data System (ADS)

Gill, D.; Luckananurung, P.

1992-01-01

The Ground Water Division of the Thai Department of Mineral Resources maintains a large archive of groundwater data with information on some 50,000 water wells. Each well file contains information on well location, well completion, borehole geology, water levels, water quality, and pumping tests. In order to enable efficient use of this information a computer-based system for information management and analysis was created. The project was sponsored by the United Nations Development Program and the Thai Department of Mineral Resources. The system was designed to serve users who lack prior training in automated data processing. Access is through a friendly user/system dialogue. Tasks are segmented into a number of logical steps, each of which is managed by a separate screen. Selective retrieval is possible by four different methods of area definition and by compliance with user-specified constraints on any combination of database variables. The main types of outputs are: (1) files of retrieved data, screened according to users' specifications; (2) an assortment of pre-formatted reports; (3) computed geochemical parameters and various diagrams of water chemistry derived therefrom; (4) bivariate scatter diagrams and linear regression analysis; (5) posting of data and computed results on maps; and (6) hydraulic aquifer characteristics as computed from pumping tests. Data are entered directly from formatted screens. Most records can be copied directly from hand-written documents. The database-management program performs data integrity checks in real time, enabling corrections at the time of input. The system software can be grouped into: (1) database administration and maintenance—these functions are carried out by the SIR/DBMS software package; (2) user communication interface for task definition and execution control—the interface is written in the operating system command language (VMS/DCL) and in FORTRAN 77; and (3) scientific data-processing programs, written in FORTRAN 77. The system was implemented on a DEC MicroVAX II computer.

Modulation format identification enabled by the digital frequency-offset loading technique for hitless coherent transceiver.

PubMed

Fu, Songnian; Xu, Zuying; Lu, Jianing; Jiang, Hexun; Wu, Qiong; Hu, Zhouyi; Tang, Ming; Liu, Deming; Chan, Calvin Chun-Kit

2018-03-19

We propose a blind and fast modulation format identification (MFI) enabled by the digital frequency-offset (FO) loading technique for hitless coherent transceiver. Since modulation format information is encoded to the FO distribution during digital signal processing (DSP) at the transmitter side (Tx), we can use the fast Fourier transformation based FO estimation (FFT-FOE) method to obtain the FO distribution of individual data block after constant modulus algorithm (CMA) pre-equalization at the receiver side, in order to realize non-data-aided (NDA) and fast MFI. The obtained FO can be also used for subsequent FO compensation (FOC), without additional complexity. We numerically investigate and experimentally verify the proposed MFI with high accuracy and fast format switching among 28 Gbaud dual-polarization (DP)-4/8/16/64QAM, time domain hybrid-4/16QAM, and set partitioning (SP)-128QAM. In particular, the proposed MFI brings no performance degradation, in term of tolerance of amplified spontaneous emission (ASE) noise, laser linewidth, and fiber nonlinearity. Finally, a hitless coherent transceiver enabled by the proposed MFI with switching-block of only 2048 symbols is demonstrated over 1500 km standard single mode fiber (SSMF) transmission.

MIiSR: Molecular Interactions in Super-Resolution Imaging Enables the Analysis of Protein Interactions, Dynamics and Formation of Multi-protein Structures.

PubMed

Caetano, Fabiana A; Dirk, Brennan S; Tam, Joshua H K; Cavanagh, P Craig; Goiko, Maria; Ferguson, Stephen S G; Pasternak, Stephen H; Dikeakos, Jimmy D; de Bruyn, John R; Heit, Bryan

2015-12-01

Our current understanding of the molecular mechanisms which regulate cellular processes such as vesicular trafficking has been enabled by conventional biochemical and microscopy techniques. However, these methods often obscure the heterogeneity of the cellular environment, thus precluding a quantitative assessment of the molecular interactions regulating these processes. Herein, we present Molecular Interactions in Super Resolution (MIiSR) software which provides quantitative analysis tools for use with super-resolution images. MIiSR combines multiple tools for analyzing intermolecular interactions, molecular clustering and image segmentation. These tools enable quantification, in the native environment of the cell, of molecular interactions and the formation of higher-order molecular complexes. The capabilities and limitations of these analytical tools are demonstrated using both modeled data and examples derived from the vesicular trafficking system, thereby providing an established and validated experimental workflow capable of quantitatively assessing molecular interactions and molecular complex formation within the heterogeneous environment of the cell.

Warthog: A MOOSE-Based Application for the Direct Code Coupling of BISON and PROTEUS

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

McCaskey, Alexander J.; Slattery, Stuart; Billings, Jay Jay

The Nuclear Energy Advanced Modeling and Simulation (NEAMS) program from the Department of Energy's Office of Nuclear Energy provides a robust toolkit for the modeling and simulation of current and future advanced nuclear reactor designs. This toolkit provides these technologies organized across product lines: two divisions targeted at fuels and end-to-end reactor modeling, and a third for integration, coupling, and high-level workflow management. The Fuels Product Line and the Reactor Product line provide advanced computational technologies that serve each respective field well, however, their current lack of integration presents a major impediment to future improvements of simulation solution fidelity. Theremore » is a desire for the capability to mix and match tools across Product Lines in an effort to utilize the best from both to improve NEAMS modeling and simulation technologies. This report details a new effort to provide this Product Line interoperability through the development of a new application called Warthog. This application couples the BISON Fuel Performance application from the Fuels Product Line and the PROTEUS Core Neutronics application from the Reactors Product Line in an effort to utilize the best from all parts of the NEAMS toolkit and improve overall solution fidelity of nuclear fuel simulations. To achieve this, Warthog leverages as much prior work from the NEAMS program as possible, and in doing so, enables interoperability between the disparate MOOSE and SHARP frameworks, and the libMesh and MOAB mesh data formats. This report describes this work in full. We begin with a detailed look at the individual NEAMS framework technologies used and developed in the various Product Lines, and the current status of their interoperability. We then introduce the Warthog application: its overall architecture and the ways it leverages the best existing tools from across the NEAMS toolkit to enable BISON-PROTEUS integration. Furthermore, we show how Warthog leverages a tool known as DataTransferKit to seamlessly enable the transfer for solution data between disparate frameworks and mesh formats. To end, we demonstrate tests for the direct software coupling of BISON and PROTEUS using Warthog, and discuss current impediments and solutions to the construction of physically realistic input models for this coupled BISON-PROTEUS system.« less

Thermodynamic Presynthetic Considerations for Ring-Opening Polymerization

PubMed Central

2016-01-01

The need for polymers for high-end applications, coupled with the desire to mimic nature’s macromolecular machinery fuels the development of innovative synthetic strategies every year. The recently acquired macromolecular-synthetic tools increase the precision and enable the synthesis of polymers with high control and low dispersity. However, regardless of the specificity, the polymerization behavior is highly dependent on the monomeric structure. This is particularly true for the ring-opening polymerization of lactones, in which the ring size and degree of substitution highly influence the polymer formation properties. In other words, there are two important factors to contemplate when considering the particular polymerization behavior of a specific monomer: catalytic specificity and thermodynamic equilibrium behavior. This perspective focuses on the latter and undertakes a holistic approach among the different lactones with regard to the equilibrium thermodynamic polymerization behavior and its relation to polymer synthesis. This is summarized in a monomeric overview diagram that acts as a presynthetic directional cursor for synthesizing highly specific macromolecules; the means by which monomer equilibrium conversion relates to starting temperature, concentration, ring size, degree of substitution, and its implications for polymerization behavior are discussed. These discussions emphasize the importance of considering not only the catalytic system but also the monomer size and structure relations to thermodynamic equilibrium behavior. The thermodynamic equilibrium behavior relation with a monomer structure offers an additional layer of complexity to our molecular toolbox and, if it is harnessed accordingly, enables a powerful route to both monomer formation and intentional macromolecular design. PMID:26795940

Thermodynamic Presynthetic Considerations for Ring-Opening Polymerization.

PubMed

Olsén, Peter; Odelius, Karin; Albertsson, Ann-Christine

2016-03-14

The need for polymers for high-end applications, coupled with the desire to mimic nature's macromolecular machinery fuels the development of innovative synthetic strategies every year. The recently acquired macromolecular-synthetic tools increase the precision and enable the synthesis of polymers with high control and low dispersity. However, regardless of the specificity, the polymerization behavior is highly dependent on the monomeric structure. This is particularly true for the ring-opening polymerization of lactones, in which the ring size and degree of substitution highly influence the polymer formation properties. In other words, there are two important factors to contemplate when considering the particular polymerization behavior of a specific monomer: catalytic specificity and thermodynamic equilibrium behavior. This perspective focuses on the latter and undertakes a holistic approach among the different lactones with regard to the equilibrium thermodynamic polymerization behavior and its relation to polymer synthesis. This is summarized in a monomeric overview diagram that acts as a presynthetic directional cursor for synthesizing highly specific macromolecules; the means by which monomer equilibrium conversion relates to starting temperature, concentration, ring size, degree of substitution, and its implications for polymerization behavior are discussed. These discussions emphasize the importance of considering not only the catalytic system but also the monomer size and structure relations to thermodynamic equilibrium behavior. The thermodynamic equilibrium behavior relation with a monomer structure offers an additional layer of complexity to our molecular toolbox and, if it is harnessed accordingly, enables a powerful route to both monomer formation and intentional macromolecular design.

Development of fusogenic glass surfaces that impart spatiotemporal control over macrophage fusion: Direct visualization of multinucleated giant cell formation.

PubMed

Faust, James J; Christenson, Wayne; Doudrick, Kyle; Ros, Robert; Ugarova, Tatiana P

2017-06-01

Implantation of synthetic material, including vascular grafts, pacemakers, etc. results in the foreign body reaction and the formation of multinucleated giant cells (MGCs) at the exterior surface of the implant. Despite the long-standing premise that fusion of mononucleated macrophages results in the formation of MGCs, to date, no published study has shown fusion in context with living specimens. This is due to the fact that optical-quality glass, which is required for the majority of live imaging techniques, does not promote macrophage fusion. Consequently, the morphological changes that macrophages undergo during fusion as well as the mechanisms that govern this process remain ill-defined. In this study, we serendipitously identified a highly fusogenic glass surface and discovered that the capacity to promote fusion was due to oleamide contamination. When adsorbed on glass, oleamide and other molecules that contain long-chain hydrocarbons promoted high levels of macrophage fusion. Adhesion, an essential step for macrophage fusion, was apparently mediated by Mac-1 integrin (CD11b/CD18, α M β 2 ) as determined by single cell force spectroscopy and adhesion assays. Micropatterned glass further increased fusion and enabled a remarkable degree of spatiotemporal control over MGC formation. Using these surfaces, we reveal the kinetics that govern MGC formation in vitro. We anticipate that the spatiotemporal control afforded by these surfaces will expedite studies designed to identify the mechanism(s) of macrophage fusion and MGC formation with implication for the design of novel biomaterials. Copyright © 2017 Elsevier Ltd. All rights reserved.

Nanoscale Confinement Controls the Crystallization of Calcium Phosphate: Relevance to Bone Formation

PubMed Central

Cantaert, Bram; Beniash, Elia; Meldrum, Fiona C.

2015-01-01

A key feature of biomineralization processes is that they take place within confined volumes, in which the local environment can have significant effects on mineral formation. Herein, we investigate the influence of confinement on the formation mechanism and structure of calcium phosphate (CaP). This is of particular relevance to the formation of dentine and bone, structures of which are based on highly mineralized collagen fibrils. CaP was precipitated within 25–300 nm diameter, cylindrical pores of track etched and anodised alumina membranes under physiological conditions, in which this system enables systematic study of the effects of the pore size in the absence of a structural match between the matrix and the growing crystals. Our results show that the main products were polycrystalline hydroxapatite (HAP) rods, together with some single crystal octacalcium phosphate (OCP) rods. Notably, we demonstrate that these were generated though an intermediate amorphous calcium phosphate (ACP) phase, and that ACP is significantly stabilised in confinement. This effect may have significance to the mineralization of bone, which can occur through a transient ACP phase. We also show that orientation of the HAP comparable, or even superior to that seen in bone can be achieved through confinement effects alone. Although this simple experimental system cannot be considered, a direct mimic of the in vivo formation of ultrathin HAP platelets within collagen fibrils, our results show that the effects of physical confinement should not be neglected when considering the mechanisms of formation of structures, such as bones and teeth. PMID:24115275

Nanoscale confinement controls the crystallization of calcium phosphate: relevance to bone formation.

PubMed

Cantaert, Bram; Beniash, Elia; Meldrum, Fiona C

2013-10-25

A key feature of biomineralization processes is that they take place within confined volumes, in which the local environment can have significant effects on mineral formation. Herein, we investigate the influence of confinement on the formation mechanism and structure of calcium phosphate (CaP). This is of particular relevance to the formation of dentine and bone, structures of which are based on highly mineralized collagen fibrils. CaP was precipitated within 25-300 nm diameter, cylindrical pores of track etched and anodised alumina membranes under physiological conditions, in which this system enables systematic study of the effects of the pore size in the absence of a structural match between the matrix and the growing crystals. Our results show that the main products were polycrystalline hydroxapatite (HAP) rods, together with some single crystal octacalcium phosphate (OCP) rods. Notably, we demonstrate that these were generated though an intermediate amorphous calcium phosphate (ACP) phase, and that ACP is significantly stabilised in confinement. This effect may have significance to the mineralization of bone, which can occur through a transient ACP phase. We also show that orientation of the HAP comparable, or even superior to that seen in bone can be achieved through confinement effects alone. Although this simple experimental system cannot be considered, a direct mimic of the in vivo formation of ultrathin HAP platelets within collagen fibrils, our results show that the effects of physical confinement should not be neglected when considering the mechanisms of formation of structures, such as bones and teeth. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structural features of silver-doped phosphate glasses in zone of femtosecond laser-induced modification

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

Vasileva, A.A., E-mail: anvsilv@gmail.com; Nazarov, I.A.; Olshin, P.K.

2015-10-15

Femtosecond (fs) laser writing of two-dimensional microstructures (waveguides) is demonstrated in bulk phosphate glasses doped with silver ions. Silver-content phosphate and silver-content niobium–phosphate glasses with high concentration of silver oxide 55 mol% were used as samples for fs laser writing. The chemical network structure of the synthesized samples is analyzed through Raman spectroscopy and was found to be strongly sensitive to Nb incorporation. It was found that the direct laser writing process enables not only reorganization of glass network, but also formation of color centers and silver nanoparticles that are revealed in appearance of luminescence signal and plasmon absorption. Themore » process of NPs' formation is more efficient for Nb-phosphate glass, while color centers are preferably formed in phosphate glass. - Graphical abstract: Formation of silver NPs on the surface of 0.5Ag{sub 2}O–0.4P{sub 2}O{sub 5}–0,1Nb{sub 2}O{sub 5} glass induced by CW laser irradiation. - Highlights: • The structure of 0.5Ag{sub 2}O–0.1Nb{sub 2}O{sub 5}–0.4P{sub 2}O{sub 5} and 0.55Ag{sub 2}O–0.45P{sub 2}O{sub 5} glasses was investigated by Raman spectroscopy. • Fs laser writing induces formation of silver NPs in investigated glasses. • Surface plasmon resonance in the absorption spectra confirms the formation of NP. • The possibility of CW laser induced formation of silver NPs on the surface of sample with niobium is shown.« less

Novel microfluidic system for online monitoring of biofilm dynamics by electrical impedance spectroscopy and amperometry

NASA Astrophysics Data System (ADS)

Bruchmann, Julia; Sachsenheimer, Kai; Schwartz, Thomas; Rapp, Bastian E.

2016-03-01

Biofilm formation is ubiquitous in nature where microorganisms attach to surfaces and form highly adapted and protected communities. In technical and industrial systems like drinking water supply, food production or shipping industry biofilms are a major cause of product contamination, biofouling, and biocorrosion. Therefore, understanding of biofilm formation and means of preventing biofilm formation is important to develop novel biofilm treatment strategies. A system allowing directly online detection and monitoring biofilm formation is necessary. However, until today, there are little to none technical systems featuring a non-destructive real-time characterization of biofilm formation in a highthroughput manner. This paper presents such a microfluidic system based on electrical impedance spectroscopy (EIS) and amperomertic current measurement. The sensor consists of four modules, each housing 24 independent electrodes within 12 microfluidic channels. Attached biomass on the electrodes is monitored as increased inhibition in charge transfer by EIS and a change in metabolic activity is measured as change in produced electric current by amperometry. This modular sensor system is highly adaptable and suitable for a broad range of microbiological applications. Among others, biofilm formation processes can be characterized online, biofilm manipulation like inactivation or destabilization can be monitored in real-time and gene expression can be analyzed in parallel. The use of different electrode designs allows effective biofilm studies during all biofilm phases. The whole system was recently extended by an integrated pneumatic microfluidic pump which enables easy handling procedures. Further developments of this pumping module will allow a fully- automated computer-controlled valving and pumping.

Enabling Soldiers with Robots

DTIC Science & Technology

2012-04-17

difficult to imagine that lethal robots would find themselves among the list of particularly inhumane weapons. Albert Einstein whose research was...REPORT DATE (DD-MM-YYYY) 17-04-2012 2. REPORT TYPE Strategy Research Project 3. DATES COVERED (From - To) 4. TITLE AND SUBTITLE Enabling...Enabling Soldiers with Robots FORMAT: Strategy Research Project DATE : 17 April 2012 WORD COUNT: 5202 PAGES: 26 KEY TERMS: Ethics, Doctrine

4D reconstruction of the past

NASA Astrophysics Data System (ADS)

Doulamis, Anastasios; Ioannides, Marinos; Doulamis, Nikolaos; Hadjiprocopis, Andreas; Fritsch, Dieter; Balet, Olivier; Julien, Martine; Protopapadakis, Eftychios; Makantasis, Kostas; Weinlinger, Guenther; Johnsons, Paul S.; Klein, Michael; Fellner, Dieter; Stork, Andre; Santos, Pedro

2013-08-01

One of the main characteristics of the Internet era we are living in, is the free and online availability of a huge amount of data. This data is of varied reliability and accuracy and exists in various forms and formats. Often, it is cross-referenced and linked to other data, forming a nexus of text, images, animation and audio enabled by hypertext and, recently, by the Web3.0 standard. Search engines can search text for keywords using algorithms of varied intelligence and with limited success. Searching images is a much more complex and computationally intensive task but some initial steps have already been made in this direction, mainly in face recognition. This paper aims to describe our proposed pipeline for integrating data available on Internet repositories and social media, such as photographs, animation and text to produce 3D models of archaeological monuments as well as enriching multimedia of cultural / archaeological interest with metadata and harvesting the end products to EUROPEANA. Our main goal is to enable historians, architects, archaeologists, urban planners and affiliated professionals to reconstruct views of historical monuments from thousands of images floating around the web.

Technology Required to Image and Characterize an exo-Earth from Space

NASA Astrophysics Data System (ADS)

Crill, Brendan

2018-01-01

NASA's Exoplanet Exploration Program (ExEP) guides the development of technology that enables the direct imaging and characterization of exo-Earths in the habitable zone of Sun-like stars with future space observatories. Here we present the 2018 ExEP Technology Gap List, an annual update to ExEP's list of technologies, to be advanced in the next 1-5 years. Key technology gaps are starlight suppression with a coronagraph (internal occulters) or a starshade (external occulters), enabling imaging at extreme contrast (more than 10 billion) by blocking on-axis starlight, while allowing the reflected light of off-axis exoplanets be detected. Building and operating a space coronagraph capable of imaging an exo-Earth will require new technologies beyond those of WFIRST, the first high-contrast coronagraph in space. A starshade has never been used in a space mission and requires new capabilities in precision deployment of large structures, starlight suppression, and in formation sensing and control. We review the current state-of-the-art in coronagraph and starshade technology and the performance level that must be achieved to discover and characterize Earth analogs.

Electrochemical detection of synthetic DNA and native 16S rRNA fragments on a microarray using a biotinylated intercalator as coupling site for an enzyme label.

PubMed

Zimdars, Andreas; Gebala, Magdalena; Hartwich, Gerhard; Neugebauer, Sebastian; Schuhmann, Wolfgang

2015-10-01

The direct electrochemical detection of synthetic DNA and native 16S rRNA fragments isolated from Escherichia coli is described. Oligonucleotides are detected via selective post-labeling of double stranded DNA and DNA-RNA duplexes with a biotinylated intercalator that enables high-specific binding of a streptavidin/alkaline phosphatase conjugate. The alkaline phosphatase catalyzes formation of p-aminophenol that is subsequently oxidized at the underlying gold electrode and hence enables the detection of complementary hybridization of the DNA capture strands due to the enzymatic signal amplification. The hybridization assay was performed on microarrays consisting of 32 individually addressable gold microelectrodes. Synthetic DNA strands with sequences representing six different pathogens which are important for the diagnosis of urinary tract infections could be detected at concentrations of 60 nM. Native 16S rRNA isolated from the different pathogens could be detected at a concentration of 30 fM. Optimization of the sensing surface is described and influences on the assay performance are discussed. Copyright © 2015 Elsevier B.V. All rights reserved.

Mesoplasticity approach to studies of the cutting mechanism in ultra-precision machining

NASA Astrophysics Data System (ADS)

Lee, Rongbin W. B.; Wang, Hao; To, Suet; Cheung, Chi Fai; Chan, Chang Yuen

2014-03-01

There have been various theoretical attempts by researchers worldwide to link up different scales of plasticity studies from the nano-, micro- and macro-scale of observation, based on molecular dynamics, crystal plasticity and continuum mechanics. Very few attempts, however, have been reported in ultra-precision machining studies. A mesoplasticity approach advocated by Lee and Yang is adopted by the authors and is successfully applied to studies of the micro-cutting mechanisms in ultra-precision machining. Traditionally, the shear angle in metal cutting, as well as the cutting force variation, can only be determined from cutting tests. In the pioneering work of the authors, the use of mesoplasticity theory enables prediction of the fluctuation of the shear angle and micro-cutting force, shear band formation, chip morphology in diamond turning and size effect in nano-indentation. These findings are verified by experiments. The mesoplasticity formulation opens up a new direction of studies to enable how the plastic behaviour of materials and their constitutive representations in deformation processing, such as machining can be predicted, assessed and deduced from the basic properties of the materials measurable at the microscale.

Consumer-based technology for distribution of surgical videos for objective evaluation.

PubMed

Gonzalez, Ray; Martinez, Jose M; Lo Menzo, Emanuele; Iglesias, Alberto R; Ro, Charles Y; Madan, Atul K

2012-08-01

The Global Operative Assessment of Laparoscopic Skill (GOALS) is one validated metric utilized to grade laparoscopic skills and has been utilized to score recorded operative videos. To facilitate easier viewing of these recorded videos, we are developing novel techniques to enable surgeons to view these videos. The objective of this study is to determine the feasibility of utilizing widespread current consumer-based technology to assist in distributing appropriate videos for objective evaluation. Videos from residents were recorded via a direct connection from the camera processor via an S-video output via a cable into a hub to connect to a standard laptop computer via a universal serial bus (USB) port. A standard consumer-based video editing program was utilized to capture the video and record in appropriate format. We utilized mp4 format, and depending on the size of the file, the videos were scaled down (compressed), their format changed (using a standard video editing program), or sliced into multiple videos. Standard available consumer-based programs were utilized to convert the video into a more appropriate format for handheld personal digital assistants. In addition, the videos were uploaded to a social networking website and video sharing websites. Recorded cases of laparoscopic cholecystectomy in a porcine model were utilized. Compression was required for all formats. All formats were accessed from home computers, work computers, and iPhones without difficulty. Qualitative analyses by four surgeons demonstrated appropriate quality to grade for these formats. Our preliminary results show promise that, utilizing consumer-based technology, videos can be easily distributed to surgeons to grade via GOALS via various methods. Easy accessibility may help make evaluation of resident videos less complicated and cumbersome.

New modes of electron microscopy for materials science enabled by fast direct electron detectors

NASA Astrophysics Data System (ADS)

Minor, Andrew

There is an ongoing revolution in the development of electron detector technology that has enabled modes of electron microscopy imaging that had only before been theorized. The age of electron microscopy as a tool for imaging is quickly giving way to a new frontier of multidimensional datasets to be mined. These improvements in electron detection have enabled cryo-electron microscopy to resolve the three-dimensional structures of non-crystalized proteins, revolutionizing structural biology. In the physical sciences direct electron detectors has enabled four-dimensional reciprocal space maps of materials at atomic resolution, providing all the structural information about nanoscale materials in one experiment. This talk will highlight the impact of direct electron detectors for materials science, including a new method of scanning nanobeam diffraction. With faster detectors we can take a series of 2D diffraction patterns at each position in a 2D STEM raster scan resulting in a four-dimensional data set. For thin film analysis, direct electron detectors hold the potential to enable strain, polarization, composition and electrical field mapping over relatively large fields of view, all from a single experiment.

XML schemas for common bioinformatic data types and their application in workflow systems

PubMed Central

Seibel, Philipp N; Krüger, Jan; Hartmeier, Sven; Schwarzer, Knut; Löwenthal, Kai; Mersch, Henning; Dandekar, Thomas; Giegerich, Robert

2006-01-01

Background Today, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create such workflows, the tools involved have to be able to work with each other's data – therefore, a common set of well-defined data formats is needed. Unfortunately, current bioinformatic tools use a great variety of heterogeneous formats. Results Acknowledging the need for common formats, the Helmholtz Open BioInformatics Technology network (HOBIT) identified several basic data types used in bioinformatics and developed appropriate format descriptions, formally defined by XML schemas, and incorporated them in a Java library (BioDOM). These schemas currently cover sequence, sequence alignment, RNA secondary structure and RNA secondary structure alignment formats in a form that is independent of any specific program, thus enabling seamless interoperation of different tools. All XML formats are available at , the BioDOM library can be obtained at . Conclusion The HOBIT XML schemas and the BioDOM library simplify adding XML support to newly created and existing bioinformatic tools, enabling these tools to interoperate seamlessly in workflow scenarios. PMID:17087823

An immunoassay for dibutyl phthalate based on direct hapten linkage to the polystyrene surface of microtiter plates.

PubMed

Wei, Chenxi; Ding, Shumao; You, Huihui; Zhang, Yaran; Wang, Yao; Yang, Xu; Yuan, Junlin

2011-01-01

Dibutyl phthalate (DBP) is predominantly used as a plasticizer inplastics to make them flexible. Extensive use of phthalates in both industrial processes and other consumer products has resulted in the ubiquitous presence of phthalates in the environment. In order to better determine the level of pollution in the environment and evaluate the potential adverse effects of exposure to DBP, immunoassay for DBP was developed. A monoclonal antibody specific to DBP was produced from a stable hybridoma cell line generated by lymphocyte hybridoma technique. An indirect competitive enzyme-linked immunosorbent assay (icELISA) employing direct coating of hapten on polystyrene microtiter plates was established for the detection of DBP. Polystyrene surface was first oxidized by permanganate in dilute sulfuric acid to generate carboxyl groups. Then dibutyl 4-aminophthalate, which is an analogue of DBP, was covalently linked to the carboxyl groups of polystyrene surface with 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC). Compared with conjugate coated format (IC(50)=106 ng/mL), the direct hapten coated format (IC(50)=14.6 ng/mL) improved assay sensitivity after careful optimization of assay conditions. The average recovery of DBP from spiked water sample was 104.4% and the average coefficient of variation was 9.95%. Good agreement of the results obtained by the hapten coated icELISA and gas chromatography-mass spectrometry further confirmed the reliability and accuracy of the icELISA for the detection of DBP in certain plastic and cosmetic samples. The stable and efficient hybridoma cell line obtained is an unlimited source of sensitive and specific antibody to DBP. The hapten coated format is proposed as generally applicable because the carboxyl groups on modified microtiter plate surface enables stable immobilization of aminated or hydroxylated hapten with EDC. The developed hapten coated icELISA can be used as a convenient quantitative tool for the sensitive and accurate monitoring DBP in water, plastic and cosmetic samples. © 2011 Wei et al.

Total synthesis of feglymycin based on a linear/convergent hybrid approach using micro-flow amide bond formation

NASA Astrophysics Data System (ADS)

Fuse, Shinichiro; Mifune, Yuto; Nakamura, Hiroyuki; Tanaka, Hiroshi

2016-11-01

Feglymycin is a naturally occurring, anti-HIV and antimicrobial 13-mer peptide that includes highly racemizable 3,5-dihydroxyphenylglycines (Dpgs). Here we describe the total synthesis of feglymycin based on a linear/convergent hybrid approach. Our originally developed micro-flow amide bond formation enabled highly racemizable peptide chain elongation based on a linear approach that was previously considered impossible. Our developed approach will enable the practical preparation of biologically active oligopeptides that contain highly racemizable amino acids, which are attractive drug candidates.

Real-space identification of intermolecular bonding with atomic force microscopy.

PubMed

Zhang, Jun; Chen, Pengcheng; Yuan, Bingkai; Ji, Wei; Cheng, Zhihai; Qiu, Xiaohui

2013-11-01

We report a real-space visualization of the formation of hydrogen bonding in 8-hydroxyquinoline (8-hq) molecular assemblies on a Cu(111) substrate, using noncontact atomic force microscopy (NC-AFM). The atomically resolved molecular structures enable a precise determination of the characteristics of hydrogen bonding networks, including the bonding sites, orientations, and lengths. The observation of bond contrast was interpreted by ab initio density functional calculations, which indicated the electron density contribution from the hybridized electronic state of the hydrogen bond. Intermolecular coordination between the dehydrogenated 8-hq and Cu adatoms was also revealed by the submolecular resolution AFM characterization. The direct identification of local bonding configurations by NC-AFM would facilitate detailed investigations of intermolecular interactions in complex molecules with multiple active sites.

Direct Measurement of S-Nitrosothiols with an Orbitrap Fusion Mass Spectrometer: S-Nitrosoglutathione Reductase as a Model Protein.

PubMed

Guerra, Damian; Truebridge, Ian; Eyles, Stephen J; Treffon, Patrick; Vierling, Elizabeth

2018-01-01

Recent studies suggest cysteine S-nitrosation of S-nitrosoglutathione reductase (GSNOR) could regulate protein redox homeostasis. "Switch" assays enable discovery of putatively S-nitrosated proteins. However, with few exceptions, researchers have not examined the kinetics and biophysical consequences of S-nitrosation. Methods to quantify protein S-nitrosothiol (SNO) abundance and formation kinetics would bridge this mechanistic gap and allow interpretation of the consequences of specific modifications, as well as facilitate development of specific S-nitrosation inhibitors. Here, we describe a rapid assay to estimate protein SNO abundance with intact protein electrospray ionization mass spectrometry. Originally designed using recombinant GSNOR, these methods are applicable to any purified protein to test for or further study nitrosatable cysteines.

Generation of binary holograms for deep scenes captured with a camera and a depth sensor

NASA Astrophysics Data System (ADS)

Leportier, Thibault; Park, Min-Chul

2017-01-01

This work presents binary hologram generation from images of a real object acquired from a Kinect sensor. Since hologram calculation from a point-cloud or polygon model presents a heavy computational burden, we adopted a depth-layer approach to generate the holograms. This method enables us to obtain holographic data of large scenes quickly. Our investigations focus on the performance of different methods, iterative and noniterative, to convert complex holograms into binary format. Comparisons were performed to examine the reconstruction of the binary holograms at different depths. We also propose to modify the direct binary search algorithm to take into account several reference image planes. Then, deep scenes featuring multiple planes of interest can be reconstructed with better efficiency.

Dense Tracking and Mapping with a Quadrocopter

NASA Astrophysics Data System (ADS)

Sturm, J.; Bylow, E.; Kerl, C.; Kahl, F.; Cremers, D.

2013-08-01

In this paper, we present an approach for acquiring textured 3D models of room-sized indoor spaces using a quadrocopter. Such room models are for example useful for architects and interior designers as well as for factory planners and construction managers. The model is internally represented by a signed distance function (SDF) and the SDF is used to directly track the camera with respect to the model. Our solution enables accurate position control of the quadrocopter, so that it can automatically follow a pre-defined flight pattern. Our system provides live feedback of the acquired 3D model to the user. The final model consisting of a textured 3D triangle mesh can be saved in several standard CAD file formats.

An innovative and highly drug-tolerant approach for detecting neutralizing antibodies directed to therapeutic antibodies.

PubMed

Sloan, John H; Conway, Richard G; Pottanat, Thomas G; Troutt, Jason S; Higgs, Richard E; Konrad, Robert J; Qian, Yue-Wei

2016-10-01

Immunogenicity testing of biotherapeutic drugs is a regulatory requirement. Herein, we describe a drug-tolerant assay for detecting neutralizing antibodies against a therapeutic antibody. Excess target of the therapeutic antibody was incorporated into the detection step of an affinity capture elution assay. Signal generated from binding of antidrug antibody (ADA) to the therapeutic antibody was compared with signal from binding of ADA to the therapeutic antibody preincubated with its target. The results demonstrated that the target blocked binding of the therapeutic antibody to neutralizing monkey ADA and to two anti-idiotypic antibodies. This highly drug-tolerant novel approach enables the detection of neutralizing antibodies and allows for one basic assay format to achieve complete characterization of ADA responses.

Dielectric Covered Planar Antennas

NASA Technical Reports Server (NTRS)

Llombart Juan, Nuria (Inventor); Lee, Choonsup (Inventor); Chattopadhyay, Goutam (Inventor); Gill, John J. (Inventor); Skalare, Anders J. (Inventor); Siegel, Peter H. (Inventor)

2014-01-01

An antenna element suitable for integrated arrays at terahertz frequencies is disclosed. The antenna element comprises an extended spherical (e.g. hemispherical) semiconductor lens, e.g. silicon, antenna fed by a leaky wave waveguide feed. The extended spherical lens comprises a substantially spherical lens adjacent a substantially planar lens extension. A couple of TE/TM leaky wave modes are excited in a resonant cavity formed between a ground plane and the substantially planar lens extension by a waveguide block coupled to the ground plane. Due to these modes, the primary feed radiates inside the lens with a directive pattern that illuminates a small sector of the lens. The antenna structure is compatible with known semiconductor fabrication technology and enables production of large format imaging arrays.

Restoring voluntary control of locomotion after paralyzing spinal cord injury.

PubMed

van den Brand, Rubia; Heutschi, Janine; Barraud, Quentin; DiGiovanna, Jack; Bartholdi, Kay; Huerlimann, Michèle; Friedli, Lucia; Vollenweider, Isabel; Moraud, Eduardo Martin; Duis, Simone; Dominici, Nadia; Micera, Silvestro; Musienko, Pavel; Courtine, Grégoire

2012-06-01

Half of human spinal cord injuries lead to chronic paralysis. Here, we introduce an electrochemical neuroprosthesis and a robotic postural interface designed to encourage supraspinally mediated movements in rats with paralyzing lesions. Despite the interruption of direct supraspinal pathways, the cortex regained the capacity to transform contextual information into task-specific commands to execute refined locomotion. This recovery relied on the extensive remodeling of cortical projections, including the formation of brainstem and intraspinal relays that restored qualitative control over electrochemically enabled lumbosacral circuitries. Automated treadmill-restricted training, which did not engage cortical neurons, failed to promote translesional plasticity and recovery. By encouraging active participation under functional states, our training paradigm triggered a cortex-dependent recovery that may improve function after similar injuries in humans.

Positron annihilation lifetime spectroscopy study of Kapton thin foils

NASA Astrophysics Data System (ADS)

Kanda, G. S.; Ravelli, L.; Löwe, B.; Egger, W.; Keeble, D. J.

2016-01-01

Variable energy positron annihilation lifetime spectroscopy (VE-PALS) experiments on polyimide material Kapton are reported. Thin Kapton foils are widely used in a variety of mechanical, electronic applications. PALS provides a sensitive probe of vacancy-related defects in a wide range of materials, including open volume in polymers. Varying the positron implantation energy enables direct measurement of thin foils. Thin Kapton foils are also commonly used to enclose the positron source material in conventional PALS measurements performed with unmoderated radionuclide sources. The results of depth-profiled positron lifetime measurements on 7.6 μm and 25 μm Kapton foils are reported and determine a dominant 385(1) ps lifetime component. The absence of significant nanosecond lifetime component due to positronium formation is confirmed.

VisBOL: Web-Based Tools for Synthetic Biology Design Visualization.

PubMed

McLaughlin, James Alastair; Pocock, Matthew; Mısırlı, Göksel; Madsen, Curtis; Wipat, Anil

2016-08-19

VisBOL is a Web-based application that allows the rendering of genetic circuit designs, enabling synthetic biologists to visually convey designs in SBOL visual format. VisBOL designs can be exported to formats including PNG and SVG images to be embedded in Web pages, presentations and publications. The VisBOL tool enables the automated generation of visualizations from designs specified using the Synthetic Biology Open Language (SBOL) version 2.0, as well as a range of well-known bioinformatics formats including GenBank and Pigeoncad notation. VisBOL is provided both as a user accessible Web site and as an open-source (BSD) JavaScript library that can be used to embed diagrams within other content and software.

Ultrahigh-throughput–directed enzyme evolution by absorbance-activated droplet sorting (AADS)

PubMed Central

Gielen, Fabrice; Hours, Raphaelle; Emond, Stephane; Fischlechner, Martin; Schell, Ursula

2016-01-01

Ultrahigh-throughput screening, in which members of enzyme libraries compartmentalized in water-in-oil emulsion droplets are assayed, has emerged as a powerful format for directed evolution and functional metagenomics but is currently limited to fluorescence readouts. Here we describe a highly efficient microfluidic absorbance-activated droplet sorter (AADS) that extends the range of assays amenable to this approach. Using this module, microdroplets can be sorted based on absorbance readout at rates of up to 300 droplets per second (i.e., >1 million droplets per hour). To validate this device, we implemented a miniaturized coupled assay for NAD+-dependent amino acid dehydrogenases. The detection limit (10 μM in a coupled assay producing a formazan dye) enables accurate kinetic readouts sensitive enough to detect a minimum of 1,300 turnovers per enzyme molecule, expressed in a single cell, and released by lysis within a droplet. Sorting experiments showed that the AADS successfully enriched active variants up to 2,800-fold from an overwhelming majority of inactive ones at ∼100 Hz. To demonstrate the utility of this module for protein engineering, two rounds of directed evolution were performed to improve the activity of phenylalanine dehydrogenase toward its native substrate. Fourteen hits showed increased activity (improved >4.5-fold in lysate; kcat increased >2.7-fold), soluble protein expression levels (up 60%), and thermostability (Tm, 12 °C higher). The AADS module makes the most widely used optical detection format amenable to screens of unprecedented size, paving the way for the implementation of chromogenic assays in droplet microfluidics workflows. PMID:27821774

The FluxCompensator: Making Radiative Transfer Models of Hydrodynamical Simulations Directly Comparable to Real Observations

NASA Astrophysics Data System (ADS)

Koepferl, Christine M.; Robitaille, Thomas P.

2017-11-01

When modeling astronomical objects throughout the universe, it is important to correctly treat the limitations of the data, for instance finite resolution and sensitivity. In order to simulate these effects, and to make radiative transfer models directly comparable to real observations, we have developed an open-source Python package called the FluxCompensator that enables the post-processing of the output of 3D Monte Carlo radiative transfer codes, such as Hyperion. With the FluxCompensator, realistic synthetic observations can be generated by modeling the effects of convolution with arbitrary point-spread functions, transmission curves, finite pixel resolution, noise, and reddening. Pipelines can be applied to compute synthetic observations that simulate observatories, such as the Spitzer Space Telescope or the Herschel Space Observatory. Additionally, this tool can read in existing observations (e.g., FITS format) and use the same settings for the synthetic observations. In this paper, we describe the package as well as present examples of such synthetic observations.

Heterobimetallic Zeolite, InV-ZSM-5, Enables Efficient Conversion of Biomass Derived Ethanol to Renewable Hydrocarbons

NASA Astrophysics Data System (ADS)

Narula, Chaitanya K.; Li, Zhenglong; Casbeer, Erik M.; Geiger, Robert A.; Moses-Debusk, Melanie; Keller, Martin; Buchanan, Michelle V.; Davison, Brian H.

2015-11-01

Direct catalytic conversion of ethanol to hydrocarbon blend-stock can increase biofuels use in current vehicles beyond the ethanol blend-wall of 10-15%. Literature reports describe quantitative conversion of ethanol over zeolite catalysts but high C2 hydrocarbon formation renders this approach unsuitable for commercialization. Furthermore, the prior mechanistic studies suggested that ethanol conversion involves endothermic dehydration step. Here, we report the complete conversion of ethanol to hydrocarbons over InV-ZSM-5 without added hydrogen and which produces lower C2 (<13%) as compared to that over H-ZSM-5. Experiments with C2H5OD and in situ DRIFT suggest that most of the products come from the hydrocarbon pool type mechanism and dehydration step is not necessary. Thus, our method of direct conversion of ethanol offers a pathway to produce suitable hydrocarbon blend-stock that may be blended at a refinery to produce fuels such as gasoline, diesel, JP-8, and jet fuel, or produce commodity chemicals such as BTX.

Heterobimetallic Zeolite, InV-ZSM-5, Enables Efficient Conversion of Biomass Derived Ethanol to Renewable Hydrocarbons.

PubMed

Narula, Chaitanya K; Li, Zhenglong; Casbeer, Erik M; Geiger, Robert A; Moses-Debusk, Melanie; Keller, Martin; Buchanan, Michelle V; Davison, Brian H

2015-11-03

Direct catalytic conversion of ethanol to hydrocarbon blend-stock can increase biofuels use in current vehicles beyond the ethanol blend-wall of 10-15%. Literature reports describe quantitative conversion of ethanol over zeolite catalysts but high C2 hydrocarbon formation renders this approach unsuitable for commercialization. Furthermore, the prior mechanistic studies suggested that ethanol conversion involves endothermic dehydration step. Here, we report the complete conversion of ethanol to hydrocarbons over InV-ZSM-5 without added hydrogen and which produces lower C2 (<13%) as compared to that over H-ZSM-5. Experiments with C2H5OD and in situ DRIFT suggest that most of the products come from the hydrocarbon pool type mechanism and dehydration step is not necessary. Thus, our method of direct conversion of ethanol offers a pathway to produce suitable hydrocarbon blend-stock that may be blended at a refinery to produce fuels such as gasoline, diesel, JP-8, and jet fuel, or produce commodity chemicals such as BTX.

The FluxCompensator: Making Radiative Transfer Models of Hydrodynamical Simulations Directly Comparable to Real Observations

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

Koepferl, Christine M.; Robitaille, Thomas P., E-mail: koepferl@usm.lmu.de

When modeling astronomical objects throughout the universe, it is important to correctly treat the limitations of the data, for instance finite resolution and sensitivity. In order to simulate these effects, and to make radiative transfer models directly comparable to real observations, we have developed an open-source Python package called the FluxCompensator that enables the post-processing of the output of 3D Monte Carlo radiative transfer codes, such as Hyperion. With the FluxCompensator, realistic synthetic observations can be generated by modeling the effects of convolution with arbitrary point-spread functions, transmission curves, finite pixel resolution, noise, and reddening. Pipelines can be applied tomore » compute synthetic observations that simulate observatories, such as the Spitzer Space Telescope or the Herschel Space Observatory . Additionally, this tool can read in existing observations (e.g., FITS format) and use the same settings for the synthetic observations. In this paper, we describe the package as well as present examples of such synthetic observations.« less

Live-cell confocal microscopy and quantitative 4D image analysis of anchor cell invasion through the basement membrane in C. elegans

PubMed Central

Kelley, Laura C.; Wang, Zheng; Hagedorn, Elliott J.; Wang, Lin; Shen, Wanqing; Lei, Shijun; Johnson, Sam A.; Sherwood, David R.

2018-01-01

Cell invasion through basement membrane (BM) barriers is crucial during development, leukocyte trafficking, and for the spread of cancer. Despite its importance in normal and diseased states, the mechanisms that direct invasion are poorly understood, in large part because of the inability to visualize dynamic cell-basement membrane interactions in vivo. This protocol describes multi-channel time-lapse confocal imaging of anchor cell invasion in live C. elegans. Methods presented include outline slide preparation and worm growth synchronization (15 min), mounting (20 min), image acquisition (20-180 min), image processing (20 min), and quantitative analysis (variable timing). Images acquired enable direct measurement of invasive dynamics including invadopodia formation, cell membrane protrusions, and BM removal. This protocol can be combined with genetic analysis, molecular activity probes, and optogenetic approaches to uncover molecular mechanisms underlying cell invasion. These methods can also be readily adapted for real-time analysis of cell migration, basement membrane turnover, and cell membrane dynamics by any worm laboratory. PMID:28880279

Heat of supersaturation-limited amyloid burst directly monitored by isothermal titration calorimetry.

PubMed

Ikenoue, Tatsuya; Lee, Young-Ho; Kardos, József; Yagi, Hisashi; Ikegami, Takahisa; Naiki, Hironobu; Goto, Yuji

2014-05-06

Amyloid fibrils form in supersaturated solutions via a nucleation and growth mechanism. Although the structural features of amyloid fibrils have become increasingly clearer, knowledge on the thermodynamics of fibrillation is limited. Furthermore, protein aggregation is not a target of calorimetry, one of the most powerful approaches used to study proteins. Here, with β2-microglobulin, a protein responsible for dialysis-related amyloidosis, we show direct heat measurements of the formation of amyloid fibrils using isothermal titration calorimetry (ITC). The spontaneous fibrillation after a lag phase was accompanied by exothermic heat. The thermodynamic parameters of fibrillation obtained under various protein concentrations and temperatures were consistent with the main-chain dominated structural model of fibrils, in which overall packing was less than that of the native structures. We also characterized the thermodynamics of amorphous aggregation, enabling the comparison of protein folding, amyloid fibrillation, and amorphous aggregation. These results indicate that ITC will become a promising approach for clarifying comprehensively the thermodynamics of protein folding and misfolding.

How half-coated janus particles enter cells.

PubMed

Gao, Yuan; Yu, Yan

2013-12-26

Janus particles possess functional asymmetry and directionality within a single entity and thus are predicted to enable many promising biomedical applications that are not offered by homogeneous particles. However, it remains elusive what role the Janus principle plays in Janus particle-cell interactions, particularly in cellular uptake. We studied how asymmetric distribution of ligands on half-coated Janus microparticles dictates the membrane dynamics during receptor-mediated particle uptake, and found key differences from those characteristic of homogeneous particles. Live-cell fluorescence imaging combined with single-particle level quantification of particle-cell membrane interactions shows that the asymmetric distribution of ligands leads to a three-step endocytic process: membrane cup formation on the ligand-coated hemisphere, stalling at the Janus interface, and rapid membrane protrusion on the ligand-absent hemisphere to complete the particle engulfment. The direct correlation between the spatial presentation of ligands on Janus particles and the temporal changes of membrane dynamics revealed in this work elucidates the potential of using the Janus principle to fine-tune particle-cell interactions.

GOS hook type wells, directional planning, techniques applied and problems encountered

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

A /Azim, M.; Fahmy, H.; Salem, A.

1995-10-01

This paper addresses the various aspects of hook type wells introduced and drilled within GUPCO operations during he last two years. The first well of this category was October-G10, drilled in October 1992 from October ``G`` platform to a target point in the Nubia formation. Several wells of the same type have been drilled through 1993 and 1994. This group includes October-H1, Ramadan 3-57, July 62-69 and SB 374-3. Drilling hook type well profiles has resulted in increased production and more reserve recovery. The driving force behind using this profile was the reservoir requirements where it was required to hitmore » a target within few meters at a certain angle and direction. Torque and drag models have been used to optimize well path planning, resulting in lower torque and drag values. Daily pot appraisal of the drilling operations to monitor hole cleaning effectiveness. Combination of advanced steerable systems and PDC bits enabled GUPCO to drill these wells cost effectively.« less

Magneto-Adaptive Surfactants Showing Anti-Curie Behavior and Tunable Surface Tension as Porogens for Mesoporous Particles with 12-Fold Symmetry.

PubMed

Hermann, Stefanie; Wessig, Martin; Kollofrath, Dennis; Gerigk, Melanie; Hagedorn, Kay; Odendal, James A; Hagner, Matthias; Drechsler, Markus; Erler, Philipp; Fonin, Mikhail; Maret, Georg; Polarz, Sebastian

2017-05-08

Gaining external control over self-organization is of vital importance for future smart materials. Surfactants are extremely valuable for the synthesis of diverse nanomaterials. Their self-assembly is dictated by microphase separation, the hydrophobic effect, and head-group repulsion. It is desirable to supplement surfactants with an added mode of long-range and directional interaction. Magnetic forces are ideal, as they are not shielded in water. We report on surfactants with heads containing tightly bound transition-metal centers. The magnetic moment of the head was varied systematically while keeping shape and charge constant. Changes in the magnetic moment of the head led to notable differences in surface tension, aggregate size, and contact angle, which could also be altered by an external magnetic field. The most astonishing result was that the use of magnetic surfactants as structure-directing agents enabled the formation of porous solids with 12-fold rotational symmetry. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Active inference and learning.

PubMed

Friston, Karl; FitzGerald, Thomas; Rigoli, Francesco; Schwartenbeck, Philipp; O Doherty, John; Pezzulo, Giovanni

2016-09-01

This paper offers an active inference account of choice behaviour and learning. It focuses on the distinction between goal-directed and habitual behaviour and how they contextualise each other. We show that habits emerge naturally (and autodidactically) from sequential policy optimisation when agents are equipped with state-action policies. In active inference, behaviour has explorative (epistemic) and exploitative (pragmatic) aspects that are sensitive to ambiguity and risk respectively, where epistemic (ambiguity-resolving) behaviour enables pragmatic (reward-seeking) behaviour and the subsequent emergence of habits. Although goal-directed and habitual policies are usually associated with model-based and model-free schemes, we find the more important distinction is between belief-free and belief-based schemes. The underlying (variational) belief updating provides a comprehensive (if metaphorical) process theory for several phenomena, including the transfer of dopamine responses, reversal learning, habit formation and devaluation. Finally, we show that active inference reduces to a classical (Bellman) scheme, in the absence of ambiguity. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Massive Star Formation Viewed through Extragalactic-Tinted Glasses

NASA Astrophysics Data System (ADS)

Willis, Sarah; Marengo, M.; Smith, H. A.; Allen, L.

2014-01-01

Massive Galactic star forming regions are the local analogs to the luminous star forming regions that dominate the emission from star forming galaxies. Their proximity to us enables the characterization of the full range of stellar masses that form in these more massive environments, improving our understanding of star formation tracers used in extragalactic studies. We have surveyed a sample of massive star forming regions with a range of morphologies and luminosities to probe the star formation activity in a variety of environments. We have used Spitzer IRAC and deep ground based J, H, Ks observations to characterize the Young Stellar Object (YSO) content of 6 massive star forming regions. These YSOs provide insight into the rate and efficiency of star formation within these regions, and enable comparison with nearby, low mass star forming regions as well as extreme cases of Galactic star formation including ‘mini-starburst’ regions. In addition, we have conducted an in-depth analysis of NGC 6334 to investigate how the star formation activity varies within an individual star forming region, using Herschel data in the far-infrared to probe the earliest stages of the ongoing star formation activity.

Determination of dew point conditions for CO2 with impurities using microfluidics.

PubMed

Song, Wen; Fadaei, Hossein; Sinton, David

2014-03-18

Impurities can greatly modify the phase behavior of carbon dioxide (CO2), with significant implications on the safety and cost of transport in pipelines. In this paper we demonstrate a microfluidic approach to measure the dew point of such mixtures, specifically the point at which water in supercritical CO2 mixtures condenses to a liquid state. The method enables direct visualization of dew formation (∼ 1-2 μm diameter droplets) at industrially relevant concentrations, pressures, and temperatures. Dew point measurements for the well-studied case of pure CO2-water agreed well with previous theoretical and experimental data over the range of pressure (up to 13.17 MPa), temperature (up to 50 °C), and water content (down to 0.00229 mol fraction) studied. The microfluidic approach showed a nearly 3-fold reduction in error as compared to previous methods. When applied to a mixture with nitrogen (2.5%) and oxygen (5.8%) impurities--typical of flue gas from natural gas oxy-fuel combustion processes--the measured dew point pressure increased on average 17.55 ± 5.4%, indicating a more stringent minimum pressure for pipeline transport. In addition to increased precision, the microfluidic method offers a direct measurement of dew formation, requires very small volumes (∼ 10 μL), and is applicable to ultralow water contents (<0.005 mol fractions), circumventing the limits of previous methods.

Tracking Equilibrium and Nonequilibrium Shifts in Data with TREND.

PubMed

Xu, Jia; Van Doren, Steven R

2017-01-24

Principal component analysis (PCA) discovers patterns in multivariate data that include spectra, microscopy, and other biophysical measurements. Direct application of PCA to crowded spectra, images, and movies (without selecting peaks or features) was shown recently to identify their equilibrium or temporal changes. To enable the community to utilize these capabilities with a wide range of measurements, we have developed multiplatform software named TREND to Track Equilibrium and Nonequilibrium population shifts among two-dimensional Data frames. TREND can also carry this out by independent component analysis. We highlight a few examples of finding concurrent processes. TREND extracts dual phases of binding to two sites directly from the NMR spectra of the titrations. In a cardiac movie from magnetic resonance imaging, TREND resolves principal components (PCs) representing breathing and the cardiac cycle. TREND can also reconstruct the series of measurements from selected PCs, as illustrated for a biphasic, NMR-detected titration and the cardiac MRI movie. Fidelity of reconstruction of series of NMR spectra or images requires more PCs than needed to plot the largest population shifts. TREND reads spectra from many spectroscopies in the most common formats (JCAMP-DX and NMR) and multiple movie formats. The TREND package thus provides convenient tools to resolve the processes recorded by diverse biophysical methods. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Direct formation of a current collector layer on a partially reduced graphite oxide film using sputter-assisted metal deposition to fabricate high-power micro-supercapacitor electrodes

NASA Astrophysics Data System (ADS)

Byun, Segi; Yu, Jin

2016-03-01

When a reduced graphite oxide (RGO) freestanding film is fabricated on a supercapacitor cell via compression onto a current collector, there are gaps between the film and the current collector, even if the cell is carefully assembled. These gaps can induce increases in the electrical series resistance (ESR) of the cell, resulting in degradation of the cell's electrochemical performance. Here, to effectively reduce the ESR of the supercapacitor, metal sputtering deposition is introduced. This enables the direct formation of the current collector layer on a partially reduced GO (pRGO) film, the model system. Using metal sputtering, a nickel (Ni) layer with a thickness <1 μm can be created easily on one side of the pRGO film. Good electrical interconnection between the pRGO film and the current collector can be obtained using a Ni layer formed on the pRGO film. The pRGO film sustains its film form with high packing density (∼1.31 g cm-3). Furthermore, the Ni-sputtered pRGO film with optimized Ni thickness exhibits remarkable enhancement of its electrochemical performance. This includes a superior rate capability and semi-permanent cycle life compared with the untreated pRGO film. This is due to the significant decrease in the ESR of the film.

Collaborative Project: Development of an Isotope-Enabled CESM for Testing Abrupt Climate Changes

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

Liu, Zhengyu

One of the most important validations for a state-of-art Earth System Model (ESM) with respect to climate changes is the simulation of the climate evolution and abrupt climate change events in the Earth’s history of the last 21,000 years. However, one great challenge for model validation is that ESMs usually do not directly simulate geochemical variables that can be compared directly with past proxy records. In this proposal, we have met this challenge by developing the simulation capability of major isotopes in a state-of-art ESM, the Community Earth System Model (CESM), enabling us to make direct model-data comparison by comparingmore » the model directly against proxy climate records. Our isotope-enabled ESM incorporates the capability of simulating key isotopes and geotracers, notably δ 18O, δD, δ 14C, and δ 13C, Nd and Pa/Th. The isotope-enabled ESM have been used to perform some simulations for the last 21000 years. The direct comparison of these simulations with proxy records has shed light on the mechanisms of important climate change events.« less

Behavioral and Neural Representations of Spatial Directions across Words, Schemas, and Images.

PubMed

Weisberg, Steven M; Marchette, Steven A; Chatterjee, Anjan

2018-05-23

Modern spatial navigation requires fluency with multiple representational formats, including visual scenes, signs, and words. These formats convey different information. Visual scenes are rich and specific but contain extraneous details. Arrows, as an example of signs, are schematic representations in which the extraneous details are eliminated, but analog spatial properties are preserved. Words eliminate all spatial information and convey spatial directions in a purely abstract form. How does the human brain compute spatial directions within and across these formats? To investigate this question, we conducted two experiments on men and women: a behavioral study that was preregistered and a neuroimaging study using multivoxel pattern analysis of fMRI data to uncover similarities and differences among representational formats. Participants in the behavioral study viewed spatial directions presented as images, schemas, or words (e.g., "left"), and responded to each trial, indicating whether the spatial direction was the same or different as the one viewed previously. They responded more quickly to schemas and words than images, despite the visual complexity of stimuli being matched. Participants in the fMRI study performed the same task but responded only to occasional catch trials. Spatial directions in images were decodable in the intraparietal sulcus bilaterally but were not in schemas and words. Spatial directions were also decodable between all three formats. These results suggest that intraparietal sulcus plays a role in calculating spatial directions in visual scenes, but this neural circuitry may be bypassed when the spatial directions are presented as schemas or words. SIGNIFICANCE STATEMENT Human navigators encounter spatial directions in various formats: words ("turn left"), schematic signs (an arrow showing a left turn), and visual scenes (a road turning left). The brain must transform these spatial directions into a plan for action. Here, we investigate similarities and differences between neural representations of these formats. We found that bilateral intraparietal sulci represent spatial directions in visual scenes and across the three formats. We also found that participants respond quickest to schemas, then words, then images, suggesting that spatial directions in abstract formats are easier to interpret than concrete formats. These results support a model of spatial direction interpretation in which spatial directions are either computed for real world action or computed for efficient visual comparison. Copyright © 2018 the authors 0270-6474/18/384996-12$15.00/0.

A Multi-Faceted Formative Assessment Approach: Better Recognising the Learning Needs of Students

ERIC Educational Resources Information Center

Jenkins, James O.

2010-01-01

Students are increasingly subject to a series of learning pressures that prevent effective engagement in assessment. Thus, the aim of this study was to create a multi-faceted formative assessment approach that better enabled students to engage in the assessment process. A formative assessment approach, consisting of six key initiatives, is…

Catalytic alkylation of remote C-H bonds enabled by proton-coupled electron transfer

NASA Astrophysics Data System (ADS)

Choi, Gilbert J.; Zhu, Qilei; Miller, David C.; Gu, Carol J.; Knowles, Robert R.

2016-11-01

Despite advances in hydrogen atom transfer (HAT) catalysis, there are currently no molecular HAT catalysts that are capable of homolysing the strong nitrogen-hydrogen (N-H) bonds of N-alkyl amides. The motivation to develop amide homolysis protocols stems from the utility of the resultant amidyl radicals, which are involved in various synthetically useful transformations, including olefin amination and directed carbon-hydrogen (C-H) bond functionalization. In the latter process—a subset of the classical Hofmann-Löffler-Freytag reaction—amidyl radicals remove hydrogen atoms from unactivated aliphatic C-H bonds. Although powerful, these transformations typically require oxidative N-prefunctionalization of the amide starting materials to achieve efficient amidyl generation. Moreover, because these N-activating groups are often incorporated into the final products, these methods are generally not amenable to the direct construction of carbon-carbon (C-C) bonds. Here we report an approach that overcomes these limitations by homolysing the N-H bonds of N-alkyl amides via proton-coupled electron transfer. In this protocol, an excited-state iridium photocatalyst and a weak phosphate base cooperatively serve to remove both a proton and an electron from an amide substrate in a concerted elementary step. The resultant amidyl radical intermediates are shown to promote subsequent C-H abstraction and radical alkylation steps. This C-H alkylation represents a catalytic variant of the Hofmann-Löffler-Freytag reaction, using simple, unfunctionalized amides to direct the formation of new C-C bonds. Given the prevalence of amides in pharmaceuticals and natural products, we anticipate that this method will simplify the synthesis and structural elaboration of amine-containing targets. Moreover, this study demonstrates that concerted proton-coupled electron transfer can enable homolytic activation of common organic functional groups that are energetically inaccessible using traditional HAT-based approaches.

Catalytic alkylation of remote C-H bonds enabled by proton-coupled electron transfer.

PubMed

Choi, Gilbert J; Zhu, Qilei; Miller, David C; Gu, Carol J; Knowles, Robert R

2016-11-10

Despite advances in hydrogen atom transfer (HAT) catalysis, there are currently no molecular HAT catalysts that are capable of homolysing the strong nitrogen-hydrogen (N-H) bonds of N-alkyl amides. The motivation to develop amide homolysis protocols stems from the utility of the resultant amidyl radicals, which are involved in various synthetically useful transformations, including olefin amination and directed carbon-hydrogen (C-H) bond functionalization. In the latter process-a subset of the classical Hofmann-Löffler-Freytag reaction-amidyl radicals remove hydrogen atoms from unactivated aliphatic C-H bonds. Although powerful, these transformations typically require oxidative N-prefunctionalization of the amide starting materials to achieve efficient amidyl generation. Moreover, because these N-activating groups are often incorporated into the final products, these methods are generally not amenable to the direct construction of carbon-carbon (C-C) bonds. Here we report an approach that overcomes these limitations by homolysing the N-H bonds of N-alkyl amides via proton-coupled electron transfer. In this protocol, an excited-state iridium photocatalyst and a weak phosphate base cooperatively serve to remove both a proton and an electron from an amide substrate in a concerted elementary step. The resultant amidyl radical intermediates are shown to promote subsequent C-H abstraction and radical alkylation steps. This C-H alkylation represents a catalytic variant of the Hofmann-Löffler-Freytag reaction, using simple, unfunctionalized amides to direct the formation of new C-C bonds. Given the prevalence of amides in pharmaceuticals and natural products, we anticipate that this method will simplify the synthesis and structural elaboration of amine-containing targets. Moreover, this study demonstrates that concerted proton-coupled electron transfer can enable homolytic activation of common organic functional groups that are energetically inaccessible using traditional HAT-based approaches.

Using modern imaging techniques to old HST data: a summary of the ALICE program.

NASA Astrophysics Data System (ADS)

Choquet, Elodie; Soummer, Remi; Perrin, Marshall; Pueyo, Laurent; Hagan, James Brendan; Zimmerman, Neil; Debes, John Henry; Schneider, Glenn; Ren, Bin; Milli, Julien; Wolff, Schuyler; Stark, Chris; Mawet, Dimitri; Golimowski, David A.; Hines, Dean C.; Roberge, Aki; Serabyn, Eugene

2018-01-01

Direct imaging of extrasolar systems is a powerful technique to study the physical properties of exoplanetary systems and understand their formation and evolution mechanisms. The detection and characterization of these objects are challenged by their high contrast with their host star. Several observing strategies and post-processing algorithms have been developed for ground-based high-contrast imaging instruments, enabling the discovery of directly-imaged and spectrally-characterized exoplanets. The Hubble Space Telescope (HST), pioneer in directly imaging extrasolar systems, has yet been often limited to the detection of bright debris disks systems, with sensitivity limited by the difficulty to implement an optimal PSF subtraction stategy, which is readily offered on ground-based telescopes in pupil tracking mode.The Archival Legacy Investigations of Circumstellar Environments (ALICE) program is a consistent re-analysis of the 10 year old coronagraphic archive of HST's NICMOS infrared imager. Using post-processing methods developed for ground-based observations, we used the whole archive to calibrate PSF temporal variations and improve NICMOS's detection limits. We have now delivered ALICE-reprocessed science products for the whole NICMOS archival data back to the community. These science products, as well as the ALICE pipeline, were used to prototype the JWST coronagraphic data and reduction pipeline. The ALICE program has enabled the detection of 10 faint debris disk systems never imaged before in the near-infrared and several substellar companion candidates, which we are all in the process of characterizing through follow-up observations with both ground-based facilities and HST-STIS coronagraphy. In this publication, we provide a summary of the results of the ALICE program, advertise its science products and discuss the prospects of the program.

First Results from a Hardware-in-the-Loop Demonstration of Closed-Loop Autonomous Formation Flying

NASA Technical Reports Server (NTRS)

Gill, E.; Naasz, Bo; Ebinuma, T.

2003-01-01

A closed-loop system for the demonstration of autonomous satellite formation flying technologies using hardware-in-the-loop has been developed. Making use of a GPS signal simulator with a dual radio frequency outlet, the system includes two GPS space receivers as well as a powerful onboard navigation processor dedicated to the GPS-based guidance, navigation, and control of a satellite formation in real-time. The closed-loop system allows realistic simulations of autonomous formation flying scenarios, enabling research in the fields of tracking and orbit control strategies for a wide range of applications. The autonomous closed-loop formation acquisition and keeping strategy is based on Lyapunov's direct control method as applied to the standard set of Keplerian elements. This approach not only assures global and asymptotic stability of the control but also maintains valuable physical insight into the applied control vectors. Furthermore, the approach can account for system uncertainties and effectively avoids a computationally expensive solution of the two point boundary problem, which renders the concept particularly attractive for implementation in onboard processors. A guidance law has been developed which strictly separates the relative from the absolute motion, thus avoiding the numerical integration of a target trajectory in the onboard processor. Moreover, upon using precise kinematic relative GPS solutions, a dynamical modeling or filtering is avoided which provides for an efficient implementation of the process on an onboard processor. A sample formation flying scenario has been created aiming at the autonomous transition of a Low Earth Orbit satellite formation from an initial along-track separation of 800 m to a target distance of 100 m. Assuming a low-thrust actuator which may be accommodated on a small satellite, a typical control accuracy of less than 5 m has been achieved which proves the applicability of autonomous formation flying techniques to formations of satellites as close as 50 m.

Bone Balance within a Cortical BMU: Local Controls of Bone Resorption and Formation

PubMed Central

Smith, David W.; Gardiner, Bruce S.; Dunstan, Colin

2012-01-01

Maintaining bone volume during bone turnover by a BMU is known as bone balance. Balance is required to maintain structural integrity of the bone and is often dysregulated in disease. Consequently, understanding how a BMU controls bone balance is of considerable interest. This paper develops a methodology for identifying potential balance controls within a single cortical BMU. The theoretical framework developed offers the possibility of a directed search for biological processes compatible with the constraints of balance control. We first derive general control constraint equations and then introduce constitutive equations to identify potential control processes that link key variables that describe the state of the BMU. The paper describes specific local bone volume balance controls that may be associated with bone resorption and bone formation. Because bone resorption and formation both involve averaging over time, short-term fluctuations in the environment are removed, leaving the control systems to manage deviations in longer-term trends back towards their desired values. The length of time for averaging is much greater for bone formation than for bone resorption, which enables more filtering of variability in the bone formation environment. Remarkably, the duration for averaging of bone formation may also grow to control deviations in long-term trends of bone formation. Providing there is sufficient bone formation capacity by osteoblasts, this leads to an extraordinarily robust control mechanism that is independent of either osteoblast number or the cellular osteoid formation rate. A complex picture begins to emerge for the control of bone volume. Different control relationships may achieve the same objective, and the ‘integration of information’ occurring within a BMU may be interpreted as different sets of BMU control systems coming to the fore as different information is supplied to the BMU, which in turn leads to different observable BMU behaviors. PMID:22844401

Australia's TERN: Advancing Ecosystem Data Management in Australia

NASA Astrophysics Data System (ADS)

Phinn, S. R.; Christensen, R.; Guru, S.

2013-12-01

Globally, there is a consistent movement towards more open, collaborative and transparent science, where the publication and citation of data is considered standard practice. Australia's Terrestrial Ecosystem Research Network (TERN) is a national research infrastructure investment designed to support the ecosystem science community through all stages of the data lifecycle. TERN has developed and implemented a comprehensive network of ';hard' and ';soft' infrastructure that enables Australia's ecosystem scientists to collect, publish, store, share, discover and re-use data in ways not previously possible. The aim of this poster is to demonstrate how TERN has successfully delivered infrastructure that is enabling a significant cultural and practical shift in Australia's ecosystem science community towards consistent approaches for data collection, meta-data, data licensing, and data publishing. TERN enables multiple disciplines, within the ecosystem sciences to more effectively and efficiently collect, store and publish their data. A critical part of TERN's approach has been to build on existing data collection activities, networks and skilled people to enable further coordination and collaboration to build each data collection facility and coordinate data publishing. Data collection in TERN is through discipline based facilities, covering long term collection of: (1) systematic plot based measurements of vegetation structure, composition and faunal biodiversity; (2) instrumented towers making systematic measurements of solar, water and gas fluxes; and (3) satellite and airborne maps of biophysical properties of vegetation, soils and the atmosphere. Several other facilities collect and integrate environmental data to produce national products for fauna and vegetation surveys, soils and coastal data, as well as integrated or synthesised products for modelling applications. Data management, publishing and sharing in TERN are implemented through a tailored data licensing framework suitable for ecosystem data, national standards for metadata, a DOI-minting service, and context-appropriate data repositories and portals. The TERN Data infrastructure is based on loosely coupled 'network of networks.' Overall, the data formats used across the TERN facilities vary from NetCDF, comma-separated values and descriptive documents. Metadata standards include ISO19115, Ecological Metadata Language and rich semantic enabled contextual information. Data services vary from Web Mapping Service, Web Feature Service, OpeNDAP, file servers and KNB Metacat. These approaches enable each data collection facility to maintain their discipline based data collection and storage protocols. TERN facility meta-data are harvested regularly for the central TERN Data Discovery Portal and converted to a national standard format. This approach enables centralised discovery, access, and re-use of data simply and effectively, while maintaining disciplinary diversity. Effort is still required to support the cultural shift towards acceptance of effective data management, publication, sharing and re-use as standard practice. To this end TERN's future activities will be directed to supporting this transformation and undertaking ';education' to enable ecosystem scientists to take full advantage of TERN's infrastructure, and providing training and guidance for best practice data management.

The effects of Dark Matter annihilation on cosmic reionization

DOE PAGES

Kaurov, Alexander A.; Hooper, Dan; Gnedin, Nickolay Y.

2016-12-15

We revisit the possibility of constraining the properties of dark matter (DM) by studying the epoch of cosmic reionization. Previous studies have shown that DM annihilation was unlikely to have provided a large fraction of the photons that ionized the universe, but instead played a subdominant role relative to stars and quasars. The DM, however, begins to efficiently annihilate with the formation of primordial microhalos atmore » $$z\\sim100-200$$, much earlier than the formation of the first stars. Therefore, if DM annihilation ionized the universe at even the percent level over the interval $$z \\sim 20-100$$, it can leave a significant imprint on the global optical depth, $$\\tau$$. Moreover, we show that cosmic microwave background (CMB) polarization data and future 21 cm measurements will enable us to more directly probe the DM contribution to the optical depth. In order to compute the annihilation rate throughout the epoch of reionization, we adopt the latest results from structure formation studies and explore the impact of various free parameters on our results. Here, we show that future measurements could make it possible to place constraints on the dark matter's annihilation cross section that are at a level comparable to those obtained from the observations of dwarf galaxies, cosmic ray measurements, and studies of recombination.« less

Phase Transition Control for High Performance Ruddlesden-Popper Perovskite Solar Cells.

PubMed

Zhang, Xu; Munir, Rahim; Xu, Zhuo; Liu, Yucheng; Tsai, Hsinhan; Nie, Wanyi; Li, Jianbo; Niu, Tianqi; Smilgies, Detlef-M; Kanatzidis, Mercouri G; Mohite, Aditya D; Zhao, Kui; Amassian, Aram; Liu, Shengzhong Frank

2018-05-01

Ruddlesden-Popper reduced-dimensional hybrid perovskite (RDP) semiconductors have attracted significant attention recently due to their promising stability and excellent optoelectronic properties. Here, the RDP crystallization mechanism in real time from liquid precursors to the solid film is investigated, and how the phase transition kinetics influences phase purity, quantum well orientation, and photovoltaic performance is revealed. An important template-induced nucleation and growth of the desired (BA) 2 (MA) 3 Pb 4 I 13 phase, which is achieved only via direct crystallization without formation of intermediate phases, is observed. As such, the thermodynamically preferred perpendicular crystal orientation and high phase purity are obtained. At low temperature, the formation of intermediate phases, including PbI 2 crystals and solvate complexes, slows down intercalation of ions and increases nucleation barrier, leading to formation of multiple RDP phases and orientation randomness. These insights enable to obtain high quality (BA) 2 (MA) 3 Pb 4 I 13 films with preferentially perpendicular quantum well orientation, high phase purity, smooth film surface, and improved optoelectronic properties. The resulting devices exhibit high power conversion efficiency of 12.17%. This work should help guide the perovskite community to better control Ruddlesden-Popper perovskite structure and further improve optoelectronic and solar cell devices. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Role of different chelating agent in synthesis of copper doped tin oxide (Cu-SnO2) nanoparticles

NASA Astrophysics Data System (ADS)

Saravanakumar, B.; Anusiya, A.; Rani, B. Jansi; Ravi, G.; Yuvakkumar, R.

2018-05-01

An attempt was made to synthesis the copper doped tin oxide (Cu-SnO2) nanoparticles by adopting different chelating agents (NaOH, KOH and C2H2O4) by Sol-gel process. The synthesized products were characterized by XRD, Photoluminescence (PL), Infra- Red (FTIR) and SEM analysis. The XRD confirms the formation of Cu-SnO2 shows the maximum peak at 33.8° with lattice plane (101). The PL peak at 361 and 382 nm due to the recombination of electron in conduction band to valence band infers the optical properties. The IR spectra correspond to the peak at 551 and 620 cm-1 attributed to the characteristics peak for Cu-SnO2 nanoparticles. The SEM images for all three Cu-SnO2 nanoparticles formed by three chelating agent (NaOH, KOH and C2H2O4) facilitates the formation mechanism and the chelating agent Oxalic acid results in formation of nano flowers with diverse layers orientated in random direction. Further SEM studies reveal that, the Cu-SnO2 nanoparticles formed by oxalic acid could posses high surface area with large number layered structured enables the better electrochemical properties and its applications.

A study of suppressed formation of low-conductivity phases in doped Li 7La 3Zr 2O 12 garnets by in situ neutron diffraction

DOE PAGES

Chen, Yan; Rangasamy, Ezhiylmurugan; dela Cruz, Clarina R.; ...

2015-09-28

Doped Li 7La 3Zr 2O 12 garnets, oxide-based solids with good Li + conductivity and compatibility, show great potential as leading electrolyte material candidates for all-solid-state lithium ion batteries. Still yet, the conductive bulk usually suffers from the presence of secondary phases and the transition towards a low-conductivity tetragonal phase during synthesis. Dopants are designed to stabilize the high-conductive cubic phase and suppress the formation of the low-conductivity phases. In situ neutron diffraction enables a direct observation of the doping effects by monitoring the phase evolutions during garnet synthesis. It reveals the reaction mechanism involving the temporary presence of intermediatemore » phases. The off-stoichiometry due to the liquid Li 2CO 3 evaporation leads to the residual of the low-conductivity intermediate phase in the as-synthesized bulk. Appropriate doping of an active element may alter the component of the intermediate phases and promote the completion of the reaction. While the dopants aid to stabilize most of the cubic phase, a small amount of tetragonal phase tends to form under a diffusion process. Lastly, the in situ observations provide the guideline of process optimization to suppress the formation of unwanted low-conductivity phases.« less

Hydrolysis of Mg(BH4)2 and its coordination compounds as a way to obtain hydrogen

NASA Astrophysics Data System (ADS)

Solovev, Mikhail V.; Chashchikhin, Oleg V.; Dorovatovskii, Pavel V.; Khrustalev, Victor N.; Zyubin, A. S.; Zyubina, T. S.; Kravchenko, O. V.; Zaytsev, Alexey A.; Dobrovolsky, Yu. A.

2018-02-01

Three ligand-stabilized Mg(BH4)2-based complexes have been synthesized and evaluated as potential hydrogen storage media for portable fuel cell applications. The new borohydrides: Mg(BH4)2 × 0.5Et2O and Mg(BH4)2 × diglyme (diglyme - CH3O(CH2)2O(CH2)2OCH3) have been synthesized and examined by X-ray single crystal diffraction method. Hydrolysis reactions of the compounds liberate hydrogen in quantities ranging from 46 to 96% of the theoretical yield. The hydrolysis of Mg(BH4)2 and other borohydrides is also accompanied by the diborane formation. The amount of liberated diborane depends on the Mg-coordination environment. To explain this fact quantum-chemical calculations have been performed. It is shown that formation of Mg-O-Mg-bridges enables the side process of diborane generation. It means that the size and denticity of the ligand directly affects the amount of released diborane. In general, the larger the ligand and the higher its denticity, the smaller is amount of diborane produced. The new compound Mg(BH4)2 × diglyme decomposes without diborane formation that allows one to be considered as a new promising chemical hydrogen storage compound for the practical usage.

Radio data archiving system

NASA Astrophysics Data System (ADS)

Knapic, C.; Zanichelli, A.; Dovgan, E.; Nanni, M.; Stagni, M.; Righini, S.; Sponza, M.; Bedosti, F.; Orlati, A.; Smareglia, R.

2016-07-01

Radio Astronomical Data models are becoming very complex since the huge possible range of instrumental configurations available with the modern Radio Telescopes. What in the past was the last frontiers of data formats in terms of efficiency and flexibility is now evolving with new strategies and methodologies enabling the persistence of a very complex, hierarchical and multi-purpose information. Such an evolution of data models and data formats require new data archiving techniques in order to guarantee data preservation following the directives of Open Archival Information System and the International Virtual Observatory Alliance for data sharing and publication. Currently, various formats (FITS, MBFITS, VLBI's XML description files and ancillary files) of data acquired with the Medicina and Noto Radio Telescopes can be stored and handled by a common Radio Archive, that is planned to be released to the (inter)national community by the end of 2016. This state-of-the-art archiving system for radio astronomical data aims at delegating as much as possible to the software setting how and where the descriptors (metadata) are saved, while the users perform user-friendly queries translated by the web interface into complex interrogations on the database to retrieve data. In such a way, the Archive is ready to be Virtual Observatory compliant and as much as possible user-friendly.

Informatics in radiology (infoRAD): free DICOM image viewing and processing software for the Macintosh computer: what's available and what it can do for you.

PubMed

Escott, Edward J; Rubinstein, David

2004-01-01

It is often necessary for radiologists to use digital images in presentations and conferences. Most imaging modalities produce images in the Digital Imaging and Communications in Medicine (DICOM) format. The image files tend to be large and thus cannot be directly imported into most presentation software, such as Microsoft PowerPoint; the large files also consume storage space. There are many free programs that allow viewing and processing of these files on a personal computer, including conversion to more common file formats such as the Joint Photographic Experts Group (JPEG) format. Free DICOM image viewing and processing software for computers running on the Microsoft Windows operating system has already been evaluated. However, many people use the Macintosh (Apple Computer) platform, and a number of programs are available for these users. The World Wide Web was searched for free DICOM image viewing or processing software that was designed for the Macintosh platform or is written in Java and is therefore platform independent. The features of these programs and their usability were evaluated. There are many free programs for the Macintosh platform that enable viewing and processing of DICOM images. (c) RSNA, 2004.

Odorants selectively activate distinct G protein subtypes in olfactory cilia.

PubMed

Schandar, M; Laugwitz, K L; Boekhoff, I; Kroner, C; Gudermann, T; Schultz, G; Breer, H

1998-07-03

Chemoelectrical signal transduction in olfactory neurons appears to involve intracellular reaction cascades mediated by heterotrimeric GTP-binding proteins. In this study attempts were made to identify the G protein subtype(s) in olfactory cilia that are activated by the primary (odorant) signal. Antibodies directed against the alpha subunits of distinct G protein subtypes interfered specifically with second messenger reponses elicited by defined subsets of odorants; odor-induced cAMP-formation was attenuated by Galphas antibodies, whereas Galphao antibodies blocked odor-induced inositol 1,4, 5-trisphosphate (IP3) formation. Activation-dependent photolabeling of Galpha subunits with [alpha-32P]GTP azidoanilide followed by immunoprecipitation using subtype-specific antibodies enabled identification of particular individual G protein subtypes that were activated upon stimulation of isolated olfactory cilia by chemically distinct odorants. For example odorants that elicited a cAMP response resulted in labeling of a Galphas-like protein, whereas odorants that elicited an IP3 response led to the labeling of a Galphao-like protein. Since odorant-induced IP3 formation was also blocked by Gbeta antibodies, activation of olfactory phospholipase C might be mediated by betagamma subunits of a Go-like G protein. These results indicate that different subsets of odorants selectively trigger distinct reaction cascades and provide evidence for dual transduction pathways in olfactory signaling.

Histone-Targeted Nucleic Acid Delivery for Tissue Regenerative Applications

NASA Astrophysics Data System (ADS)

Munsell, Erik V.

Nucleic acid delivery has garnered significant attention as an innovative therapeutic approach for treating a wide variety of diseases. However, the design of non-viral delivery systems that negotiate efficient intracellular trafficking and nuclear entry represents a significant challenge. Overcoming these hurdles requires a combination of well-controlled materials approaches with techniques to understand and direct cellular delivery. Recent investigations have highlighted the roles histone tail sequences play in directing nuclear delivery and retention, as well as activating DNA transcription. We established the ability to recapitulate these natural histone tail activities within non-viral gene nanocarriers, driving gene transfer/expression by enabling effective navigation to the nucleus via retrograde vesicular trafficking. A unique finding of this histone-targeted approach was that nanocarriers gained enhanced access to the nucleus during mitosis. The work described in this dissertation builds off of these fundamental insights to facilitate the translation of this histone-targeted delivery approach toward regenerative medicine applications. During native tissue repair, actively proliferating mesenchymal stem cells (MSCs) respond to a complex series of growth factor signals that direct their differentiation. Accordingly, the investigations in this work focused on utilizing the histone-targeted nanocarriers to enhance osteogenic growth factor gene transfer in dividing MSCs leading to augmented MSC chondrogenic differentiation, an essential first step in skeletal tissue repair. Concurrently, additional studies focused on optimizing the histone-targeted nanocarrier design strategy to enable improved plasmid DNA (pDNA) binding stability and tunable harnessing of native cellular processing pathways for enhanced gene transfer. Overall, the work presented herein demonstrated substantial increases in growth factor expression following histone-targeted gene transfer. This enhanced expression enabled more robust levels of chondrogenesis in MSCs than treatments with equivalent amounts of recombinant growth factor protein. Additionally, nanocarrier design optimization provided effective pDNA condensation and controllable interactions with native histone effectors. Importantly, these optimized nanocarriers conferred stable nanoplex formation and maintained transfection efficiency under physiologically relevant conditions. Taken together, these advances may help drive the clinical translation of histone-targeted nucleic acid delivery strategies for the regeneration of damaged tissue following traumatic injury.

j5 v2.8.4

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

Hillson, Nathan

j5 automates and optimizes the design of the molecular biological process of cloning/constructing DNA. j5 enables users to benefit from (combinatorial) multi-part scar-less SLIC, Gibson, CPEC, Golden Gate assembly, or variants thereof, for which automation software does not currently exist, without the intense labor currently associated with the process. j5 inputs a list of the DNA sequences to be assembled, along with a Genbank, FASTA, jbei-seq, or SBOL v1.1 format sequence file for each DNA source. Given the list of DNA sequences to be assembled, j5 first determines the cost-minimizing assembly strategy for each part (direct synthesis, PCR/SOE, or oligo-embedding),more » designs DNA oligos with Primer3, adds flanking homology sequences (SLIC, Gibson, and CPEC; optimized with Primer3 for CPEC) or optimized overhang sequences (Golden Gate) to the oligos and direct synthesis pieces, and utilizes BLAST to check against oligo mis-priming and assembly piece incompatibility events. After identifying DNA oligos that are already contained within a local collection for reuse, the program estimates the total cost of direct synthesis and new oligos to be ordered. In the instance that j5 identifies putative assembly piece incompatibilities (multiple pieces with high flanking sequence homology), the program suggests hierarchical subassemblies where possible. The program outputs a comma-separated value (CSV) file, viewable via Excel or other spreadsheet software, that contains assembly design information (such as the PCR/SOE reactions to perform, their anticipated sizes and sequences, etc.) as well as a properly annotated genbank file containing the sequence resulting from the assembly, and appends the local oligo library with the oligos to be ordered j5 condenses multiple independent assembly projects into 96-well format for high-throughput liquid-handling robotics platforms, and generates configuration files for the PR-PR biology-friendly robot programming language. j5 thus provides a new way to design DNA assembly procedures much more productively and efficiently, not only in terms of time, but also in terms of cost. To a large extent, however, j5 does not allow people to do something that could not be done before by hand given enough time and effort. An exception to this is that, since the very act of using j5 to design the DNA assembly process standardizes the experimental details and workflow, j5 enables a single person to concurrently perform the independent DNA construction tasks of an entire group of researchers. Currently, this is not readily possible, since separate researchers employ disparate design strategies and workflows, and furthermore, their designs and workflows are very infrequently fully captured in an electronic format which is conducive to automation.« less

One-dimensional polaritons with size-tunable and enhanced coupling strengths in semiconductor nanowires.

PubMed

van Vugt, Lambert K; Piccione, Brian; Cho, Chang-Hee; Nukala, Pavan; Agarwal, Ritesh

2011-06-21

Strong coupling of light with excitons in direct bandgap semiconductors leads to the formation of composite photonic-electronic quasi-particles (polaritons), in which energy oscillates coherently between the photonic and excitonic states with the vacuum Rabi frequency. The light-matter coherence is maintained until the oscillator dephases or the photon escapes. Exciton-polariton formation has enabled the observation of Bose-Einstein condensation in the solid-state, low-threshold polariton lasing and is also useful for terahertz and slow-light applications. However, maintaining coherence for higher carrier concentration and temperature applications still requires increased coupling strengths. Here, we report on size-tunable, exceptionally high exciton-polariton coupling strengths characterized by a vacuum Rabi splitting of up to 200 meV as well as a reduction in group velocity, in surface-passivated, self-assembled semiconductor nanowire cavities. These experiments represent systematic investigations on light-matter coupling in one-dimensional optical nanocavities, demonstrating the ability to engineer light-matter coupling strengths at the nanoscale, even in non-quantum-confined systems, to values much higher than in bulk.

One-dimensional polaritons with size-tunable and enhanced coupling strengths in semiconductor nanowires

PubMed Central

van Vugt, Lambert K.; Piccione, Brian; Cho, Chang-Hee; Nukala, Pavan; Agarwal, Ritesh

2011-01-01

Strong coupling of light with excitons in direct bandgap semiconductors leads to the formation of composite photonic-electronic quasi-particles (polaritons), in which energy oscillates coherently between the photonic and excitonic states with the vacuum Rabi frequency. The light-matter coherence is maintained until the oscillator dephases or the photon escapes. Exciton-polariton formation has enabled the observation of Bose-Einstein condensation in the solid-state, low-threshold polariton lasing and is also useful for terahertz and slow-light applications. However, maintaining coherence for higher carrier concentration and temperature applications still requires increased coupling strengths. Here, we report on size-tunable, exceptionally high exciton-polariton coupling strengths characterized by a vacuum Rabi splitting of up to 200 meV as well as a reduction in group velocity, in surface-passivated, self-assembled semiconductor nanowire cavities. These experiments represent systematic investigations on light-matter coupling in one-dimensional optical nanocavities, demonstrating the ability to engineer light-matter coupling strengths at the nanoscale, even in non-quantum-confined systems, to values much higher than in bulk. PMID:21628582

The Large UV/Optical/Infrared Surveyor (LUVOIR): Decadal Mission concept technology development overview

NASA Astrophysics Data System (ADS)

Bolcar, Matthew R.

2017-09-01

The Large Ultraviolet / Optical / Infrared (LUVOIR) Surveyor is one of four large mission concept studies being developed by NASA for consideration in the 2020 Astrophysics Decadal Survey. LUVOIR will support a broad range of science objectives, including the direct imaging and spectral characterization of habitable exoplanets around sun-like stars, the study of galaxy formation and evolution, the epoch of reionization, star and planet formation, and the remote sensing of Solar System bodies. The LUVOIR Science and Technology Definition Team (STDT) has tasked a Technology Working Group (TWG), with more than 60 members from NASA centers, academia, industry, and international partners, with identifying technologies that enable or enhance the LUVOIR science mission. The TWG has identified such technologies in the areas of Coronagraphy, Ultra-Stable Opto-mechanical Systems, Detectors, Coatings, Starshades, and Instrument Components, and has completed a detailed assessment of the state-of-the-art. We present here a summary of this technology assessment effort, as well as the current progress in defining a technology development plan to mature these technologies to the required technology readiness level (TRL).

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

Singh, Sadanand; Pablo, Juan J. de

Recently, novel organic glassy materials that exhibit remarkable stability have been prepared by vapor deposition. The thermophysical properties of these new ''stable'' glasses are equivalent to those that common glasses would exhibit after aging over periods lasting thousands of years. The origin of such enhanced stability has been elusive; in the absence of detailed models, past studies have discussed the formation of new polyamorphs or that of nanocrystals to explain the observed behavior. In this work, an atomistic molecular model of trehalose, a disaccharide of glucose, is used to examine the properties of vapor-deposited stable glasses. Consistent with experiment, themore » model predicts the formation of stable glasses having a higher density, a lower enthalpy, and higher onset temperatures than those of the corresponding ''ordinary'' glass formed by quenching the bulk liquid. Simulations reveal that newly formed layers of the growing vapor-deposited film exhibit greater mobility than the remainder of the material, thereby enabling a reorganization of the film as it is grown. They also reveal that ''stable'' glasses exhibit a distinct layered structure in the direction normal to the substrate that is responsible for their unusual properties.« less

Structure Basis for Directional R-loop Formation and Substrate Handover Mechanisms in Type I CRISPR-Cas System.

PubMed

Xiao, Yibei; Luo, Min; Hayes, Robert P; Kim, Jonathan; Ng, Sherwin; Ding, Fang; Liao, Maofu; Ke, Ailong

2017-06-29

Type I CRISPR systems feature a sequential dsDNA target searching and degradation process, by crRNA-displaying Cascade and nuclease-helicase fusion enzyme Cas3, respectively. Here we present two cryo-EM snapshots of the Thermobifida fusca type I-E Cascade: (1) unwinding 11 bp of dsDNA at the seed-sequence region to scout for sequence complementarity, and (2) further unwinding of the entire protospacer to form a full R-loop. These structures provide the much-needed temporal and spatial resolution to resolve key mechanistic steps leading to Cas3 recruitment. In the early steps, PAM recognition causes severe DNA bending, leading to spontaneous DNA unwinding to form a seed-bubble. The full R-loop formation triggers conformational changes in Cascade, licensing Cas3 to bind. The same process also generates a bulge in the non-target DNA strand, enabling its handover to Cas3 for cleavage. The combination of both negative and positive checkpoints ensures stringent yet efficient target degradation in type I CRISPR-Cas systems. Copyright © 2017 Elsevier Inc. All rights reserved.

Temperature Dependence in Homogeneous and Heterogeneous Nucleation

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

McGraw R. L.; Winkler, P. M.; Wagner, P. E.

2017-08-01

Heterogeneous nucleation on stable (sub-2 nm) nuclei aids the formation of atmospheric cloud condensation nuclei (CCN) by circumventing or reducing vapor pressure barriers that would otherwise limit condensation and new particle growth. Aerosol and cloud formation depend largely on the interaction between a condensing liquid and the nucleating site. A new paper published this year reports the first direct experimental determination of contact angles as well as contact line curvature and other geometric properties of a spherical cap nucleus at nanometer scale using measurements from the Vienna Size Analyzing Nucleus Counter (SANC) (Winkler et al., 2016). For water nucleating heterogeneouslymore » on silver oxide nanoparticles we find contact angles around 15 degrees compared to around 90 degrees for the macroscopically measured equilibrium angle for water on bulk silver. The small microscopic contact angles can be attributed via the generalized Young equation to a negative line tension that becomes increasingly dominant with increasing curvature of the contact line. These results enable a consistent theoretical description of heterogeneous nucleation and provide firm insight to the wetting of nanosized objects.« less

Adding the 'heart' to hanging drop networks for microphysiological multi-tissue experiments.

PubMed

Rismani Yazdi, Saeed; Shadmani, Amir; Bürgel, Sebastian C; Misun, Patrick M; Hierlemann, Andreas; Frey, Olivier

2015-11-07

Microfluidic hanging-drop networks enable culturing and analysis of 3D microtissue spheroids derived from different cell types under controlled perfusion and investigating inter-tissue communication in multi-tissue formats. In this paper we introduce a compact on-chip pumping approach for flow control in hanging-drop networks. The pump includes one pneumatic chamber located directly above one of the hanging drops and uses the surface tension at the liquid-air-interface for flow actuation. Control of the pneumatic protocol provides a wide range of unidirectional pulsatile and continuous flow profiles. With the proposed concept several independent hanging-drop networks can be operated in parallel with only one single pneumatic actuation line at high fidelity. Closed-loop medium circulation between different organ models for multi-tissue formats and multiple simultaneous assays in parallel are possible. Finally, we implemented a real-time feedback control-loop of the pump actuation based on the beating of a human iPS-derived cardiac microtissue cultured in the same system. This configuration allows for simulating physiological effects on the heart and their impact on flow circulation between the organ models on chip.

Cloud Microphysics Parameterization in a Shallow Cumulus Cloud Simulated by a Largrangian Cloud Model

NASA Astrophysics Data System (ADS)

Oh, D.; Noh, Y.; Hoffmann, F.; Raasch, S.

2017-12-01

Lagrangian cloud model (LCM) is a fundamentally new approach of cloud simulation, in which the flow field is simulated by large eddy simulation and droplets are treated as Lagrangian particles undergoing cloud microphysics. LCM enables us to investigate raindrop formation and examine the parameterization of cloud microphysics directly by tracking the history of individual Lagrangian droplets simulated by LCM. Analysis of the magnitude of raindrop formation and the background physical conditions at the moment at which every Lagrangian droplet grows from cloud droplets to raindrops in a shallow cumulus cloud reveals how and under which condition raindrops are formed. It also provides information how autoconversion and accretion appear and evolve within a cloud, and how they are affected by various factors such as cloud water mixing ratio, rain water mixing ratio, aerosol concentration, drop size distribution, and dissipation rate. Based on these results, the parameterizations of autoconversion and accretion, such as Kessler (1969), Tripoli and Cotton (1980), Beheng (1994), and Kharioutdonov and Kogan (2000), are examined, and the modifications to improve the parameterizations are proposed.

FIR/THz Space Interferometry: Science Opportunities, Mission Concepts, and Technical Challenges

NASA Technical Reports Server (NTRS)

Leisawitz, David

2007-01-01

Sensitive far-IR imaging and spectroscopic measurements of astronomical objects on sub-arcsecond angular scales are essential to our understanding of star and planet formation, the formation and evolution of galaxies, and to the detection and characterization of extrasolar planets. Cold single-aperture telescopes in space, such as the Spitzer Space Telescope and the Herschel Space Observatory, are very sensitive, but they lack the necessary angular resolution by two or more orders of magnitude. Far-IR space interferometers will address this need in the coming decades. Several mission concepts have already been studied, including in the US the Space Infrared Interferometric Telescope (SPIRIT) and the more ambitious Submillimeter Probe of the Evolution of Cosmic Structure (SPECS). This talk will describe science goals and summarize alternative concepts for future FIR/THz space interferometry missions. Small arrays of sensitive, fast, direct detectors are a key enabling technology for SPIRIT and SPECS. I will describe the technology requirements for far-IR interferometry, including the detector requirements, and their derivation from the mission science goals and instrument concepts.

Lithium dendrite growth through solid polymer electrolyte membranes

NASA Astrophysics Data System (ADS)

Harry, Katherine; Schauser, Nicole; Balsara, Nitash

2015-03-01

Replacing the graphite-based anode in current batteries with a lithium foil will result in a qualitative increase in the energy density of lithium batteries. The primary reason for not adopting lithium-foil anodes is the formation of dendrites during cell charging. In this study, stop-motion X-ray microtomography experiments were used to directly monitor the growth of lithium dendrites during electrochemical cycling of symmetric lithium-lithium cells with a block copolymer electrolyte. In an attempt to understand the relationship between viscoelastic properties of the electrolyte on dendrite formation, a series of complementary experiments including cell cycling, tomography, ac impedance, and rheology, were conducted above and below the glass transition temperature of the non-conducting poly(styrene) block; the conducting phase is a mixture of rubbery poly(ethylene oxide) and a lithium salt. The tomography experiments enable quantification of the evolution of strain in the block copolymer electrolyte. Our work provides fundamental insight into the dynamics of electrochemical deposition of metallic films in contact with high modulus polymer electrolytes. Rational approaches for slowing down and, perhaps, eliminating dendrite growth are proposed.

Mechanistic insights into plasmonic photocatalysts in utilizing visible light.

PubMed

Leong, Kah Hon; Aziz, Azrina Abd; Sim, Lan Ching; Saravanan, Pichiah; Jang, Min; Bahnemann, Detlef

2018-01-01

The utilisation of sunlight as an abundant and renewable resource has motivated the development of sustainable photocatalysts that can collectively harvest visible light. However, the bottleneck in utilising the low energy photons has led to the discovery of plasmonic photocatalysts. The presence of noble metal on the plasmonic photocatalyst enables the harvesting of visible light through the unique characteristic features of the noble metal nanomaterials. Moreover, the formation of interfaces between noble metal particles and semiconductor materials further results in the formation of a Schottky junction. Thereby, the plasmonic characteristics have opened up a new direction in promoting an alternative path that can be of value to the society through sustainable development derived through energy available for all for diverse applications. We have comprehensively prepared this review to specifically focus on fundamental insights into plasmonic photocatalysts, various synthesis routes, together with their strengths and weaknesses, and the interaction of the plasmonic photocatalyst with pollutants as well as the role of active radical generation and identification. The review ends with a pinnacle insight into future perspectives regarding realistic applications of plasmonic photocatalysts.

The Large UV/Optical/Infrared Surveyor (LUVOIR): Decadal Mission Concept Technology Development Overview

NASA Technical Reports Server (NTRS)

Bolcar, Matthew R.

2017-01-01

The Large Ultraviolet / Optical / Infrared (LUVOIR) Surveyor is one of four large mission concept studies being developed by NASA for consideration in the 2020 Astrophysics Decadal Survey. LUVOIR will support a broad range of science objectives, including the direct imaging and spectral characterization of habitable exoplanets around sun-like stars, the study of galaxy formation and evolution, the epoch of reionization, star and planet formation, and the remote sensing of Solar System bodies. The LUVOIR Science and Technology Definition Team (STDT) has tasked a Technology Working Group (TWG), with more than 60 members from NASA centers, academia, industry, and international partners, with identifying technologies that enable or enhance the LUVOIR science mission. The TWG has identified such technologies in the areas of Coronagraphy, Ultra-Stable Opto-mechanical Systems, Detectors, Coatings, Starshades, and Instrument Components, and has completed a detailed assessment of the state-of-the-art. We present here a summary of this technology assessment effort, as well as the current progress in defining a technology development plan to mature these technologies to the required technology readiness level (TRL).

Lattice model for self-assembly with application to the formation of cytoskeletal-like structures

NASA Astrophysics Data System (ADS)

Stewman, Shannon F.; Dinner, Aaron R.

2007-07-01

We introduce a stochastic approach for self-assembly in systems far from equilibrium. The building blocks are represented by a lattice of discrete variables (Potts-like spins), and physically meaningful mechanisms are obtained by restricting transitions through spatially local rules based on experimental data. We use the method to study nucleation of filopodia-like bundles in a system consisting of purified actin, fascin, actin-related protein 2/3 , and beads coated with Wiskott-Aldrich syndrome protein. Consistent with previous speculation based on static experimental images, we find that bundles derive from Λ -precursor-like patterns of spins on the lattice. The ratcheting of the actin network relative to the surface that represents beads plays an important role in determining the number and orientation of bundles due to the fact that branching is the primary means for generating barbed ends pointed in directions that allow rapid filament growth. By enabling the de novo formation of coexisting morphologies without the computational cost of explicit representation of proteins, the approach introduced complements earlier models of cytoskeletal behavior in vitro and in vivo.

Probing Human Telomeric DNA and RNA Topology and Ligand Binding in a Cellular Model by Using Responsive Fluorescent Nucleoside Probes.

PubMed

Manna, Sudeshna; Panse, Cornelia H; Sontakke, Vyankat A; Sangamesh, Sarangamath; Srivatsan, Seergazhi G

2017-08-17

The development of biophysical systems that enable an understanding of the structure and ligand-binding properties of G-quadruplex (GQ)-forming nucleic acid sequences in cells or models that mimic the cellular environment would be highly beneficial in advancing GQ-directed therapeutic strategies. Herein, the establishment of a biophysical platform to investigate the structure and recognition properties of human telomeric (H-Telo) DNA and RNA repeats in a cell-like confined environment by using conformation-sensitive fluorescent nucleoside probes and a widely used cellular model, bis(2-ethylhexyl) sodium sulfosuccinate reverse micelles (RMs), is described. The 2'-deoxy and ribonucleoside probes, composed of a 5-benzofuran uracil base analogue, faithfully report the aqueous micellar core through changes in their fluorescence properties. The nucleoside probes incorporated into different loops of H-Telo DNA and RNA oligonucleotide repeats are minimally perturbing and photophysically signal the formation of respective GQ structures in both aqueous buffer and RMs. Furthermore, these sensors enable a direct comparison of the binding affinity of a ligand to H-Telo DNA and RNA GQ structures in the bulk and confined environment of RMs. These results demonstrate that this combination of a GQ nucleoside probe and easy-to-handle RMs could provide new opportunities to study and devise screening-compatible assays in a cell-like environment to discover GQ binders of clinical potential. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dynamic Receptor Team Formation Can Explain the High Signal Transduction Gain in Escherichia coli

PubMed Central

Albert, Réka; Chiu, Yu-wen; Othmer, Hans G.

2004-01-01

Evolution has provided many organisms with sophisticated sensory systems that enable them to respond to signals in their environment. The response frequently involves alteration in the pattern of movement, either by directed movement, a process called taxis, or by altering the speed or frequency of turning, which is called kinesis. Chemokinesis has been most thoroughly studied in the peritrichous bacterium Escherichia coli, which has four helical flagella distributed over the cell surface, and swims by rotating them. When rotated counterclockwise the flagella coalesce into a propulsive bundle, producing a relatively straight “run,” and when rotated clockwise they fly apart, resulting in a “tumble” which reorients the cell with little translocation. A stochastic process generates the runs and tumbles, and in a chemoeffector gradient, runs that carry the cell in a favorable direction are extended. The cell senses spatial gradients as temporal changes in receptor occupancy and changes the probability of counterclockwise rotation (the bias) on a fast timescale, but adaptation returns the bias to baseline on a slow timescale, enabling the cell to detect and respond to further concentration changes. The overall structure of the signal transduction pathways is well characterized in E. coli, but important details are still not understood. Only recently has a source of gain in the signal transduction network been identified experimentally, and here we present a mathematical model based on dynamic assembly of receptor teams that can explain this observation. PMID:15111386

Dynamic receptor team formation can explain the high signal transduction gain in Escherichia coli.

PubMed

Albert, Réka; Chiu, Yu-Wen; Othmer, Hans G

2004-05-01

Evolution has provided many organisms with sophisticated sensory systems that enable them to respond to signals in their environment. The response frequently involves alteration in the pattern of movement, either by directed movement, a process called taxis, or by altering the speed or frequency of turning, which is called kinesis. Chemokinesis has been most thoroughly studied in the peritrichous bacterium Escherichia coli, which has four helical flagella distributed over the cell surface, and swims by rotating them. When rotated counterclockwise the flagella coalesce into a propulsive bundle, producing a relatively straight "run," and when rotated clockwise they fly apart, resulting in a "tumble" which reorients the cell with little translocation. A stochastic process generates the runs and tumbles, and in a chemoeffector gradient, runs that carry the cell in a favorable direction are extended. The cell senses spatial gradients as temporal changes in receptor occupancy and changes the probability of counterclockwise rotation (the bias) on a fast timescale, but adaptation returns the bias to baseline on a slow timescale, enabling the cell to detect and respond to further concentration changes. The overall structure of the signal transduction pathways is well characterized in E. coli, but important details are still not understood. Only recently has a source of gain in the signal transduction network been identified experimentally, and here we present a mathematical model based on dynamic assembly of receptor teams that can explain this observation.

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

Aytug, Tolga; Lupini, Andrew R.; Jellison, Gerald E.

The design of multifunctional coatings impact impact the performance of many optical systems and components. Such coatings should be mechanically robust, and combine user-defined optical and wetting functions with scalable fabrication formulations. By taking cues from the properties of some natural biological structures, we report here the formation of low-refractive index antireflective glass films that embody omni-directional optical properties over a wide range of wavelengths, while also possessing specific wetting capabilities. The coatings comprise an interconnected network of nanoscale pores surrounded by a nanostructured silica framework. These structures result from a novel fabrication method that utilizes metastable spinodal phase separationmore » in glass-based materials. The approach not only enables design of surface microstructures with graded-index antireflection characteristics, where the surface reflection is suppressed through optical impedance matching between interfaces, but also facilitates self-cleaning ability through modification of the surface chemistry. Based on near complete elimination of Fresnel reflections (yielding >95% transmission through a single-side coated glass) and corresponding increase in broadband transmission, the fabricated nanostructured surfaces are found to promote a general and an invaluable ~3–7% relative increase in current output of multiple direct/indirect bandgap photovoltaic cells. Moreover, these antireflective surfaces also demonstrate superior resistance against mechanical wear and abrasion. Unlike conventional counterparts, the present antireflective coatings are essentially monolithic, enabling simultaneous realization of graded index anti-reflectivity, self-cleaning capability, and mechanical stability within the same surface. Moreover, the concept represents a fundamental basis for development of advanced coated optical quality products, especially where environmental exposure is required.« less

How Copper Nanowires Grow and How To Control Their Properties.

PubMed

Ye, Shengrong; Stewart, Ian E; Chen, Zuofeng; Li, Bo; Rathmell, Aaron R; Wiley, Benjamin J

2016-03-15

Scalable, solution-phase nanostructure synthesis has the promise to produce a wide variety of nanomaterials with novel properties at a cost that is low enough for these materials to be used to solve problems. For example, solution-synthesized metal nanowires are now being used to make low cost, flexible transparent electrodes in touch screens, organic light-emitting diodes (OLEDs), and solar cells. There has been a tremendous increase in the number of solution-phase syntheses that enable control over the assembly of atoms into nanowires in the last 15 years, but proposed mechanisms for nanowire formation are usually qualitative, and for many syntheses there is little consensus as to how nanowires form. It is often not clear what species is adding to a nanowire growing in solution or what mechanistic step limits its rate of growth. A deeper understanding of nanowire growth is important for efficiently directing the development of nanowire synthesis toward producing a wide variety of nanostructure morphologies for structure-property studies or producing precisely defined nanostructures for a specific application. This Account reviews our progress over the last five years toward understanding how copper nanowires form in solution, how to direct their growth into nanowires with dimensions ideally suited for use in transparent conducting films, and how to use copper nanowires as a template to grow core-shell nanowires. The key advance enabling a better understanding of copper nanowire growth is the first real-time visualization of nanowire growth in solution, enabling the acquisition of nanowire growth kinetics. By measuring the growth rate of individual nanowires as a function of concentration of the reactants and temperature, we show that a growing copper nanowire can be thought of as a microelectrode that is charged with electrons by hydrazine and grows through the diffusion-limited addition of Cu(OH)2(-). This deeper mechanistic understanding, coupled to an understanding of the structure-property relationship of nanowires in transparent conducting films, enabled the production of copper nanowires that can be coated from solution to make films with properties that rival the dominant transparent conductor, indium tin oxide. Finally, we show how copper nanowires can be coated with Zn, Sn, In, Ni, Co, Ag, Au, and Pt to protect them from oxidation or enable their use as transparent electrocatalysts.

Digital direct electron imaging of energy-filtered electron backscatter diffraction patterns

NASA Astrophysics Data System (ADS)

Vespucci, S.; Winkelmann, A.; Naresh-Kumar, G.; Mingard, K. P.; Maneuski, D.; Edwards, P. R.; Day, A. P.; O'Shea, V.; Trager-Cowan, C.

2015-11-01

Electron backscatter diffraction is a scanning electron microscopy technique used to obtain crystallographic information on materials. It allows the nondestructive mapping of crystal structure, texture, and strain with a lateral and depth resolution on the order of tens of nanometers. Electron backscatter diffraction patterns (EBSPs) are presently acquired using a detector comprising a scintillator coupled to a digital camera, and the crystallographic information obtainable is limited by the conversion of electrons to photons and then back to electrons again. In this article we will report the direct acquisition of energy-filtered EBSPs using a digital complementary metal-oxide-semiconductor hybrid pixel detector, Timepix. We show results from a range of samples with different mass and density, namely diamond, silicon, and GaN. Direct electron detection allows the acquisition of EBSPs at lower (≤5 keV) electron beam energies. This results in a reduction in the depth and lateral extension of the volume of the specimen contributing to the pattern and will lead to a significant improvement in lateral and depth resolution. Direct electron detection together with energy filtering (electrons having energy below a specific value are excluded) also leads to an improvement in spatial resolution but in addition provides an unprecedented increase in the detail in the acquired EBSPs. An increase in contrast and higher-order diffraction features are observed. In addition, excess-deficiency effects appear to be suppressed on energy filtering. This allows the fundamental physics of pattern formation to be interrogated and will enable a step change in the use of electron backscatter diffraction (EBSD) for crystal phase identification and the mapping of strain. The enhancement in the contrast in high-pass energy-filtered EBSD patterns is found to be stronger for lighter, less dense materials. The improved contrast for such materials will enable the application of the EBSD technique to be expanded to materials for which conventional EBSD analysis is not presently practicable.

Direct observation of a single nanoparticle-ubiquitin corona formation

NASA Astrophysics Data System (ADS)

Ding, Feng; Radic, Slaven; Chen, Ran; Chen, Pengyu; Geitner, Nicholas K.; Brown, Jared M.; Ke, Pu Chun

2013-09-01

The advancement of nanomedicine and the increasing applications of nanoparticles in consumer products have led to administered biological exposure and unintentional environmental accumulation of nanoparticles, causing concerns over the biocompatibility and sustainability of nanotechnology. Upon entering physiological environments, nanoparticles readily assume the form of a nanoparticle-protein corona that dictates their biological identity. Consequently, understanding the structure and dynamics of a nanoparticle-protein corona is essential for predicting the fate, transport, and toxicity of nanomaterials in living systems and for enabling the vast applications of nanomedicine. Here we combined multiscale molecular dynamics simulations and complementary experiments to characterize the silver nanoparticle-ubiquitin corona formation. Notably, ubiquitins competed with citrates for the nanoparticle surface, governed by specific electrostatic interactions. Under a high protein/nanoparticle stoichiometry, ubiquitins formed a multi-layer corona on the particle surface. The binding exhibited an unusual stretched-exponential behavior, suggesting a rich binding kinetics. Furthermore, the binding destabilized the α-helices while increasing the β-sheet content of the proteins. This study revealed the atomic and molecular details of the structural and dynamic characteristics of nanoparticle-protein corona formation.The advancement of nanomedicine and the increasing applications of nanoparticles in consumer products have led to administered biological exposure and unintentional environmental accumulation of nanoparticles, causing concerns over the biocompatibility and sustainability of nanotechnology. Upon entering physiological environments, nanoparticles readily assume the form of a nanoparticle-protein corona that dictates their biological identity. Consequently, understanding the structure and dynamics of a nanoparticle-protein corona is essential for predicting the fate, transport, and toxicity of nanomaterials in living systems and for enabling the vast applications of nanomedicine. Here we combined multiscale molecular dynamics simulations and complementary experiments to characterize the silver nanoparticle-ubiquitin corona formation. Notably, ubiquitins competed with citrates for the nanoparticle surface, governed by specific electrostatic interactions. Under a high protein/nanoparticle stoichiometry, ubiquitins formed a multi-layer corona on the particle surface. The binding exhibited an unusual stretched-exponential behavior, suggesting a rich binding kinetics. Furthermore, the binding destabilized the α-helices while increasing the β-sheet content of the proteins. This study revealed the atomic and molecular details of the structural and dynamic characteristics of nanoparticle-protein corona formation. Electronic supplementary information (ESI) available: Experimental and computational methods as well as supporting figures. See DOI: 10.1039/c3nr02147e

Venous-derived angioblasts generate organ-specific vessels during zebrafish embryonic development.

PubMed

Hen, Gideon; Nicenboim, Julian; Mayseless, Oded; Asaf, Lihee; Shin, Masahiro; Busolin, Giorgia; Hofi, Roy; Almog, Gabriella; Tiso, Natascia; Lawson, Nathan D; Yaniv, Karina

2015-12-15

Formation and remodeling of vascular beds are complex processes orchestrated by multiple signaling pathways. Although it is well accepted that vessels of a particular organ display specific features that enable them to fulfill distinct functions, the embryonic origins of tissue-specific vessels and the molecular mechanisms regulating their formation are poorly understood. The subintestinal plexus of the zebrafish embryo comprises vessels that vascularize the gut, liver and pancreas and, as such, represents an ideal model in which to investigate the early steps of organ-specific vessel formation. Here, we show that both arterial and venous components of the subintestinal plexus originate from a pool of specialized angioblasts residing in the floor of the posterior cardinal vein (PCV). Using live imaging of zebrafish embryos, in combination with photoconvertable transgenic reporters, we demonstrate that these angioblasts undergo two phases of migration and differentiation. Initially, a subintestinal vein forms and expands ventrally through a Bone Morphogenetic Protein-dependent step of collective migration. Concomitantly, a Vascular Endothelial Growth Factor-dependent shift in the directionality of migration, coupled to the upregulation of arterial markers, is observed, which culminates with the generation of the supraintestinal artery. Together, our results establish the zebrafish subintestinal plexus as an advantageous model for the study of organ-specific vessel development and provide new insights into the molecular mechanisms controlling its formation. More broadly, our findings suggest that PCV-specialized angioblasts contribute not only to the formation of the early trunk vasculature, but also to the establishment of late-forming, tissue-specific vascular beds. © 2015. Published by The Company of Biologists Ltd.

Disaggregation and separation dynamics of magnetic particles in a microfluidic flow under an alternating gradient magnetic field

NASA Astrophysics Data System (ADS)

Cao, Quanliang; Li, Zhenhao; Wang, Zhen; Qi, Fan; Han, Xiaotao

2018-05-01

How to prevent particle aggregation in the magnetic separation process is of great importance for high-purity separation, while it is a challenging issue in practice. In this work, we report a novel method to solve this problem for improving the selectivity of size-based separation by use of a gradient alternating magnetic field. The specially designed magnetic field is capable of dynamically adjusting the magnetic field direction without changing the direction of magnetic gradient force acting on the particles. Using direct numerical simulations, we show that particles within a certain center-to-center distance are inseparable under a gradient static magnetic field since they are easy aggregated and then start moving together. By contrast, it has been demonstrated that alternating repulsive and attractive interaction forces between particles can be generated to avoid the formation of aggregations when the alternating gradient magnetic field with a given alternating frequency is applied, enabling these particles to be continuously separated based on size-dependent properties. The proposed magnetic separation method and simulation results have the significance for fundamental understanding of particle dynamic behavior and improving the separation efficiency.

Grand canonical electronic density-functional theory: Algorithms and applications to electrochemistry

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

Sundararaman, Ravishankar; Goddard, III, William A.; Arias, Tomas A.

First-principles calculations combining density-functional theory and continuum solvation models enable realistic theoretical modeling and design of electrochemical systems. When a reaction proceeds in such systems, the number of electrons in the portion of the system treated quantum mechanically changes continuously, with a balancing charge appearing in the continuum electrolyte. A grand-canonical ensemble of electrons at a chemical potential set by the electrode potential is therefore the ideal description of such systems that directly mimics the experimental condition. We present two distinct algorithms: a self-consistent field method and a direct variational free energy minimization method using auxiliary Hamiltonians (GC-AuxH), to solvemore » the Kohn-Sham equations of electronic density-functional theory directly in the grand canonical ensemble at fixed potential. Both methods substantially improve performance compared to a sequence of conventional fixed-number calculations targeting the desired potential, with the GC-AuxH method additionally exhibiting reliable and smooth exponential convergence of the grand free energy. Lastly, we apply grand-canonical density-functional theory to the under-potential deposition of copper on platinum from chloride-containing electrolytes and show that chloride desorption, not partial copper monolayer formation, is responsible for the second voltammetric peak.« less

Direct Depth- and Lateral- Imaging of Nanoscale Magnets Generated by Ion Impact

PubMed Central

Röder, Falk; Hlawacek, Gregor; Wintz, Sebastian; Hübner, René; Bischoff, Lothar; Lichte, Hannes; Potzger, Kay; Lindner, Jürgen; Fassbender, Jürgen; Bali, Rantej

2015-01-01

Nanomagnets form the building blocks for a variety of spin-transport, spin-wave and data storage devices. In this work we generated nanoscale magnets by exploiting the phenomenon of disorder-induced ferromagnetism; disorder was induced locally on a chemically ordered, initially non-ferromagnetic, Fe60Al40 precursor film using  nm diameter beam of Ne+ ions at 25 keV energy. The beam of energetic ions randomized the atomic arrangement locally, leading to the formation of ferromagnetism in the ion-affected regime. The interaction of a penetrating ion with host atoms is known to be spatially inhomogeneous, raising questions on the magnetic homogeneity of nanostructures caused by ion-induced collision cascades. Direct holographic observations of the flux-lines emergent from the disorder-induced magnetic nanostructures were made in order to measure the depth- and lateral- magnetization variation at ferromagnetic/non-ferromagnetic interfaces. Our results suggest that high-resolution nanomagnets of practically any desired 2-dimensional geometry can be directly written onto selected alloy thin films using a nano-focussed ion-beam stylus, thus enabling the rapid prototyping and testing of novel magnetization configurations for their magneto-coupling and spin-wave properties. PMID:26584789

Grand canonical electronic density-functional theory: Algorithms and applications to electrochemistry.

PubMed

Sundararaman, Ravishankar; Goddard, William A; Arias, Tomas A

2017-03-21

First-principles calculations combining density-functional theory and continuum solvation models enable realistic theoretical modeling and design of electrochemical systems. When a reaction proceeds in such systems, the number of electrons in the portion of the system treated quantum mechanically changes continuously, with a balancing charge appearing in the continuum electrolyte. A grand-canonical ensemble of electrons at a chemical potential set by the electrode potential is therefore the ideal description of such systems that directly mimics the experimental condition. We present two distinct algorithms: a self-consistent field method and a direct variational free energy minimization method using auxiliary Hamiltonians (GC-AuxH), to solve the Kohn-Sham equations of electronic density-functional theory directly in the grand canonical ensemble at fixed potential. Both methods substantially improve performance compared to a sequence of conventional fixed-number calculations targeting the desired potential, with the GC-AuxH method additionally exhibiting reliable and smooth exponential convergence of the grand free energy. Finally, we apply grand-canonical density-functional theory to the under-potential deposition of copper on platinum from chloride-containing electrolytes and show that chloride desorption, not partial copper monolayer formation, is responsible for the second voltammetric peak.

Digital-Direct-RT-PCR: a sensitive and specific method for quantification of CTC in patients with cervical carcinoma.

PubMed

Pfitzner, Claudia; Schröder, Isabel; Scheungraber, Cornelia; Dogan, Askin; Runnebaum, Ingo Bernhard; Dürst, Matthias; Häfner, Norman

2014-02-05

The detection of circulating tumour cells (CTC) in cancer patients may be useful for therapy monitoring and prediction of relapse. A sensitive assay based on HPV-oncogene transcripts which are highly specific for cervical cancer cells was established. The Digital-Direct-RT-PCR (DD-RT-PCR) combines Ficoll-separation, ThinPrep-fixation and one-step RT-PCR in a low-throughput digital-PCR format enabling the direct analysis and detection of individual CTC without RNA isolation. Experimental samples demonstrated a sensitivity of one HPV-positive cell in 500,000 HPV-negative cells. Spike-in experiments with down to 5 HPV-positive cells per millilitre EDTA-blood resulted in concordant positive results by PCR and immunocytochemistry. Blood samples from 3 of 10 CxCa patients each contained a single HPV-oncogene transcript expressing CTC among 5 to 15*10(5) MNBC. Only 1 of 7 patients with local but 2 of 3 women with systemic disease had CTC. This highly sensitive DD-RT-PCR for the detection of CTC may also be applied to other tumour entities which express tumour-specific transcripts.

In situ observations of the atomistic mechanisms of Ni catalyzed low temperature graphene growth.

PubMed

Patera, Laerte L; Africh, Cristina; Weatherup, Robert S; Blume, Raoul; Bhardwaj, Sunil; Castellarin-Cudia, Carla; Knop-Gericke, Axel; Schloegl, Robert; Comelli, Giovanni; Hofmann, Stephan; Cepek, Cinzia

2013-09-24

The key atomistic mechanisms of graphene formation on Ni for technologically relevant hydrocarbon exposures below 600 °C are directly revealed via complementary in situ scanning tunneling microscopy and X-ray photoelectron spectroscopy. For clean Ni(111) below 500 °C, two different surface carbide (Ni2C) conversion mechanisms are dominant which both yield epitaxial graphene, whereas above 500 °C, graphene predominantly grows directly on Ni(111) via replacement mechanisms leading to embedded epitaxial and/or rotated graphene domains. Upon cooling, additional carbon structures form exclusively underneath rotated graphene domains. The dominant graphene growth mechanism also critically depends on the near-surface carbon concentration and hence is intimately linked to the full history of the catalyst and all possible sources of contamination. The detailed XPS fingerprinting of these processes allows a direct link to high pressure XPS measurements of a wide range of growth conditions, including polycrystalline Ni catalysts and recipes commonly used in industrial reactors for graphene and carbon nanotube CVD. This enables an unambiguous and consistent interpretation of prior literature and an assessment of how the quality/structure of as-grown carbon nanostructures relates to the growth modes.

Grand canonical electronic density-functional theory: Algorithms and applications to electrochemistry

DOE PAGES

Sundararaman, Ravishankar; Goddard, III, William A.; Arias, Tomas A.

2017-03-16

First-principles calculations combining density-functional theory and continuum solvation models enable realistic theoretical modeling and design of electrochemical systems. When a reaction proceeds in such systems, the number of electrons in the portion of the system treated quantum mechanically changes continuously, with a balancing charge appearing in the continuum electrolyte. A grand-canonical ensemble of electrons at a chemical potential set by the electrode potential is therefore the ideal description of such systems that directly mimics the experimental condition. We present two distinct algorithms: a self-consistent field method and a direct variational free energy minimization method using auxiliary Hamiltonians (GC-AuxH), to solvemore » the Kohn-Sham equations of electronic density-functional theory directly in the grand canonical ensemble at fixed potential. Both methods substantially improve performance compared to a sequence of conventional fixed-number calculations targeting the desired potential, with the GC-AuxH method additionally exhibiting reliable and smooth exponential convergence of the grand free energy. Lastly, we apply grand-canonical density-functional theory to the under-potential deposition of copper on platinum from chloride-containing electrolytes and show that chloride desorption, not partial copper monolayer formation, is responsible for the second voltammetric peak.« less

Hydrodynamical processes in planet-forming accretion disks

NASA Astrophysics Data System (ADS)

Lin, Min-Kai

Understanding the physics of accretion flows in circumstellar disk provides the foundation to any theory of planet formation. The last few years have witnessed dramatic a revision in the fundamental fluid dynamics of protoplanetary accretion disks. There is growing evidence that the key to answering some of the most pressing questions, such as the origin of disk turbulence, mass transport, and planetesimal formation, may lie within, and intimately linked to, purely hydrodynamical processes in protoplanetary disks. Recent studies, including those from the proposal team, have discovered and highlighted the significance of several new hydrodynamical instabilities in the planet-forming regions of these disks. These include, but not limited to: the vertical shear instability, active between 10 to 100 AU; the zombie vortex instability, operating in regions interior to about 1AU; and the convective over-stability at intermediate radii. Secondary Rossbywave and elliptic instabilities may also be triggered, feeding off the structures that emerge from the above primary instabilities. The result of these hydrodynamic processes range from small-scale turbulence that transports angular momentum, to large-scale vortices that concentrate dust particles and enhance planetesimal formation. Hydrodynamic processes pertain to a wide range of disk conditions, meaning that at least one of these processes are active at any given disk location and evolutionary epoch. This remains true even after planet formation, which affects their subsequent orbital evolution. Hydrodynamical processes also have direct observable consequences. For example, vortices have being invoked to explain recent ALMA images of asymmetric `dust-traps' in transition disks. Hydrodynamic activities thus play a crucial role at every stage of planet formation and disk evolution. We propose to develop theoretical models of the above hydrodynamic processes under physical disk conditions by properly accounting for disk thermodynamics, dust dynamics, disk self-gravity and three-dimensional effects. By including these effects, we go wellbeyond previous works based on idealized disk models. This effort is necessary to understand how these instabilities operate and interact in realistic protoplanetary disks. This will enable us to provide a unified picture of how various hydrodynamic activities fit together to drive global disk evolution. We will address key questions including the strength of the resulting hydrodynamic turbulence, the lifetime of large-scale vortices under realistic disk conditions, and their impact on the evolution of solids within the disk. Inclusion of these additional physics will likely uncover new, yet-unknown hydrodynamic processes. Our generalized models enables a direct link between theory and observations. For example, a self-consistent incorporation of dust dynamics into the theory of hydrodynamic instabilities is particularly important, since it is the dust component that is usually observed. We will also establish the connection between the properties of large-scale, observable structures such as vortices, to the underlying disk properties, such as disk mass, and vertical structure, which are difficult to infer directly from observations. We also propose to study, for the first time, the dynamical interaction between hydrodynamic turbulence and proto-planets, as well as the influence of largescale vortices on disk-planet interaction. This is necessary towards a realistic modeling of the orbital evolution of proto planets, and thus in predicting the final architecture of planetary systems. The proposal team's expertise and experience, ranging from mathematical analyses to state-of the-art numerical simulations in astrophysical fluid dynamics, provides a multi-method approach to these problems. This is necessary towards establishing a rigorous understanding of these fundamental hydrodynamical processes in protoplanetary accretion disks.

Phospholipid micelle-based magneto-plasmonic nanoformulation for magnetic field-directed, imaging-guided photo-induced cancer therapy.

PubMed

Ohulchanskyy, Tymish Y; Kopwitthaya, Atcha; Jeon, Mansik; Guo, Moran; Law, Wing-Cheung; Furlani, Edward P; Kim, Chulhong; Prasad, Paras N

2013-11-01

We present a magnetoplasmonic nanoplatform combining gold nanorods (GNR) and iron-oxide nanoparticles within phospholipid-based polymeric nanomicelles (PGRFe). The gold nanorods exhibit plasmon resonance absorbance at near infrared wavelengths to enable photoacoustic imaging and photothermal therapy, while the Fe3O4 nanoparticles enable magnetophoretic control of the nanoformulation. The fabricated nanoformulation can be directed and concentrated by an external magnetic field, which provides enhancement of a photoacoustic signal. Application of an external field also leads to enhanced uptake of the magnetoplasmonic formulation by cancer cells in vitro. Under laser irradiation at the wavelength of the GNR absorption peak, the PGRFe formulation efficiently generates plasmonic nanobubbles within cancer cells, as visualized by confocal microscopy, causing cell destruction. The combined magnetic and plasmonic functionalities of the nanoplatform enable magnetic field-directed, imaging-guided, enhanced photo-induced cancer therapy. In this study, a nano-formulation of gold nanorods and iron oxide nanoparticles is presented using a phospholipid micelle-based delivery system for magnetic field-directed and imaging-guided photo-induced cancer therapy. The gold nanorods enable photoacoustic imaging and photothermal therapy, while the Fe3O4 nanoparticles enable magnetophoretic control of the formulation. This and similar systems could enable more precise and efficient cancer therapy, hopefully in the near future, after additional testing. Copyright © 2013 Elsevier Inc. All rights reserved.

XML schemas for common bioinformatic data types and their application in workflow systems.

PubMed

Seibel, Philipp N; Krüger, Jan; Hartmeier, Sven; Schwarzer, Knut; Löwenthal, Kai; Mersch, Henning; Dandekar, Thomas; Giegerich, Robert

2006-11-06

Today, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create such workflows, the tools involved have to be able to work with each other's data--therefore, a common set of well-defined data formats is needed. Unfortunately, current bioinformatic tools use a great variety of heterogeneous formats. Acknowledging the need for common formats, the Helmholtz Open BioInformatics Technology network (HOBIT) identified several basic data types used in bioinformatics and developed appropriate format descriptions, formally defined by XML schemas, and incorporated them in a Java library (BioDOM). These schemas currently cover sequence, sequence alignment, RNA secondary structure and RNA secondary structure alignment formats in a form that is independent of any specific program, thus enabling seamless interoperation of different tools. All XML formats are available at http://bioschemas.sourceforge.net, the BioDOM library can be obtained at http://biodom.sourceforge.net. The HOBIT XML schemas and the BioDOM library simplify adding XML support to newly created and existing bioinformatic tools, enabling these tools to interoperate seamlessly in workflow scenarios.

Plasma membrane H+-ATPase regulation is required for auxin gradient formation preceding phototropic growth

PubMed Central

Hohm, Tim; Demarsy, Emilie; Quan, Clément; Allenbach Petrolati, Laure; Preuten, Tobias; Vernoux, Teva; Bergmann, Sven; Fankhauser, Christian

2014-01-01

Phototropism is a growth response allowing plants to align their photosynthetic organs toward incoming light and thereby to optimize photosynthetic activity. Formation of a lateral gradient of the phytohormone auxin is a key step to trigger asymmetric growth of the shoot leading to phototropic reorientation. To identify important regulators of auxin gradient formation, we developed an auxin flux model that enabled us to test in silico the impact of different morphological and biophysical parameters on gradient formation, including the contribution of the extracellular space (cell wall) or apoplast. Our model indicates that cell size, cell distributions, and apoplast thickness are all important factors affecting gradient formation. Among all tested variables, regulation of apoplastic pH was the most important to enable the formation of a lateral auxin gradient. To test this prediction, we interfered with the activity of plasma membrane H+-ATPases that are required to control apoplastic pH. Our results show that H+-ATPases are indeed important for the establishment of a lateral auxin gradient and phototropism. Moreover, we show that during phototropism, H+-ATPase activity is regulated by the phototropin photoreceptors, providing a mechanism by which light influences apoplastic pH. PMID:25261457

An integrated healthcare information system for end-to-end standardized exchange and homogeneous management of digital ECG formats.

PubMed

Trigo, Jesús Daniel; Martínez, Ignacio; Alesanco, Alvaro; Kollmann, Alexander; Escayola, Javier; Hayn, Dieter; Schreier, Günter; García, José

2012-07-01

This paper investigates the application of the enterprise information system (EIS) paradigm to standardized cardiovascular condition monitoring. There are many specifications in cardiology, particularly in the ECG standardization arena. The existence of ECG formats, however, does not guarantee the implementation of homogeneous, standardized solutions for ECG management. In fact, hospital management services need to cope with various ECG formats and, moreover, several different visualization applications. This heterogeneity hampers the normalization of integrated, standardized healthcare information systems, hence the need for finding an appropriate combination of ECG formats and a suitable EIS-based software architecture that enables standardized exchange and homogeneous management of ECG formats. Determining such a combination is one objective of this paper. The second aim is to design and develop the integrated healthcare information system that satisfies the requirements posed by the previous determination. The ECG formats selected include ISO/IEEE11073, Standard Communications Protocol for Computer-Assisted Electrocardiography, and an ECG ontology. The EIS-enabling techniques and technologies selected include web services, simple object access protocol, extensible markup language, or business process execution language. Such a selection ensures the standardized exchange of ECGs within, or across, healthcare information systems while providing modularity and accessibility.

Direct writing of metal nanostructures: lithographic tools for nanoplasmonics research.

PubMed

Leggett, Graham J

2011-03-22

Continued progress in the fast-growing field of nanoplasmonics will require the development of new methods for the fabrication of metal nanostructures. Optical lithography provides a continually expanding tool box. Two-photon processes, as demonstrated by Shukla et al. (doi: 10.1021/nn103015g), enable the fabrication of gold nanostructures encapsulated in dielectric material in a simple, direct process and offer the prospect of three-dimensional fabrication. At higher resolution, scanning probe techniques enable nanoparticle particle placement by localized oxidation, and near-field sintering of nanoparticulate films enables direct writing of nanowires. Direct laser "printing" of single gold nanoparticles offers a remarkable capability for the controlled fabrication of model structures for fundamental studies, particle-by-particle. Optical methods continue to provide a powerful support for research into metamaterials.

Grouper: a compact, streamable triangle mesh data structure.

PubMed

Luffel, Mark; Gurung, Topraj; Lindstrom, Peter; Rossignac, Jarek

2014-01-01

We present Grouper: an all-in-one compact file format, random-access data structure, and streamable representation for large triangle meshes. Similarly to the recently published SQuad representation, Grouper represents the geometry and connectivity of a mesh by grouping vertices and triangles into fixed-size records, most of which store two adjacent triangles and a shared vertex. Unlike SQuad, however, Grouper interleaves geometry with connectivity and uses a new connectivity representation to ensure that vertices and triangles can be stored in a coherent order that enables memory-efficient sequential stream processing. We present a linear-time construction algorithm that allows streaming out Grouper meshes using a small memory footprint while preserving the initial ordering of vertices. As a part of this construction, we show how the problem of assigning vertices and triangles to groups reduces to a well-known NP-hard optimization problem, and present a simple yet effective heuristic solution that performs well in practice. Our array-based Grouper representation also doubles as a triangle mesh data structure that allows direct access to vertices and triangles. Storing only about two integer references per triangle--i.e., less than the three vertex references stored with each triangle in a conventional indexed mesh format--Grouper answers both incidence and adjacency queries in amortized constant time. Our compact representation enables data-parallel processing on multicore computers, instant partitioning and fast transmission for distributed processing, as well as efficient out-of-core access. We demonstrate the versatility and performance benefits of Grouper using a suite of example meshes and processing kernels.

Biocatalytic Self-Assembly on Magnetic Nanoparticles.

PubMed

Conte, Maria P; Sahoo, Jugal Kishore; Abul-Haija, Yousef M; Lau, K H Aaron; Ulijn, Rein V

2018-01-24

Combining (bio)catalysis and molecular self-assembly provides an effective approach for the production and processing of self-assembled materials by exploiting catalysis to direct the assembly kinetics and hence controlling the formation of ordered nanostructures. Applications of (bio)catalytic self-assembly in biologically interfacing systems and in nanofabrication have recently been reported. Inspired by self-assembly in biological cells, efforts to confine catalysts on flat or patterned surfaces to exert spatial control over molecular gelator generation and nanostructure self-assembly have also emerged. Building on our previous work in the area, we demonstrate in this report the use of enzymes immobilized onto magnetic nanoparticles (NPs) to spatially localize the initiation of peptide self-assembly into nanofibers around NPs. The concept is generalized for both an equilibrium biocatalytic system that forms stable hydrogels and a nonequilibrium system that normally has a preset lifetime. Characterization of the hydrogels shows that self-assembly occurs at the site of enzyme immobilization on the NPs to give rise to gels with a "hub-and-spoke" morphology, where the nanofibers are linked through the enzyme-NP conjugates. This NP-controlled arrangement of self-assembled nanofibers enables both remarkable enhancements in the shear strength of hydrogel systems and a dramatic extension of the hydrogel stability in the nonequilibrium system. We are also able to show that the use of magnetic NPs enables the external control of both the formation of the hydrogel and its overall structure by application of an external magnetic field. We anticipate that the enhanced properties and stimuli-responsiveness of our NP-enzyme system will have applications ranging from nanomaterial fabrication to biomaterials and biosensing.

Grouper: A Compact, Streamable Triangle Mesh Data Structure

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

Luffel, Mark; Gurung, Topraj; Lindstrom, Peter

2014-01-01

Here, we present Grouper: an all-in-one compact file format, random-access data structure, and streamable representation for large triangle meshes. Similarly to the recently published SQuad representation, Grouper represents the geometry and connectivity of a mesh by grouping vertices and triangles into fixed-size records, most of which store two adjacent triangles and a shared vertex. Unlike SQuad, however, Grouper interleaves geometry with connectivity and uses a new connectivity representation to ensure that vertices and triangles can be stored in a coherent order that enables memory-efficient sequential stream processing. We also present a linear-time construction algorithm that allows streaming out Grouper meshesmore » using a small memory footprint while preserving the initial ordering of vertices. In this construction, we show how the problem of assigning vertices and triangles to groups reduces to a well-known NP-hard optimization problem, and present a simple yet effective heuristic solution that performs well in practice. Our array-based Grouper representation also doubles as a triangle mesh data structure that allows direct access to vertices and triangles. Storing only about two integer references per triangle-i.e., less than the three vertex references stored with each triangle in a conventional indexed mesh format-Grouper answers both incidence and adjacency queries in amortized constant time. Our compact representation enables data-parallel processing on multicore computers, instant partitioning and fast transmission for distributed processing, as well as efficient out-of-core access. We demonstrate the versatility and performance benefits of Grouper using a suite of example meshes and processing kernels.« less

Demotivating infant feeding counselling encounters in southern Africa: do counsellors need more or different training?

PubMed

Buskens, I; Jaffe, A

2008-03-01

Ethnographic research was conducted in eleven low-resource settings across Swaziland, Namibia and South Africa to explore how the perceptions and experiences of counselling health workers, pregnant women and recent mothers could be used to improve infant feeding counselling in the context of mother to child transmission (MTCT) of HIV. We found many counselling encounters to be demotivating. Mothers often reported feeling judged, stigmatised and shamed. Counsellors complained of mothers' poor compliance and passive resistance and reported suffering from stress, depression and burnout. We observed a rift between the mothers and counselling nurses, with both parties holding opposing agendas grounded in conflicting realities, expectations, experiences and needs. While the clients framed the visit as a consultation, counsellors framed it as health education, towards one exclusive purpose; to save the baby. Two communication modes prevailed in the counselling encounter: in theory, the counselling format was non-directive and client-centred but, in practice, most encounters reverted to information-based health education. Neither counselling format enabled the counsellors to acknowledge the reality of the two opposing agendas in the conversation and manage its dynamics. In order to achieve success - which, for the health service, is framed as persuading mothers to test for HIV and disclose the result - counsellors often felt compelled to be prescriptive and authoritative and reverted at times to confronting, judging and shaming mothers. Yet to adhere to their feeding choice consistently, mothers need to be motivated towards the significant behaviour change that this implies: to change their traditional roles and identities as women. For infant feeding counselling in the context of HIV/AIDS to become effective in southern Africa, a different format is therefore required; one that can acknowledge and manage these opposing agendas and conflicting realities and also enable counsellors to motivate mothers to make significant behaviour change.

Early science from the Pan-STARRS1 Optical Galaxy Survey (POGS): Maps of stellar mass and star formation rate surface density obtained from distributed-computing pixel-SED fitting

NASA Astrophysics Data System (ADS)

Thilker, David A.; Vinsen, K.; Galaxy Properties Key Project, PS1

2014-01-01

To measure resolved galactic physical properties unbiased by the mask of recent star formation and dust features, we are conducting a citizen-scientist enabled nearby galaxy survey based on the unprecedented optical (g,r,i,z,y) imaging from Pan-STARRS1 (PS1). The PS1 Optical Galaxy Survey (POGS) covers 3π steradians (75% of the sky), about twice the footprint of SDSS. Whenever possible we also incorporate ancillary multi-wavelength image data from the ultraviolet (GALEX) and infrared (WISE, Spitzer) spectral regimes. For each cataloged nearby galaxy with a reliable redshift estimate of z < 0.05 - 0.1 (dependent on donated CPU power), publicly-distributed computing is being harnessed to enable pixel-by-pixel spectral energy distribution (SED) fitting, which in turn provides maps of key physical parameters such as the local stellar mass surface density, crude star formation history, and dust attenuation. With pixel SED fitting output we will then constrain parametric models of galaxy structure in a more meaningful way than ordinarily achieved. In particular, we will fit multi-component (e.g. bulge, bar, disk) galaxy models directly to the distribution of stellar mass rather than surface brightness in a single band, which is often locally biased. We will also compute non-parametric measures of morphology such as concentration, asymmetry using the POGS stellar mass and SFR surface density images. We anticipate studying how galactic substructures evolve by comparing our results with simulations and against more distant imaging surveys, some of which which will also be processed in the POGS pipeline. The reliance of our survey on citizen-scientist volunteers provides a world-wide opportunity for education. We developed an interactive interface which highlights the science being produced by each volunteer’s own CPU cycles. The POGS project has already proven popular amongst the public, attracting about 5000 volunteers with nearly 12,000 participating computers, and is growing rapidly.

Route Network Construction with Location-Direction-Enabled Photographs

NASA Astrophysics Data System (ADS)

Fujita, Hideyuki; Sagara, Shota; Ohmori, Tadashi; Shintani, Takahiko

2018-05-01

We propose a method for constructing a geometric graph for generating routes that summarize a geographical area and also have visual continuity by using a set of location-direction-enabled photographs. A location- direction-enabled photograph is a photograph that has information about the location (position of the camera at the time of shooting) and the direction (direction of the camera at the time of shooting). Each nodes of the graph corresponds to a location-direction-enabled photograph. The location of each node is the location of the corresponding photograph, and a route on the graph corresponds to a route in the geographic area and a sequence of photographs. The proposed graph is constructed to represent characteristic spots and paths linking the spots, and it is assumed to be a kind of a spatial summarization of the area with the photographs. Therefore, we call the routes on the graph as spatial summary route. Each route on the proposed graph also has a visual continuity, which means that we can understand the spatial relationship among the continuous photographs on the route such as moving forward, backward, turning right, etc. In this study, when the changes in the shooting position and shooting direction satisfied a given threshold, the route was defined to have visual continuity. By presenting the photographs in order along the generated route, information can be presented sequentially, while maintaining visual continuity to a great extent.

Evaluation of the Self-Directed Personal Services Program Operated through Enable.

ERIC Educational Resources Information Center

Walker, Pam; And Others

This report evaluates a self-directed personal service (SDPS) program operated through the larger Enable Program for people with disabilities in Onondaga County, New York. First, it contrasts characteristics of traditional personal assistance services (such as low pay, agency-determined, limited types/levels of support, and program management…

High-power, format-flexible, 885-nm vertical-cavity surface-emitting laser arrays

NASA Astrophysics Data System (ADS)

Wang, Chad; Talantov, Fedor; Garrett, Henry; Berdin, Glen; Cardellino, Terri; Millenheft, David; Geske, Jonathan

2013-03-01

High-power, format flexible, 885 nm vertical-cavity surface-emitting laser (VCSEL) arrays have been developed for solid-state pumping and illumination applications. In this approach, a common VCSEL size format was designed to enable tiling into flexible formats and operating configurations. The fabrication of a common chip size on ceramic submount enables low-cost volume manufacturing of high-power VCSEL arrays. This base VCSEL chip was designed to be 5x3.33 mm2, and produced up to 50 Watts of peak continuous wave (CW) power. To scale to higher powers, multiple chips can be tiled into a combination of series or parallel configurations tailored to the application driver conditions. In actively cooled CW operation, the VCSEL array chips were packaged onto a single water channel cooler, and we have demonstrated 0.5x1, 1x1, and 1x3 cm2 formats, producing 150, 250, and 500 Watts of peak power, respectively, in under 130 A operating current. In QCW operation, the 1x3 cm2 VCSEL module, which contains 18 VCSEL array chips packaged on a single water cooler, produced over 1.3 kW of peak power. In passively cooled packages, multiple chip configurations have been developed for illumination applications, producing over 300 Watts of peak power in QCW operating conditions. These VCSEL chips use a substrate-removed structure to allow for efficient thermal heatsinking to enable high-power operation. This scalable, format flexible VCSEL architecture can be applied to wavelengths ranging from 800 to 1100 nm, and can be used to tailor emission spectral widths and build high-power hyperspectral sources.

Apparatus for providing directional permeability measurements in subterranean earth formations

DOEpatents

Shuck, Lowell Z.

1977-01-01

Directional permeability measurements are provided in a subterranean earth formation by injecting a high-pressure gas from a wellbore into the earth formation in various azimuthal directions with the direction having the largest pressure drop being indicative of the maximum permeability direction. These measurements are provided by employing an inflatable boot containing a plurality of conduits in registry with a like plurality of apertures penetrating the housing at circumferentially spaced-apart locations. These conduits are, in turn, coupled through a valved manifold to a source of pressurized gas so that the high-pressure gas may be selectively directed through any conduit into the earth formation defining the bore with the resulting difference in the pressure drop through the various conduits providing the permeability measurements.

New perspectives on neuronal development via microfluidic environments

PubMed Central

Millet, Larry J.; Gillette, Martha U.

2012-01-01

Understanding the signals that guide neuronal development and direct formation of axons, dendrites, and synapses during wiring of the brain is a fundamental challenge of developmental neuroscience. Discovering how local signals shape developing neurons has been impeded by the inability of conventional culture methods to interrogate micro-environments of complex neuronal cytoarchitectures, where different sub-domains encounter distinct chemical, physical, and fluidic features. Micro-fabrication techniques are enabling the creation of micro-environments tailored to neuronal structures and sub-domains, with unprecedented access and control. The design, fabrication, and properties of microfluidic devices offer significant advantages for addressing unresolved issues of neuronal development. These high-resolution approaches are poised to contribute new insights into mechanisms for restoring neuronal function and connectivity compromised by injury, stress, and neurodegeneration. PMID:23031246

Detection of carbon monoxide and water absorption lines in an exoplanet atmosphere.

PubMed

Konopacky, Quinn M; Barman, Travis S; Macintosh, Bruce A; Marois, Christian

2013-03-22

Determining the atmospheric structure and chemical composition of an exoplanet remains a formidable goal. Fortunately, advancements in the study of exoplanets and their atmospheres have come in the form of direct imaging--spatially resolving the planet from its parent star--which enables high-resolution spectroscopy of self-luminous planets in jovian-like orbits. Here, we present a spectrum with numerous, well-resolved molecular lines from both water and carbon monoxide from a massive planet orbiting less than 40 astronomical units from the star HR 8799. These data reveal the planet's chemical composition, atmospheric structure, and surface gravity, confirming that it is indeed a young planet. The spectral lines suggest an atmospheric carbon-to-oxygen ratio that is greater than that of the host star, providing hints about the planet's formation.

Differentiation of grain orientation with corrosive and colour etching on a granular bainitic steel.

PubMed

Reisinger, S; Ressel, G; Eck, S; Marsoner, S

2017-08-01

This study presents a detailed verification of the etching methods with Nital and Klemm on a granular bainitic steel. It is shown that both methods allow the identification of the crystal orientation, whereas Klemm etching enables also a quantification of the apparent phases, as also retained austenite can be distinguished from the other bainitic microstructures. A combination of atom probe tomography with electron-back-scattered-diffraction showed that both etching methods emphasize the bainitic {100} crystal orientation. However, a cross-section produced by focused ion beam evidenced that Klemm etching leads to the formation of a topography of the different oriented bainitic crystals that directly affects the thickness and therefore the apparent colour of the deposited layer formed during etching. Copyright © 2017 Elsevier Ltd. All rights reserved.

Interatomic Coulombic Decay: The Mechanism for Rapid Deexcitation of Hollow Atoms.

PubMed

Wilhelm, Richard A; Gruber, Elisabeth; Schwestka, Janine; Kozubek, Roland; Madeira, Teresa I; Marques, José P; Kobus, Jacek; Krasheninnikov, Arkady V; Schleberger, Marika; Aumayr, Friedrich

2017-09-08

The impact of a highly charged ion onto a solid gives rise to charge exchange between the ion and target atoms, so that a slow ion gets neutralized in the vicinity of the surface. Using highly charged Ar and Xe ions and the surface-only material graphene as a target, we show that the neutralization and deexcitation of the ions proceeds on a sub-10 fs time scale. We further demonstrate that a multiple Interatomic Coulombic Decay (ICD) model can describe the observed ultrafast deexcitation. Other deexcitation mechanisms involving nonradiative decay and quasimolecular orbital formation during the impact are not important, as follows from the comparison of our experimental data with the results of first-principles calculations. Our method also enables the estimation of ICD rates directly.

Shock-induced reaction synthesis of cubic boron nitride

NASA Astrophysics Data System (ADS)

Beason, M. T.; Pauls, J. M.; Gunduz, I. E.; Rouvimov, S.; Manukyan, K. V.; Matouš, K.; Son, S. F.; Mukasyan, A.

2018-04-01

Here, we report ultra-fast (0.1-5 μs) shock-induced reactions in the 3B-TiN system, leading to the direct synthesis of cubic boron nitride, which is extremely rare in nature and is the second hardest material known. Composite powders were produced through high-energy ball milling to provide intimate mixing and subsequently shocked using an explosive charge. High-resolution transmission electron microscopy and X-ray diffraction confirm the formation of nanocrystalline grains of c-BN produced during the metathetical reaction between boron and titanium nitride. Our results illustrate the possibility of rapid reactions enabled by high-energy ball milling possibly occurring in the solid state on incredibly short timescales. This process may provide a route for the discovery and fabrication of advanced compounds.

Parameters Free Computational Characterization of Defects in Transition Metal Oxides with Diffusion Quantum Monte Carlo

NASA Astrophysics Data System (ADS)

Santana, Juan A.; Krogel, Jaron T.; Kent, Paul R.; Reboredo, Fernando

Materials based on transition metal oxides (TMO's) are among the most challenging systems for computational characterization. Reliable and practical computations are possible by directly solving the many-body problem for TMO's with quantum Monte Carlo (QMC) methods. These methods are very computationally intensive, but recent developments in algorithms and computational infrastructures have enabled their application to real materials. We will show our efforts on the application of the diffusion quantum Monte Carlo (DMC) method to study the formation of defects in binary and ternary TMO and heterostructures of TMO. We will also outline current limitations in hardware and algorithms. This work is supported by the Materials Sciences & Engineering Division of the Office of Basic Energy Sciences, U.S. Department of Energy (DOE).

High-definition Fourier transform infrared spectroscopic imaging of prostate tissue

NASA Astrophysics Data System (ADS)

Wrobel, Tomasz P.; Kwak, Jin Tae; Kadjacsy-Balla, Andre; Bhargava, Rohit

2016-03-01

Histopathology forms the gold standard for cancer diagnosis and therapy, and generally relies on manual examination of microscopic structural morphology within tissue. Fourier-Transform Infrared (FT-IR) imaging is an emerging vibrational spectroscopic imaging technique, especially in a High-Definition (HD) format, that provides the spatial specificity of microscopy at magnifications used in diagnostic surgical pathology. While it has been shown for standard imaging that IR absorption by tissue creates a strong signal where the spectrum at each pixel is a quantitative "fingerprint" of the molecular composition of the sample, here we show that this fingerprint also enables direct digital pathology without the need for stains or dyes for HD imaging. An assessment of the potential of HD imaging to improve diagnostic pathology accuracy is presented.

The formation mechanism for printed silver-contacts for silicon solar cells.

PubMed

Fields, Jeremy D; Ahmad, Md Imteyaz; Pool, Vanessa L; Yu, Jiafan; Van Campen, Douglas G; Parilla, Philip A; Toney, Michael F; van Hest, Maikel F A M

2016-04-01

Screen-printing provides an economically attractive means for making Ag electrical contacts to Si solar cells, but the use of Ag substantiates a significant manufacturing cost, and the glass frit used in the paste to enable contact formation contains Pb. To achieve optimal electrical performance and to develop pastes with alternative, abundant and non-toxic materials, a better understanding the contact formation process during firing is required. Here, we use in situ X-ray diffraction during firing to reveal the reaction sequence. The findings suggest that between 500 and 650 °C PbO in the frit etches the SiNx antireflective-coating on the solar cell, exposing the Si surface. Then, above 650 °C, Ag(+) dissolves into the molten glass frit - key for enabling deposition of metallic Ag on the emitter surface and precipitation of Ag nanocrystals within the glass. Ultimately, this work clarifies contact formation mechanisms and suggests approaches for development of inexpensive, nontoxic solar cell contacting pastes.

The formation mechanism for printed silver-contacts for silicon solar cells

DOE PAGES

Fields, Jeremy D.; Ahmad, Md. Imteyaz; Pool, Vanessa L.; ...

2016-04-01

Screen-printing provides an economically attractive means for making Ag electrical contacts to Si solar cells, but the use of Ag substantiates a significant manufacturing cost, and the glass frit used in the paste to enable contact formation contains Pb. To achieve optimal electrical performance and to develop pastes with alternative, abundant, and non-toxic materials requires understanding the contact formation process during firing. Here, we use in-situ X-ray diffraction during firing to reveal the reaction sequence. The findings suggest that between 500 degrees C and 650 degrees C PbO in the frit etches the SiNx antireflective-coating on the solar cell, exposingmore » the Si surface. Then, above 650 degrees C, Ag+ dissolves into the molten glass frit -- key for enabling deposition of metallic Ag on the emitter surface and precipitation of Ag nanocrystals within the glass. Ultimately, this work clarifies contact formation mechanisms and suggests approaches for development of inexpensive, nontoxic solar cell contacting pastes.« less

Integrated approaches to spatiotemporally directing angiogenesis in host and engineered tissues.

PubMed

Kant, Rajeev J; Coulombe, Kareen L K

2018-03-15

The field of tissue engineering has turned towards biomimicry to solve the problem of tissue oxygenation and nutrient/waste exchange through the development of vasculature. Induction of angiogenesis and subsequent development of a vascular bed in engineered tissues is actively being pursued through combinations of physical and chemical cues, notably through the presentation of topographies and growth factors. Presenting angiogenic signals in a spatiotemporal fashion is beginning to generate improved vascular networks, which will allow for the creation of large and dense engineered tissues. This review provides a brief background on the cells, mechanisms, and molecules driving vascular development (including angiogenesis), followed by how biomaterials and growth factors can be used to direct vessel formation and maturation. Techniques to accomplish spatiotemporal control of vascularization include incorporation or encapsulation of growth factors, topographical engineering, and 3D bioprinting. The vascularization of engineered tissues and their application in angiogenic therapy in vivo is reviewed herein with an emphasis on the most densely vascularized tissue of the human body - the heart. Vascularization is vital to wound healing and tissue regeneration, and development of hierarchical networks enables efficient nutrient transfer. In tissue engineering, vascularization is necessary to support physiologically dense engineered tissues, and thus the field seeks to induce vascular formation using biomaterials and chemical signals to provide appropriate, pro-angiogenic signals for cells. This review critically examines the materials and techniques used to generate scaffolds with spatiotemporal cues to direct vascularization in engineered and host tissues in vitro and in vivo. Assessment of the field's progress is intended to inspire vascular applications across all forms of tissue engineering with a specific focus on highlighting the nuances of cardiac tissue engineering for the greater regenerative medicine community. Copyright © 2018 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Cutting a Drop of Water Pinned by Wire Loops Using a Superhydrophobic Surface and Knife

PubMed Central

Yanashima, Ryan; García, Antonio A.; Aldridge, James; Weiss, Noah; Hayes, Mark A.; Andrews, James H.

2012-01-01

A water drop on a superhydrophobic surface that is pinned by wire loops can be reproducibly cut without formation of satellite droplets. Drops placed on low-density polyethylene surfaces and Teflon-coated glass slides were cut with superhydrophobic knives of low-density polyethylene and treated copper or zinc sheets, respectively. Distortion of drop shape by the superhydrophobic knife enables a clean break. The driving force for droplet formation arises from the lower surface free energy for two separate drops, and it is modeled as a 2-D system. An estimate of the free energy change serves to guide when droplets will form based on the variation of drop volume, loop spacing and knife depth. Combining the cutting process with an electrofocusing driving force could enable a reproducible biomolecular separation without troubling satellite drop formation. PMID:23029297

Using Formative Assessment to Facilitate Learner Self-Regulation: A Case Study of Assessment Practices and Student Perceptions in Hong Kong

ERIC Educational Resources Information Center

Jing Jing, Ma

2017-01-01

One of the key aims of formative assessment in higher education is to enable students to become self-regulated learners (Nicol & Macfarlane-Dick, 2006). Based on Nicol and Macfarlane-Dick's (2006) framework, this exploratory study investigates which formative assessment practices proposed by them were used by one college EFL writing teacher to…

Implications of Martian Phyllosilicate Formation Conditions to the Early Climate on Mars

NASA Astrophysics Data System (ADS)

Bishop, J. L.; Baker, L.; Fairén, A. G.; Michalski, J. R.; Gago-Duport, L.; Velbel, M. A.; Gross, C.; Rampe, E. B.

2017-12-01

We propose that short-term warmer and wetter environments, occurring sporadically in a generally cold early Mars, enabled formation of phyllosilicate-rich outcrops on the surface of Mars without requiring long-term warm and wet conditions. We are investigating phyllosilicate formation mechanisms including CO2 and H2O budgets to provide constraints on the early martian climate. We have evaluated the nature and stratigraphy of phyllosilicate-bearing surface units on Mars based on i) phyllosilicate-forming environments on Earth, ii) phyllosilicate reactions in the lab, and iii) modeling experiments involving phyllosilicates and short-range ordered (SRO) materials. The type of phyllosilicates that form on Mars depends on temperature, water/rock ratio, acidity, salinity and available ions. Mg-rich trioctahedral smectite mixtures are more consistent with subsurface formation environments (crustal, hydrothermal or alkaline lakes) up to 400 °C and are not associated with martian surface environments. In contrast, clay profiles dominated by dioctahedral Al/Fe-smectites are typically formed in subaqueous or subaerial surface environments. We propose models describing formation of smectite-rich outcrops and laterally extensive vertical profiles of Fe/Mg-smectites, sulfates, and Al-rich clay assemblages formed in surface environments. Further, the presence of abundant SRO materials without phyllosilicates could mark the end of the last warm and wet episode on Mars supporting smectite formation. Climate Implications for Early Mars: Clay formation reactions proceed extremely slowly at cool temperatures. The thick smectite outcrops observed on Mars through remote sensing would require standing water on Mars for hundreds of millions of years if they formed in waters 10-15 °C. However, warmer temperatures could have enabled faster production of these smectite-rich beds. Sporadic warming episodes to 30-40 °C could have enabled formation of these smectites over only tens or hundreds of thousands of years instead. Our analyses of the phyllosilicate record on Mars point to a scenario of brief warm and wet conditions that accounts for formation of substantial smectite clays in many locations, geologic features resulting from liquid water across the planet, and a generally cold and dry climate.

DELLA proteins regulate arbuscule formation in arbuscular mycorrhizal symbiosis

PubMed Central

Floss, Daniela S.; Levy, Julien G.; Lévesque-Tremblay, Véronique; Pumplin, Nathan; Harrison, Maria J.

2013-01-01

Most flowering plants are able to form endosymbioses with arbuscular mycorrhizal fungi. In this mutualistic association, the fungus colonizes the root cortex and establishes elaborately branched hyphae, called arbuscules, within the cortical cells. Arbuscule development requires the cellular reorganization of both symbionts, and the resulting symbiotic interface functions in nutrient exchange. A plant symbiosis signaling pathway controls the development of the symbiosis. Several components of the pathway have been identified, but transcriptional regulators that control downstream pathways for arbuscule formation are still unknown. Here we show that DELLA proteins, which are repressors of gibberellic acid (GA) signaling and function at the nexus of several signaling pathways, are required for arbuscule formation. Arbuscule formation is severely impaired in a Medicago truncatula Mtdella1/Mtdella2 double mutant; GA treatment of wild-type roots phenocopies the della double mutant, and a dominant DELLA protein (della1-Δ18) enables arbuscule formation in the presence of GA. Ectopic expression of della1-Δ18 suggests that DELLA activity in the vascular tissue and endodermis is sufficient to enable arbuscule formation in the inner cortical cells. In addition, expression of della1-Δ18 restores arbuscule formation in the symbiosis signaling pathway mutant cyclops/ipd3, indicating an intersection between DELLA and symbiosis signaling for arbuscule formation. GA signaling also influences arbuscule formation in monocots, and a Green Revolution wheat variety carrying dominant DELLA alleles shows enhanced colonization but a limited growth response to arbuscular mycorrhizal symbiosis. PMID:24297892

DELLA proteins regulate arbuscule formation in arbuscular mycorrhizal symbiosis.

PubMed

Floss, Daniela S; Levy, Julien G; Lévesque-Tremblay, Véronique; Pumplin, Nathan; Harrison, Maria J

2013-12-17

Most flowering plants are able to form endosymbioses with arbuscular mycorrhizal fungi. In this mutualistic association, the fungus colonizes the root cortex and establishes elaborately branched hyphae, called arbuscules, within the cortical cells. Arbuscule development requires the cellular reorganization of both symbionts, and the resulting symbiotic interface functions in nutrient exchange. A plant symbiosis signaling pathway controls the development of the symbiosis. Several components of the pathway have been identified, but transcriptional regulators that control downstream pathways for arbuscule formation are still unknown. Here we show that DELLA proteins, which are repressors of gibberellic acid (GA) signaling and function at the nexus of several signaling pathways, are required for arbuscule formation. Arbuscule formation is severely impaired in a Medicago truncatula Mtdella1/Mtdella2 double mutant; GA treatment of wild-type roots phenocopies the della double mutant, and a dominant DELLA protein (della1-Δ18) enables arbuscule formation in the presence of GA. Ectopic expression of della1-Δ18 suggests that DELLA activity in the vascular tissue and endodermis is sufficient to enable arbuscule formation in the inner cortical cells. In addition, expression of della1-Δ18 restores arbuscule formation in the symbiosis signaling pathway mutant cyclops/ipd3, indicating an intersection between DELLA and symbiosis signaling for arbuscule formation. GA signaling also influences arbuscule formation in monocots, and a Green Revolution wheat variety carrying dominant DELLA alleles shows enhanced colonization but a limited growth response to arbuscular mycorrhizal symbiosis.

The Role of e-Portfolios in Supporting Productive Learning

ERIC Educational Resources Information Center

Yang, Min; Tai, Mui; Lim, Cher Ping

2016-01-01

e-Portfolios are a form of authentic assessment with formative functions that include showcasing and sharing learning artifacts, documenting reflective learning processes, connecting learning across various stages and enabling frequent feedback for improvements. This paper examines how e-portfolios take up these formative roles to support…

dPCR: A Technology Review

PubMed Central

Quan, Phenix-Lan; Sauzade, Martin

2018-01-01

Digital Polymerase Chain Reaction (dPCR) is a novel method for the absolute quantification of target nucleic acids. Quantification by dPCR hinges on the fact that the random distribution of molecules in many partitions follows a Poisson distribution. Each partition acts as an individual PCR microreactor and partitions containing amplified target sequences are detected by fluorescence. The proportion of PCR-positive partitions suffices to determine the concentration of the target sequence without a need for calibration. Advances in microfluidics enabled the current revolution of digital quantification by providing efficient partitioning methods. In this review, we compare the fundamental concepts behind the quantification of nucleic acids by dPCR and quantitative real-time PCR (qPCR). We detail the underlying statistics of dPCR and explain how it defines its precision and performance metrics. We review the different microfluidic digital PCR formats, present their underlying physical principles, and analyze the technological evolution of dPCR platforms. We present the novel multiplexing strategies enabled by dPCR and examine how isothermal amplification could be an alternative to PCR in digital assays. Finally, we determine whether the theoretical advantages of dPCR over qPCR hold true by perusing studies that directly compare assays implemented with both methods. PMID:29677144

Evolution of Satellite Imagers and Sounders for Low Earth Orbit and Technology Directions at NASA

NASA Technical Reports Server (NTRS)

Pagano, Thomas S.; McClain, Charles R.

2010-01-01

Imagers and Sounders for Low Earth Orbit (LEO) provide fundamental global daily observations of the Earth System for scientists, researchers, and operational weather agencies. The imager provides the nominal 1-2 km spatial resolution images with global coverage in multiple spectral bands for a wide range of uses including ocean color, vegetation indices, aerosol, snow and cloud properties, and sea surface temperature. The sounder provides vertical profiles of atmospheric temperature, water vapor cloud properties, and trace gases including ozone, carbon monoxide, methane and carbon dioxide. Performance capabilities of these systems has evolved with the optical and sensing technologies of the decade. Individual detectors were incorporated on some of the first imagers and sounders that evolved to linear array technology in the '80's. Signal-to-noise constraints limited these systems to either broad spectral resolution as in the case of the imager, or low spatial resolution as in the case of the sounder. Today's area 2-dimensional large format array technology enables high spatial and high spectral resolution to be incorporated into a single instrument. This places new constraints on the design of these systems and enables new capabilities for scientists to examine the complex processes governing the Earth System.

Non-Covalent Photo-Patterning of Gelatin Matrices Using Caged Collagen Mimetic Peptides

PubMed Central

Li, Yang; Hoa San, Boi; L. Kessler, Julian; Hwan Kim, Jin; Xu, Qingguo; Hanes, Justin; Yu, Seungju Michael

2015-01-01

Advancements in photolithography have enabled us to spatially encode biochemical cues in biocompatible platforms such as synthetic hydrogels. Conventional patterning works through photo-activated chemical reactions on inert polymer networks. However, these techniques cannot be directly applied to protein hydrogels without chemically altering the protein scaffolds. To this end, we developed a non-covalent photo-patterning strategy for gelatin (denatured collagen) hydrogels utilizing a caged collagen mimetic peptide (caged CMP) which binds to gelatin strands through UV activated, triple helix hybridization. Here we present 2D and 3D photo-patterning of gelatin hydrogels enabled by the caged CMPs as well as creation of concentration gradients of CMPs. We show that photo-patterning of PEG-conjugated caged CMPs can be used to spatially control cell adhesion on gelatin films. CMP’s specificity for binding to gelatin allows patterning of almost any synthetic or natural gelatin-containing matrix, such as zymograms, gelatin-methacrylate hydrogels, and even a corneal tissue. Since the CMP is a chemically and biologically inert peptide which is proven to be an ideal carrier for bioactive molecules, our patterning method provides a radically new tool for immobilizing drugs to natural tissues and for functionalizing scaffolds for complex tissue formation. PMID:25476588

Shuttle-Data-Tape XML Translator

NASA Technical Reports Server (NTRS)

Barry, Matthew R.; Osborne, Richard N.

2005-01-01

JSDTImport is a computer program for translating native Shuttle Data Tape (SDT) files from American Standard Code for Information Interchange (ASCII) format into databases in other formats. JSDTImport solves the problem of organizing the SDT content, affording flexibility to enable users to choose how to store the information in a database to better support client and server applications. JSDTImport can be dynamically configured by use of a simple Extensible Markup Language (XML) file. JSDTImport uses this XML file to define how each record and field will be parsed, its layout and definition, and how the resulting database will be structured. JSDTImport also includes a client application programming interface (API) layer that provides abstraction for the data-querying process. The API enables a user to specify the search criteria to apply in gathering all the data relevant to a query. The API can be used to organize the SDT content and translate into a native XML database. The XML format is structured into efficient sections, enabling excellent query performance by use of the XPath query language. Optionally, the content can be translated into a Structured Query Language (SQL) database for fast, reliable SQL queries on standard database server computers.

Facile One-pot Transformation of Iron Oxides from Fe2O3 Nanoparticles to Nanostructured Fe3O4@C Core-Shell Composites via Combustion Waves

PubMed Central

Shin, Jungho; Lee, Kang Yeol; Yeo, Taehan; Choi, Wonjoon

2016-01-01

The development of a low-cost, fast, and large-scale process for the synthesis and manipulation of nanostructured metal oxides is essential for incorporating materials with diverse practical applications. Herein, we present a facile one-pot synthesis method using combustion waves that simultaneously achieves fast reduction and direct formation of carbon coating layers on metal oxide nanostructures. Hybrid composites of Fe2O3 nanoparticles and nitrocellulose on the cm scale were fabricated by a wet impregnation process. We demonstrated that self-propagating combustion waves along interfacial boundaries between the surface of the metal oxide and the chemical fuels enabled the release of oxygen from Fe2O3. This accelerated reaction directly transformed Fe2O3 into Fe3O4 nanostructures. The distinctive color change from reddish-brown Fe2O3 to dark-gray Fe3O4 confirmed the transition of oxidation states and the change in the fundamental properties of the material. Furthermore, it simultaneously formed carbon layers of 5–20 nm thickness coating the surfaces of the resulting Fe3O4 nanoparticles, which may aid in maintaining the nanostructures and improving the conductivity of the composites. This newly developed use of combustion waves in hybridized nanostructures may permit the precise manipulation of the chemical compositions of other metal oxide nanostructures, as well as the formation of organic/inorganic hybrid nanostructures. PMID:26902260

Netmeld v. 1.0

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

BERG, MICHAEL; RILEY, MARSHALL

System assessments typically yield large quantities of data from disparate sources for an analyst to scrutinize for issues. Netmeld is used to parse input from different file formats, store the data in a common format, allow users to easily query it, and enable analysts to tie different analysis tools together using a common back-end.

Language Technologies to Support Formative Feedback

ERIC Educational Resources Information Center

Berlanga, Adriana J.; Kalz, Marco; Stoyanov, Slavi; van Rosmalen, Peter; Smithies, Alisdair; Braidman, Isobel

2011-01-01

Formative feedback enables comparison to be made between a learner's current understanding and a desired learning goal. Obtaining this information is a time consuming task that most tutors cannot afford. We therefore wished to develop a support software tool, which provides tutors and learners with information that identifies a learner's progress,…

ORGANIC AEROSOL FORMATION IN THE HUMID, PHOTOCHEMICALLY-ACTIVE SOUTHEASTERN US: SOAS EXPERIMENTS AND SIMULATIONS

EPA Science Inventory

A better understanding of SOA formation, properties and behavior in the humid eastern U.S. including dependence on anthropogenic emissions (RFA Q #1, 2). More accurate air quality prediction enabling more accurate air quality management (EPA Goal #1). Scientific insights co...

Plasma membrane H⁺ -ATPase regulation is required for auxin gradient formation preceding phototropic growth.

PubMed

Hohm, Tim; Demarsy, Emilie; Quan, Clément; Allenbach Petrolati, Laure; Preuten, Tobias; Vernoux, Teva; Bergmann, Sven; Fankhauser, Christian

2014-09-26

Phototropism is a growth response allowing plants to align their photosynthetic organs toward incoming light and thereby to optimize photosynthetic activity. Formation of a lateral gradient of the phytohormone auxin is a key step to trigger asymmetric growth of the shoot leading to phototropic reorientation. To identify important regulators of auxin gradient formation, we developed an auxin flux model that enabled us to test in silico the impact of different morphological and biophysical parameters on gradient formation, including the contribution of the extracellular space (cell wall) or apoplast. Our model indicates that cell size, cell distributions, and apoplast thickness are all important factors affecting gradient formation. Among all tested variables, regulation of apoplastic pH was the most important to enable the formation of a lateral auxin gradient. To test this prediction, we interfered with the activity of plasma membrane H⁺ -ATPases that are required to control apoplastic pH. Our results show that H⁺ -ATPases are indeed important for the establishment of a lateral auxin gradient and phototropism. Moreover, we show that during phototropism, H⁺ -ATPase activity is regulated by the phototropin photoreceptors, providing a mechanism by which light influences apoplastic pH. © 2014 The Authors. Published under the terms of the CC BY 4.0 license.

Bio-inspired direct patterning functional nanothin microlines: controllable liquid transfer.

PubMed

Wang, Qianbin; Meng, Qingan; Wang, Pengwei; Liu, Huan; Jiang, Lei

2015-04-28

Developing a general and low-cost strategy that enables direct patterning of microlines with nanometer thickness from versatile liquid-phase functional materials and precise positioning of them on various substrates remains a challenge. Herein, with inspiration from the oriental wisdom to control ink transfer by Chinese brushes, we developed a facile and general writing strategy to directly pattern various functional microlines with homogeneous distribution and nanometer-scale thickness. It is demonstrated that the width and thickness of the microlines could be well-controlled by tuning the writing method, providing guidance for the adaptation of this technique to various systems. It is also shown that various functional liquid-phase materials, such as quantum dots, small molecules, polymers, and suspensions of nanoparticles, could directly write on the substrates with intrinsic physicochemical properties well-preserved. Moreover, this technique enabled direct patterning of liquid-phase materials on certain microdomains, even in multiple layered style, thus a microdomain localized chemical reaction and the patterned surface chemical modification were enabled. This bio-inspired direct writing device will shed light on the template-free printing of various functional micropatterns, as well as the integrated functional microdevices.

Development of the High-Order Decoupled Direct Method in Three Dimensions for Particulate Matter: Enabling Advanced Sensitivity Analysis in Air Quality Models

EPA Science Inventory

The high-order decoupled direct method in three dimensions for particular matter (HDDM-3D/PM) has been implemented in the Community Multiscale Air Quality (CMAQ) model to enable advanced sensitivity analysis. The major effort of this work is to develop high-order DDM sensitivity...

Enabling Self-Directed Computer Use for Individuals with Cerebral Palsy: A Systematic Review of Assistive Devices and Technologies

ERIC Educational Resources Information Center

Davies, T. Claire; Mudge, Suzie; Ameratunga, Shanthi; Stott, N. Susan

2010-01-01

Aim: The purpose of this study was to systematically review published evidence on the development, use, and effectiveness of devices and technologies that enable or enhance self-directed computer access by individuals with cerebral palsy (CP). Methods: Nine electronic databases were searched using keywords "computer", "software", "spastic",…

Ocean data management in OMP Data Service

NASA Astrophysics Data System (ADS)

Fleury, Laurence; André, François; Belmahfoud, Nizar; Boichard, Jean-Luc; Brissebrat, Guillaume; Ferré, Hélène; Mière, Arnaud

2014-05-01

The Observatoire Midi-Pyrénées Data Service (SEDOO) is a development team, dedicated to environmental data management and dissemination application set up, in the framework of intensive field campaigns and long term observation networks. SEDOO developped some applications dealing with ocean data only, but also generic databases that enable to store and distribute multidisciplinary datasets. SEDOO is in charge of the in situ data management and the data portal for international and multidisciplinary programmes as large as African Monsoon Multidisciplinary Analyses (AMMA) and Mediterranean Integrated STudies at Regional And Local Scales (MISTRALS). The AMMA and MISTRALS databases are distributed and the data portals enable to access datasets managed by other data centres (IPSL, CORIOLIS...) through interoperability protocols (OPeNDAP, xml requests...). AMMA and MISTRALS metadata (data description) are standardized and comply with international standards (ISO 19115-19139; INSPIRE European Directive; Global Change Master Directory Thesaurus). Most of the AMMA and MISTRALS in situ ocean data sets are homogenized and inserted in a relational database, in order to enable accurate data selection and download of different data sets in a shared format. Data selection criteria are location, period, physical property name, physical property range... The data extraction procedure include format output selection among CSV, NetCDF, Nasa Ames... The AMMA database - http://database.amma-international.org/ - contains field campaign observations in the Guinea Gulf (EGEE 2005-2007) and Atlantic Tropical Ocean (AEROSE-II 2006...), as well as long term monitoring data (PIRATA, ARGO...). Operational analysis (MERCATOR) and satellite products (TMI, SSMI...) are managed by IPSL data centre and can be accessed too. They have been projected over regular latitude-longitude grids and converted into the NetCDF format. The MISTRALS data portal - http://mistrals.sedoo.fr/ - enables to access ocean datasets produced by the contributing programmes: Hydrological cycle in the Mediterranean eXperiment (HyMeX), Chemistry-Aerosol Mediterranean eXperiment (ChArMEx), Marine Mediterranean eXperiment (MERMeX)... The programmes include many field campaigns from 2011 to 2015, collecting general and specific properties. Long term monitoring networks, like Mediterranean Ocean Observing System on Environment (MOOSE) or Mediterranean Eurocentre for Underwater Sciences and Technologies (MEUST-SE), contribute to the MISTRALS data portal as well. Relevant model outputs and satellite products managed by external data centres (IPSL, ENEA...) can be accessed too. SEDOO manages the SSS (Sea Surface Salinity) national observation service data: http://sss.sedoo.fr/. SSS aims at collecting, validating, archiving and distributing in situ SSS measurements derived from Voluntary Observing Ship programs. The SSS data user interface enables to built multicriteria data request and download relevant datasets. SEDOO contributes to the SOLWARA project that aims at understanding the oceanic circulation in the Coral Sea and the Solomon Sea and their role in both the climate system and the oceanic chemistry. The research programme include in situ measurements, numerical modelling and compiled analyses of past data. The website http://thredds.sedoo.fr/solwara/ enables to access, visualize and download Solwara gridded data and model simulations, using Thredds associated services (OPEnDAP, NCSS and WMS). In order to improve the application user-friendliness, SSS and SOLWARA web interfaces are JEE applications build with GWT Framework, and share many modules.

Step-gate polysilicon nanowires field effect transistor compatible with CMOS technology for label-free DNA biosensor.

PubMed

Wenga, G; Jacques, E; Salaün, A-C; Rogel, R; Pichon, L; Geneste, F

2013-02-15

Currently, detection of DNA hybridization using fluorescence-based detection technique requires expensive optical systems and complex bioinformatics tools. Hence, the development of new low cost devices that enable direct and highly sensitive detection stimulates a lot of research efforts. Particularly, devices based on silicon nanowires are emerging as ultrasensitive electrical sensors for the direct detection of biological species thanks to their high surface to volume ratio. In this study, we propose innovative devices using step-gate polycrystalline silicon nanowire FET (poly-Si NW FETs), achieved with simple and low cost fabrication process, and used as ultrasensitive electronic sensor for DNA hybridization. The poly-SiNWs are synthesized using the sidewall spacer formation technique. The detailed fabrication procedure for a step-gate NWFET sensor is described in this paper. No-complementary and complementary DNA sequences were clearly discriminated and detection limit to 1 fM range is observed. This first result using this nano-device is promising for the development of low cost and ultrasensitive polysilicon nanowires based DNA sensors compatible with the CMOS technology. Copyright © 2012 Elsevier B.V. All rights reserved.

Heterobimetallic Zeolite, InV-ZSM-5, Enables Efficient Conversion of Biomass Derived Ethanol to Renewable Hydrocarbons

PubMed Central

Narula, Chaitanya K.; Li, Zhenglong; Casbeer, Erik M.; Geiger, Robert A.; Moses-Debusk, Melanie; Keller, Martin; Buchanan, Michelle V.; Davison, Brian H.

2015-01-01

Direct catalytic conversion of ethanol to hydrocarbon blend-stock can increase biofuels use in current vehicles beyond the ethanol blend-wall of 10–15%. Literature reports describe quantitative conversion of ethanol over zeolite catalysts but high C2 hydrocarbon formation renders this approach unsuitable for commercialization. Furthermore, the prior mechanistic studies suggested that ethanol conversion involves endothermic dehydration step. Here, we report the complete conversion of ethanol to hydrocarbons over InV-ZSM-5 without added hydrogen and which produces lower C2 (<13%) as compared to that over H-ZSM-5. Experiments with C2H5OD and in situ DRIFT suggest that most of the products come from the hydrocarbon pool type mechanism and dehydration step is not necessary. Thus, our method of direct conversion of ethanol offers a pathway to produce suitable hydrocarbon blend-stock that may be blended at a refinery to produce fuels such as gasoline, diesel, JP-8, and jet fuel, or produce commodity chemicals such as BTX. PMID:26526963

Constraint-based modeling of carbon fixation and the energetics of electron transfer in Geobacter metallireducens.

PubMed

Feist, Adam M; Nagarajan, Harish; Rotaru, Amelia-Elena; Tremblay, Pier-Luc; Zhang, Tian; Nevin, Kelly P; Lovley, Derek R; Zengler, Karsten

2014-04-01

Geobacter species are of great interest for environmental and biotechnology applications as they can carry out direct electron transfer to insoluble metals or other microorganisms and have the ability to assimilate inorganic carbon. Here, we report on the capability and key enabling metabolic machinery of Geobacter metallireducens GS-15 to carry out CO2 fixation and direct electron transfer to iron. An updated metabolic reconstruction was generated, growth screens on targeted conditions of interest were performed, and constraint-based analysis was utilized to characterize and evaluate critical pathways and reactions in G. metallireducens. The novel capability of G. metallireducens to grow autotrophically with formate and Fe(III) was predicted and subsequently validated in vivo. Additionally, the energetic cost of transferring electrons to an external electron acceptor was determined through analysis of growth experiments carried out using three different electron acceptors (Fe(III), nitrate, and fumarate) by systematically isolating and examining different parts of the electron transport chain. The updated reconstruction will serve as a knowledgebase for understanding and engineering Geobacter and similar species.

Mechanisms of Furfural Reduction on Metal Electrodes: Distinguishing Pathways for Selective Hydrogenation of Bioderived Oxygenates.

PubMed

Chadderdon, Xiaotong H; Chadderdon, David J; Matthiesen, John E; Qiu, Yang; Carraher, Jack M; Tessonnier, Jean-Philippe; Li, Wenzhen

2017-10-11

Electrochemical reduction of biomass-derived platform molecules is an emerging route for the sustainable production of fuels and chemicals. However, understanding gaps between reaction conditions, underlying mechanisms, and product selectivity have limited the rational design of active, stable, and selective catalyst systems. In this work, the mechanisms of electrochemical reduction of furfural, an important biobased platform molecule and model for aldehyde reduction, are explored through a combination of voltammetry, preparative electrolysis, thiol-electrode modifications, and kinetic isotope studies. It is demonstrated that two distinct mechanisms are operable on metallic Cu electrodes in acidic electrolytes: (i) electrocatalytic hydrogenation (ECH) and (ii) direct electroreduction. The contributions of each mechanism to the observed product distribution are clarified by evaluating the requirement for direct chemical interactions with the electrode surface and the role of adsorbed hydrogen. Further analysis reveals that hydrogenation and hydrogenolysis products are generated by parallel ECH pathways. Understanding the underlying mechanisms enables the manipulation of furfural reduction by rationally tuning the electrode potential, electrolyte pH, and furfural concentration to promote selective formation of important biobased polymer precursors and fuels.

Characterization of VOCs Emissions from Industrial Facilities and Natural Gas Production Sites: A Mobile Sensing Approach

NASA Astrophysics Data System (ADS)

Zhou, X.; Gu, J.; Trask, B.; Lyon, D. R.; Albertson, J. D.

2017-12-01

With the recent expansion of U.S. oil and gas (O&G) production, many studies have focused on the quantification of fugitive methane emissions. However, only a few studies have explored the emissions of volatile organic compounds (VOCs) from O&G production sites that affect human health in adjacent communities, both directly through exposure to toxic chemical compounds and indirectly via formation of ground-level ozone. In this study, we seek to quantify emissions of VOCs from O&G production sites and petrochemical facilities using a mobile sensing approach, with both high-end analyzers and relatively low-cost sensors. A probabilistic source characterization approach is used to estimate emission rates of VOCs, directly taking into account quantitative measure of sensor accuracy. This work will provide data with proper spatiotemporal resolution and coverage, so as to improve the understanding of VOCs emission from O&G production sites, VOCs-exposure of local communities, and explore the feasibility of low-cost sensors for VOCs monitoring. The project will provide an important foundational step to enable large scale studies.

Mechanisms of Furfural Reduction on Metal Electrodes: Distinguishing Pathways for Selective Hydrogenation of Bioderived Oxygenates

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

Chadderdon, Xiaotong H.; Chadderdon, David J.; Matthiesen, John E.

Electrochemical reduction of biomass-derived platform molecules is an emerging route for the sustainable production of fuels and chemicals. Understanding gaps between reaction conditions, underlying mechanisms, and product selectivity have limited the rational design of active, stable, and selective catalyst systems. Here, the mechanisms of electrochemical reduction of furfural, an important biobased platform molecule and model for aldehyde reduction, are explored through a combination of voltammetry, preparative electrolysis, thiol-electrode modifications, and kinetic isotope studies. It is demonstrated that two distinct mechanisms are operable on metallic Cu electrodes in acidic electrolytes: (i) electrocatalytic hydrogenation (ECH) and (ii) direct electroreduction. The contributions ofmore » each mechanism to the observed product distribution are clarified by evaluating the requirement for direct chemical interactions with the electrode surface and the role of adsorbed hydrogen. Further analysis reveals that hydrogenation and hydrogenolysis products are generated by parallel ECH pathways. By understanding the underlying mechanisms it enables the manipulation of furfural reduction by rationally tuning the electrode potential, electrolyte pH, and furfural concentration to promote selective formation of important biobased polymer precursors and fuels.« less

Heterobimetallic zeolite, InV-ZSM-5, enables efficient conversion of biomass derived ethanol to renewable hydrocarbons

DOE PAGES

Narula, Chaitanya K.; Li, Zhenglong; Casbeer, Erik M.; ...

2015-11-03

Here, direct catalytic conversion of ethanol to hydrocarbon blend-stock can increase biofuels use in current vehicles beyond the ethanol blend-wall of 10–15%. Literature reports describe quantitative conversion of ethanol over zeolite catalysts but high C 2 hydrocarbon formation renders this approach unsuitable for commercialization. Furthermore, the prior mechanistic studies suggested that ethanol conversion involves endothermic dehydration step. Here, we report the complete conversion of ethanol to hydrocarbons over InV-ZSM-5 without added hydrogen and which produces lower C 2 (<13%) as compared to that over H-ZSM-5. Experiments with C 2H 5OD and in situ DRIFT suggest that most of the productsmore » come from the hydrocarbon pool type mechanism and dehydration step is not necessary. Thus, our method of direct conversion of ethanol offers a pathway to produce suitable hydrocarbon blend-stock that may be blended at a refinery to produce fuels such as gasoline, diesel, JP-8, and jet fuel, or produce commodity chemicals such as BTX.« less

Novel nanometer-level uniform amorphous carbon coating for boron powders by direct pyrolysis of coronene without solvent.

PubMed

Ye, ShuJun; Song, MingHui; Kumakura, Hiroaki

2015-01-30

A 3 nm coronene coating and a 4 nm amorphous carbon coating with a uniform shell-core encapsulation structure for nanosized boron (B) powders are formed by a simple process in which coronene is directly mixed with boron particles without a solvent and heated at 520 °C for 1 h or at 630 °C for 3 h in a vacuum-sealed silica tube. Coronene has a melting point lower than its decomposition temperature, which enables liquid coronene to cover B particles by liquid diffusion and penetration without the need for a solvent. The diffusion and penetration of coronene can extend to the boundaries of particles and to inside the agglomerated nanoparticles to form a complete shell-core encapsulated structure. As the temperature is increased, thermal decomposition of coronene on the B particles results in the formation of a uniform amorphous carbon coating layer. This novel and simple nanometer-level uniform amorphous carbon coating method can possibly be applied to many other powders; thus, it has potential applications in many fields at low cost.

Engineered 3D vascular and neuronal networks in a microfluidic platform.

PubMed

Osaki, Tatsuya; Sivathanu, Vivek; Kamm, Roger D

2018-03-26

Neurovascular coupling plays a key role in the pathogenesis of neurodegenerative disorders including motor neuron disease (MND). In vitro models provide an opportunity to understand the pathogenesis of MND, and offer the potential for drug screening. Here, we describe a new 3D microvascular and neuronal network model in a microfluidic platform to investigate interactions between these two systems. Both 3D networks were established by co-culturing human embryonic stem (ES)-derived MN spheroids and endothelial cells (ECs) in microfluidic devices. Co-culture with ECs improves neurite elongation and neuronal connectivity as measured by Ca 2+ oscillation. This improvement was regulated not only by paracrine signals such as brain-derived neurotrophic factor secreted by ECs but also through direct cell-cell interactions via the delta-notch pathway, promoting neuron differentiation and neuroprotection. Bi-directional signaling was observed in that the neural networks also affected vascular network formation under perfusion culture. This in vitro model could enable investigations of neuro-vascular coupling, essential to understanding the pathogenesis of neurodegenerative diseases including MNDs such as amyotrophic lateral sclerosis.

Direct bonding in diastema closure--high drama, immediate resolution.

PubMed

Blitz, N

1996-07-01

Aesthetic rehabilitation in complex diastema closure cases is guided by the principles of proportion. The width to length ratio of the centrals must be pleasing. Achievement of this proper balance dictates treatment. It determines the following: 1) the amount of distal proximal reduction; 2) the decision to completely veneer the incisors vs. just adding to the interproximal; 3) the number of teeth to be treated; 4) the placement and location of naturally occurring prominences and concavities to create the illusion of a narrower tooth. The proper accommodation of these four topics will permit the maintenance or restoration of acceptable dimensions in the centrals. If they are made to appear harmonious then the principle of "golden proportion" (1.6:1:0.6) can be achieved among the centrals, laterals and cuspids. Direct bonding in diastema closure cases allow the dentist and the patient complete control in the formation of that smile. This treatment modality is challenging and ultimately rewarding for the patient and the dentist. At times it enables us to restore form and function and to make our patients whole again not just figuratively but literally.

Mechanisms of Furfural Reduction on Metal Electrodes: Distinguishing Pathways for Selective Hydrogenation of Bioderived Oxygenates

DOE PAGES

Chadderdon, Xiaotong H.; Chadderdon, David J.; Matthiesen, John E.; ...

2017-09-13

Electrochemical reduction of biomass-derived platform molecules is an emerging route for the sustainable production of fuels and chemicals. Understanding gaps between reaction conditions, underlying mechanisms, and product selectivity have limited the rational design of active, stable, and selective catalyst systems. Here, the mechanisms of electrochemical reduction of furfural, an important biobased platform molecule and model for aldehyde reduction, are explored through a combination of voltammetry, preparative electrolysis, thiol-electrode modifications, and kinetic isotope studies. It is demonstrated that two distinct mechanisms are operable on metallic Cu electrodes in acidic electrolytes: (i) electrocatalytic hydrogenation (ECH) and (ii) direct electroreduction. The contributions ofmore » each mechanism to the observed product distribution are clarified by evaluating the requirement for direct chemical interactions with the electrode surface and the role of adsorbed hydrogen. Further analysis reveals that hydrogenation and hydrogenolysis products are generated by parallel ECH pathways. By understanding the underlying mechanisms it enables the manipulation of furfural reduction by rationally tuning the electrode potential, electrolyte pH, and furfural concentration to promote selective formation of important biobased polymer precursors and fuels.« less

Portable device and method for determining permeability characteristics of earth formations

DOEpatents

Shuck, Lowell Z.

1977-01-01

The invention is directed to a device which is used for determining permeability characteristics of earth formations at the surface thereof. The determination of the maximum permeability direction and the magnitude of permeability are achieved by employing a device comprising a housing having a central fluid-injection port surrounded by a plurality of spaced-apart fluid flow and pressure monitoring ports radially extending from the central injection port. With the housing resting on the earth formation in a relatively fluid-tight manner as provided by an elastomeric pad disposed therebetween, fluid is injected through the central port into the earth formation and into registry with the fluid-monitoring ports disposed about the injection port. The fluid-monitoring ports are selectively opened and the flow of the fluid through the various fluid ports is measured so as to provide a measurement of flow rates and pressure distribution about the center hole which is indicative on the earth formation permeability direction and magnitude. For example, the azimuthal direction of the fluid-monitoring ports in the direction through which the greatest amount of injected fluid flows as determined by the lowest pressure distribution corresponds to the direction of maximum permeability in the earth formation.

Influence of the formation- and passivation rate of boron-oxygen defects for mitigating carrier-induced degradation in silicon within a hydrogen-based model

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

Hallam, Brett, E-mail: brett.hallam@unsw.edu.au; Abbott, Malcolm; Nampalli, Nitin

2016-02-14

A three-state model is used to explore the influence of defect formation- and passivation rates of carrier-induced degradation related to boron-oxygen complexes in boron-doped p-type silicon solar cells within a hydrogen-based model. The model highlights that the inability to effectively mitigate carrier-induced degradation at elevated temperatures in previous studies is due to the limited availability of defects for hydrogen passivation, rather than being limited by the defect passivation rate. An acceleration of the defect formation rate is also observed to increase both the effectiveness and speed of carrier-induced degradation mitigation, whereas increases in the passivation rate do not lead tomore » a substantial acceleration of the hydrogen passivation process. For high-throughput mitigation of such carrier-induced degradation on finished solar cell devices, two key factors were found to be required, high-injection conditions (such as by using high intensity illumination) to enable an acceleration of defect formation whilst simultaneously enabling a rapid passivation of the formed defects, and a high temperature to accelerate both defect formation and defect passivation whilst still ensuring an effective mitigation of carrier-induced degradation.« less

Natural remanent magnetization and rock magnetic parameters from the North-East Atlantic continental margin : Insights from a new, automated cryogenic magnetometer at the Geological Survey of Norway

NASA Astrophysics Data System (ADS)

Klug, Martin; Fabian, Karl; Knies, Jochen; Sauer, Simone

2017-04-01

Natural remanent magnetization (NRM) and rock magnetic parameters from two locations, West Barents Sea ( 71.6°N,16.2°E) and Vestnesa Ridge, NW Svalbard ( 79.0°N, 6.9°E), were acquired using a new, automatically operating cryogenic magnetometer system at the Geological Survey of Norway. The magnetometer setup comprises an automated robot sample feeding, dynamic operation and measurement monitoring, and customised output-to-database data handling. The setup is designed to dynamically enable a variety of parallel measurements with several coupled devices (e.g. balance, MS2B) to effectively use dead-time in between the otherwise time-consuming measurements with the cryogen magnetometer. Web-based access allows remote quality control and interaction 24/7 and enables high sample throughput. The magnetic properties are combined with geophysical, geochemical measurements and optical imaging, both radiographic and colour images, from high-resolution core-logging. The multidisciplinary approach enables determination and interpretation of content and formation of the magnetic fraction, and its development during diagenetic processes. Besides palaeomagnetic age determination the results offer the opportunity to study sediment transformation processes that have implications for the burial and degradation of organic matter. The results also help to understand long and short-term variability of sediment accumulation. Chemical sediment stability is directly linked to environmental and climate variability in the polar marine environment during the recent past.

Reconsidering plant memory: Intersections between stress recovery, RNA turnover, and epigenetics

PubMed Central

Crisp, Peter A.; Ganguly, Diep; Eichten, Steven R.; Borevitz, Justin O.; Pogson, Barry J.

2016-01-01

Plants grow in dynamic environments where they can be exposed to a multitude of stressful factors, all of which affect their development, yield, and, ultimately, reproductive success. Plants are adept at rapidly acclimating to stressful conditions and are able to further fortify their defenses by retaining memories of stress to enable stronger or more rapid responses should an environmental perturbation recur. Indeed, one mechanism that is often evoked regarding environmental memories is epigenetics. Yet, there are relatively few examples of such memories; neither is there a clear understanding of their duration, considering the plethora of stresses in nature. We propose that this field would benefit from investigations into the processes and mechanisms enabling recovery from stress. An understanding of stress recovery could provide fresh insights into when, how, and why environmental memories are created and regulated. Stress memories may be maladaptive, hindering recovery and affecting development and potential yield. In some circumstances, it may be advantageous for plants to learn to forget. Accordingly, the recovery process entails a balancing act between resetting and memory formation. During recovery, RNA metabolism, posttranscriptional gene silencing, and RNA-directed DNA methylation have the potential to play key roles in resetting the epigenome and transcriptome and in altering memory. Exploration of this emerging area of research is becoming ever more tractable with advances in genomics, phenomics, and high-throughput sequencing methodology that will enable unprecedented profiling of high-resolution stress recovery time series experiments and sampling of large natural populations. PMID:26989783

Implementation of orthogonal frequency division multiplexing (OFDM) and advanced signal processing for elastic optical networking in accordance with networking and transmission constraints

NASA Astrophysics Data System (ADS)

Johnson, Stanley

An increasing adoption of digital signal processing (DSP) in optical fiber telecommunication has brought to the fore several interesting DSP enabled modulation formats. One such format is orthogonal frequency division multiplexing (OFDM), which has seen great success in wireless and wired RF applications, and is being actively investigated by several research groups for use in optical fiber telecom. In this dissertation, I present three implementations of OFDM for elastic optical networking and distributed network control. The first is a field programmable gate array (FPGA) based real-time implementation of a version of OFDM conventionally known as intensity modulation and direct detection (IMDD) OFDM. I experimentally demonstrate the ability of this transmission system to dynamically adjust bandwidth and modulation format to meet networking constraints in an automated manner. To the best of my knowledge, this is the first real-time software defined networking (SDN) based control of an OFDM system. In the second OFDM implementation, I experimentally demonstrate a novel OFDM transmission scheme that supports both direct detection and coherent detection receivers simultaneously using the same OFDM transmitter. This interchangeable receiver solution enables a trade-off between bit rate and equipment cost in network deployment and upgrades. I show that the proposed transmission scheme can provide a receiver sensitivity improvement of up to 1.73 dB as compared to IMDD OFDM. I also present two novel polarization analyzer based detection schemes, and study their performance using experiment and simulation. In the third implementation, I present an OFDM pilot-tone based scheme for distributed network control. The first instance of an SDN-based OFDM elastic optical network with pilot-tone assisted distributed control is demonstrated. An improvement in spectral efficiency and a fast reconfiguration time of 30 ms have been achieved in this experiment. Finally, I experimentally demonstrate optical re-timing of a 10.7 Gb/s data stream utilizing the property of bound soliton pairs (or "soliton molecules") to relax to an equilibrium temporal separation after propagation through a nonlinear dispersion alternating fiber span. Pulses offset up to 16 ps from bit center are successfully re-timed. The optical re-timing scheme studied here is a good example of signal processing in the optical domain and such a technique can overcome the bandwidth bottleneck present in DSP. An enhanced version of this re-timing scheme is analyzed using numerical simulations.

Catalysis of Dialanine Formation by Glycine in the Salt-Induced Peptide Formation Reaction.

NASA Astrophysics Data System (ADS)

Suwannachot, Yuttana; Rode, Bernd M.

1998-02-01

Mutual catalysis of amino acids in the salt-induced peptide formation (SIPF) reaction is demonstrated for the case of glycine/alanine. The presence of glycine enhances dialanine formation by a factor up to 50 and enables dialanine formation at much lower alanine concentrations. The actual amounts of glycine play an important role for this catalytic effect, the optimal glycine concentration is 1/8 of the alanine concentration. The mechanism appears to be based on the formation of the intermediate Gly-Ala-Ala tripeptide, connected to one coordination site of copper(II) ion, and subsequent hydrolysis to dialanine and glycine.

Catalysis of dialanine formation by glycine in the salt-induced peptide formation reaction.

PubMed

Suwannachot, Y; Rode, B M

1998-02-01

Mutual catalysis of amino acids in the salt-induced peptide formation (SIPF) reaction is demonstrated for the case of glycine/alanine. The presence of glycine enhances dialanine formation by a factor up to 50 and enables dialanine formation at much lower alanine concentrations. The actual amounts of glycine play an important role for this catalytic effect, the optimal glycine concentration is 1/8 of the alanine concentration. The mechanism appears to be based on the formation of the intermediate Gly-Ala-Ala tripeptide, connected to one coordination site of copper(II) ion, and subsequent hydrolysis to dialanine and glycine.

Prediction of 3D chip formation in the facing cutting with lathe machine using FEM

NASA Astrophysics Data System (ADS)

Prasetyo, Yudhi; Tauviqirrahman, Mohamad; Rusnaldy

2016-04-01

This paper presents the prediction of the chip formation at the machining process using a lathe machine in a more specific way focusing on facing cutting (face turning). The main purpose is to propose a new approach to predict the chip formation with the variation of the cutting directions i.e., the backward and forward direction. In addition, the interaction between stress analysis and chip formation on cutting process was also investigated. The simulations were conducted using three dimensional (3D) finite element method based on ABAQUS software with aluminum and high speed steel (HSS) as the workpiece and the tool materials, respectively. The simulation result showed that the chip resulted using a backward direction depicts a better formation than that using a conventional (forward) direction.

Digital-Direct-RT-PCR: a sensitive and specific method for quantification of CTC in patients with cervical carcinoma

PubMed Central

Pfitzner, Claudia; Schröder, Isabel; Scheungraber, Cornelia; Dogan, Askin; Runnebaum, Ingo Bernhard; Dürst, Matthias; Häfner, Norman

2014-01-01

The detection of circulating tumour cells (CTC) in cancer patients may be useful for therapy monitoring and prediction of relapse. A sensitive assay based on HPV-oncogene transcripts which are highly specific for cervical cancer cells was established. The Digital-Direct-RT-PCR (DD-RT-PCR) combines Ficoll-separation, ThinPrep-fixation and one-step RT-PCR in a low-throughput digital-PCR format enabling the direct analysis and detection of individual CTC without RNA isolation. Experimental samples demonstrated a sensitivity of one HPV-positive cell in 500,000 HPV-negative cells. Spike-in experiments with down to 5 HPV-positive cells per millilitre EDTA-blood resulted in concordant positive results by PCR and immunocytochemistry. Blood samples from 3 of 10 CxCa patients each contained a single HPV-oncogene transcript expressing CTC among 5 to 15*105 MNBC. Only 1 of 7 patients with local but 2 of 3 women with systemic disease had CTC. This highly sensitive DD-RT-PCR for the detection of CTC may also be applied to other tumour entities which express tumour-specific transcripts. Abbreviations: CTC – circulating tumour cells, CxCa – cervical cancer, DD-RT-PCR – Digital-Direct Reverse Transcriptase PCR, HPV – Human Papilloma Virus, MNBC – mononuclear blood cells, ICC – immunocytochemistry. PMID:24496006

A new model for simulating 3-d crystal growth and its application to the study of antifreeze proteins.

PubMed

Wathen, Brent; Kuiper, Michael; Walker, Virginia; Jia, Zongchao

2003-01-22

A novel computational technique for modeling crystal formation has been developed that combines three-dimensional (3-D) molecular representation and detailed energetics calculations of molecular mechanics techniques with the less-sophisticated probabilistic approach used by statistical techniques to study systems containing millions of molecules undergoing billions of interactions. Because our model incorporates both the structure of and the interaction energies between participating molecules, it enables the 3-D shape and surface properties of these molecules to directly affect crystal formation. This increase in model complexity has been achieved while simultaneously increasing the number of molecules in simulations by several orders of magnitude over previous statistical models. We have applied this technique to study the inhibitory effects of antifreeze proteins (AFPs) on ice-crystal formation. Modeling involving both fish and insect AFPs has produced results consistent with experimental observations, including the replication of ice-etching patterns, ice-growth inhibition, and specific AFP-induced ice morphologies. Our work suggests that the degree of AFP activity results more from AFP ice-binding orientation than from AFP ice-binding strength. This technique could readily be adapted to study other crystal and crystal inhibitor systems, or to study other noncrystal systems that exhibit regularity in the structuring of their component molecules, such as those associated with the new nanotechnologies.

Defining the Core Archive Data Standards of the International Planetary Data Alliance (IPDA)

NASA Technical Reports Server (NTRS)

Hughes, J. Steven; Crichton, Dan; Beebe, Reta; Guinness, Ed; Heather, David; Zender, Joe

2007-01-01

A goal of the International Planetary Data Alliance (lPDA) is to develop a set of archive data standards that enable the sharing of scientific data across international agencies and missions. To help achieve this goal, the IPDA steering committee initiated a six month proj ect to write requirements for and draft an information model based on the Planetary Data System (PDS) archive data standards. The project had a special emphasis on data formats. A set of use case scenarios were first developed from which a set of requirements were derived for the IPDA archive data standards. The special emphasis on data formats was addressed by identifying data formats that have been used by PDS nodes and other agencies in the creation of successful data sets for the Planetary Data System (PDS). The dependency of the IPDA information model on the PDS archive standards required the compilation of a formal specification of the archive standards currently in use by the PDS. An ontology modelling tool was chosen to capture the information model from various sources including the Planetary Science Data Dictionary [I] and the PDS Standards Reference [2]. Exports of the modelling information from the tool database were used to produce the information model document using an object-oriented notation for presenting the model. The tool exports can also be used for software development and are directly accessible by semantic web applications.

Synthetic niches for differentiation of human embryonic stem cells bypassing embryoid body formation.

PubMed

Liu, Yarong; Fox, Victoria; Lei, Yuning; Hu, Biliang; Joo, Kye-Il; Wang, Pin

2014-07-01

The unique self-renewal and pluripotency features of human embryonic stem cells (hESCs) offer the potential for unlimited development of novel cell therapies. Currently, hESCs are cultured and differentiated using methods, such as monolayer culture and embryoid body (EB) formation. As such, achieving efficient differentiation into higher order structures remains a challenge, as well as maintaining cell viability during differentiation into homogeneous cell populations. Here, we describe the application of highly porous polymer scaffolds as synthetic stem cell niches. Bypassing the EB formation step, these scaffolds are capable of three-dimensional culture of undifferentiated hESCs and subsequent directed differentiation into three primary germ layers. H9 hESCs were successfully maintained and proliferated in biodegradable polymer scaffolds based on poly (lactic-co-glycolic acid) (PLGA). The results showed that cells within PLGA scaffolds retained characteristics of undifferentiated pluripotent stem cells. Moreover, the scaffolds allowed differentiation towards the lineage of interest by the addition of growth factors to the culture system. The in vivo transplantation study revealed that the scaffolds could provide a microenvironment that enabled hESCs to interact with their surroundings, thereby promoting cell differentiation. Therefore, this approach, which provides a unique culture/differentiation system for hESCs, will find its utility in various stem cell-based tissue-engineering applications. © 2013 Wiley Periodicals, Inc.

Assessment of femtosecond laser induced periodic surface structures on polymer films.

PubMed

Rebollar, Esther; Vázquez de Aldana, Javier R; Martín-Fabiani, Ignacio; Hernández, Margarita; Rueda, Daniel R; Ezquerra, Tiberio A; Domingo, Concepción; Moreno, Pablo; Castillejo, Marta

2013-07-21

In this work we present the formation of laser induced periodic surface structures (LIPSS) on spin-coated thin films of several model aromatic polymers including poly(ethylene terephthalate), poly(trimethylene terephthalate) and poly carbonate bis-phenol A upon irradiation with femtosecond pulses of 795 and 265 nm at fluences well below the ablation threshold. LIPSS are formed with period lengths similar to the laser wavelength and parallel to the direction of the laser polarization vector. Formation of LIPSS upon IR irradiation at 795 nm, a wavelength at which the polymers absorb weakly, contrasts with the absence of LIPSS in this spectral range upon irradiation with nanosecond pulses. Real and reciprocal space characterization of LIPSS obtained by Atomic Force Microscopy (AFM) and Grazing Incidence Small Angle X-ray Scattering (GISAXS), respectively, yields well correlated morphological information. Comparison of experimental and simulated GISAXS patterns suggests that LIPSS can be suitably described considering a quasi-one-dimensional paracrystalline lattice and that irradiation parameters have an influence on the order of such a lattice. Fluorescence measurements, after laser irradiation, provide indirect information about dynamics and structure of the polymer at the molecular level. Our results indicate that the LIPSS are formed by interference of the incident and surface scattered waves. As a result of this process, heating of the polymer surface above its glass transition temperature takes place enabling LIPSS formation.

Highly Manufacturable Deep (Sub-Millimeter) Etching Enabled High Aspect Ratio Complex Geometry Lego-Like Silicon Electronics.

PubMed

Ghoneim, Mohamed Tarek; Hussain, Muhammad Mustafa

2017-04-01

A highly manufacturable deep reactive ion etching based process involving a hybrid soft/hard mask process technology shows high aspect ratio complex geometry Lego-like silicon electronics formation enabling free-form (physically flexible, stretchable, and reconfigurable) electronic systems. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Integration of cell-free protein coexpression with an enzyme-linked immunosorbent assay enables rapid analysis of protein–protein interactions directly from DNA

PubMed Central

Layton, Curtis J; Hellinga, Homme W

2011-01-01

Assays that integrate detection of binding with cell-free protein expression directly from DNA can dramatically increase the pace at which protein–protein interactions (PPIs) can be analyzed by mutagenesis. In this study, we present a method that combines in vitro protein production with an enzyme-linked immunosorbent assay (ELISA) to measure PPIs. This method uses readily available commodity instrumentation and generic antibody–affinity tag interactions. It is straightforward and rapid to execute, enabling many interactions to be assessed in parallel. In traditional ELISAs, reporter complexes are assembled stepwise with one layer at a time. In the method presented here, all the members of the reporter complex are present and assembled together. The signal strength is dependent on all the intercomponent interaction affinities and concentrations. Although this assay is straightforward to execute, establishing proper conditions and analysis of the results require a thorough understanding of the processes that determine the signal strength. The formation of the fully assembled reporter sandwich can be modeled as a competition between Langmuir adsorption isotherms for the immobilized components and binding equilibria of the solution components. We have shown that modeling this process provides semiquantitative understanding of the effects of affinity and concentration and can guide strategies for the development of experimental protocols. We tested the method experimentally using the interaction between a synthetic ankyrin repeat protein (Off7) and maltose-binding protein. Measurements obtained for a collection of alanine mutations in the interface between these two proteins demonstrate that a range of affinities can be analyzed. PMID:21674663

Monolithic graded-refractive-index glass-based antireflective coatings. Broadband/omnidirectional light harvesting and self-cleaning characteristics

DOE PAGES

Aytug, Tolga; Lupini, Andrew R.; Jellison, Gerald E.; ...

2015-04-23

The design of multifunctional coatings impact impact the performance of many optical systems and components. Such coatings should be mechanically robust, and combine user-defined optical and wetting functions with scalable fabrication formulations. By taking cues from the properties of some natural biological structures, we report here the formation of low-refractive index antireflective glass films that embody omni-directional optical properties over a wide range of wavelengths, while also possessing specific wetting capabilities. The coatings comprise an interconnected network of nanoscale pores surrounded by a nanostructured silica framework. These structures result from a novel fabrication method that utilizes metastable spinodal phase separationmore » in glass-based materials. The approach not only enables design of surface microstructures with graded-index antireflection characteristics, where the surface reflection is suppressed through optical impedance matching between interfaces, but also facilitates self-cleaning ability through modification of the surface chemistry. Based on near complete elimination of Fresnel reflections (yielding >95% transmission through a single-side coated glass) and corresponding increase in broadband transmission, the fabricated nanostructured surfaces are found to promote a general and an invaluable ~3–7% relative increase in current output of multiple direct/indirect bandgap photovoltaic cells. Moreover, these antireflective surfaces also demonstrate superior resistance against mechanical wear and abrasion. Unlike conventional counterparts, the present antireflective coatings are essentially monolithic, enabling simultaneous realization of graded index anti-reflectivity, self-cleaning capability, and mechanical stability within the same surface. Moreover, the concept represents a fundamental basis for development of advanced coated optical quality products, especially where environmental exposure is required.« less

Emerging feed-forward inhibition allows the robust formation of direction selectivity in the developing ferret visual cortex

PubMed Central

Escobar, Gina M.; Maffei, Arianna; Miller, Paul

2014-01-01

The computation of direction selectivity requires that a cell respond to joint spatial and temporal characteristics of the stimulus that cannot be separated into independent components. Direction selectivity in ferret visual cortex is not present at the time of eye opening but instead develops in the days and weeks following eye opening in a process that requires visual experience with moving stimuli. Classic Hebbian or spike timing-dependent modification of excitatory feed-forward synaptic inputs is unable to produce direction-selective cells from unselective or weakly directionally biased initial conditions because inputs eventually grow so strong that they can independently drive cortical neurons, violating the joint spatial-temporal activation requirement. Furthermore, without some form of synaptic competition, cells cannot develop direction selectivity in response to training with bidirectional stimulation, as cells in ferret visual cortex do. We show that imposing a maximum lateral geniculate nucleus (LGN)-to-cortex synaptic weight allows neurons to develop direction-selective responses that maintain the requirement for joint spatial and temporal activation. We demonstrate that a novel form of inhibitory plasticity, postsynaptic activity-dependent long-term potentiation of inhibition (POSD-LTPi), which operates in the developing cortex at the time of eye opening, can provide synaptic competition and enables robust development of direction-selective receptive fields with unidirectional or bidirectional stimulation. We propose a general model of the development of spatiotemporal receptive fields that consists of two phases: an experience-independent establishment of initial biases, followed by an experience-dependent amplification or modification of these biases via correlation-based plasticity of excitatory inputs that compete against gradually increasing feed-forward inhibition. PMID:24598528

Flightless I interacts with NMMIIA to promote cell extension formation, which enables collagen remodeling

PubMed Central

Arora, Pamma D.; Wang, Yongqiang; Bresnick, Anne; Janmey, Paul A.; McCulloch, Christopher A.

2015-01-01

We examined the role of the actin-capping protein flightless I (FliI) in collagen remodeling by mouse fibroblasts. FliI-overexpressing cells exhibited reduced spreading on collagen but formed elongated protrusions that stained for myosin10 and fascin and penetrated pores of collagen-coated membranes. Inhibition of Cdc42 blocked formation of cell protrusions. In FliI-knockdown cells, transfection with constitutively active Cdc42 did not enable protrusion formation. FliI-overexpressing cells displayed increased uptake and degradation of exogenous collagen and strongly compacted collagen fibrils, which was blocked by blebbistatin. Mass spectrometry analysis of FliI immunoprecipitates showed that FliI associated with nonmuscle myosin IIA (NMMIIA), which was confirmed by immunoprecipitation. GFP-FliI colocalized with NMMIIA at cell protrusions. Purified FliI containing gelsolin-like domains (GLDs) 1–6 capped actin filaments efficiently, whereas FliI GLD 2–6 did not. Binding assays showed strong interaction of purified FliI protein (GLD 1–6) with the rod domain of NMMIIA (kD = 0.146 μM), whereas FliI GLD 2–6 showed lower binding affinity (kD = 0.8584 μM). Cells expressing FliI GLD 2–6 exhibited fewer cell extensions, did not colocalize with NMMIIA, and showed reduced collagen uptake compared with cells expressing FliI GLD 1–6. We conclude that FliI interacts with NMMIIA to promote cell extension formation, which enables collagen remodeling in fibroblasts. PMID:25877872

The Nature of the Microstructure and Interface Boundary Formation in Directionally Solidified Ceramic Boride Composites

DTIC Science & Technology

2015-02-19

boride composites *Volodymyr Borysovych Filipov SCIENCE AND TECHNOLOGY CENTER IN UKRAINE METALISTIV 7A, KYIV, UKRAINE *FRANTSEVICH...microstructure and interface boundary formation in directionally solidified ceramic boride composites 5a. CONTRACT NUMBER STCU P-512 5b. GRANT NUMBER...BOUNDARY FORMATION IN DIRECTIONALLY SOLIDIFIED CERAMIC BORIDE COMPOSITES Project manager: Filipov Volodymyr Borysovych Phone: (+380.44) 424-13-67

Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format.

PubMed

Webb, Ryan L; Ma'ayan, Avi

2011-03-21

The World Wide Web plays a critical role in enabling molecular, cell, systems and computational biologists to exchange, search, visualize, integrate, and analyze experimental data. Such efforts can be further enhanced through the development of semantic web concepts. The semantic web idea is to enable machines to understand data through the development of protocol free data exchange formats such as Resource Description Framework (RDF) and the Web Ontology Language (OWL). These standards provide formal descriptors of objects, object properties and their relationships within a specific knowledge domain. However, the overhead of converting datasets typically stored in data tables such as Excel, text or PDF into RDF or OWL formats is not trivial for non-specialists and as such produces a barrier to seamless data exchange between researchers, databases and analysis tools. This problem is particularly of importance in the field of network systems biology where biochemical interactions between genes and their protein products are abstracted to networks. For the purpose of converting biochemical interactions into the BioPAX format, which is the leading standard developed by the computational systems biology community, we developed an open-source command line tool that takes as input tabular data describing different types of molecular biochemical interactions. The tool converts such interactions into the BioPAX level 3 OWL format. We used the tool to convert several existing and new mammalian networks of protein interactions, signalling pathways, and transcriptional regulatory networks into BioPAX. Some of these networks were deposited into PathwayCommons, a repository for consolidating and organizing biochemical networks. The software tool Sig2BioPAX is a resource that enables experimental and computational systems biologists to contribute their identified networks and pathways of molecular interactions for integration and reuse with the rest of the research community.

Rapid Gorge Formation in an Artificially Created Waterfall

NASA Astrophysics Data System (ADS)

Anton, L.; Mather, A. E.; Stokes, M.; Munoz Martin, A.

2014-12-01

A number of studies have examined rates of gorge formation, nick point retreat, and the controls on those rates via bedrock erodibility, the effectiveness of bedrock erosion mechanisms and the role of hillslope processes. Most findings are based on conceptual / empirical models or long term landscape analysis; but studies of recent quantifiable events are scarce yet highly valuable. Here we present expert eye witness account and quantitative survey of large and rapid fluvial erosion events that occurred over an artificially created waterfall at a spillway mouth. In 6 years a ~270 m long, ~100 m deep and ~100 to 160 m wide canyon was carved, and ~1.58 x106 m3 of granite bedrock was removed from the spillway site. Available flow data indicates that the erosion took place under unremarkable flood discharge conditions. The analysis of historic topographic maps enables the reconstruction of the former topography and successive erosion events, enabling the quantification of bedrock erosion amounts, and rates. Analysis of bedrock erodibility and discontinuity patterns demonstrates that the bedrock is mechanically strong, and that similar rock strength and fracture patterns are found throughout the region. It is apparent that structural pre-conditioning through fracture density and orientation in relation to flow and slope direction is of paramount importance in the gorge development. The presented example provides an exceptional opportunity for studying the evolution process of a bedrock canyon and to precisely measure the rate of bedrock channel erosion over a six year period. Results illustrate the highly episodic nature of the erosion and highlight several key observations for the adjustability of bedrock rivers. The observations have implications for the efficiency of bedrock erosion and raise important questions about incision rates, driving mechanisms and timescale assumptions' in models of landscape change.

OA8 Caring for the family caregiver: working with volunteers to implement and improve a service to enable family caregivers to maintain their own wellbeing.

PubMed

Cohen, S Robin; Keats, Susan; Cherba, Maria; Allen, Dawn; MacKinnon, Christopher J; Bitzas, Vasiliki; Kogan, Naomi; Penner, Jamie L; Calislar, Monica Parmar; Feindel, Anna; Lapointe, Bernard; Baxter, Sharon; O'Brien, Suzanne; Stajduhar, Kelli

2015-04-01

Family caregivers suffer physically, mentally, and spiritually. Community volunteers play an important role in supporting patients at the end of life or former caregivers in bereavement. However, there are no research reports of volunteer services focused on maintaining the wellbeing of end-of-life caregivers. To have volunteers, a hired volunteer coordinator, health care providers, and researchers implement and formatively evaluate a volunteer service to enable family caregivers to maintain their well being while providing care and subsequent bereavement. This presentation will focus on the volunteers' roles with the project as both agents of change to the service and as support for the caregivers. A qualitative formative evaluation informed by Guba and Lincoln's Fourth Generation Evaluation (1989) participatory design was conducted. Data was collected through individual interviews, focus groups, participant observation during volunteer support meetings, and through volunteers' written reflections. Amongst the volunteers, volunteer coordinator, and principal investigator, there was mutual respect for and interest in learning about everyone's roles and experiences in the project. The experience was rewarding because they felt they helped the family caregiver and enjoyed developing and improving the service and working in a supportive team. Volunteers' challenges included being nervous for their first meeting with a caregiver, and frustration with some rules put in place to protect them (e.g. not helping the caregiver with direct care for the patient). Volunteers can be an effective part of the research team, while providing valuable support and encouragement for family caregivers to maintain their own wellbeing. © 2015, Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Extractive alkylation of 6-mercaptopurine and determination in plasma by gas chromatography-mass spectrometry.

PubMed

Floberg, S; Hartvig, P; Lindström, B; Lönner-Holm, G; Odlind, B

1981-09-11

An analytical procedure was developed for the determination of 6-mercaptopurine in plasma. Owing to the polar character and low plasma concentration of the compound, extraction and derivatization was carried out directly from the plasma sample by extractive alkylation. Determination was made using gas chromatography-mass spectrometry with multiple-ion detection. Conditions with respect to the rate of formation and the stability of the derivative formed in the extractive alkylation step were evaluated. The selectively of the method to azathioprine and to metabolites was thoroughly investigated. No 6-mercaptopurine was formed from azathioprine added to water or plasma and run through the method. The method enables the detection of 2 ng of 6 mercaptopurine in a 1.0-ml plasma sample. Quantitative determinations were done down to 10 ng/ml 6 mercaptopurine in plasma.

Image Formation in High Contrast Optical Systems: The Role of Polarization

NASA Technical Reports Server (NTRS)

Breckinridge, James B.

2004-01-01

To find evidence of life in the Universe outside our solar system is one of the most compelling and visionary adventures of the 21st century. The technologies to create the telescopes and instruments that will enable this discovery are now within the grasp of mankind. Direct imaging of a very faint planet around a neighboring bright star requires high contrast or a hypercontrast optical imaging system capable of controlling unwanted radiation within the system to one part in ten to the 11th. This paper identifies several physical phenomena that affect image quality in high contrast imaging systems. Polarization induced at curved metallic surfaces and by anisotropy in the deposition process (Smith-Purcell effect) along with beam shifts introduced by the Goos-Hachen effect are discussed. A typical configuration is analyzed, and technical risk mitigation concepts are discussed.

Scientific Resource EXplorer

NASA Astrophysics Data System (ADS)

Xing, Z.; Wormuth, A.; Smith, A.; Arca, J.; Lu, Y.; Sayfi, E.

2014-12-01

Inquisitive minds in our society are never satisfied with curatedimages released by a typical public affairs office. They always want tolook deeper and play directly on original data. However, most scientificdata products are notoriously hard to use. They are immensely large,highly distributed and diverse in format. In this presentation,we will demonstrate Resource EXplorer (REX), a novel webtop applicationthat allows anyone to conveniently explore and visualize rich scientificdata repositories, using only a standard web browser. This tool leverageson the power of Webification Science (w10n-sci), a powerful enabling technologythat simplifies the use of scientific data on the web platform.W10n-sci is now being deployed at an increasing number of NASA data centers,some of which are the largest digital treasure troves in our nation.With REX, these wonderful scientific resources are open for teachers andstudents to learn and play.

Electrochemical deposition onto self-assembled monolayers: new insights into micro- and nanofabrication.

PubMed

Schilardi, Patricia L; Dip, Patricio; dos Santos Claro, Paula C; Benítez, Guillermo A; Fonticelli, Mariano H; Azzaroni, Omar; Salvarezza, Roberto C

2005-12-16

Pattern transfer with high resolution is a frontier topic in the emerging field of nanotechnologies. Electrochemical molding is a possible route for nanopatterning metal, alloys and oxide surfaces with high resolution in a simple and inexpensive way. This method involves electrodeposition onto a conducting master covered by a self-assembled alkanethiolate monolayer (SAMs). This molecular film enables direct surface-relief pattern transfer from the conducting master to the inner face of the electrodeposit, and also allows an easy release of the electrodeposited film due their excellent anti-adherent properties. Replicas of the original conductive master can be also obtained by a simple two-step procedure. SAM quality and stability under electrodeposition conditions combined with the formation of smooth electrodeposits are crucial to obtain high-quality pattern transfer with sub-50 nm resolution.

Application of isotope labeling experiments and (13)C flux analysis to enable rational pathway engineering.

PubMed

McAtee, Allison G; Jazmin, Lara J; Young, Jamey D

2015-12-01

Isotope labeling experiments (ILEs) and (13)C flux analysis provide actionable information for metabolic engineers to identify knockout, overexpression, and/or media optimization targets. ILEs have been used in both academic and industrial labs to increase product formation, discover novel metabolic functions in previously uncharacterized organisms, and enhance the metabolic efficiency of host cell factories. This review highlights specific examples of how ILEs have been used in conjunction with enzyme or metabolic engineering to elucidate host cell metabolism and improve product titer, rate, or yield in a directed manner. We discuss recent progress and future opportunities involving the use of ILEs and (13)C flux analysis to characterize non-model host organisms and to identify and subsequently eliminate wasteful byproduct pathways or metabolic bottlenecks. Copyright © 2015 Elsevier Ltd. All rights reserved.

A new technique in reference based DNA sequence compression algorithm: Enabling partial decompression

NASA Astrophysics Data System (ADS)

Banerjee, Kakoli; Prasad, R. A.

2014-10-01

The whole gamut of Genetic data is ever increasing exponentially. The human genome in its base format occupies almost thirty terabyte of data and doubling its size every two and a half year. It is well-know that computational resources are limited. The most important resource which genetic data requires in its collection, storage and retrieval is its storage space. Storage is limited. Computational performance is also dependent on storage and execution time. Transmission capabilities are also directly dependent on the size of the data. Hence Data compression techniques become an issue of utmost importance when we confront with the task of handling such giganticdatabases like GenBank. Decompression is also an issue when such huge databases are being handled. This paper is intended not only to provide genetic data compression but also partially decompress the genetic sequences.

Rhombohedral cubic semiconductor materials on trigonal substrate with single crystal properties and devices based on such materials

NASA Technical Reports Server (NTRS)

Park, Yeonjoon (Inventor); Choi, Sang Hyouk (Inventor); King, Glen C. (Inventor); Elliott, James R. (Inventor)

2012-01-01

Growth conditions are developed, based on a temperature-dependent alignment model, to enable formation of cubic group IV, group II-V and group II-VI crystals in the [111] orientation on the basal (0001) plane of trigonal crystal substrates, controlled such that the volume percentage of primary twin crystal is reduced from about 40% to about 0.3%, compared to the majority single crystal. The control of stacking faults in this and other embodiments can yield single crystalline semiconductors based on these materials that are substantially without defects, or improved thermoelectric materials with twinned crystals for phonon scattering while maintaining electrical integrity. These methods can selectively yield a cubic-on-trigonal epitaxial semiconductor material in which the cubic layer is substantially either directly aligned, or 60 degrees-rotated from, the underlying trigonal material.

Quantitative 3D evolution of colloidal nanoparticle oxidation in solution

DOE PAGES

Sun, Yugang; Zuo, Xiaobing; Sankaranarayanan, Subramanian K. R. S.; ...

2017-04-21

Real-time tracking three-dimensional (3D) evolution of colloidal nanoparticles in solution is essential for understanding complex mechanisms involved in nanoparticle growth and transformation. We simultaneously use time-resolved small-angle and wide-angle x-ray scattering to monitor oxidation of highly uniform colloidal iron nanoparticles, enabling the reconstruction of intermediate 3D morphologies of the nanoparticles with a spatial resolution of ~5 Å. The in-situ probing combined with large-scale reactive molecular dynamics simulations reveals the transformational details from the solid metal nanoparticles to hollow metal oxide nanoshells via nanoscale Kirkendall process, for example, coalescence of voids upon their growth, reversing of mass diffusion direction depending onmore » crystallinity, and so forth. In conclusion, our results highlight the complex interplay between defect chemistry and defect dynamics in determining nanoparticle transformation and formation.« less

Nanoaquariums Fabricated by Femtosecond Laser for Exploration of Dynamics and Functions of Microorganisms

NASA Astrophysics Data System (ADS)

Sugioka, Koji; Hanada, Yasutaka; Kawano, Hiroyuki; Ishikawa, Ikuko S.; Miyawaki, Atsushi; Midorikawa, Katsumi

2010-10-01

We demonstrate to fabricate microfluidic chips integrated with some functional elements such as optical attenuators and optical waveguides by femtosecond (fs) laser direct writing for mechanism study of gliding movement of Phormidium to a seedling root. Femtosecond laser irradiation followed by annealing and wet etching in dilute hydrofluoric (HF) acid solution resulted in formation of three-dimensional (3D) hollow microstructures embedded in a photosensitive glass. The embedded microfludic structures enabled us to easily and efficiently observe Phormidium gliding to the seedling root, which accelerates growth of the vegetable seedling. In addition, integration of optical attenuators and optical waveguides into the microfluidic structures in the microchip clarified the mechanism of the gliding movement of Phormidium. Such microchips, referred to as nanoaquariums, realized the highly efficient and functional observation and analysis of various microorganisms.

Nano-aquarium fabrication with cut-off filter for mechanism study of Phormidium assemblage

NASA Astrophysics Data System (ADS)

Hanada, Y.; Sugioka, K.; Ishikawa, I.; Kawano, H.; Miyawaki, A.; Midorikawa, K.

2010-02-01

We demonstrate fabrication of microfluidic chips integrated with different functional elements such as optical filters and optical waveguide for mechanism study of gliding movement of Phormidium to a seedling root using a femtosecond (fs) laser. Fs laser direct writing followed by annealing and successive wet etching in dilute hydrofluoric (HF) acid solution resulted in formation of three dimensional (3D) hollow microstructures embedded in a photostructurable glass. The embedded microfludic structures enabled us to easily and efficiently observe Phormidium gliding to the seedling root, which accelerates growth of the seedling. In addition, fabrication of optical filter and optical waveguide integrated with the microfluidic structures in the microchip clarified the mechanism of the gliding movement. Such microchips, referred to as a nano-aquarium, realize the efficient and highly functional observation and analysis of the gliding movement of Phormidium.

Evolution and Biological Roles of Alternative 3'UTRs.

PubMed

Mayr, Christine

2016-03-01

More than half of human genes use alternative cleavage and polyadenylation to generate alternative 3' untranslated region (3'UTR) isoforms. Most efforts have focused on transcriptome-wide mapping of alternative 3'UTRs and on the question of how 3'UTR isoform ratios may be regulated. However, it remains less clear why alternative 3'UTRs have evolved and what biological roles they play. This review summarizes our current knowledge of the functional roles of alternative 3'UTRs, including mRNA localization, mRNA stability, and translational efficiency. Recent work suggests that alternative 3'UTRs may also enable the formation of protein-protein interactions to regulate protein localization or to diversify protein functions. These recent findings open an exciting research direction for the investigation of new biological roles of alternative 3'UTRs. Copyright © 2015 Elsevier Ltd. All rights reserved.

Solution-processed, Self-organized Organic Single Crystal Arrays with Controlled Crystal Orientation

PubMed Central

Kumatani, Akichika; Liu, Chuan; Li, Yun; Darmawan, Peter; Takimiya, Kazuo; Minari, Takeo; Tsukagoshi, Kazuhito

2012-01-01

A facile solution process for the fabrication of organic single crystal semiconductor devices which meets the demand for low-cost and large-area fabrication of high performance electronic devices is demonstrated. In this paper, we develop a bottom-up method which enables direct formation of organic semiconductor single crystals at selected locations with desired orientations. Here oriented growth of one-dimensional organic crystals is achieved by using self-assembly of organic molecules as the driving force to align these crystals in patterned regions. Based upon the self-organized organic single crystals, we fabricate organic field effect transistor arrays which exhibit an average field-effect mobility of 1.1 cm2V−1s−1. This method can be carried out under ambient atmosphere at room temperature, thus particularly promising for production of future plastic electronics. PMID:22563523

Virtualization of open-source secure web services to support data exchange in a pediatric critical care research network

PubMed Central

Sward, Katherine A; Newth, Christopher JL; Khemani, Robinder G; Cryer, Martin E; Thelen, Julie L; Enriquez, Rene; Shaoyu, Su; Pollack, Murray M; Harrison, Rick E; Meert, Kathleen L; Berg, Robert A; Wessel, David L; Shanley, Thomas P; Dalton, Heidi; Carcillo, Joseph; Jenkins, Tammara L; Dean, J Michael

2015-01-01

Objectives To examine the feasibility of deploying a virtual web service for sharing data within a research network, and to evaluate the impact on data consistency and quality. Material and Methods Virtual machines (VMs) encapsulated an open-source, semantically and syntactically interoperable secure web service infrastructure along with a shadow database. The VMs were deployed to 8 Collaborative Pediatric Critical Care Research Network Clinical Centers. Results Virtual web services could be deployed in hours. The interoperability of the web services reduced format misalignment from 56% to 1% and demonstrated that 99% of the data consistently transferred using the data dictionary and 1% needed human curation. Conclusions Use of virtualized open-source secure web service technology could enable direct electronic abstraction of data from hospital databases for research purposes. PMID:25796596

Quantitative 3D evolution of colloidal nanoparticle oxidation in solution

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

Sun, Yugang; Zuo, Xiaobing; Sankaranarayanan, Subramanian K. R. S.

Real-time tracking three-dimensional (3D) evolution of colloidal nanoparticles in solution is essential for understanding complex mechanisms involved in nanoparticle growth and transformation. We simultaneously use time-resolved small-angle and wide-angle x-ray scattering to monitor oxidation of highly uniform colloidal iron nanoparticles, enabling the reconstruction of intermediate 3D morphologies of the nanoparticles with a spatial resolution of ~5 Å. The in-situ probing combined with large-scale reactive molecular dynamics simulations reveals the transformational details from the solid metal nanoparticles to hollow metal oxide nanoshells via nanoscale Kirkendall process, for example, coalescence of voids upon their growth, reversing of mass diffusion direction depending onmore » crystallinity, and so forth. In conclusion, our results highlight the complex interplay between defect chemistry and defect dynamics in determining nanoparticle transformation and formation.« less

Apollo2Go: a web service adapter for the Apollo genome viewer to enable distributed genome annotation.

PubMed

Klee, Kathrin; Ernst, Rebecca; Spannagl, Manuel; Mayer, Klaus F X

2007-08-30

Apollo, a genome annotation viewer and editor, has become a widely used genome annotation and visualization tool for distributed genome annotation projects. When using Apollo for annotation, database updates are carried out by uploading intermediate annotation files into the respective database. This non-direct database upload is laborious and evokes problems of data synchronicity. To overcome these limitations we extended the Apollo data adapter with a generic, configurable web service client that is able to retrieve annotation data in a GAME-XML-formatted string and pass it on to Apollo's internal input routine. This Apollo web service adapter, Apollo2Go, simplifies the data exchange in distributed projects and aims to render the annotation process more comfortable. The Apollo2Go software is freely available from ftp://ftpmips.gsf.de/plants/apollo_webservice.

Apollo2Go: a web service adapter for the Apollo genome viewer to enable distributed genome annotation

PubMed Central

Klee, Kathrin; Ernst, Rebecca; Spannagl, Manuel; Mayer, Klaus FX

2007-01-01

Background Apollo, a genome annotation viewer and editor, has become a widely used genome annotation and visualization tool for distributed genome annotation projects. When using Apollo for annotation, database updates are carried out by uploading intermediate annotation files into the respective database. This non-direct database upload is laborious and evokes problems of data synchronicity. Results To overcome these limitations we extended the Apollo data adapter with a generic, configurable web service client that is able to retrieve annotation data in a GAME-XML-formatted string and pass it on to Apollo's internal input routine. Conclusion This Apollo web service adapter, Apollo2Go, simplifies the data exchange in distributed projects and aims to render the annotation process more comfortable. The Apollo2Go software is freely available from . PMID:17760972

Microinverters for employment in connection with photovoltaic modules

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

Lentine, Anthony L.; Nielson, Gregory N.; Okandan, Murat

2015-09-22

Microinverters useable in association with photovoltaic modules are described. A three phase-microinverter receives direct current output generated by a microsystems-enabled photovoltaic cell and converts such direct current output into three-phase alternating current out. The three-phase microinverter is interleaved with other three-phase-microinverters, wherein such microinverters are integrated in a photovoltaic module with the microsystems-enabled photovoltaic cell.

Hydrogenation of silyl formates: sustainable production of silanol and methanol from hydrosilane and carbon dioxide.

PubMed

Koo, Jangwoo; Kim, Seung Hyo; Hong, Soon Hyeok

2018-05-10

A new process for simultaneously obtaining two chemical building blocks, methanol and silanol, was realized starting from silyl formates which can be derived from silane and carbon dioxide. Understanding the reaction mechanism enabled us to improve the reaction efficiency by the addition of a small amount of methanol.

Exploring Tensions in Developing Assessment for Learning

ERIC Educational Resources Information Center

Webb, Mary; Jones, Jane

2009-01-01

This paper is based on a study of classroom practice of primary school teachers who were engaged in a programme of professional development to implement formative assessment in their classrooms. The programme sought to develop the skills and expertise of teachers to enable formative assessment to be used to support and improve the learning of…

The Integrity of FPGA Designs: Capabilities Enabled by Unlocking Bitstreams and 3rd-Party IP

DTIC Science & Technology

2012-03-01

represented in an HDL such as Verilog or in another common electronic design format such as the Electronic Design Interchange Format ( EDIF ). Whether...Verilog or EDIF , however, the synthesized netlist is expressed as a connected and configured arrangement of the FPGA resources necessary to realize

Tough Choices in Designing a Formative Assessment System

ERIC Educational Resources Information Center

Sharkey, Nancy S.; Murnane, Richard J.

2006-01-01

A growing number of school districts in the United States are introducing formative assessment systems to measure student skills in core subjects throughout the year. The underlying logic is that providing teachers with timely information on student skills will enable them to improve instruction and better prepare students to excel on high-stakes,…

Fostering Critical Reflection in a Computer-Based, Asynchronously Delivered Diversity Training Course

ERIC Educational Resources Information Center

Givhan, Shawn T.

2013-01-01

This dissertation study chronicles the creation of a computer-based, asynchronously delivered diversity training course for a state agency. The course format enabled efficient delivery of a mandatory curriculum to the Massachusetts Department of State Police workforce. However, the asynchronous format posed a challenge to achieving the learning…

Nanocrystalline Precursors for the Co-Assembly of Crack-Free Metal Oxide Inverse Opals.

PubMed

Phillips, Katherine R; Shirman, Tanya; Shirman, Elijah; Shneidman, Anna V; Kay, Theresa M; Aizenberg, Joanna

2018-05-01

Inorganic microstructured materials are ubiquitous in nature. However, their formation in artificial self-assembly systems is challenging as it involves a complex interplay of competing forces during and after assembly. For example, colloidal assembly requires fine-tuning of factors such as the size and surface charge of the particles and electrolyte strength of the solvent to enable successful self-assembly and minimize crack formation. Co-assembly of templating colloidal particles together with a sol-gel matrix precursor material helps to release stresses that accumulate during drying and solidification, as previously shown for the formation of high-quality inverse opal (IO) films out of amorphous silica. Expanding this methodology to crystalline materials would result in microscale architectures with enhanced photonic, electronic, and catalytic properties. This work describes tailoring the crystallinity of metal oxide precursors that enable the formation of highly ordered, large-area (mm 2 ) crack-free titania, zirconia, and alumina IO films. The same bioinspired approach can be applied to other crystalline materials as well as structures beyond IOs. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Murai Reaction on Furfural Derivatives Enabled by Removable N,N'-Bidentate Directing Groups.

PubMed

Pezzetta, Cristofer; Veiros, Luis F; Oble, Julie; Poli, Giovanni

2017-06-22

Furfural and related compounds are industrially relevant building blocks obtained from lignocellulosic biomass. To enhance the added value of these renewable resources, a Ru-catalyzed hydrofurylation of alkenes, involving a directed C-H activation at C3 of the furan ring, was developed. A thorough experimental study revealed that a bidentate amino-imine directing group enabled the desired coupling. Removal of the directing group occurred during the purification step, directly releasing the C3-functionalized furfurals. Development of the reaction as well as optimization and scope of the method were described. A mechanism was proposed on the basis of DFT calculations. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Enhanced van der Waals epitaxy via electron transfer enabled interfacial dative bond formation

DOE PAGES

Xie, Weiyu; Lu, Toh -Ming; Wang, Gwo -Ching; ...

2017-11-14

Enhanced van der Waals (vdW) epitaxy of semiconductors on a layered vdW substrate is identified as the formation of dative bonds. For example, despite that NbSe 2 is a vdW layeredmaterial, first-principles calculations reveal that the bond strength at a CdTe-NbSe 2 interface is five times as large as that of vdW interactions at a CdTe-graphene interface. Finally, the unconventional chemistry here is enabled by an effective net electron transfer from Cd dangling-bond states at a CdTe surface to metallic nonbonding NbSe 2 states, which is a necessary condition to activate the Cd for enhanced binding with Se.

Enhanced van der Waals epitaxy via electron transfer enabled interfacial dative bond formation

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

Xie, Weiyu; Lu, Toh -Ming; Wang, Gwo -Ching

Enhanced van der Waals (vdW) epitaxy of semiconductors on a layered vdW substrate is identified as the formation of dative bonds. For example, despite that NbSe 2 is a vdW layeredmaterial, first-principles calculations reveal that the bond strength at a CdTe-NbSe 2 interface is five times as large as that of vdW interactions at a CdTe-graphene interface. Finally, the unconventional chemistry here is enabled by an effective net electron transfer from Cd dangling-bond states at a CdTe surface to metallic nonbonding NbSe 2 states, which is a necessary condition to activate the Cd for enhanced binding with Se.

Analysis of Borderline Substitution/Electron Transfer Pathways from Direct ab initio MD Simulations

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

Yamataka, H; Aida, M A.; Dupuis, Michel

Ab initio molecular dynamics simulations were carried out for the borderline reaction pathways in the reaction of CH2O?- with CH3Cl. The simulations reveal distinctive features of three types of mechanisms passing through the SN2-like transition state (TS): (i) a direct formation of SN2 products, (ii) a direct formation of ET products, and (iii) a 2-step formation of ET products via the SN2 valley. The direct formation of the ET product through the SN2-like TS appears to be more favorable at higher temperatures. The 2-step process depends on the amount of energy that goes into the C-C stretching mode.

Strategies for specifically directing metal functionalization of protein nanotubes: constructing protein coated silver nanowires

NASA Astrophysics Data System (ADS)

Carreño-Fuentes, Liliana; Ascencio, Jorge A.; Medina, Ariosto; Aguila, Sergio; Palomares, Laura A.; Ramírez, Octavio T.

2013-06-01

Biological molecules that self-assemble in the nanoscale range are useful multifunctional materials. Rotavirus VP6 protein self-assembles into tubular structures in the absence of other rotavirus proteins. Here, we present strategies for selectively directing metal functionalization to the lumen of VP6 nanotubes. The specific in situ metal reduction in the inner surface of nanotube walls was achieved by the simple modification of a method previously reported to functionalize the nanotube outer surface. Silver nanorods and nanowires as long as 1.5 μm were formed inside the nanotubes by coalescence of nanoparticles. Such one-dimensional structures were longer than others previously obtained using bioscaffolds. The interactions between silver ions and the nanotube were simulated to understand the conditions that allowed nanowire formation. Molecular docking showed that a naturally occurring arrangement of aspartate residues enabled the stabilization of silver ions on the internal surface of the VP6 nanotubes. This is the first time that such a spatial arrangement has been proposed for the nucleation of silver nanoparticles, opening the possibility of using such an array to direct functionalization of other biomolecules. These results demonstrate the natural capabilities of VP6 nanotubes to function as a versatile biotemplate for nanomaterials.

Application of small-size antennas for estimation of angles of arrival of HF signals scattered by ionospheric irregularities

NASA Astrophysics Data System (ADS)

Guo, Qiang; Galushko, Volodymyr G.; Zalizovski, Andriy V.; Kashcheyev, Sergiy B.; Zheng, Yu

2018-05-01

A modification of the Doppler Interferometry Technique is suggested to enable estimating angles of arrival of comparatively broadband HF signals scattered by random irregularities of the ionospheric plasma with the use of small-size weakly directional antennas. The technique is based on the measurements of cross-spectra phases of the probe radiation recorded at least in three spatially separated points. The developed algorithm has been used to investigate the angular and frequency-time characteristics of HF signals propagating at frequencies above the maximum usable one (MUF) for the direct radio path Moscow-Kharkiv. The received signal spectra show presence of three families of spatial components attributed, respectively, to scattering by plasma irregularities near the middle point of the radio path, ground backscatter signals and scattering of the sounding signals by the intense plasma turbulence associated with auroral activations. It has been shown that the regions responsible for the formation of the third family components are located well inside the auroral oval. The drift velocity and direction of the auroral ionosphere plasma have been determined. The obtained estimates are consistent with the classical conception of the ionospheric plasma convection at high latitudes and do not contradict the results of investigations of the auroral ionosphere dynamics using the SuperDARN network.

Using repetitive transcranial magnetic stimulation to study the underlying neural mechanisms of human motor learning and memory.

PubMed

Censor, Nitzan; Cohen, Leonardo G

2011-01-01

In the last two decades, there has been a rapid development in the research of the physiological brain mechanisms underlying human motor learning and memory. While conventional memory research performed on animal models uses intracellular recordings, microfusion of protein inhibitors to specific brain areas and direct induction of focal brain lesions, human research has so far utilized predominantly behavioural approaches and indirect measurements of neural activity. Repetitive transcranial magnetic stimulation (rTMS), a safe non-invasive brain stimulation technique, enables the study of the functional role of specific cortical areas by evaluating the behavioural consequences of selective modulation of activity (excitation or inhibition) on memory generation and consolidation, contributing to the understanding of the neural substrates of motor learning. Depending on the parameters of stimulation, rTMS can also facilitate learning processes, presumably through purposeful modulation of excitability in specific brain regions. rTMS has also been used to gain valuable knowledge regarding the timeline of motor memory formation, from initial encoding to stabilization and long-term retention. In this review, we summarize insights gained using rTMS on the physiological and neural mechanisms of human motor learning and memory. We conclude by suggesting possible future research directions, some with direct clinical implications.

Formation and resuscitation of viable but nonculturable Salmonella typhi.

PubMed

Zeng, Bin; Zhao, Guozhong; Cao, Xiaohong; Yang, Zhen; Wang, Chunling; Hou, Lihua

2013-01-01

Salmonella typhi is a pathogen that causes the human disease of typhoid fever. The aim of this study was to investigate the viable but nonculturable (VBNC) state of S. typhi. Some samples were stimulated at 4°C or -20°C, while others were induced by different concentrations of CuSO4. Total cell counts remained constant throughout several days by acridine orange direct counting; however, plate counts declined to undetectable levels within 48 hours by plate counting at -20°C. The direct viable counts remained fairly constant at this level by direct viable counting. Carbon and nitrogen materials slowly decreased which indicated that a large population of cells existed in the VBNC state and entered the VBNC state in response to exposure to 0.01 or 0.015 mmol/L CuSO4 for more than 14 or 12 days, respectively. Adding 3% Tween 20 or 1% catalase enabled cells to become culturable again, with resuscitation times of 48 h and 24 h, respectively. The atomic force microscope results showed that cells gradually changed in shape from short rods to coccoids, and decreased in size when they entered the VBNC state. Further animal experiments suggested that resuscitated cells might regain pathogenicity.

Probing individual star-forming regions in maximal starburst galaxiesat redshifts z=2-4 with the SMA (and other major facilities): Planck's Dusty GEMS.

NASA Astrophysics Data System (ADS)

Nesvadba, Nicole

2018-01-01

Strongly gravitationally lensed galaxies are veritable gems for our understanding of high-redshift galaxy evolution, allowing us to study dust, gas, and star formation even in the most intense starbursts on scales of individual star-forming regions. On these scales, below one to few 100 pc in the source plane, kpc-scale rotational support no longer dominates, and star formation is regulated by the local gas and stellar mass surface densities and energy injection from turbulence and winds driven by star formation and AGN. I will report on our on-going follow-up of Planck's Dusty GEMS, a small sample of 11 of the brightest, gravitationally lensed high-redshift galaxies on the extragalactic sub-mm sky. SMA 850-micron imaging is playing a critical role in identifying and characterizing the dusty starburst regions, their star-formation properties, and the gravitational lens modeling, and has been paving the way towards a rich multi-wavelength program, which would not have been possible without. This includes VLT, HST and ALMA high-resolution studies of the gas and stellar populations, amongst others. These observations enabled us, e.g., to study theinterplay between gravity and turbulence in an Eddington-limited starburst for the first time, and to detect the first absorption line of [CII] from diffuse gas outside the Milky Way. I will also discussthe first direct lensing estimate of a (bottom-heavy) initial mass function in the early Universe and outline how these and similar observations would benefit from increased bandwidth.

Native chemical ligation at Asx-Cys, Glx-Cys: chemical synthesis and high-resolution X-ray structure of ShK toxin by racemic protein crystallography.

PubMed

Dang, Bobo; Kubota, Tomoya; Mandal, Kalyaneswar; Bezanilla, Francisco; Kent, Stephen B H

2013-08-14

We have re-examined the utility of native chemical ligation at -Gln/Glu-Cys- [Glx-Cys] and -Asn/Asp-Cys- [Asx-Cys] sites. Using the improved thioaryl catalyst 4-mercaptophenylacetic acid (MPAA), native chemical ligation could be performed at -Gln-Cys- and Asn-Cys- sites without side reactions. After optimization, ligation at a -Glu-Cys- site could also be used as a ligation site, with minimal levels of byproduct formation. However, -Asp-Cys- is not appropriate for use as a site for native chemical ligation because of formation of significant amounts of β-linked byproduct. The feasibility of native chemical ligation at -Gln-Cys- enabled a convergent total chemical synthesis of the enantiomeric forms of the ShK toxin protein molecule. The D-ShK protein molecule was ~50,000-fold less active in blocking the Kv1.3 channel than the L-ShK protein molecule. Racemic protein crystallography was used to obtain high-resolution X-ray diffraction data for ShK toxin. The structure was solved by direct methods and showed significant differences from the previously reported NMR structures in some regions of the ShK protein molecule.

Packed Bed Bioreactor for the Isolation and Expansion of Placental-Derived Mesenchymal Stromal Cells

PubMed Central

Osiecki, Michael J.; Michl, Thomas D.; Kul Babur, Betul; Kabiri, Mahboubeh; Atkinson, Kerry; Lott, William B.; Griesser, Hans J.; Doran, Michael R.

2015-01-01

Large numbers of Mesenchymal stem/stromal cells (MSCs) are required for clinical relevant doses to treat a number of diseases. To economically manufacture these MSCs, an automated bioreactor system will be required. Herein we describe the development of a scalable closed-system, packed bed bioreactor suitable for large-scale MSCs expansion. The packed bed was formed from fused polystyrene pellets that were air plasma treated to endow them with a surface chemistry similar to traditional tissue culture plastic. The packed bed was encased within a gas permeable shell to decouple the medium nutrient supply and gas exchange. This enabled a significant reduction in medium flow rates, thus reducing shear and even facilitating single pass medium exchange. The system was optimised in a small-scale bioreactor format (160 cm2) with murine-derived green fluorescent protein-expressing MSCs, and then scaled-up to a 2800 cm2 format. We demonstrated that placental derived MSCs could be isolated directly within the bioreactor and subsequently expanded. Our results demonstrate that the closed system large-scale packed bed bioreactor is an effective and scalable tool for large-scale isolation and expansion of MSCs. PMID:26660475

Probing Cometary Chemistry with ALMA

NASA Technical Reports Server (NTRS)

Milam, Stefanie N.

2010-01-01

Comets are considered to bear the record of the primitive Solar nebula as remnants of planetesimals that formed the outer planets. To date there are just over two dozen known cometary species compared to the >150 known interstellar molecules. This is likely due to the challenges posed when attempting to measure the composition of these small bodies. With the significant improvement in sensitivity, ALMA will likely enable the detection of new molecules to help us gain better understanding of the chemical complexity found in comets. This advancement in sensitivity will also assist in the measurement of isotope ratios in various species. These values are imperative for determining the conditions during cometary formation as well as provide insight into ongoing speculations of parent species, the possible delivery of H2O to Earth, and a direct comparison to protostellar disk chemistry. The high angular resolution obtained with ALMA will be capable of resolving any compact distributions or density enhancements in the more extended distribution that may lead to a better understanding of the formation of these species in the outer coma. By studying comet compositions we gain insight into the composition of the early Solar System as well as their astrobiological implications.

Bioactive carbon-PEEK composites prepared by chemical surface treatment.

PubMed

Miyazaki, Toshiki; Matsunami, Chisato; Shirosaki, Yuki

2017-01-01

Polyetheretherketone (PEEK) has attracted much attention as an artificial intervertebral spacer for spinal reconstruction. Furthermore, PEEK plastic reinforced with carbon fiber has twice the bending strength of pure PEEK. However, the PEEK-based materials do not show ability for direct bone bonding, i.e., bioactivity. Although several trials have been conducted for enabling PEEK with bioactivity, few studies have reported on bioactive surface modification of carbon-PEEK composites. In the present study, we attempted the preparation of bioactive carbon-PEEK composites by chemical treatments with H 2 SO 4 and CaCl 2 . Bioactivity was evaluated by in vitro apatite formation in simulated body fluid (SBF). The apatite formation on the carbon-PEEK composite was compared with that of pure PEEK. Both pure PEEK and carbon-PEEK composite formed the apatite in SBF when they were treated with H 2 SO 4 and CaCl 2 ; the latter showed higher apatite-forming ability than the former. It is conjectured that many functional groups able to induce the apatite nucleation, such as sulfo and carboxyl groups, are incorporated into the dispersed carbon phase in the carbon-PEEK composites. Copyright © 2016 Elsevier B.V. All rights reserved.

Large Format, Background Limited Arrays of Kinetic Inductance Detectors for Sub-mm Astronomy

NASA Astrophysics Data System (ADS)

Baselmans, Jochem

2018-01-01

We present the development of large format imaging arrays for sub-mm astronomy based upon microwave Kinetic Inductance detectors and their read-out. In particular we focus on the arrays developed for the A-MKID instrument for the APEX telescope. AMKID contains 2 focal plane arrays, covering a field of view of 15?x15?. One array is optimized for the 350 GHz telluric window, the other for the 850 GHz window. Both arrays are constructed from four 61 x 61 mm detector chips, each of which contains up to 3400 detectors and up to 880 detectors per readout line. The detectors are lens antenna coupled MKIDs made from NbTiN and Aluminium that reach photon noise limited sensitivity in combination with a high optical coupling. The lens-antenna radiation coupling enables the use of 4K optics and Lyot stop due to the intrinsic directivity of the detector beam, allowing a simple cryogenic architecture. We discuss the pixel design and verification, detector packaging and the array performance. We will also discuss the readout system, which is a combination of a digital and analog back-end that can read-out up to 4000 pixels simultaneously using frequency division multiplexing.

Orthotopic lung cancer murine model by nonoperative transbronchial approach.

PubMed

Nakajima, Takahiro; Anayama, Takashi; Matsuda, Yasushi; Hwang, David M; McVeigh, Patrick Z; Wilson, Brian C; Zheng, Gang; Keshavjee, Shaf; Yasufuku, Kazuhiro

2014-05-01

The aim of this work was to establish a novel orthotopic human non-small cell lung cancer (NSCLC) murine xenograft model by a nonsurgical, transbronchial approach. Male athymic nude mice and human NSCLC cell lines, including A549, H460, and H520 were used. Under direct visualization of the vocal cords, a 23-gauge blunt-tip slightly curved metal catheter was introduced into the trachea to the bronchus, and 2.5×10(5) tumor cells mixed with Matrigel (BD Biosciences, Mississauga, Ontario, Canada) were administered into the lung. Mice were monitored using weekly microcomputed tomography scans for tumor formation. When the tumor size reached more than 4 mm in diameter, the animals were euthanized, and the tumor tissue was evaluated histopathologically. Of 37 mice studied, 34 were confirmed to have tumor formation: 29 developed solitary tumors and 5 had multifocal lesions. There was no evidence of extrapleural dissemination or effusion. Transbronchial delivery of tumor cells enabled the establishment of a novel orthotopic human NSCLC murine xenograft model. This clinically relevant preclinical model bearing a solitary nodule is of value for a variety of in vivo research studies. Copyright © 2014 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

Mechanistic understanding of the cysteine capping modifications of antibodies enables selective chemical engineering in live mammalian cells.

PubMed

Zhong, Xiaotian; He, Tao; Prashad, Amar S; Wang, Wenge; Cohen, Justin; Ferguson, Darren; Tam, Amy S; Sousa, Eric; Lin, Laura; Tchistiakova, Lioudmila; Gatto, Scott; D'Antona, Aaron; Luan, Yen-Tung; Ma, Weijun; Zollner, Richard; Zhou, Jing; Arve, Bo; Somers, Will; Kriz, Ronald

2017-04-20

Protein modifications by intricate cellular machineries often redesign the structure and function of existing proteins to impact biological networks. Disulfide bond formation between cysteine (Cys) pairs is one of the most common modifications found in extracellularly-destined proteins, key to maintaining protein structure. Unpaired surface cysteines on secreted mammalian proteins are also frequently found disulfide-bonded with free Cys or glutathione (GSH) in circulation or culture, the mechanism for which remains unknown. Here we report that these so-called Cys-capping modifications take place outside mammalian cells, not in the endoplasmic reticulum (ER) where oxidoreductase-mediated protein disulfide formation occurs. Unpaired surface cysteines of extracellularly-arrived proteins such as antibodies are uncapped upon secretion before undergoing disulfide exchange with cystine or oxidized GSH in culture medium. This observation has led to a feasible way to selectively modify the nucleophilic thiol side-chain of cell-surface or extracellular proteins in live mammalian cells, by applying electrophiles with a chemical handle directly into culture medium. These findings provide potentially an effective approach for improving therapeutic conjugates and probing biological systems. Copyright © 2017 Elsevier B.V. All rights reserved.

Hip joint replacement using monofilament polypropylene surgical mesh: an animal model.

PubMed

Białecki, Jacek; Majchrzycki, Marian; Szymczak, Antoni; Klimowicz-Bodys, Małgorzata Dorota; Wierzchoś, Edward; Kołomecki, Krzysztof

2014-01-01

Hip joint dysplasia is a deformation of the articular elements (pelvic acetabulum, head of the femur, and/or ligament of the head of the femur) leading to laxity of the hip components and dislocation of the femoral head from the pelvic acetabulum. Diagnosis is based on symptoms observed during clinical and radiological examinations. There are two treatment options: conservative and surgical. The classic surgical procedures are juvenile pubic symphysiodesis (JPS), triple pelvic osteotomy (TPO), total hip replacement (THR), and femoral head and neck resection (FHNE). The aim of this experiment was to present an original technique of filling the acetabulum with a polypropylene implant, resting the femoral neck directly on the mesh. The experiment was performed on eight sheep. The clinical value of the new surgical technique was evaluated using clinical, radiological, and histological methods. This technique helps decrease the loss of limb length by supporting the femoral neck on the mesh equivalent to the femoral head. It also reduces joint pain and leads to the formation of stable and mobile pseudarthrosis. The mesh manifested osteoprotective properties and enabled the formation of a stiff-elastic connection within the hip joint. The method is very cost-effective and the technique itself is simple to perform.

Packed Bed Bioreactor for the Isolation and Expansion of Placental-Derived Mesenchymal Stromal Cells.

PubMed

Osiecki, Michael J; Michl, Thomas D; Kul Babur, Betul; Kabiri, Mahboubeh; Atkinson, Kerry; Lott, William B; Griesser, Hans J; Doran, Michael R

2015-01-01

Large numbers of Mesenchymal stem/stromal cells (MSCs) are required for clinical relevant doses to treat a number of diseases. To economically manufacture these MSCs, an automated bioreactor system will be required. Herein we describe the development of a scalable closed-system, packed bed bioreactor suitable for large-scale MSCs expansion. The packed bed was formed from fused polystyrene pellets that were air plasma treated to endow them with a surface chemistry similar to traditional tissue culture plastic. The packed bed was encased within a gas permeable shell to decouple the medium nutrient supply and gas exchange. This enabled a significant reduction in medium flow rates, thus reducing shear and even facilitating single pass medium exchange. The system was optimised in a small-scale bioreactor format (160 cm2) with murine-derived green fluorescent protein-expressing MSCs, and then scaled-up to a 2800 cm2 format. We demonstrated that placental derived MSCs could be isolated directly within the bioreactor and subsequently expanded. Our results demonstrate that the closed system large-scale packed bed bioreactor is an effective and scalable tool for large-scale isolation and expansion of MSCs.

Millisecond-Timescale Monitoring of PbS Nanoparticle Nucleation and Growth Using Droplet-Based Microfluidics.

PubMed

Lignos, Ioannis; Stavrakis, Stavros; Kilaj, Ardita; deMello, Andrew J

2015-08-26

The early-time kinetics (<1 s) of lead sulfide (PbS) quantum dot formation are probed using a novel droplet-based microfluidic platform, which allows for high-throughput and real-time optical analysis of the reactive process with millisecond time resolution. The reaction platform enables the concurrent investigation of the emission characteristics of PbS quantum dots and a real-time estimation of their size and concentration during nucleation and growth. These investigations reveal a two-stage mechanism for PbS nanoparticle formation. The first stage corresponds to the fast conversion of precursor species to PbS crystals, followed by the growth of the formed particles. The growth kinetics of the PbS nanoparticles follow the Lifshitz-Slyozov-Wagner model for Ostwald ripening, allowing direct estimation of the rate constants for the process. In addition, the extraction of absorption spectra of ultrasmall quantum dots is demonstrated for first time in an online manner. The droplet-based microfluidic platform integrated with online spectroscopic analysis provides a new tool for the quantitative extraction of high temperature kinetics for systems with rapid nucleation and growth stages. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Adding the ‘heart’ to hanging drop networks for microphysiological multi-tissue experiments†

PubMed Central

Yazdi, Saeed Rismani; Shadmani, Amir; Bürgel, Sebastian C.; Misun, Patrick M.; Hierlemann, Andreas; Frey, Olivier

2017-01-01

Microfluidic hanging-drop networks enable culturing and analysis of 3D microtissue spheroids derived from different cell types under controlled perfusion and investigating inter-tissue communication in multi-tissue formats. In this paper we introduce a compact on-chip pumping approach for flow control in hanging-drop networks. The pump includes one pneumatic chamber located directly above one of the hanging drops and uses the surface tension at the liquid–air-interface for flow actuation. Control of the pneumatic protocol provides a wide range of unidirectional pulsatile and continuous flow profiles. With the proposed concept several independent hanging-drop networks can be operated in parallel with only one single pneumatic actuation line at high fidelity. Closed-loop medium circulation between different organ models for multi-tissue formats and multiple simultaneous assays in parallel are possible. Finally, we implemented a real-time feedback control-loop of the pump actuation based on the beating of a human iPS-derived cardiac microtissue cultured in the same system. This configuration allows for simulating physiological effects on the heart and their impact on flow circulation between the organ models on chip. PMID:26401602

Visualization of seismic tomography on Google Earth: Improvement of KML generator and its web application to accept the data file in European standard format

NASA Astrophysics Data System (ADS)

Yamagishi, Y.; Yanaka, H.; Tsuboi, S.

2009-12-01

We have developed a conversion tool for the data of seismic tomography into KML, called KML generator, and made it available on the web site (http://www.jamstec.go.jp/pacific21/google_earth). The KML generator enables us to display vertical and horizontal cross sections of the model on Google Earth in three-dimensional manner, which would be useful to understand the Earth's interior. The previous generator accepts text files of grid-point data having longitude, latitude, and seismic velocity anomaly. Each data file contains the data for each depth. Metadata, such as bibliographic reference, grid-point interval, depth, are described in other information file. We did not allow users to upload their own tomographic model to the web application, because there is not standard format to represent tomographic model. Recently European seismology research project, NEIRES (Network of Research Infrastructures for European Seismology), advocates that the data of seismic tomography should be standardized. They propose a new format based on JSON (JavaScript Object Notation), which is one of the data-interchange formats, as a standard one for the tomography. This format consists of two parts, which are metadata and grid-point data values. The JSON format seems to be powerful to handle and to analyze the tomographic model, because the structure of the format is fully defined by JavaScript objects, thus the elements are directly accessible by a script. In addition, there exist JSON libraries for several programming languages. The International Federation of Digital Seismograph Network (FDSN) adapted this format as a FDSN standard format for seismic tomographic model. There might be a possibility that this format would not only be accepted by European seismologists but also be accepted as the world standard. Therefore we improve our KML generator for seismic tomography to accept the data file having also JSON format. We also improve the web application of the generator so that the JSON formatted data file can be uploaded. Users can convert any tomographic model data to KML. The KML obtained through the new generator should provide an arena to compare various tomographic models and other geophysical observations on Google Earth, which may act as a common platform for geoscience browser.

Heart disease management by women: does intervention format matter?

PubMed

Clark, Noreen M; Janz, Nancy K; Dodge, Julia A; Lin, Xihong; Trabert, Britton L; Kaciroti, Niko; Mosca, Lori; Wheeler, John R; Keteyian, Steven

2014-10-01

A randomized controlled trial of two formats of a program (Women Take PRIDE) to enhance management of heart disease by patients was conducted. Older women (N = 575) were randomly assigned to a group or self-directed format or to a control group. Data regarding symptoms, functional health status, and weight were collected at baseline and at 4, 12, and 18 months. The formats produced different outcomes. At 18 months, the self-directed format was better than the control in reducing the number (p ≤ .02), frequency (p ≤ .03), and bothersomeness (p ≤ .02) of cardiac symptoms. The self-directed format was also better than the group format in reducing symptom frequency of all types (p ≤ .04). The group format improved ambulation at 12 months (p ≤ .04) and weight loss at 18 months (p ≤ .03), and group participants were more likely to complete the program (p ≤ .05). The availability of different learning formats could enhance management of cardiovascular disease by patients. © 2014 Society for Public Health Education.

Heart disease management by women: does intervention format matter?

PubMed

Clark, Noreen M; Janz, Nancy K; Dodge, Julia A; Lin, Xihong; Trabert, Britton L; Kaciroti, Niko; Mosca, Lori; Wheeler, John R; Keteyian, Steven

2009-04-01

A randomized controlled trial of two formats of a program (Women Take PRIDE) to enhance management of heart disease by patients was conducted. Older women (N = 575) were randomly assigned to a group or self-directed format or to a control group. Data regarding symptoms, functional health status, and weight were collected at baseline and at 4, 12, and 18 months. The formats produced different outcomes. At 18 months, the self-directed format was better than the control in reducing the number (p < or = .02), frequency (p < or = .03), and bothersomeness (p < or = .02) of cardiac symptoms. The self-directed format was also better than the group format in reducing symptom frequency of all types (p < or = .04). The group format improved ambulation at 12 months (p < or = .04) and weight loss at 18 months (p < or = .03), and group participants were more likely to complete the program ( p < or = .05). The availability of different learning formats could enhance management of cardiovascular disease by patients.

An open-architecture approach to defect analysis software for mask inspection systems

NASA Astrophysics Data System (ADS)

Pereira, Mark; Pai, Ravi R.; Reddy, Murali Mohan; Krishna, Ravi M.

2009-04-01

Industry data suggests that Mask Inspection represents the second biggest component of Mask Cost and Mask Turn Around Time (TAT). Ever decreasing defect size targets lead to more sensitive mask inspection across the chip, thus generating too many defects. Hence, more operator time is being spent in analyzing and disposition of defects. Also, the fact that multiple Mask Inspection Systems and Defect Analysis strategies would typically be in use in a Mask Shop or a Wafer Foundry further complicates the situation. In this scenario, there is a need for a versatile, user friendly and extensible Defect Analysis software that reduces operator analysis time and enables correct classification and disposition of mask defects by providing intuitive visual and analysis aids. We propose a new vendor-neutral defect analysis software, NxDAT, based on an open architecture. The open architecture of NxDAT makes it easily extensible to support defect analysis for mask inspection systems from different vendors. The capability to load results from mask inspection systems from different vendors either directly or through a common interface enables the functionality of establishing correlation between inspections carried out by mask inspection systems from different vendors. This capability of NxDAT enhances the effectiveness of defect analysis as it directly addresses the real-life scenario where multiple types of mask inspection systems from different vendors co-exist in mask shops or wafer foundries. The open architecture also potentially enables loading wafer inspection results as well as loading data from other related tools such as Review Tools, Repair Tools, CD-SEM tools etc, and correlating them with the corresponding mask inspection results. A unique concept of Plug-In interface to NxDAT further enhances the openness of the architecture of NxDAT by enabling end-users to add their own proprietary defect analysis and image processing algorithms. The plug-in interface makes it possible for the end-users to make use of their collected knowledge through the years of experience in mask inspection process by encapsulating the knowledge into software utilities and plugging them into NxDAT. The plug-in interface is designed with the intent of enabling the pro-active mask defect analysis teams to build competitive differentiation into their defect analysis process while protecting their knowledge internally within their company. By providing interface with all major standard layout and mask data formats, NxDAT enables correlation of defect data on reticles with design and mask databases, further extending the effectiveness of defect analysis for D2DB inspection. NxDAT also includes many other advanced features for easy and fast navigation, visual display of defects, defect selection, multi-tier classification, defect clustering and gridding, sophisticated CD and contact measurement analysis, repeatability analysis such as adder analysis, defect trend, capture rate etc.

The Effect of Patient Choice of Intervention on Health Outcomes

PubMed Central

Clark, Noreen M.; Janz, Nancy K.; Dodge, Julia A.; Mosca, Lori; Lin, Xihong; Long, Qi; Little, Roderick J; Wheeler, John R.C.; Keteyian, Steven; Liang, Jersey

2008-01-01

Background Patient preference may influence intervention effects, but has not been extensively studied. Randomized controlled design (N=1075) assessed outcomes when women (60 years +) were given a choice of two formats of a program to enhance heart disease management. Methods Randomization to "no choice" or "choice" study arms. Further randomization of "no choice” to: 1) Group intervention program format, 2) Self-Directed program format, 3) Control Group. "Choice" arm selected their preferred program format. Baseline, four, twelve, and eighteen month follow-up data collected. Two analyses: health outcomes for choice compared to being randomized; and preference effect on treatment efficacy. Results Women who chose a format compared to being assigned a format had better psychosocial functioning at four months (p=0.02) and tended toward better physical functioning at twelve months (p=0.07). At eighteen months women who chose versus being assigned a format had more symptoms measured as: number (p=0.004), frequency (p=0.006) and bother (p=0.004). At four months women who preferred the Group format had better psychosocial functioning when assigned the Group format than when they were assigned the Self Directed format (p=0.03). At eighteen months women preferring a Group format had more symptoms: number (p=0.001), frequency (p=0.001), bother (p=0.001) when assigned the Group format than when assigned the Self Directed format. Conclusions Choice and preference for the Group format each enhanced psychosocial and physical functioning up to one year. Despite the preference for Group format, over the longer term (eighteen months) cardiac symptoms were fewer when assigned the Self-Directed format. PMID:18515187

Understanding the solution phase chemistry and solid state thermodynamic behavior of pharmaceutical cocrystals

NASA Astrophysics Data System (ADS)

Maheshwari, Chinmay

Cocrystals have drawn a lot of research interest in the last decade due to their potential to favorably alter the physicochemical and biopharmaceutical properties of active pharmaceutical ingredients. This dissertation focuses on the thermodynamic stability and solubility of pharmaceutical cocrystals. Specifically, the objectives are to; (i) investigate the influence of coformer properties such as solubility and ionization characteristics on cocrystal solubility and stability as a function of pH, (ii) to measure the thermodynamic solubility of metastable cocrystals, and study the solubility differences measured by kinetic and equilibrium methods, (iii) investigate the role of surfactants on the solubility and synthesis of cocrystals, (iv) investigate the solid state phase transformation of reactants to cocrystals and the factors that influence the reaction kinetics and, (v) provide models that enable the prediction of cocrystal formation by calculating the free energy of formation for a solid to solid transformation of reactants to cocrystals. Cocrystal solubilities were measured directly when cocrystals were thermodynamically stable, while solubilities were calculated from eutectic concentration measurements when cocrystals were of higher solubility than its components. Cocrystal solubility was highly dependent on coformer solubilities for gabapentin-lactam and lamotrigine cocrystals. It was found that melting point is not a good indicator of cocrystal solubility as solute-solvent interactions quantified by the activity coefficient play a huge role in the observed solubility. Similar to salts, cocrystals also exhibit pHmax, however the salts and cocrystals have different dependencies on the parameters that govern the value of pHmax. It is also shown that cocrystals could provide solubility advantage over salts as lamotrigine-nicotinamide cocrystal hydrate has about 6 fold higher solubility relative to lamotrigine-saccharin salt. In the case of mixtures of solid reactants, it was observed that cocrystals can form spontaneously when the reactants are in physical contact and that temperature, relative humidity, and disorder in the reactants caused by mechanical stress such as milling can enhance the reaction rates. Prediction of spontaneous cocrystal formation was investigated by developing models to calculate the Gibbs free energy of formation. Thermal behavior of cocrystal reactants was investigated by calorimetry and the interaction between the reactants is explained by investigating the heats of mixing in the melt. These principles are applied on cocrystals that are divided into two categories; (i) Where the cocrystal melting point is between that of its reactants and, (ii) where the cocrystal melting point is below that of its components. Generalized equations were developed that enable the calculation of Gibbs free energy of formation from fusion temperatures, enthalpy and entropy of fusion.

Solar Wind Electrons Alphas and Protons (SWEAP) Investigation: Design of the Solar Wind and Coronal Plasma Instrument Suite for Solar Probe Plus

NASA Astrophysics Data System (ADS)

Kasper, Justin C.; Abiad, Robert; Austin, Gerry; Balat-Pichelin, Marianne; Bale, Stuart D.; Belcher, John W.; Berg, Peter; Bergner, Henry; Berthomier, Matthieu; Bookbinder, Jay; Brodu, Etienne; Caldwell, David; Case, Anthony W.; Chandran, Benjamin D. G.; Cheimets, Peter; Cirtain, Jonathan W.; Cranmer, Steven R.; Curtis, David W.; Daigneau, Peter; Dalton, Greg; Dasgupta, Brahmananda; DeTomaso, David; Diaz-Aguado, Millan; Djordjevic, Blagoje; Donaskowski, Bill; Effinger, Michael; Florinski, Vladimir; Fox, Nichola; Freeman, Mark; Gallagher, Dennis; Gary, S. Peter; Gauron, Tom; Gates, Richard; Goldstein, Melvin; Golub, Leon; Gordon, Dorothy A.; Gurnee, Reid; Guth, Giora; Halekas, Jasper; Hatch, Ken; Heerikuisen, Jacob; Ho, George; Hu, Qiang; Johnson, Greg; Jordan, Steven P.; Korreck, Kelly E.; Larson, Davin; Lazarus, Alan J.; Li, Gang; Livi, Roberto; Ludlam, Michael; Maksimovic, Milan; McFadden, James P.; Marchant, William; Maruca, Bennet A.; McComas, David J.; Messina, Luciana; Mercer, Tony; Park, Sang; Peddie, Andrew M.; Pogorelov, Nikolai; Reinhart, Matthew J.; Richardson, John D.; Robinson, Miles; Rosen, Irene; Skoug, Ruth M.; Slagle, Amanda; Steinberg, John T.; Stevens, Michael L.; Szabo, Adam; Taylor, Ellen R.; Tiu, Chris; Turin, Paul; Velli, Marco; Webb, Gary; Whittlesey, Phyllis; Wright, Ken; Wu, S. T.; Zank, Gary

2016-12-01

The Solar Wind Electrons Alphas and Protons (SWEAP) Investigation on Solar Probe Plus is a four sensor instrument suite that provides complete measurements of the electrons and ionized helium and hydrogen that constitute the bulk of solar wind and coronal plasma. SWEAP consists of the Solar Probe Cup (SPC) and the Solar Probe Analyzers (SPAN). SPC is a Faraday Cup that looks directly at the Sun and measures ion and electron fluxes and flow angles as a function of energy. SPAN consists of an ion and electron electrostatic analyzer (ESA) on the ram side of SPP (SPAN-A) and an electron ESA on the anti-ram side (SPAN-B). The SPAN-A ion ESA has a time of flight section that enables it to sort particles by their mass/charge ratio, permitting differentiation of ion species. SPAN-A and -B are rotated relative to one another so their broad fields of view combine like the seams on a baseball to view the entire sky except for the region obscured by the heat shield and covered by SPC. Observations by SPC and SPAN produce the combined field of view and measurement capabilities required to fulfill the science objectives of SWEAP and Solar Probe Plus. SWEAP measurements, in concert with magnetic and electric fields, energetic particles, and white light contextual imaging will enable discovery and understanding of solar wind acceleration and formation, coronal and solar wind heating, and particle acceleration in the inner heliosphere of the solar system. SPC and SPAN are managed by the SWEAP Electronics Module (SWEM), which distributes power, formats onboard data products, and serves as a single electrical interface to the spacecraft. SWEAP data products include ion and electron velocity distribution functions with high energy and angular resolution. Full resolution data are stored within the SWEM, enabling high resolution observations of structures such as shocks, reconnection events, and other transient structures to be selected for download after the fact. This paper describes the implementation of the SWEAP Investigation, the driving requirements for the suite, expected performance of the instruments, and planned data products, as of mission preliminary design review.

The Hubble Deep UV Legacy Survey (HDUV)

NASA Astrophysics Data System (ADS)

Montes, Mireia; Oesch, Pascal

2015-08-01

Deep HST imaging has shown that the overall star formation density and UV light density at z>3 is dominated by faint, blue galaxies. Remarkably, very little is known about the equivalent galaxy population at lower redshifts. Understanding how these galaxies evolve across the epoch of peak cosmic star-formation is key to a complete picture of galaxy evolution. Here, we present a new HST WFC3/UVIS program, the Hubble Deep UV (HDUV) legacy survey. The HDUV is a 132 orbit program to obtain deep imaging in two filters (F275W and F336W) over the two CANDELS Deep fields. We will cover ~100 arcmin2 sampling the rest-frame far-UV at z>~0.5, this will provide a unique legacy dataset with exquisite HST multi-wavelength imaging as well as ancillary HST grism NIR spectroscopy for a detailed study of faint, star-forming galaxies at z~0.5-2. The HDUV will enable a wealth of research by the community, which includes tracing the evolution of the FUV luminosity function over the peak of the star formation rate density from z~3 down to z~0.5, measuring the physical properties of sub-L* galaxies, and characterizing resolved stellar populations to decipher the build-up of the Hubble sequence from sub-galactic clumps. This poster provides an overview of the HDUV survey and presents the reduced data products and catalogs which will be released to the community, reaching down to 27.5-28.0 mag at 5 sigma. By directly sampling the rest-frame far-UV at z>~0.5, this will provide a unique legacy dataset with exquisite HST multi-wavelength imaging as well as ancillary HST grism NIR spectroscopy for a detailed study of faint, star-forming galaxies at z~0.5-2. The HDUV will enable a wealth of research by the community, which includes tracing the evolution of the FUV luminosity function over the peak of the star formation rate density from z~3 down to z~0.5, measuring the physical properties of sub-L* galaxies, and characterizing resolved stellar populations to decipher the build-up of the Hubble sequence from sub-galactic clumps. This poster provides an overview of the HDUV survey and presents reduced data products and catalogs which will be released to the community.

Fabrication, Densification, and Replica Molding of 3D Carbon Nanotube Microstructures

PubMed Central

Copic, Davor; Park, Sei Jin; Tawfick, Sameh; De Volder, Michael; Hart, A. John

2012-01-01

The introduction of new materials and processes to microfabrication has, in large part, enabled many important advances in microsystems, lab-on-a-chip devices, and their applications. In particular, capabilities for cost-effective fabrication of polymer microstructures were transformed by the advent of soft lithography and other micromolding techniques 1, 2, and this led a revolution in applications of microfabrication to biomedical engineering and biology. Nevertheless, it remains challenging to fabricate microstructures with well-defined nanoscale surface textures, and to fabricate arbitrary 3D shapes at the micro-scale. Robustness of master molds and maintenance of shape integrity is especially important to achieve high fidelity replication of complex structures and preserving their nanoscale surface texture. The combination of hierarchical textures, and heterogeneous shapes, is a profound challenge to existing microfabrication methods that largely rely upon top-down etching using fixed mask templates. On the other hand, the bottom-up synthesis of nanostructures such as nanotubes and nanowires can offer new capabilities to microfabrication, in particular by taking advantage of the collective self-organization of nanostructures, and local control of their growth behavior with respect to microfabricated patterns. Our goal is to introduce vertically aligned carbon nanotubes (CNTs), which we refer to as CNT "forests", as a new microfabrication material. We present details of a suite of related methods recently developed by our group: fabrication of CNT forest microstructures by thermal CVD from lithographically patterned catalyst thin films; self-directed elastocapillary densification of CNT microstructures; and replica molding of polymer microstructures using CNT composite master molds. In particular, our work shows that self-directed capillary densification ("capillary forming"), which is performed by condensation of a solvent onto the substrate with CNT microstructures, significantly increases the packing density of CNTs. This process enables directed transformation of vertical CNT microstructures into straight, inclined, and twisted shapes, which have robust mechanical properties exceeding those of typical microfabrication polymers. This in turn enables formation of nanocomposite CNT master molds by capillary-driven infiltration of polymers. The replica structures exhibit the anisotropic nanoscale texture of the aligned CNTs, and can have walls with sub-micron thickness and aspect ratios exceeding 50:1. Integration of CNT microstructures in fabrication offers further opportunity to exploit the electrical and thermal properties of CNTs, and diverse capabilities for chemical and biochemical functionalization 3. PMID:22806089

Fabrication, densification, and replica molding of 3D carbon nanotube microstructures.

PubMed

Copic, Davor; Park, Sei Jin; Tawfick, Sameh; De Volder, Michael; Hart, A John

2012-07-02

The introduction of new materials and processes to microfabrication has, in large part, enabled many important advances in microsystems, lab-on-a-chip devices, and their applications. In particular, capabilities for cost-effective fabrication of polymer microstructures were transformed by the advent of soft lithography and other micromolding techniques (1, 2), and this led a revolution in applications of microfabrication to biomedical engineering and biology. Nevertheless, it remains challenging to fabricate microstructures with well-defined nanoscale surface textures, and to fabricate arbitrary 3D shapes at the micro-scale. Robustness of master molds and maintenance of shape integrity is especially important to achieve high fidelity replication of complex structures and preserving their nanoscale surface texture. The combination of hierarchical textures, and heterogeneous shapes, is a profound challenge to existing microfabrication methods that largely rely upon top-down etching using fixed mask templates. On the other hand, the bottom-up synthesis of nanostructures such as nanotubes and nanowires can offer new capabilities to microfabrication, in particular by taking advantage of the collective self-organization of nanostructures, and local control of their growth behavior with respect to microfabricated patterns. Our goal is to introduce vertically aligned carbon nanotubes (CNTs), which we refer to as CNT "forests", as a new microfabrication material. We present details of a suite of related methods recently developed by our group: fabrication of CNT forest microstructures by thermal CVD from lithographically patterned catalyst thin films; self-directed elastocapillary densification of CNT microstructures; and replica molding of polymer microstructures using CNT composite master molds. In particular, our work shows that self-directed capillary densification ("capillary forming"), which is performed by condensation of a solvent onto the substrate with CNT microstructures, significantly increases the packing density of CNTs. This process enables directed transformation of vertical CNT microstructures into straight, inclined, and twisted shapes, which have robust mechanical properties exceeding those of typical microfabrication polymers. This in turn enables formation of nanocomposite CNT master molds by capillary-driven infiltration of polymers. The replica structures exhibit the anisotropic nanoscale texture of the aligned CNTs, and can have walls with sub-micron thickness and aspect ratios exceeding 50:1. Integration of CNT microstructures in fabrication offers further opportunity to exploit the electrical and thermal properties of CNTs, and diverse capabilities for chemical and biochemical functionalization (3).

Use of electrospinning and dynamic air focusing to create three-dimensional cell culture scaffolds in microfluidic devices.

PubMed

Chen, Chengpeng; Mehl, Benjamin T; Sell, Scott A; Martin, R Scott

2016-09-21

Organs-on-a-chip has emerged as a powerful tool for pharmacological and physiological studies. A key part in the construction of such a model is the ability to pattern or culture cells in a biomimetic fashion. Most of the reported cells-on-a-chip models integrate cells on a flat surface, which does not accurately represent the extracellular matrix that they experience in vivo. Electrospinning, a technique used to generate sub-micron diameter polymer fibers, has been used as an in vitro cell culture substrate and for tissue engineering applications. Electrospinning of fibers directly into a fully sealed fluidic channel using a conventional setup has not been possible due to issues of confining the fibers into a discrete network. In this work, a dynamic focusing method was developed, with this approach enabling direct deposition of electrospun fibers into a fully sealed fluidic channel, to act as a matrix for cell culture and subsequent studies under continuous flowing conditions. Scanning electron microscopy of electrospun polycaprolactone fibers shows that this method enables the formation of fibrous layers on the inner wall of a 3D-printed fluidic device (mean fiber size = 1.6 ± 0.6 μm and average pore size = 113 ± 19 μm(2)). Cells were able to be cultured in this 3D scaffold without the addition of adhesion proteins. Media was pumped through the channel at high flow rates (up to 400 μL min(-1)) during a dynamic cell culture process and both the fibers and the cells were found to be strongly adherent. A PDMS fluidic device was also prepared (from a 3D printed mold) and coated with polycaprolactone fibers. The PDMS device enables optical detection and confocal imaging of cultured cells on the fibers. Finally, macrophages were cultured in the devices to study how the fibrous scaffold can affect cell behavior. It was found that under lipopolysaccharide stimulation, macrophages cultured on PCL fibers inside of a channel secreted significantly more cytokines than those cultured on a thin layer of PCL in a channel or directly on the inner channel wall. Overall, this study represents a new approach for in vitro cell studies, where electrospinning can be used to easily and quickly create 3D scaffolds that can improve the culture conditions in microfluidic devices.

Presidential Space Policy Directs NASA to Return Humans to Moon

NASA Image and Video Library

2017-12-11

President Donald Trump signed a new Space Policy Directive-1 at the White House on Monday, Dec. 11, directing NASA’s human spaceflight program back to the Moon, as recommended by the National Space Council.    The directive calls for NASA to lead an innovative and sustainable program of exploration with commercial and international partners to enable human expansion across the solar system, and to bring back to Earth new knowledge and opportunities for human advancement. This effort will more effectively organize government, private industry, and international efforts toward returning humans on the Moon, and will lay the foundation that will eventually enable human exploration of Mars.

Debris Disk Structure and Morphology as Revealed by Aggressive STIS Multi-Roll Coronagraphy: A New Look at Some Old Friends

NASA Technical Reports Server (NTRS)

Grady, Carol A; Kuchner, Marc; Woodgate, Bruce E.

2012-01-01

We present new imaging results from a well-selected sample of II circumstellar debris disks, all with HST pedigree, using STIS visible-light 6-roll PSF-template subtracted coronagraphy (PSFTSC). These new observations, pushing HST to its highest levels of coronagraphic performance, simultaneously probe both the interior regions of these debris systems, with inner working distances < app 8 AU for half the stars in this sample (corresponding to the giant planet and Kuiper belt regions within our own solar system), and the exterior regions far beyond. These new images enable direct inter-comparison of the architectures of these exoplanetary debris systems in the context of our own Solar System: These observations also permit us, for the first time, to characterize material in these regions at high spatial resolution and identify disk sub-structures that are signposts of planet formation and evolution; in particular, asymmetries and non-uniform debris structures that signal the presence of co-orbiting perturbing planets, and dynamical interactions (e.g., resulting in posited small grain stripping and disk "pollution") with the ISM. We focus here on recently acquired and reduced images of he circumstellar debris systems about: AU Mic (edge-on, and @ 10 pc the closest star in our sample), HD 61005, HD 32297 and HD 15115 (all with morphologies strongly suggestive of ISM wind interactions), HD 181327 & HDI07146 (close to face-on with respectively narrow and broad debris rings), and MP Mus (a "mature" proto-planetary disk hosted by a cTTS). All of our objects were previously observed in the near-IR with inferior spatial resolution and imaging efficacy, but with NICMOS r = 0.3" inner working angle (IWA) comparable to STIS multi-roll coronagraphy. The combination of new optical and existing near-IR imaging can strongly constrain the dust properties, thus enabling an assessment of grain processing and planetesimal populations. These results will directly inform upon the posited planet formation mechanisms that occur after the approximately 10 My epoch of gas depletion, a time in our solar system when giant planets were migrating and terrestrial planets were forming, and directly test theoretical models of these processes. These observations lmiquely probe both into the interior regions of these systems and are sensitive to and spatially resolve low surface-brightness (SB) material at large stellocentric distances with spatial resolution comparable to ACS and with augmenting NICMOS near-IR disk photometry in hand.

A Concept for In-space, System-level Validation of Spacecraft Precision Formation Flying

NASA Technical Reports Server (NTRS)

Leitner, Jesse; Carpenter, J. Russell; Naasz, Bo J.; Scharf, Daniel P.; Hadaegh, Fred Y.; Ahmed, Asif

2007-01-01

A number of international space agencies and organizations, to include the National Aeronautics and Space Administration (NASA), the European Space Agency (ESA), and the Centre National d'Etudes Spatiales (CNES), to name a few, have embraced the concept of spacecraft formation flying to revolutionize the capabilities of astronomy and Earth remote sensing from space. The concept has been around well over a decade and a wide array of technologies and capabilities have been developed to enable multiple spacecraft to collaborate in a highly-coupled manner as would be required for a formation flying mission. Furthermore, many relevant capabilities for formation flying have been demonstrated in the area of rendezvous and docking, loosely-controlled formations, and in missions with collaborating spacecraft with very precise metrology. .However, in considering the case of precision formation flying (PFF), i.e, when the relative geometry of multiple vehicles must be controlled on-board in a continuous and precise manner, there have been several missions proposed, but the realization in space has not yet occurred due to a range of issues. This paper will briefly examine those issues and present a concept for demonstrating a core capability for performing PFF, necessary for virtually any PFF mission concept, that will help to overcome the problems encountered in prior attempts and help to allay the risks to enable future PFF science missions.

Analysis of borderline substitution/electron transfer pathways from direct ab initio MD simulations

NASA Astrophysics Data System (ADS)

Yamataka, Hiroshi; Aida, Misako; Dupuis, Michel

2002-02-01

Ab initio molecular dynamics simulations were carried out for the borderline reaction pathways in the reaction of CH 2O rad - with CH 3Cl. The simulations reveal distinctive features of three types of mechanisms passing through the S N2-like transition state (TS): (i) a direct formation of S N2 products, (ii) a direct formation of ET products, and (iii) a two-step formation of ET products via the S N2 valley. The direct formation of the ET product through the S N2-like TS appears to be more favorable at higher temperatures. The two-step process depends on the amount of energy that goes into the C-C stretching mode.

GVE-Based Dynamics and Control for Formation Flying Spacecraft

NASA Technical Reports Server (NTRS)

Breger, Louis; How, Jonathan P.

2004-01-01

Formation flying is an enabling technology for many future space missions. This paper presents extensions to the equations of relative motion expressed in Keplerian orbital elements, including new initialization techniques for general formation configurations. A new linear time-varying form of the equations of relative motion is developed from Gauss Variational Equations and used in a model predictive controller. The linearizing assumptions for these equations are shown to be consistent with typical formation flying scenarios. Several linear, convex initialization techniques are presented, as well as a general, decentralized method for coordinating a tetrahedral formation using differential orbital elements. Control methods are validated using a commercial numerical propagator.

Final Report: Mechanisms of sputter ripple formation: coupling among energetic ions, surface kinetics, stress and composition

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

Chason, Eric; Shenoy, Vivek

Self-organized pattern formation enables the creation of nanoscale surface structures over large areas based on fundamental physical processes rather than an applied template. Low energy ion bombardment is one such method that induces the spontaneous formation of a wide variety of interesting morphological features (e.g., sputter ripples and/or quantum dots). This program focused on the processes controlling sputter ripple formation and the kinetics controlling the evolution of surfaces and nanostructures in high flux environments. This was done by using systematic, quantitative experiments to measure ripple formation under a variety of processing conditions coupled with modeling to interpret the results.

Debiasing comparative optimism and increasing worry for health outcomes.

PubMed

Rose, Jason P

2012-11-01

Comparative optimism - feeling at less personal risk for negative outcomes than one's peers - has been linked to reduced prevention efforts. This study examined a novel debiasing technique aimed at simultaneously reducing both indirectly and directly measured comparative optimism. Before providing direct comparative estimates, participants provided absolute self and peer estimates in a joint format (same computer screen) or a separate format (different computer screens). Relative to the separate format condition, participants in the joint format condition showed (1) lower comparative optimism in absolute/indirect measures, (2) lower direct comparative optimism, and (3) heightened worry. Implications for risk perception screening are discussed.

Why Video Games Can Be a Good Fit for Formative Assessment

ERIC Educational Resources Information Center

Bauer, Malcolm; Wylie, Caroline; Jackson, Tanner; Mislevy, Bob; Hoffman-John, Erin; John, Michael; Corrigan, Seth

2017-01-01

This paper explores the relation between formative assessment principles and their analogues in video games that game designers have been developing over the past 35 years. We identify important parallels between the two that should enable effective and efficient use of well-designed video games in the classroom as part of an overall learning…

Higher Education as Self-Formation. IOE Inaugural Professorial Lectures

ERIC Educational Resources Information Center

Marginson, Simon

2018-01-01

Higher education can be understood as a process of self-formation or self-cultivation, immersed in complex knowledge, that enables the student to become more capable and more autonomous and self-determining. In this lecture Professor Simon Marginson draws on a sweep of ideas from the fields of education and social science, including the late work…

FASTQ quality control dashboard

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

2016-07-25

FQCDB builds up existing open source software, FastQC, implementing a modern web interface for across parsed output of FastQC. In addition, FQCDB is extensible as a web service to include additional plots of type line, boxplot, or heatmap, across data formatted according to guidelines. The interface is also configurable via more readable JSON format, enabling customization by non-web programmers.

Living in the Age of Imposed Amnesia: The Eclipse of Democratic Formative Culture

ERIC Educational Resources Information Center

Giroux, Henry A.

2011-01-01

This article argues that under neoliberal casino capitalism there has been a wholesale attack not only on the social state but also on those public spheres that enable the formative cultures necessary to produce critical agents, engaged subjects, and the literacies necessary to make power and authority accountable. In this instance, the struggle…

Calibration Procedures in Mid Format Camera Setups

NASA Astrophysics Data System (ADS)

Pivnicka, F.; Kemper, G.; Geissler, S.

2012-07-01

A growing number of mid-format cameras are used for aerial surveying projects. To achieve a reliable and geometrically precise result also in the photogrammetric workflow, awareness on the sensitive parts is important. The use of direct referencing systems (GPS/IMU), the mounting on a stabilizing camera platform and the specific values of the mid format camera make a professional setup with various calibration and misalignment operations necessary. An important part is to have a proper camera calibration. Using aerial images over a well designed test field with 3D structures and/or different flight altitudes enable the determination of calibration values in Bingo software. It will be demonstrated how such a calibration can be performed. The direct referencing device must be mounted in a solid and reliable way to the camera. Beside the mechanical work especially in mounting the camera beside the IMU, 2 lever arms have to be measured in mm accuracy. Important are the lever arms from the GPS Antenna to the IMU's calibrated centre and also the lever arm from the IMU centre to the Camera projection centre. In fact, the measurement with a total station is not a difficult task but the definition of the right centres and the need for using rotation matrices can cause serious accuracy problems. The benefit of small and medium format cameras is that also smaller aircrafts can be used. Like that, a gyro bases stabilized platform is recommended. This causes, that the IMU must be mounted beside the camera on the stabilizer. The advantage is, that the IMU can be used to control the platform, the problematic thing is, that the IMU to GPS antenna lever arm is floating. In fact we have to deal with an additional data stream, the values of the movement of the stabiliser to correct the floating lever arm distances. If the post-processing of the GPS-IMU data by taking the floating levers into account, delivers an expected result, the lever arms between IMU and camera can be applied. However, there is a misalignment (bore side angle) that must be evaluated by photogrammetric process using advanced tools e.g. in Bingo. Once, all these parameters have been determined, the system is capable for projects without or with only a few ground control points. But which effect has the photogrammetric process when directly applying the achieved direct orientation values compared with an AT based on a proper tiepoint matching? The paper aims to show the steps to be done by potential users and gives a kind of quality estimation about the importance and quality influence of the various calibration and adjustment steps.

Alginate Hydrogel Microencapsulation Inhibits Devitrification and Enables Large-Volume Low-CPA Cell Vitrification

PubMed Central

Huang, Haishui; Choi, Jung Kyu; Rao, Wei; Zhao, Shuting; Agarwal, Pranay; Zhao, Gang

2015-01-01

Cryopreservation of stem cells is important to meet their ever-increasing demand by the burgeoning cell-based medicine. The conventional slow freezing for stem cell cryopreservation suffers from inevitable cell injury associated with ice formation and the vitrification (i.e., no visible ice formation) approach is emerging as a new strategy for cell cryopreservation. A major challenge to cell vitrification is intracellular ice formation (IIF, a lethal event to cells) induced by devitrification (i.e., formation of visible ice in previously vitrified solution) during warming the vitrified cells at cryogenic temperature back to super-zero temperatures. Consequently, high and toxic concentrations of penetrating cryoprotectants (i.e., high CPAs, up to ~8 M) and/or limited sample volumes (up to ~2.5 μl) have been used to minimize IIF during vitrification. We reveal that alginate hydrogel microencapsulation can effectively inhibit devitrification during warming. Our data show that if ice formation were minimized during cooling, IIF is negligible in alginate hydrogel-microencapsulated cells during the entire cooling and warming procedure of vitrification. This enables vitrification of pluripotent and multipotent stem cells with up to ~4 times lower concentration of penetrating CPAs (up to 2 M, low CPA) in up to ~100 times larger sample volume (up to ~250 μl, large volume). PMID:26640426

Alginate Hydrogel Microencapsulation Inhibits Devitrification and Enables Large-Volume Low-CPA Cell Vitrification.

PubMed

Huang, Haishui; Choi, Jung Kyu; Rao, Wei; Zhao, Shuting; Agarwal, Pranay; Zhao, Gang; He, Xiaoming

2015-11-25

Cryopreservation of stem cells is important to meet their ever-increasing demand by the burgeoning cell-based medicine. The conventional slow freezing for stem cell cryopreservation suffers from inevitable cell injury associated with ice formation and the vitrification ( i.e. , no visible ice formation) approach is emerging as a new strategy for cell cryopreservation. A major challenge to cell vitrification is intracellular ice formation (IIF, a lethal event to cells) induced by devitrification ( i.e. , formation of visible ice in previously vitrified solution) during warming the vitrified cells at cryogenic temperature back to super-zero temperatures. Consequently, high and toxic concentrations of penetrating cryoprotectants ( i.e. , high CPAs, up to ~8 M) and/or limited sample volumes (up to ~2.5 μl) have been used to minimize IIF during vitrification. We reveal that alginate hydrogel microencapsulation can effectively inhibit devitrification during warming. Our data show that if ice formation were minimized during cooling, IIF is negligible in alginate hydrogel-microencapsulated cells during the entire cooling and warming procedure of vitrification. This enables vitrification of pluripotent and multipotent stem cells with up to ~4 times lower concentration of penetrating CPAs (up to 2 M, low CPA) in up to ~100 times larger sample volume (up to ~250 μl, large volume).

Distinguishing crystallization stages and their influence on quantum efficiency during perovskite solar cell formation in real-time.

PubMed

Wagner, Lukas; Mundt, Laura E; Mathiazhagan, Gayathri; Mundus, Markus; Schubert, Martin C; Mastroianni, Simone; Würfel, Uli; Hinsch, Andreas; Glunz, Stefan W

2017-11-02

Relating crystallization of the absorber layer in a perovskite solar cell (PSC) to the device performance is a key challenge for the process development and in-depth understanding of these types of high efficient solar cells. A novel approach that enables real-time photo-physical and electrical characterization using a graphite-based PSC is introduced in this work. In our graphite-based PSC, the device architecture of porous monolithic contact layers creates the possibility to perform photovoltaic measurements while the perovskite crystallizes within this scaffold. The kinetics of crystallization in a solution based 2-step formation process has been analyzed by real-time measurement of the external photon to electron quantum efficiency as well as the photoluminescence emission spectra of the solar cell. With this method it was in particular possible to identify a previously overlooked crystallization stage during the formation of the perovskite absorber layer. This stage has significant influence on the development of the photocurrent, which is attributed to the formation of electrical pathways between the electron and hole contact, enabling efficient charge carrier extraction. We observe that in contrast to previously suggested models, the perovskite layer formation is indeed not complete with the end of crystal growth.

Formations of Tethered Spacecraft as Stable Platforms for Far IR and Sub-mm Astronomy

NASA Technical Reports Server (NTRS)

Quadrelli, Marco B.; Hadaegh, Fred Y.; Shao, Michael; Lorenzini, Enrico C.

2004-01-01

In this paper we describe current research in tethered formations for interferometry, and a roadmap to demonstrating the required key technologies via on-ground and in-orbit testing. We propose an integrated kilometer-size tethered spacecraft formation flying concept which enables Far IR and Sub-mm astronomy observations from space. A rather general model is used to predict the dynamics, control, and estimation performance of formations of spacecraft connected by tethers in LEO and deep space. These models include the orbital and tethered formation dynamics, environmental models, and models of the formation estimator/controller/commander. Both centralized and decentralized control/sensing/estimation schemes are possible, and dynamic ranges of interest for sensing/control are described. Key component/subsystem technologies are described which need both ground-based and in-orbit demonstration prior to their utilization in precision space interferometry missions using tethered formations. Defining an orbiting formation as an ensemble of orbiting spacecraft performing a cooperative task, recent work has demonstrated the validity of the tethering the spacecraft to provide both the required formation rigidity and satisfy the formation reconfiguration needs such as interferometer baseline control. In our concept, several vehicles are connected and move along the tether, so that to reposition them the connecting tether links must vary in length. This feature enables variable and precise baseline control while the system spins around the boresight. The control architecture features an interferometer configuration composed of one central combiner spacecraft and two aligned collector spacecraft. The combiner spacecraft acts as the formation leader and is also where the centralized sensing and estimation functions reside. Some of the issues analyzed with the model are: dynamic modes of deformation of the distributed structure, architecture of the formation sensor, and sources of dynamical perturbation that need to be mitigated for precision operation in space. Examples from numerical simulation of an envisioned scenario in heliocentric orbit demonstrate the potential of the concept for space interferometry.

Formate, acetate, and propionate as substrates for sulfate reduction in sub-arctic sediments of Southwest Greenland

PubMed Central

Glombitza, Clemens; Jaussi, Marion; Røy, Hans; Seidenkrantz, Marit-Solveig; Lomstein, Bente A.; Jørgensen, Bo B.

2015-01-01

Volatile fatty acids (VFAs) are key intermediates in the anaerobic mineralization of organic matter in marine sediments. We studied the role of VFAs in the carbon and energy turnover in the sulfate reduction zone of sediments from the sub-arctic Godthåbsfjord (SW Greenland) and the adjacent continental shelf in the NE Labrador Sea. VFA porewater concentrations were measured by a new two-dimensional ion chromatography-mass spectrometry method that enabled the direct analysis of VFAs without sample pretreatment. VFA concentrations were low and surprisingly constant (4–6 μmol L−1 for formate and acetate, and 0.5 μmol L−1 for propionate) throughout the sulfate reduction zone. Hence, VFAs are turned over while maintaining a stable concentration that is suggested to be under a strong microbial control. Estimated mean diffusion times of acetate between neighboring cells were <1 s, whereas VFA turnover times increased from several hours at the sediment surface to several years at the bottom of the sulfate reduction zone. Thus, diffusion was not limiting the VFA turnover. Despite constant VFA concentrations, the Gibbs energies (ΔGr) of VFA-dependent sulfate reduction decreased downcore, from −28 to −16 kJ (mol formate)−1, −68 to −31 kJ (mol acetate)−1, and −124 to −65 kJ (mol propionate)−1. Thus, ΔGr is apparently not determining the in-situ VFA concentrations directly. However, at the bottom of the sulfate zone of the shelf station, acetoclastic sulfate reduction might operate at its energetic limit at ~ −30 kJ (mol acetate)−1. It is not clear what controls VFA concentrations in the porewater but cell physiological constraints such as energetic costs of VFA activation or uptake could be important. We suggest that such constraints control the substrate turnover and result in a minimum ΔGr that depends on cell physiology and is different for individual substrates. PMID:26379631

Modeling The Distribution Of Dark Matter And Its Connection To Galaxies

NASA Astrophysics Data System (ADS)

Mao, Yao-Yuan

2016-06-01

Despite the mysterious nature of dark matter and dark energy, the Lambda-Cold Dark Matter (LCDM) model provides a reasonably accurate description of the evolution of the cosmos and the distribution of galaxies. Today, we are set to tackle more specific and quantitative questions about the galaxy formation physics, the nature of dark matter, and the connection between the dark and the visible components. The answers to these questions are however elusive, because dark matter is not directly observable, and various unknowns lie between what we can observe and what we can calculate. Hence, mathematical models that bridge the observable and the calculable are essential for the study of modern cosmology. The aim of my thesis work is to improve existing models and also to construct new models for various aspects of the dark matter distribution, as dark matter structures the cosmic web and forms the nests of visible galaxies. Utilizing a series of cosmological dark matter simulations which span a wide dynamical range and a statistical sample of zoom-in simulations which focus on individual dark matter halos, we develop models for the spatial and velocity distribution of dark matter particles, the abundance of dark substructures, and the empirical connection between dark matter and galaxies. As more precise observational results become available, more accurate models are then required to test the consistency between these results and the LCDM predictions. For all the models we investigate, we find that the formation history of dark matter halos always plays a crucial role. Neglecting the halo formation history would result in systematic biases when we interpret various observational results, including dark matter direct detection experiments, the detection of dark substructures with strong-lensed systems, the large-scale spatial clustering of galaxies, and the abundance of dwarf galaxies. Rectifying this, our work will enable us to fully utilize the complementary power of diverse observational datasets to test the LCDM model and to seek new physics.