Sample records for throughput solution phase
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Klijn, Marieke E; Hubbuch, Jürgen
2018-04-27
Protein phase diagrams are a tool to investigate cause and consequence of solution conditions on protein phase behavior. The effects are scored according to aggregation morphologies such as crystals or amorphous precipitates. Solution conditions affect morphological features, such as crystal size, as well as kinetic features, such as crystal growth time. Common used data visualization techniques include individual line graphs or symbols-based phase diagrams. These techniques have limitations in terms of handling large datasets, comprehensiveness or completeness. To eliminate these limitations, morphological and kinetic features obtained from crystallization images generated with high throughput microbatch experiments have been visualized with radar charts in combination with the empirical phase diagram (EPD) method. Morphological features (crystal size, shape, and number, as well as precipitate size) and kinetic features (crystal and precipitate onset and growth time) are extracted for 768 solutions with varying chicken egg white lysozyme concentration, salt type, ionic strength and pH. Image-based aggregation morphology and kinetic features were compiled into a single and easily interpretable figure, thereby showing that the EPD method can support high throughput crystallization experiments in its data amount as well as its data complexity. Copyright © 2018. Published by Elsevier Inc.
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A solid-phase glycosyltransferase assay for high-throughput screening in drug discovery research.
Donovan, R S; Datti, A; Baek, M G; Wu, Q; Sas, I J; Korczak, B; Berger, E G; Roy, R; Dennis, J W
1999-10-01
Glycosyltransferases mediate changes in glycosylation patterns which, in turn, may affect the function of glycoproteins and/or glycolipids and, further downstream, processes of development, differentiation, transformation and cell-cell recognition. Such enzymes, therefore, represent valid targets for drug discovery. We have developed a solid-phase glycosyltransferase assay for use in a robotic high-throughput format. Carbohydrate acceptors coupled covalently to polyacrylamide are coated onto 96-well plastic plates. The glycosyltransferase reaction is performed with recombinant enzymes and radiolabeled sugar-nucleotide donor at 37 degrees C, followed by washing, addition of scintillation counting fluid, and measurement of radioactivity using a 96-well beta-counter. Glycopolymer construction and coating of the plastic plates, enzyme and substrate concentrations, and linearity with time were optimized using recombinant Core 2 beta1-6-N-acetylglucosaminyltransferase (Core 2 GlcNAc-T). This enzyme catalyzes a rate-limiting reaction for expression of polylactosamine and the selectin ligand sialyl-Lewis(x) in O-glycans. A glycopolymer acceptor for beta1-6-N-acetylglucosaminyltransferase V was also designed and shown to be effective in the solid-phase assay. In a high-throughput screen of a microbial extract library, the coefficient of variance for positive controls was 9.4%, and high concordance for hit validation was observed between the Core 2 GlcNAc-T solid-phase assay and a standard solution-phase assay. The solid-phase assay format, which can be adapted for a variety of glycosyltransferase enzymes, allowed a 5-6 fold increase in throughput compared to the corresponding solution-phase assay.
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High throughput integrated thermal characterization with non-contact optical calorimetry
NASA Astrophysics Data System (ADS)
Hou, Sichao; Huo, Ruiqing; Su, Ming
2017-10-01
Commonly used thermal analysis tools such as calorimeter and thermal conductivity meter are separated instruments and limited by low throughput, where only one sample is examined each time. This work reports an infrared based optical calorimetry with its theoretical foundation, which is able to provide an integrated solution to characterize thermal properties of materials with high throughput. By taking time domain temperature information of spatially distributed samples, this method allows a single device (infrared camera) to determine the thermal properties of both phase change systems (melting temperature and latent heat of fusion) and non-phase change systems (thermal conductivity and heat capacity). This method further allows these thermal properties of multiple samples to be determined rapidly, remotely, and simultaneously. In this proof-of-concept experiment, the thermal properties of a panel of 16 samples including melting temperatures, latent heats of fusion, heat capacities, and thermal conductivities have been determined in 2 min with high accuracy. Given the high thermal, spatial, and temporal resolutions of the advanced infrared camera, this method has the potential to revolutionize the thermal characterization of materials by providing an integrated solution with high throughput, high sensitivity, and short analysis time.
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Temperature control in a 30 stage, 5-cm Centrifugal Contactor Pilot Plant
DOE Office of Scientific and Technical Information (OSTI.GOV)
Jack D. Law; Troy G. Garn; David H. Meikrantz
2009-09-01
Temperature profile testing was performed using a 30 stage 5-cm centrifugal contactor pilot plant. These tests were performed to evaluate the ability to control process temperature by adjusting feed solution temperatures. This would eliminate the need for complex jacketed heat exchanger installation on the centrifugal contactors. Thermocouples were installed on the inlet and outlets of each stage, as well as directly in the mixing zone of several of the contactor stages. Lamp oil, a commercially available alkane mixture of C14 to C18 chains, and tap water adjusted to pH 2 with nitric acid were the solution feeds for the temperaturemore » profile testing. Temperature data profiles for an array of total throughputs and contactor rpm values for both single-phase and two-phase systems were collected with selected profiles. The total throughput ranged from 0.5-1.4 L/min with rotor speeds from 3500-4000 rpm. Inlet solution temperatures ranging from ambient up to 50 °C were tested. Results of the two-phase temperature profile testing are detailed« less
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Townsend, Jared B; Shaheen, Farzana; Liu, Ruiwu; Lam, Kit S
2010-09-13
A method to efficiently immobilize and partition large quantities of microbeads in an array format in microfabricated poly(dimethylsiloxane) (PDMS) cassette for ultrahigh-throughput in situ releasable solution-phase cell-based screening of one-bead-one-compound (OBOC) combinatorial libraries is described. Commercially available Jeffamine triamine T-403 (∼440 Da) was derivatized such that two of its amino groups were protected by Fmoc and the remaining amino group capped with succinic anhydride to generate a carboxyl group. This resulting trifunctional hydrophilic polymer was then sequentially coupled two times to the outer layer of topologically segregated bilayer TentaGel (TG) beads with solid phase peptide synthesis chemistry resulting in beads with increased loading capacity, hydrophilicity, and porosity at the outer layer. We have found that such bead configuration can facilitate ultrahigh-throughput in situ releasable solution-phase screening of OBOC libraries. An encoded releasable OBOC small molecule library was constructed on Jeffamine derivatized TG beads with library compounds tethered to the outer layer via a disulfide linker and coding tags in the interior of the beads. Compound-beads could be efficiently loaded (5-10 min) into a 5 cm diameter Petri dish containing a 10,000-well PDMS microbead cassette, such that over 90% of the microwells were each filled with only one compound-bead. Jurkat T-lymphoid cancer cells suspended in Matrigel were then layered over the microbead cassette to immobilize the compound-beads. After 24 h of incubation at 37 °C, dithiothreitol was added to trigger the release of library compounds. Forty-eight hours later, MTT reporter assay was used to identify regions of reduced cell viability surrounding each positive bead. From a total of about 20,000 beads screened, 3 positive beads were detected and physically isolated for decoding. A strong consensus motif was identified for these three positive compounds. These compounds were resynthesized and found to be cytotoxic (IC(50) 50-150 μM) against two T-lymphoma cell lines and less so against the MDA-MB 231 breast cancer cell line. This novel ultrahigh-throughput OBOC releasable method can potentially be adapted to many existing 96- or 384-well solution-phase cell-based or biochemical assays.
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Townsend, Jared B.; Shaheen, Farzana; Liu, Ruiwu; Lam, Kit S.
2011-01-01
A method to efficiently immobilize and partition large quantities of microbeads in an array format in microfabricated polydimethylsiloxane (PDMS) cassette for high-throughput in situ releasable solution-phase cell-based screening of one-bead-one-compound (OBOC) combinatorial libraries is described. Commercially available Jeffamine triamine T-403 (∼440 Da) was derivatized such that two of its amino groups were protected by Fmoc and the remaining amino group capped with succinic anhydride to generate a carboxyl group. This resulting tri-functional hydrophilic polymer was then sequentially coupled two times to the outer layer of topologically segregated bilayer TentaGel (TG) beads with solid phase peptide synthesis chemistry, resulting in beads with increased loading capacity, hydrophilicity and porosity at the outer layer. We have found that such bead configuration can facilitate ultra high-throughput in situ releasable solution-phase screening of OBOC libraries. An encoded releasable OBOC small molecule library was constructed on Jeffamine derivatized TG beads with library compounds tethered to the outer layer via a disulfide linker and coding tags in the interior of the beads. Compound-beads could be efficiently loaded (5-10 minutes) into a 5 cm diameter Petri dish containing a 10,000-well PDMS microbead cassette, such that over 90% of the microwells were each filled with only one compound-bead. Jurkat T-lymphoid cancer cells suspended in Matrigel® were then layered over the microbead cassette to immobilize the compound-beads. After 24 hours of incubation at 37°C, dithiothreitol was added to trigger the release of library compounds. Forty-eight hours later, MTT reporter assay was used to identify regions of reduced cell viability surrounding each positive bead. From a total of about 20,000 beads screened, 3 positive beads were detected and physically isolated for decoding. A strong consensus motif was identified for these three positive compounds. These compounds were re-synthesized and found to be cytotoxic (IC50 50-150 μM) against two T-lymphoma cell lines and less so against the MDA-MB 231 breast cancer cell line. This novel ultra high-throughput OBOC releasable method can potentially be adapted to many existing 96- or 384-well solution-phase cell-based or biochemical assays. PMID:20593859
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High Throughput, Polymeric Aqueous Two-Phase Printing of Tumor Spheroids
Atefi, Ehsan; Lemmo, Stephanie; Fyffe, Darcy; Luker, Gary D.; Tavana, Hossein
2014-01-01
This paper presents a new 3D culture microtechnology for high throughput production of tumor spheroids and validates its utility for screening anti-cancer drugs. We use two immiscible polymeric aqueous solutions and microprint a submicroliter drop of the “patterning” phase containing cells into a bath of the “immersion” phase. Selecting proper formulations of biphasic systems using a panel of biocompatible polymers results in the formation of a round drop that confines cells to facilitate spontaneous formation of a spheroid without any external stimuli. Adapting this approach to robotic tools enables straightforward generation and maintenance of spheroids of well-defined size in standard microwell plates and biochemical analysis of spheroids in situ, which is not possible with existing techniques for spheroid culture. To enable high throughput screening, we establish a phase diagram to identify minimum cell densities within specific volumes of the patterning drop to result in a single spheroid. Spheroids show normal growth over long-term incubation and dose-dependent decrease in cellular viability when treated with drug compounds, but present significant resistance compared to monolayer cultures. The unprecedented ease of implementing this microtechnology and its robust performance will benefit high throughput studies of drug screening against cancer cells with physiologically-relevant 3D tumor models. PMID:25411577
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New Bandwidth Efficient Parallel Concatenated Coding Schemes
NASA Technical Reports Server (NTRS)
Denedetto, S.; Divsalar, D.; Montorsi, G.; Pollara, F.
1996-01-01
We propose a new solution to parallel concatenation of trellis codes with multilevel amplitude/phase modulations and a suitable iterative decoding structure. Examples are given for throughputs 2 bits/sec/Hz with 8PSK and 16QAM signal constellations.
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Bhattacharyya, S; Fan, L; Vo, L; Labadie, J
2000-04-01
Amine libraries and their derivatives are important targets for high throughput synthesis because of their versatility as medicinal agents and agrochemicals. As a part of our efforts towards automated chemical library synthesis, a titanium(IV) isopropoxide mediated solution phase reductive amination protocol was successfully translated to automation on the Trident(TM) library synthesizer of Argonaut Technologies. An array of 24 secondary amines was prepared in high yield and purity from 4 primary amines and 6 carbonyl compounds. These secondary amines were further utilized in a split synthesis to generate libraries of ureas, amides and sulfonamides in solution phase on the Trident(TM). The automated runs included 192 reactions to synthesize 96 ureas in duplicate and 96 reactions to synthesize 48 amides and 48 sulfonamides. A number of polymer-assisted solution phase protocols were employed for parallel work-up and purification of the products in each step.
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Solution-Phase Photochemical Nanopatterning Enabled by High-Refractive-Index Beam Pen Arrays.
Xie, Zhuang; Gordiichuk, Pavlo; Lin, Qing-Yuan; Meckes, Brian; Chen, Peng-Cheng; Sun, Lin; Du, Jingshan S; Zhu, Jinghan; Liu, Yuan; Dravid, Vinayak P; Mirkin, Chad A
2017-08-22
A high-throughput, solution-based, scanning-probe photochemical nanopatterning approach, which does not require the use of probes with subwavelength apertures, is reported. Specifically, pyramid arrays made from high-refractive-index polymeric materials were constructed and studied as patterning tools in a conventional liquid-phase beam pen lithography experiment. Two versions of the arrays were explored with either metal-coated or metal-free tips. Importantly, light can be channeled through both types of tips and the appropriate solution phase (e.g., H 2 O or CH 3 OH) and focused on subwavelength regions of a substrate to effect a photoreaction in solution that results in localized patterning of a self-assembled monolayer (SAM)-coated Au thin film substrate. Arrays with as many as 4500 pyramid-shaped probes were used to simultaneously initiate thousands of localized free-radical photoreactions (decomposition of a lithium acylphosphinate photoinitiator in an aqueous solution) that result in oxidative removal of the SAM. The technique is attractive since it allows one to rapidly generate features less than 200 nm in diameter, and the metal-free tips afford more than 10-fold higher intensity than the tips with nanoapertures over a micrometer propagation length. In principle, this mask-free method can be utilized as a versatile tool for performing a wide variety of photochemistries across multiple scales that may be important in high-throughput combinatorial screening applications related to chemistry, biology, and materials science.
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Prakesch, Michael; Srivastava, Stuti; Leek, Donald M; Arya, Prabhat
2006-01-01
With the goal of rapidly accessing tetrahydroquinoline-based natural-product-like polycyclic architectures, herein, we report an unprecedented, in situ, stereocontrolled Aza Michael approach in solution and on the solid phase. The mild reaction conditions required to reach the desired target are highly attractive for the use of this method in library generation. To our knowledge, this approach has not been used before, and it opens a novel route leading to a wide variety of tetrahydroquinoline-derived bridged tricyclic derivatives.
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Bladergroen, Marco R.; van der Burgt, Yuri E. M.
2015-01-01
For large-scale and standardized applications in mass spectrometry- (MS-) based proteomics automation of each step is essential. Here we present high-throughput sample preparation solutions for balancing the speed of current MS-acquisitions and the time needed for analytical workup of body fluids. The discussed workflows reduce body fluid sample complexity and apply for both bottom-up proteomics experiments and top-down protein characterization approaches. Various sample preparation methods that involve solid-phase extraction (SPE) including affinity enrichment strategies have been automated. Obtained peptide and protein fractions can be mass analyzed by direct infusion into an electrospray ionization (ESI) source or by means of matrix-assisted laser desorption ionization (MALDI) without further need of time-consuming liquid chromatography (LC) separations. PMID:25692071
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Fuzzy Logic-based expert system for evaluating cake quality of freeze-dried formulations.
Trnka, Hjalte; Wu, Jian X; Van De Weert, Marco; Grohganz, Holger; Rantanen, Jukka
2013-12-01
Freeze-drying of peptide and protein-based pharmaceuticals is an increasingly important field of research. The diverse nature of these compounds, limited understanding of excipient functionality, and difficult-to-analyze quality attributes together with the increasing importance of the biosimilarity concept complicate the development phase of safe and cost-effective drug products. To streamline the development phase and to make high-throughput formulation screening possible, efficient solutions for analyzing critical quality attributes such as cake quality with minimal material consumption are needed. The aim of this study was to develop a fuzzy logic system based on image analysis (IA) for analyzing cake quality. Freeze-dried samples with different visual quality attributes were prepared in well plates. Imaging solutions together with image analytical routines were developed for extracting critical visual features such as the degree of cake collapse, glassiness, and color uniformity. On the basis of the IA outputs, a fuzzy logic system for analysis of these freeze-dried cakes was constructed. After this development phase, the system was tested with a new screening well plate. The developed fuzzy logic-based system was found to give comparable quality scores with visual evaluation, making high-throughput classification of cake quality possible. © 2013 Wiley Periodicals, Inc. and the American Pharmacists Association.
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NASA Astrophysics Data System (ADS)
Lopez, Carlos; Watanabe, Takaichi; Cabral, Joao; Graham, Peter; Porcar, Lionel; Martel, Anne
2014-03-01
The coupling of microfluidics and small angle neutron scattering (SANS) is successfully demonstrated for the first time. We have developed novel microdevices with suitably low SANS background and high pressure compatibility for the investigation of flow-induced phenomena and high throughput phase mapping of complex fluids. We successfully obtained scattering profiles from 50 micron channels, in 10s - 100s second acquisition times. The microfluidic geometry enables the variation of both flow type and magnitude, beyond traditional rheo-SANS setups, and is exceptionally well-suited for complex fluids due to the commensurability of relevant time and lengthscales. We demonstrate our approach by studying model flow responsive systems, including surfactant/co-surfactant/water mixtures, with well-known equilibrium phase behaviour,: sodium dodecyl sulfate (SDS)/octanol/brine, cetyltrimethyl ammonium chloride (C16TAC)/pentanol/water and a model microemulsion system (C10E4 /decane/ D20), as well as polyelectrolyte solutions. Finally, using an online micromixer we are able to implement a high throughput approach, scanning in excess of 10 scattering profiles/min for a continuous aqueous surfactant dilution over two decades in concentration.
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Kuroda, Noritaka; Hird, Nick; Cork, David G
2006-01-01
During further improvement of a high-throughput, solution-phase synthesis system, new workup tools and apparatus for parallel liquid-liquid extraction and evaporation have been developed. A combination of in-house design and collaboration with external manufacturers has been used to address (1) environmental issues concerning solvent emissions and (2) sample tracking errors arising from manual intervention. A parallel liquid-liquid extraction unit, containing miniature high-speed magnetic stirrers for efficient mixing of organic and aqueous phases, has been developed for use on a multichannel liquid handler. Separation of the phases is achieved by dispensing them into a newly patented filter tube containing a vertical hydrophobic porous membrane, which allows only the organic phase to pass into collection vials positioned below. The vertical positioning of the membrane overcomes the hitherto dependence on the use of heavier-than-water, bottom-phase, organic solvents such as dichloromethane, which are restricted due to environmental concerns. Both small (6-mL) and large (60-mL) filter tubes were developed for parallel phase separation in library and template synthesis, respectively. In addition, an apparatus for parallel solvent evaporation was developed to (1) remove solvent from the above samples with highly efficient recovery and (2) avoid the movement of individual samples between their collection on a liquid handler and registration to prevent sample identification errors. The apparatus uses a diaphragm pump to achieve a dynamic circulating closed system with a heating block for the rack of 96 sample vials and an efficient condenser to trap the solvents. Solvent recovery is typically >98%, and convenient operation and monitoring has made the apparatus the first choice for removal of volatile solvents.
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High-throughput measurement of polymer film thickness using optical dyes
NASA Astrophysics Data System (ADS)
Grunlan, Jaime C.; Mehrabi, Ali R.; Ly, Tien
2005-01-01
Optical dyes were added to polymer solutions in an effort to create a technique for high-throughput screening of dry polymer film thickness. Arrays of polystyrene films, cast from a toluene solution, containing methyl red or solvent green were used to demonstrate the feasibility of this technique. Measurements of the peak visible absorbance of each film were converted to thickness using the Beer-Lambert relationship. These absorbance-based thickness calculations agreed within 10% of thickness measured using a micrometer for polystyrene films that were 10-50 µm. At these thicknesses it is believed that the absorbance values are actually more accurate. At least for this solvent-based system, thickness was shown to be accurately measured in a high-throughput manner that could potentially be applied to other equivalent systems. Similar water-based films made with poly(sodium 4-styrenesulfonate) dyed with malachite green oxalate or congo red did not show the same level of agreement with the micrometer measurements. Extensive phase separation between polymer and dye resulted in inflated absorbance values and calculated thickness that was often more than 25% greater than that measured with the micrometer. Only at thicknesses below 15 µm could reasonable accuracy be achieved for the water-based films.
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Jaramillo, Thomas F; Baeck, Sung-Hyeon; Kleiman-Shwarsctein, Alan; Choi, Kyoung-Shin; Stucky, Galen D; McFarland, Eric W
2005-01-01
High-throughput electrochemical methods have been developed for the investigation of Zn1-xCo(x)O films for photoelectrochemical hydrogen production from water. A library of 120 samples containing 27 different compositions (0
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Raina, Shweta A; Alonzo, David E; Zhang, Geoff G Z; Gao, Yi; Taylor, Lynne S
2015-11-01
Highly supersaturated aqueous solutions of poorly soluble compounds can undergo liquid-liquid phase separation (LLPS) when the concentration exceeds the "amorphous solubility". This phenomenon has been widely observed during high throughput screening of new molecular entities as well as during the dissolution of amorphous solid dispersions. In this study, we have evaluated the use of environment-sensitive fluorescence probes to investigate the formation and properties of the non-crystalline drug-rich aggregates formed in aqueous solutions as a result of LLPS. Six different environment-sensitive fluorophores were employed to study LLPS in highly supersaturated solutions of several model compounds, all dihydropyridine derivatives. Each fluoroprobe exhibited a large hypsochromic shift with decreasing environment polarity. Upon drug aggregate formation, the probes partitioned into the drug-rich phase and exhibited changes in emission wavelength and intensity consistent with sensing a lower polarity environment. The LLPS onset concentrations determined using the fluorescence measurements were in good agreement with light scattering measurements as well as theoretically estimated amorphous solubility values. Environment-sensitive fluorescence probes are useful to help understand the phase behavior of highly supersaturated aqueous solutions, which in turn is important in the context of developing enabling formulations for poorly soluble compounds.
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Suram, Santosh K.; Xue, Yexiang; Bai, Junwen; ...
2016-11-21
Rapid construction of phase diagrams is a central tenet of combinatorial materials science with accelerated materials discovery efforts often hampered by challenges in interpreting combinatorial X-ray diffraction data sets, which we address by developing AgileFD, an artificial intelligence algorithm that enables rapid phase mapping from a combinatorial library of X-ray diffraction patterns. AgileFD models alloying-based peak shifting through a novel expansion of convolutional nonnegative matrix factorization, which not only improves the identification of constituent phases but also maps their concentration and lattice parameter as a function of composition. By incorporating Gibbs’ phase rule into the algorithm, physically meaningful phase mapsmore » are obtained with unsupervised operation, and more refined solutions are attained by injecting expert knowledge of the system. The algorithm is demonstrated through investigation of the V–Mn–Nb oxide system where decomposition of eight oxide phases, including two with substantial alloying, provides the first phase map for this pseudoternary system. This phase map enables interpretation of high-throughput band gap data, leading to the discovery of new solar light absorbers and the alloying-based tuning of the direct-allowed band gap energy of MnV 2O 6. Lastly, the open-source family of AgileFD algorithms can be implemented into a broad range of high throughput workflows to accelerate materials discovery.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Suram, Santosh K.; Xue, Yexiang; Bai, Junwen
Rapid construction of phase diagrams is a central tenet of combinatorial materials science with accelerated materials discovery efforts often hampered by challenges in interpreting combinatorial X-ray diffraction data sets, which we address by developing AgileFD, an artificial intelligence algorithm that enables rapid phase mapping from a combinatorial library of X-ray diffraction patterns. AgileFD models alloying-based peak shifting through a novel expansion of convolutional nonnegative matrix factorization, which not only improves the identification of constituent phases but also maps their concentration and lattice parameter as a function of composition. By incorporating Gibbs’ phase rule into the algorithm, physically meaningful phase mapsmore » are obtained with unsupervised operation, and more refined solutions are attained by injecting expert knowledge of the system. The algorithm is demonstrated through investigation of the V–Mn–Nb oxide system where decomposition of eight oxide phases, including two with substantial alloying, provides the first phase map for this pseudoternary system. This phase map enables interpretation of high-throughput band gap data, leading to the discovery of new solar light absorbers and the alloying-based tuning of the direct-allowed band gap energy of MnV 2O 6. Lastly, the open-source family of AgileFD algorithms can be implemented into a broad range of high throughput workflows to accelerate materials discovery.« less
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A high-throughput exploration of magnetic materials by using structure predicting methods
NASA Astrophysics Data System (ADS)
Arapan, S.; Nieves, P.; Cuesta-López, S.
2018-02-01
We study the capability of a structure predicting method based on genetic/evolutionary algorithm for a high-throughput exploration of magnetic materials. We use the USPEX and VASP codes to predict stable and generate low-energy meta-stable structures for a set of representative magnetic structures comprising intermetallic alloys, oxides, interstitial compounds, and systems containing rare-earths elements, and for both types of ferromagnetic and antiferromagnetic ordering. We have modified the interface between USPEX and VASP codes to improve the performance of structural optimization as well as to perform calculations in a high-throughput manner. We show that exploring the structure phase space with a structure predicting technique reveals large sets of low-energy metastable structures, which not only improve currently exiting databases, but also may provide understanding and solutions to stabilize and synthesize magnetic materials suitable for permanent magnet applications.
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Picoliter Drop-On-Demand Dispensing for Multiplex Liquid Cell Transmission Electron Microscopy
DOE Office of Scientific and Technical Information (OSTI.GOV)
Patterson, Joseph P.; Parent, Lucas R.; Cantlon, Joshua
2016-05-03
Abstract Liquid cell transmission electron microscopy (LCTEM) provides a unique insight into the dynamics of nanomaterials in solution. Controlling the addition of multiple solutions to the liquid cell remains a key hurdle in our ability to increase throughput and to study processes dependent on solution mixing including chemical reactions. Here, we report that a piezo dispensing technique allows for mixing of multiple solutions directly within the viewing area. This technique permits deposition of 50 pL droplets of various aqueous solutions onto the liquid cell window, before assembly of the cell in a fully controlled manner. This proof-of-concept study highlights themore » great potential of picoliter dispensing in combination with LCTEM for observing nanoparticle mixing in the solution phase and the creation of chemical gradients.« less
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Shinde, Aniketa; Guevarra, Dan; Haber, Joel A.; ...
2014-10-21
For many solar fuel generator designs involve illumination of a photoabsorber stack coated with a catalyst for the oxygen evolution reaction (OER). In this design, impinging light must pass through the catalyst layer before reaching the photoabsorber(s), and thus optical transmission is an important function of the OER catalyst layer. Many oxide catalysts, such as those containing elements Ni and Co, form oxide or oxyhydroxide phases in alkaline solution at operational potentials that differ from the phases observed in ambient conditions. To characterize the transparency of such catalysts during OER operation, 1031 unique compositions containing the elements Ni, Co, Ce,more » La, and Fe were prepared by a high throughput inkjet printing technique. Moreover, the catalytic current of each composition was recorded at an OER overpotential of 0.33 V with simultaneous measurement of the spectral transmission. By combining the optical and catalytic properties, the combined catalyst efficiency was calculated to identify the optimal catalysts for solar fuel applications within the material library. Our measurements required development of a new high throughput instrument with integrated electrochemistry and spectroscopy measurements, which enables various spectroelectrochemistry experiments.« less
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Yang, Jing-Hua; Shao, Jing; Wang, Hou-Yu; Dong, Jing-Yu; Fan, Liu-Yin; Cao, Cheng-Xi; Xu, Yu-Quan
2012-09-01
Herein, a simple novel free-flow electrophoresis (FFE) method was developed via introduction of organic solvent into the electrolyte system, increasing the solute solubility and throughput of the sample. As a proof of concept, phenazine-1-carboxylic acid (PCA) from Pseudomonas sp. M18 was selected as a model solute for the demonstration on feasibility of novel FFE method on account of its faint solubility in aqueous circumstance. In the developed method, the organic solvent was added into not only the sample buffer to improve the solubility of the solute, but also the background buffer to construct a uniform aqueous-organic circumstance. These factors of organic solvent percentage and types as well as pH value of background buffer were investigated for the purification of PCA in the FFE device via CE. The experiments revealed that the percentage and the types of organic solvent exerted major influence on the purification of PCA. Under the optimized conditions (30 mM phosphate buffer in 60:40 (v/v) water-methanol at an apparent pH 7.0, 3.26 mL/min background flux, 10-min residence time of injected sample, and 400 V), PCA could be continuously purified from its impurities. The flux of sample injection was 10.05 μL/min, and the recovery was up to 93.7%. An 11.9-fold improvement of throughput was found with a carrier buffer containing 40% (v/v) methanol, compared with the pure aqueous phase. The developed procedure is of evident significance for the purification of weak polarity solute via FFE. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Wang, Ying; Latypov, Ramil F; Lomakin, Aleksey; Meyer, Julie A; Kerwin, Bruce A; Vunnum, Suresh; Benedek, George B
2014-05-05
Colloidal stability of antibody solutions, i.e., the propensity of the folded protein to precipitate, is an important consideration in formulation development of therapeutic monoclonal antibodies. In a protein solution, different pathways including crystallization, colloidal aggregation, and liquid-liquid phase separation (LLPS) can lead to the formation of precipitates. The kinetics of crystallization and aggregation are often slow and vary from protein to protein. Due to the diverse mechanisms of these protein condensation processes, it is a challenge to develop a standardized test for an early evaluation of the colloidal stability of antibody solutions. LLPS would normally occur in antibody solutions at sufficiently low temperature, provided that it is not preempted by freezing of the solution. Poly(ethylene glycol) (PEG) can be used to induce LLPS at temperatures above the freezing point. Here, we propose a colloidal stability test based on inducing LLPS in antibody solutions and measuring the antibody concentration of the dilute phase. We demonstrate experimentally that such a PEG-induced LLPS test can be used to compare colloidal stability of different antibodies in different solution conditions and can be readily applied to high-throughput screening. We have derived an equation for the effects of PEG concentration and molecular weight on the results of the LLPS test. Finally, this equation defines a binding energy in the condensed phase, which can be determined in the PEG-induced LLPS test. This binding energy is a measure of attractive interactions between antibody molecules and can be used for quantitative characterization of the colloidal stability of antibody solutions.
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High-throughput state-machine replication using software transactional memory.
Zhao, Wenbing; Yang, William; Zhang, Honglei; Yang, Jack; Luo, Xiong; Zhu, Yueqin; Yang, Mary; Luo, Chaomin
2016-11-01
State-machine replication is a common way of constructing general purpose fault tolerance systems. To ensure replica consistency, requests must be executed sequentially according to some total order at all non-faulty replicas. Unfortunately, this could severely limit the system throughput. This issue has been partially addressed by identifying non-conflicting requests based on application semantics and executing these requests concurrently. However, identifying and tracking non-conflicting requests require intimate knowledge of application design and implementation, and a custom fault tolerance solution developed for one application cannot be easily adopted by other applications. Software transactional memory offers a new way of constructing concurrent programs. In this article, we present the mechanisms needed to retrofit existing concurrency control algorithms designed for software transactional memory for state-machine replication. The main benefit for using software transactional memory in state-machine replication is that general purpose concurrency control mechanisms can be designed without deep knowledge of application semantics. As such, new fault tolerance systems based on state-machine replications with excellent throughput can be easily designed and maintained. In this article, we introduce three different concurrency control mechanisms for state-machine replication using software transactional memory, namely, ordered strong strict two-phase locking, conventional timestamp-based multiversion concurrency control, and speculative timestamp-based multiversion concurrency control. Our experiments show that speculative timestamp-based multiversion concurrency control mechanism has the best performance in all types of workload, the conventional timestamp-based multiversion concurrency control offers the worst performance due to high abort rate in the presence of even moderate contention between transactions. The ordered strong strict two-phase locking mechanism offers the simplest solution with excellent performance in low contention workload, and fairly good performance in high contention workload.
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High-throughput state-machine replication using software transactional memory
Yang, William; Zhang, Honglei; Yang, Jack; Luo, Xiong; Zhu, Yueqin; Yang, Mary; Luo, Chaomin
2017-01-01
State-machine replication is a common way of constructing general purpose fault tolerance systems. To ensure replica consistency, requests must be executed sequentially according to some total order at all non-faulty replicas. Unfortunately, this could severely limit the system throughput. This issue has been partially addressed by identifying non-conflicting requests based on application semantics and executing these requests concurrently. However, identifying and tracking non-conflicting requests require intimate knowledge of application design and implementation, and a custom fault tolerance solution developed for one application cannot be easily adopted by other applications. Software transactional memory offers a new way of constructing concurrent programs. In this article, we present the mechanisms needed to retrofit existing concurrency control algorithms designed for software transactional memory for state-machine replication. The main benefit for using software transactional memory in state-machine replication is that general purpose concurrency control mechanisms can be designed without deep knowledge of application semantics. As such, new fault tolerance systems based on state-machine replications with excellent throughput can be easily designed and maintained. In this article, we introduce three different concurrency control mechanisms for state-machine replication using software transactional memory, namely, ordered strong strict two-phase locking, conventional timestamp-based multiversion concurrency control, and speculative timestamp-based multiversion concurrency control. Our experiments show that speculative timestamp-based multiversion concurrency control mechanism has the best performance in all types of workload, the conventional timestamp-based multiversion concurrency control offers the worst performance due to high abort rate in the presence of even moderate contention between transactions. The ordered strong strict two-phase locking mechanism offers the simplest solution with excellent performance in low contention workload, and fairly good performance in high contention workload. PMID:29075049
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Efficient Phase Unwrapping Architecture for Digital Holographic Microscopy
Hwang, Wen-Jyi; Cheng, Shih-Chang; Cheng, Chau-Jern
2011-01-01
This paper presents a novel phase unwrapping architecture for accelerating the computational speed of digital holographic microscopy (DHM). A fast Fourier transform (FFT) based phase unwrapping algorithm providing a minimum squared error solution is adopted for hardware implementation because of its simplicity and robustness to noise. The proposed architecture is realized in a pipeline fashion to maximize throughput of the computation. Moreover, the number of hardware multipliers and dividers are minimized to reduce the hardware costs. The proposed architecture is used as a custom user logic in a system on programmable chip (SOPC) for physical performance measurement. Experimental results reveal that the proposed architecture is effective for expediting the computational speed while consuming low hardware resources for designing an embedded DHM system. PMID:22163688
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NASA Astrophysics Data System (ADS)
Mok, Aaron T. Y.; Lee, Kelvin C. M.; Wong, Kenneth K. Y.; Tsia, Kevin K.
2018-02-01
Biophysical properties of cells could complement and correlate biochemical markers to characterize a multitude of cellular states. Changes in cell size, dry mass and subcellular morphology, for instance, are relevant to cell-cycle progression which is prevalently evaluated by DNA-targeted fluorescence measurements. Quantitative-phase microscopy (QPM) is among the effective biophysical phenotyping tools that can quantify cell sizes and sub-cellular dry mass density distribution of single cells at high spatial resolution. However, limited camera frame rate and thus imaging throughput makes QPM incompatible with high-throughput flow cytometry - a gold standard in multiparametric cell-based assay. Here we present a high-throughput approach for label-free analysis of cell cycle based on quantitative-phase time-stretch imaging flow cytometry at a throughput of > 10,000 cells/s. Our time-stretch QPM system enables sub-cellular resolution even at high speed, allowing us to extract a multitude (at least 24) of single-cell biophysical phenotypes (from both amplitude and phase images). Those phenotypes can be combined to track cell-cycle progression based on a t-distributed stochastic neighbor embedding (t-SNE) algorithm. Using multivariate analysis of variance (MANOVA) discriminant analysis, cell-cycle phases can also be predicted label-free with high accuracy at >90% in G1 and G2 phase, and >80% in S phase. We anticipate that high throughput label-free cell cycle characterization could open new approaches for large-scale single-cell analysis, bringing new mechanistic insights into complex biological processes including diseases pathogenesis.
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Computational tool for the early screening of monoclonal antibodies for their viscosities
Agrawal, Neeraj J; Helk, Bernhard; Kumar, Sandeep; Mody, Neil; Sathish, Hasige A.; Samra, Hardeep S.; Buck, Patrick M; Li, Li; Trout, Bernhardt L
2016-01-01
Highly concentrated antibody solutions often exhibit high viscosities, which present a number of challenges for antibody-drug development, manufacturing and administration. The antibody sequence is a key determinant for high viscosity of highly concentrated solutions; therefore, a sequence- or structure-based tool that can identify highly viscous antibodies from their sequence would be effective in ensuring that only antibodies with low viscosity progress to the development phase. Here, we present a spatial charge map (SCM) tool that can accurately identify highly viscous antibodies from their sequence alone (using homology modeling to determine the 3-dimensional structures). The SCM tool has been extensively validated at 3 different organizations, and has proved successful in correctly identifying highly viscous antibodies. As a quantitative tool, SCM is amenable to high-throughput automated analysis, and can be effectively implemented during the antibody screening or engineering phase for the selection of low-viscosity antibodies. PMID:26399600
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Ulaczyk-Lesanko, Agnieszka; Pelletier, Eric; Lee, Maria; Prinz, Heino; Waldmann, Herbert; Hall, Dennis G
2007-01-01
Several solid- and solution-phase strategies were evaluated for the preparation of libraries of polysubstituted piperidines of type 7 using the tandem aza[4+2]cycloaddition/allylboration multicomponent reaction between 1-aza-4-boronobutadienes, maleimides, and aldehydes. A novel four-component variant of this chemistry was developed in solution phase, and it circumvents the need for pre-forming the azabutadiene component. A parallel synthesis coupled with compound purification by HPLC with mass-based fraction collection allowed the preparation of a library of 944 polysubstituted piperidines in a high degree of purity suitable for biological screening. A representative subset of 244 compounds was screened against a panel of phosphatase enzymes, and despite the modest levels of activity obtained, this study demonstrated that piperidines of type 7 display the right physical properties (e.g., solubility) to be assayed effectively in high-throughput enzymatic tests.
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Fei, Yiyan; Landry, James P; Sun, Yungshin; Zhu, Xiangdong; Wang, Xiaobing; Luo, Juntao; Wu, Chun-Yi; Lam, Kit S
2010-01-01
We describe a high-throughput scanning optical microscope for detecting small-molecule compound microarrays on functionalized glass slides. It is based on measurements of oblique-incidence reflectivity difference and employs a combination of a y-scan galvometer mirror and an x-scan translation stage with an effective field of view of 2 cm x 4 cm. Such a field of view can accommodate a printed small-molecule compound microarray with as many as 10,000 to 20,000 targets. The scanning microscope is capable of measuring kinetics as well as endpoints of protein-ligand reactions simultaneously. We present the experimental results on solution-phase protein reactions with small-molecule compound microarrays synthesized from one-bead, one-compound combinatorial chemistry and immobilized on a streptavidin-functionalized glass slide.
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Fei, Yiyan; Landry, James P.; Sun, Yungshin; Zhu, Xiangdong; Wang, Xiaobing; Luo, Juntao; Wu, Chun-Yi; Lam, Kit S.
2010-01-01
We describe a high-throughput scanning optical microscope for detecting small-molecule compound microarrays on functionalized glass slides. It is based on measurements of oblique-incidence reflectivity difference and employs a combination of a y-scan galvometer mirror and an x-scan translation stage with an effective field of view of 2 cm×4 cm. Such a field of view can accommodate a printed small-molecule compound microarray with as many as 10,000 to 20,000 targets. The scanning microscope is capable of measuring kinetics as well as endpoints of protein-ligand reactions simultaneously. We present the experimental results on solution-phase protein reactions with small-molecule compound microarrays synthesized from one-bead, one-compound combinatorial chemistry and immobilized on a streptavidin-functionalized glass slide. PMID:20210464
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Fast iodide-SAD phasing for high-throughput membrane protein structure determination
Melnikov, Igor; Polovinkin, Vitaly; Kovalev, Kirill; Gushchin, Ivan; Shevtsov, Mikhail; Shevchenko, Vitaly; Mishin, Alexey; Alekseev, Alexey; Rodriguez-Valera, Francisco; Borshchevskiy, Valentin; Cherezov, Vadim; Leonard, Gordon A.; Gordeliy, Valentin; Popov, Alexander
2017-01-01
We describe a fast, easy, and potentially universal method for the de novo solution of the crystal structures of membrane proteins via iodide–single-wavelength anomalous diffraction (I-SAD). The potential universality of the method is based on a common feature of membrane proteins—the availability at the hydrophobic-hydrophilic interface of positively charged amino acid residues with which iodide strongly interacts. We demonstrate the solution using I-SAD of four crystal structures representing different classes of membrane proteins, including a human G protein–coupled receptor (GPCR), and we show that I-SAD can be applied using data collection strategies based on either standard or serial x-ray crystallography techniques. PMID:28508075
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Fast iodide-SAD phasing for high-throughput membrane protein structure determination.
Melnikov, Igor; Polovinkin, Vitaly; Kovalev, Kirill; Gushchin, Ivan; Shevtsov, Mikhail; Shevchenko, Vitaly; Mishin, Alexey; Alekseev, Alexey; Rodriguez-Valera, Francisco; Borshchevskiy, Valentin; Cherezov, Vadim; Leonard, Gordon A; Gordeliy, Valentin; Popov, Alexander
2017-05-01
We describe a fast, easy, and potentially universal method for the de novo solution of the crystal structures of membrane proteins via iodide-single-wavelength anomalous diffraction (I-SAD). The potential universality of the method is based on a common feature of membrane proteins-the availability at the hydrophobic-hydrophilic interface of positively charged amino acid residues with which iodide strongly interacts. We demonstrate the solution using I-SAD of four crystal structures representing different classes of membrane proteins, including a human G protein-coupled receptor (GPCR), and we show that I-SAD can be applied using data collection strategies based on either standard or serial x-ray crystallography techniques.
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Baumgartner, Kai; Galm, Lara; Nötzold, Juliane; Sigloch, Heike; Morgenstern, Josefine; Schleining, Kristina; Suhm, Susanna; Oelmeier, Stefan A; Hubbuch, Jürgen
2015-02-01
Knowledge of protein phase behavior is essential for downstream process design in the biopharmaceutical industry. Proteins can either be soluble, crystalline or precipitated. Additionally liquid-liquid phase separation, gelation and skin formation can occur. A method to generate phase diagrams in high throughput on an automated liquid handling station in microbatch scale was developed. For lysozyme from chicken egg white, human lysozyme, glucose oxidase and glucose isomerase phase diagrams were generated at four different pH values – pH 3, 5, 7 and 9. Sodium chloride, ammonium sulfate, polyethylene glycol 300 and polyethylene glycol 1000 were used as precipitants. Crystallizing conditions could be found for lysozyme from chicken egg white using sodium chloride, for human lysozyme using sodium chloride or ammonium sulfate and glucose isomerase using ammonium sulfate. PEG caused destabilization of human lysozyme and glucose oxidase solutions or a balance of stabilizing and destabilizing effects for glucose isomerase near the isoelectric point. This work presents a systematic generation and extensive study of phase diagrams of proteins. Thus, it adds to the general understanding of protein behavior in liquid formulation and presents a convenient methodology applicable to any protein solution. Copyright © 2014 Elsevier B.V. All rights reserved.
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Evans, Jack D; Jelfs, Kim E; Day, Graeme M; Doonan, Christian J
2017-06-06
Composed from discrete units, porous molecular materials (PMMs) possess unique properties not observed for conventional, extended, solids, such as solution processibility and permanent porosity in the liquid phase. However, identifying the origin of porosity is not a trivial process, especially for amorphous or liquid phases. Furthermore, the assembly of molecular components is typically governed by a subtle balance of weak intermolecular forces that makes structure prediction challenging. Accordingly, in this review we canvass the crucial role of molecular simulations in the characterisation and design of PMMs. We will outline strategies for modelling porosity in crystalline, amorphous and liquid phases and also describe the state-of-the-art methods used for high-throughput screening of large datasets to identify materials that exhibit novel performance characteristics.
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Optical determination of crystal phase in semiconductor nanocrystals
Lim, Sung Jun; Schleife, André; Smith, Andrew M.
2017-01-01
Optical, electronic and structural properties of nanocrystals fundamentally derive from crystal phase. This is especially important for polymorphic II–VI, III–V and I-III-VI2 semiconductor materials such as cadmium selenide, which exist as two stable phases, cubic and hexagonal, each with distinct properties. However, standard crystallographic characterization through diffraction yields ambiguous phase signatures when nanocrystals are small or polytypic. Moreover, diffraction methods are low-throughput, incompatible with solution samples and require large sample quantities. Here we report the identification of unambiguous optical signatures of cubic and hexagonal phases in II–VI nanocrystals using absorption spectroscopy and first-principles electronic-structure theory. High-energy spectral features allow rapid identification of phase, even in small nanocrystals (∼2 nm), and may help predict polytypic nanocrystals from differential phase contributions. These theoretical and experimental insights provide simple and accurate optical crystallographic analysis for liquid-dispersed nanomaterials, to improve the precision of nanocrystal engineering and improve our understanding of nanocrystal reactions. PMID:28513577
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An extensible framework for capturing solvent effects in computer generated kinetic models.
Jalan, Amrit; West, Richard H; Green, William H
2013-03-14
Detailed kinetic models provide useful mechanistic insight into a chemical system. Manual construction of such models is laborious and error-prone, which has led to the development of automated methods for exploring chemical pathways. These methods rely on fast, high-throughput estimation of species thermochemistry and kinetic parameters. In this paper, we present a methodology for extending automatic mechanism generation to solution phase systems which requires estimation of solvent effects on reaction rates and equilibria. The linear solvation energy relationship (LSER) method of Abraham and co-workers is combined with Mintz correlations to estimate ΔG(solv)°(T) in over 30 solvents using solute descriptors estimated from group additivity. Simple corrections are found to be adequate for the treatment of radical sites, as suggested by comparison with known experimental data. The performance of scaled particle theory expressions for enthalpic-entropic decomposition of ΔG(solv)°(T) is also presented along with the associated computational issues. Similar high-throughput methods for solvent effects on free-radical kinetics are only available for a handful of reactions due to lack of reliable experimental data, and continuum dielectric calculations offer an alternative method for their estimation. For illustration, we model liquid phase oxidation of tetralin in different solvents computing the solvent dependence for ROO• + ROO• and ROO• + solvent reactions using polarizable continuum quantum chemistry methods. The resulting kinetic models show an increase in oxidation rate with solvent polarity, consistent with experiment. Further work needed to make this approach more generally useful is outlined.
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High-throughput ab-initio dilute solute diffusion database.
Wu, Henry; Mayeshiba, Tam; Morgan, Dane
2016-07-19
We demonstrate automated generation of diffusion databases from high-throughput density functional theory (DFT) calculations. A total of more than 230 dilute solute diffusion systems in Mg, Al, Cu, Ni, Pd, and Pt host lattices have been determined using multi-frequency diffusion models. We apply a correction method for solute diffusion in alloys using experimental and simulated values of host self-diffusivity. We find good agreement with experimental solute diffusion data, obtaining a weighted activation barrier RMS error of 0.176 eV when excluding magnetic solutes in non-magnetic alloys. The compiled database is the largest collection of consistently calculated ab-initio solute diffusion data in the world.
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Solid-phase assays for small molecule screening using sol-gel entrapped proteins.
Lebert, Julie M; Forsberg, Erica M; Brennan, John D
2008-04-01
With compound libraries exceeding one million compounds, the ability to quickly and effectively screen these compounds against relevant pharmaceutical targets has become crucial. Solid-phase assays present several advantages over solution-based methods. For example, a higher degree of miniaturization can be achieved, functional- and affinity-based studies are possible, and a variety of detection methods can be used. Unfortunately, most protein immobilization methods are either too harsh or require recombinant proteins and thus are not amenable to delicate proteins such as kinases and membrane-bound receptors. Sol-gel encapsulation of proteins in an inorganic silica matrix has emerged as a novel solid-phase assay platform. In this minireview, we discuss the development of sol-gel derived protein microarrays and sol-gel based monolithic bioaffinity columns for the high-throughput screening of small molecule libraries and mixtures.
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High throughput workflow for coacervate formation and characterization in shampoo systems.
Kalantar, T H; Tucker, C J; Zalusky, A S; Boomgaard, T A; Wilson, B E; Ladika, M; Jordan, S L; Li, W K; Zhang, X; Goh, C G
2007-01-01
Cationic cellulosic polymers find wide utility as benefit agents in shampoo. Deposition of these polymers onto hair has been shown to mend split-ends, improve appearance and wet combing, as well as provide controlled delivery of insoluble actives. The deposition is thought to be enhanced by the formation of a polymer/surfactant complex that phase-separates from the bulk solution upon dilution. A standard characterization method has been developed to characterize the coacervate formation upon dilution, but the test is time and material prohibitive. We have developed a semi-automated high throughput workflow to characterize the coacervate-forming behavior of different shampoo formulations. A procedure that allows testing of real use shampoo dilutions without first formulating a complete shampoo was identified. This procedure was adapted to a Tecan liquid handler by optimizing the parameters for liquid dispensing as well as for mixing. The high throughput workflow enabled preparation and testing of hundreds of formulations with different types and levels of cationic cellulosic polymers and surfactants, and for each formulation a haze diagram was constructed. Optimal formulations and their dilutions that give substantial coacervate formation (determined by haze measurements) were identified. Results from this high throughput workflow were shown to reproduce standard haze and bench-top turbidity measurements, and this workflow has the advantages of using less material and allowing more variables to be tested with significant time savings.
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High-throughput determination of structural phase diagram and constituent phases using GRENDEL
NASA Astrophysics Data System (ADS)
Kusne, A. G.; Keller, D.; Anderson, A.; Zaban, A.; Takeuchi, I.
2015-11-01
Advances in high-throughput materials fabrication and characterization techniques have resulted in faster rates of data collection and rapidly growing volumes of experimental data. To convert this mass of information into actionable knowledge of material process-structure-property relationships requires high-throughput data analysis techniques. This work explores the use of the Graph-based endmember extraction and labeling (GRENDEL) algorithm as a high-throughput method for analyzing structural data from combinatorial libraries, specifically, to determine phase diagrams and constituent phases from both x-ray diffraction and Raman spectral data. The GRENDEL algorithm utilizes a set of physical constraints to optimize results and provides a framework by which additional physics-based constraints can be easily incorporated. GRENDEL also permits the integration of database data as shown by the use of critically evaluated data from the Inorganic Crystal Structure Database in the x-ray diffraction data analysis. Also the Sunburst radial tree map is demonstrated as a tool to visualize material structure-property relationships found through graph based analysis.
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Pan, Yuchen; Sackmann, Eric K; Wypisniak, Karolina; Hornsby, Michael; Datwani, Sammy S; Herr, Amy E
2016-12-23
High-quality immunoreagents enhance the performance and reproducibility of immunoassays and, in turn, the quality of both biological and clinical measurements. High quality recombinant immunoreagents are generated using antibody-phage display. One metric of antibody quality - the binding affinity - is quantified through the dissociation constant (K D ) of each recombinant antibody and the target antigen. To characterize the K D of recombinant antibodies and target antigen, we introduce affinity electrophoretic mobility shift assays (EMSAs) in a high-throughput format suitable for small volume samples. A microfluidic card comprised of free-standing polyacrylamide gel (fsPAG) separation lanes supports 384 concurrent EMSAs in 30 s using a single power source. Sample is dispensed onto the microfluidic EMSA card by acoustic droplet ejection (ADE), which reduces EMSA variability compared to sample dispensing using manual or pin tools. The K D for each of a six-member fragment antigen-binding fragment library is reported using ~25-fold less sample mass and ~5-fold less time than conventional heterogeneous assays. Given the form factor and performance of this micro- and mesofluidic workflow, we have developed a sample-sparing, high-throughput, solution-phase alternative for biomolecular affinity characterization.
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Pan, Yuchen; Sackmann, Eric K.; Wypisniak, Karolina; Hornsby, Michael; Datwani, Sammy S.; Herr, Amy E.
2016-01-01
High-quality immunoreagents enhance the performance and reproducibility of immunoassays and, in turn, the quality of both biological and clinical measurements. High quality recombinant immunoreagents are generated using antibody-phage display. One metric of antibody quality – the binding affinity – is quantified through the dissociation constant (KD) of each recombinant antibody and the target antigen. To characterize the KD of recombinant antibodies and target antigen, we introduce affinity electrophoretic mobility shift assays (EMSAs) in a high-throughput format suitable for small volume samples. A microfluidic card comprised of free-standing polyacrylamide gel (fsPAG) separation lanes supports 384 concurrent EMSAs in 30 s using a single power source. Sample is dispensed onto the microfluidic EMSA card by acoustic droplet ejection (ADE), which reduces EMSA variability compared to sample dispensing using manual or pin tools. The KD for each of a six-member fragment antigen-binding fragment library is reported using ~25-fold less sample mass and ~5-fold less time than conventional heterogeneous assays. Given the form factor and performance of this micro- and mesofluidic workflow, we have developed a sample-sparing, high-throughput, solution-phase alternative for biomolecular affinity characterization. PMID:28008969
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High-throughput ab-initio dilute solute diffusion database
Wu, Henry; Mayeshiba, Tam; Morgan, Dane
2016-01-01
We demonstrate automated generation of diffusion databases from high-throughput density functional theory (DFT) calculations. A total of more than 230 dilute solute diffusion systems in Mg, Al, Cu, Ni, Pd, and Pt host lattices have been determined using multi-frequency diffusion models. We apply a correction method for solute diffusion in alloys using experimental and simulated values of host self-diffusivity. We find good agreement with experimental solute diffusion data, obtaining a weighted activation barrier RMS error of 0.176 eV when excluding magnetic solutes in non-magnetic alloys. The compiled database is the largest collection of consistently calculated ab-initio solute diffusion data in the world. PMID:27434308
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Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)
DOE Office of Scientific and Technical Information (OSTI.GOV)
Hura, Greg L.; Menon, Angeli L.; Hammel, Michal
2009-07-20
We present an efficient pipeline enabling high-throughput analysis of protein structure in solution with small angle X-ray scattering (SAXS). Our SAXS pipeline combines automated sample handling of microliter volumes, temperature and anaerobic control, rapid data collection and data analysis, and couples structural analysis with automated archiving. We subjected 50 representative proteins, mostly from Pyrococcus furiosus, to this pipeline and found that 30 were multimeric structures in solution. SAXS analysis allowed us to distinguish aggregated and unfolded proteins, define global structural parameters and oligomeric states for most samples, identify shapes and similar structures for 25 unknown structures, and determine envelopes formore » 41 proteins. We believe that high-throughput SAXS is an enabling technology that may change the way that structural genomics research is done.« less
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Quesada-Cabrera, Raul; Weng, Xiaole; Hyett, Geoff; Clark, Robin J H; Wang, Xue Z; Darr, Jawwad A
2013-09-09
High-throughput continuous hydrothermal flow synthesis was used to manufacture 66 unique nanostructured oxide samples in the Ce-Zr-Y-O system. This synthesis approach resulted in a significant increase in throughput compared to that of conventional batch or continuous hydrothermal synthesis methods. The as-prepared library samples were placed into a wellplate for both automated high-throughput powder X-ray diffraction and Raman spectroscopy data collection, which allowed comprehensive structural characterization and phase mapping. The data suggested that a continuous cubic-like phase field connects all three Ce-Zr-O, Ce-Y-O, and Y-Zr-O binary systems together with a smooth and steady transition between the structures of neighboring compositions. The continuous hydrothermal process led to as-prepared crystallite sizes in the range of 2-7 nm (as determined by using the Scherrer equation).
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High-Throughput Incubation and Quantification of Agglutination Assays in a Microfluidic System.
Castro, David; Conchouso, David; Kodzius, Rimantas; Arevalo, Arpys; Foulds, Ian G
2018-06-04
In this paper, we present a two-phase microfluidic system capable of incubating and quantifying microbead-based agglutination assays. The microfluidic system is based on a simple fabrication solution, which requires only laboratory tubing filled with carrier oil, driven by negative pressure using a syringe pump. We provide a user-friendly interface, in which a pipette is used to insert single droplets of a 1.25-µL volume into a system that is continuously running and therefore works entirely on demand without the need for stopping, resetting or washing the system. These assays are incubated by highly efficient passive mixing with a sample-to-answer time of 2.5 min, a 5⁻10-fold improvement over traditional agglutination assays. We study system parameters such as channel length, incubation time and flow speed to select optimal assay conditions, using the streptavidin-biotin interaction as a model analyte quantified using optical image processing. We then investigate the effect of changing the concentration of both analyte and microbead concentrations, with a minimum detection limit of 100 ng/mL. The system can be both low- and high-throughput, depending on the rate at which assays are inserted. In our experiments, we were able to easily produce throughputs of 360 assays per hour by simple manual pipetting, which could be increased even further by automation and parallelization. Agglutination assays are a versatile tool, capable of detecting an ever-growing catalog of infectious diseases, proteins and metabolites. A system such as this one is a step towards being able to produce high-throughput microfluidic diagnostic solutions with widespread adoption. The development of analytical techniques in the microfluidic format, such as the one presented in this work, is an important step in being able to continuously monitor the performance and microfluidic outputs of organ-on-chip devices.
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Hattrick-Simpers, Jason R.; Gregoire, John M.; Kusne, A. Gilad
2016-05-26
With their ability to rapidly elucidate composition-structure-property relationships, high-throughput experimental studies have revolutionized how materials are discovered, optimized, and commercialized. It is now possible to synthesize and characterize high-throughput libraries that systematically address thousands of individual cuts of fabrication parameter space. An unresolved issue remains transforming structural characterization data into phase mappings. This difficulty is related to the complex information present in diffraction and spectroscopic data and its variation with composition and processing. Here, we review the field of automated phase diagram attribution and discuss the impact that emerging computational approaches will have in the generation of phase diagrams andmore » beyond.« less
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Xin, Huaxia; Dai, Zhuoshun; Cai, Jianfeng; Ke, Yanxiong; Shi, Hui; Fu, Qing; Jin, Yu; Liang, Xinmiao
2017-08-04
Supercritical fluid chromatography (SFC) with chiral stationary phases (CSPs) is an advanced solution for the separation of achiral compounds in Piper kadsura. Analogues and stereoisomers are abundant in natural products, but there are obstacles in separation using conventional method. In this paper, four lignan diastereoisomers, (-)-Galbelgin, (-)-Ganschisandrin, Galgravin and (-)-Veraguensin, from Piper kadsura were separated and purified by chiral SFC. Purification strategy was designed, considering of the compound enrichment, sample purity and purification throughput. Two-step achiral purification method on chiral preparative columns with stacked automated injections was developed. Unconventional mobile phase modifier dichloromethane (DCM) was applied to improve the sample solubility. Four diastereoisomers was prepared at the respective weight of 103.1mg, 10.0mg, 152.3mg and 178.6mg from 710mg extract with the purity of greater than 98%. Copyright © 2017 Elsevier B.V. All rights reserved.
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Rapid, low dose X-ray diffractive imaging of the malaria parasite Plasmodium falciparum.
Jones, Michael W M; Dearnley, Megan K; van Riessen, Grant A; Abbey, Brian; Putkunz, Corey T; Junker, Mark D; Vine, David J; McNulty, Ian; Nugent, Keith A; Peele, Andrew G; Tilley, Leann
2014-08-01
Phase-diverse X-ray coherent diffractive imaging (CDI) provides a route to high sensitivity and spatial resolution with moderate radiation dose. It also provides a robust solution to the well-known phase-problem, making on-line image reconstruction feasible. Here we apply phase-diverse CDI to a cellular sample, obtaining images of an erythrocyte infected by the sexual stage of the malaria parasite, Plasmodium falciparum, with a radiation dose significantly lower than the lowest dose previously reported for cellular imaging using CDI. The high sensitivity and resolution allow key biological features to be identified within intact cells, providing complementary information to optical and electron microscopy. This high throughput method could be used for fast tomographic imaging, or to generate multiple replicates in two-dimensions of hydrated biological systems without freezing or fixing. This work demonstrates that phase-diverse CDI is a valuable complementary imaging method for the biological sciences and ready for immediate application. © 2013 Elsevier B.V. All rights reserved.
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The planning and establishment of a sample preparation laboratory for drug discovery
Dufresne, Claude
2000-01-01
Nature has always been a productive source of new drugs. With the advent of high-throughput screening, it has now become possible to rapidly screen large sample collections. In addition to seeking greater diversity from natural product sources (micro-organisms, plants, etc.), fractionation of the crude extracts prior to screening is becoming a more important part of our efforts. As sample preparation protocols become more involved, automation can help to achieve and maintain a desired sample throughput. To address the needs of our screening program, two robotic systems were designed. The first system processes crude extracts all the way to 96-well plates, containing solutions suitable for screening in biological and biochemical assays. The system can dissolve crude extracts, fractionate them on solid-phase extraction cartridges, dry and weigh each fraction, re-dissolve them to a known concentration, and prepare mother plates. The second system replicates mother plates into a number of daughter plates. PMID:18924691
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Little information is available regarding the potential for many commercial chemicals to induce developmental toxicity. The mESC Adherent Cell Differentiation and Cytoxicity (ACDC) assay is a high-throughput screen used to close this data gap. Thus, ToxCast™ Phase I chemicals wer...
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Near-common-path interferometer for imaging Fourier-transform spectroscopy in wide-field microscopy
Wadduwage, Dushan N.; Singh, Vijay Raj; Choi, Heejin; Yaqoob, Zahid; Heemskerk, Hans; Matsudaira, Paul; So, Peter T. C.
2017-01-01
Imaging Fourier-transform spectroscopy (IFTS) is a powerful method for biological hyperspectral analysis based on various imaging modalities, such as fluorescence or Raman. Since the measurements are taken in the Fourier space of the spectrum, it can also take advantage of compressed sensing strategies. IFTS has been readily implemented in high-throughput, high-content microscope systems based on wide-field imaging modalities. However, there are limitations in existing wide-field IFTS designs. Non-common-path approaches are less phase-stable. Alternatively, designs based on the common-path Sagnac interferometer are stable, but incompatible with high-throughput imaging. They require exhaustive sequential scanning over large interferometric path delays, making compressive strategic data acquisition impossible. In this paper, we present a novel phase-stable, near-common-path interferometer enabling high-throughput hyperspectral imaging based on strategic data acquisition. Our results suggest that this approach can improve throughput over those of many other wide-field spectral techniques by more than an order of magnitude without compromising phase stability. PMID:29392168
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Controlled electrosprayed formation of non-spherical microparticles
NASA Astrophysics Data System (ADS)
Jeyhani, Morteza; Mak, Sze Yi; Sammut, Stephen; Shum, Ho Cheung; Hwang, Dae Kun; Tsai, Scott S. H.
2017-11-01
Fabrication of biocompatible microparticles, such as alginate particles, with the possibility of controlling the particles' morphology in a high-throughput manner, is essential for pharmaceutical and cosmetic industries. Even though the shape of alginate particles has been shown to be an important parameter in controlling drug delivery, there are very limited manufacturing methods to produce non-spherical alginate microparticles in a high-throughput fashion. Here, we present a system that generates non-spherical biocompatible alginate microparticles with a tunable size and shape, and at high-throughput, using an electrospray technique. Alginate solution, which is a highly biocompatible material, is flown through a needle using a constant flow rate syringe pump. The alginate phase is connected to a high-voltage power supply to charge it positively. There is a metallic ring underneath the needle that is charged negatively. The applied voltage creates an electric field that forces the dispensing droplets to pass through the metallic ring toward the collection bath. During this migration, droplets break up to smaller droplets to dissipate their energy. When the droplets reach the calcium chloride bath, polymerization happens and solidifies the droplets. We study the effects of changing the distance from the needle to the bath, and the concentration of calcium chloride in the bath, to control the size and the shape of the resulting microparticles.
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Hydraulic and Clean-in-Place Evaluations for a 12.5-cm Annular Centrifugal Contactor at INL
DOE Office of Scientific and Technical Information (OSTI.GOV)
Troy G. Garn; David H. Meikrantz; Nick R. Mann
2008-09-01
Hydraulic and Clean-in-Place Evaluations for a 12.5 cm Annular Centrifugal Contactor at the INL Troy G. Garn, Dave H. Meikrantz, Nick R. Mann, Jack D. Law, Terry A. Todd Idaho National Laboratory Commercially available, Annular Centrifugal Contactors (ACC) are currently being evaluated for processing dissolved nuclear fuel solutions to selectively partition integrated elements using solvent extraction technologies. These evaluations include hydraulic and clean-in-place (CIP) testing of a commercially available 12.5 cm unit. Data from these evaluations is used to support design of future nuclear fuel reprocessing facilities. Hydraulic testing provides contactor throughput performance data on two-phase systems for a widemore » range of operating conditions. Hydraulic testing results on a simple two-phase oil and water system followed by a 30 % Tributyl phosphate in N-dodecane / nitric acid pair are reported. Maximum total throughputs for this size contactor ranged from 20 to 32 liters per minute without significant other phase carryover. A relatively new contactor design enhancement providing Clean-in-Place capability for ACCs was also investigated. Spray nozzles installed into the central rotor shaft allow the rotor internals to be cleaned, offline. Testing of the solids capture of a diatomaceous earth/water slurry feed followed by CIP testing was performed. Solids capture efficiencies of >95% were observed for all tests and short cold water cleaning pulses proved successful at removing solids from the rotor.« less
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USDA-ARS?s Scientific Manuscript database
This study demonstrated the application of an automated high-throughput mini-cartridge solid-phase extraction (mini-SPE) cleanup for the rapid low-pressure gas chromatography – tandem mass spectrometry (LPGC-MS/MS) analysis of pesticides and environmental contaminants in QuEChERS extracts of foods. ...
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Phase Equilibria and Magnetic Phases in the Ce-Fe-Co-B System
Wang, Tian; Kevorkov, Dmytro; Medraj, Mamoun
2016-01-01
Ce-Fe-Co-B is a promising system for permanent magnets. A high-throughput screening method combining diffusion couples, key alloys, Scanning Electron Microscope/Wavelength Dispersive X-ray Spectroscope (SEM/WDS), and Magnetic Force Microscope (MFM) is used in this research to understand the phase equilibria and to explore promising magnetic phases in this system. Three magnetic phases were detected and their homogeneity ranges were determined at 900 °C, which were presented by the formulae: Ce2Fe14−xCoxB (0 ≤ x ≤ 4.76), CeCo4−xFexB (0 ≤ x ≤ 3.18), and Ce3Co11−x FexB4 (0 ≤ x ≤ 6.66). The phase relations among the magnetic phases in this system have been studied. Ce2(Fe, Co)14B appears to have stronger magnetization than Ce(Co, Fe)4B and Ce3(Co, Fe)11B4 from MFM analysis when comparing the magnetic interactions of selected key alloys. Also, a non-magnetic CeCo12−xFexB6 (0 ≤ x ≤ 8.74) phase was detected in this system. A boron-rich solid solution with Ce13FexCoyB45 (32 ≤ x ≤ 39, 3 ≤ y ≤ 10) chemical composition was also observed. However, the crystal structure of this phase could not be found in the literature. Moreover, ternary solid solutions ε1 (Ce2Fe17−xCox (0 ≤ x ≤ 12.35)) and ε2 (Ce2Co17−xFex (0 ≤ x ≤ 3.57)) were found to form between Ce2Fe17 and Ce2Co17 in the Ce-Fe-Co ternary system at 900 °C. PMID:28772374
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NASA Astrophysics Data System (ADS)
Rahmanseresht, Sheema; Milas, Peker; Ramos, Kieran P.; Gamari, Ben D.; Goldner, Lori S.
2015-05-01
Fluorescence resonance energy transfer (FRET) from individual, dye-labeled RNA molecules confined in freely-diffusing attoliter-volume aqueous droplets is carefully compared to FRET from unconfined RNA in solution. The use of freely-diffusing droplets is a remarkably simple and high-throughput technique that facilitates a substantial increase in signal-to-noise for single-molecular-pair FRET measurements. We show that there can be dramatic differences between FRET in solution and in droplets, which we attribute primarily to an altered pH in the confining environment. We also demonstrate that a sufficient concentration of a non-ionic surfactant mitigates this effect and restores FRET to its neutral-pH solution value. At low surfactant levels, even accounting for pH, we observe differences between the distribution of FRET values in solution and in droplets which remain unexplained. Our results will facilitate the use of nanoemulsion droplets as attoliter volume reactors for use in biophysical and biochemical assays, and also in applications such as protein crystallization or nanoparticle synthesis, where careful attention to the pH of the confined phase is required.
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NASA Astrophysics Data System (ADS)
Marenzana, Massimo; Hagen, Charlotte K.; Das Neves Borges, Patricia; Endrizzi, Marco; Szafraniec, Magdalena B.; Ignatyev, Konstantin; Olivo, Alessandro
2012-12-01
Being able to quantitatively assess articular cartilage in three-dimensions (3D) in small rodent animal models, with a simple laboratory set-up, would prove extremely important for the development of pre-clinical research focusing on cartilage pathologies such as osteoarthritis (OA). These models are becoming essential tools for the development of new drugs for OA, a disease affecting up to 1/3 of the population older than 50 years for which there is no cure except prosthetic surgery. However, due to limitations in imaging technology, high-throughput 3D structural imaging has not been achievable in small rodent models, thereby limiting their translational potential and their efficiency as research tools. We show that a simple laboratory system based on coded-aperture x-ray phase contrast imaging (CAXPCi) can correctly visualize the cartilage layer in slices of an excised rat tibia imaged both in air and in saline solution. Moreover, we show that small, surgically induced lesions are also correctly detected by the CAXPCi system, and we support this finding with histopathology examination. Following these successful proof-of-concept results in rat cartilage, we expect that an upgrade of the system to higher resolutions (currently underway) will enable extending the method to the imaging of mouse cartilage as well. From a technological standpoint, by showing the capability of the system to detect cartilage also in water, we demonstrate phase sensitivity comparable to other lab-based phase methods (e.g. grating interferometry). In conclusion, CAXPCi holds a strong potential for being adopted as a routine laboratory tool for non-destructive, high throughput assessment of 3D structural changes in murine articular cartilage, with a possible impact in the field similar to the revolution that conventional microCT brought into bone research.
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Morikawa, Go; Suzuka, Chihiro; Shoji, Atsushi; Shibusawa, Yoichi; Yanagida, Akio
2016-01-05
A high-throughput method for determining the octanol/water partition coefficient (P(o/w)) of a large variety of compounds exhibiting a wide range in hydrophobicity was established. The method combines a simple shake-flask method with a novel two-phase solvent system comprising an acetonitrile-phosphate buffer (0.1 M, pH 7.4)-1-octanol (25:25:4, v/v/v; AN system). The AN system partition coefficients (K(AN)) of 51 standard compounds for which log P(o/w) (at pH 7.4; log D) values had been reported were determined by single two-phase partitioning in test tubes, followed by measurement of the solute concentration in both phases using an automatic flow injection-ultraviolet detection system. The log K(AN) values were closely related to reported log D values, and the relationship could be expressed by the following linear regression equation: log D=2.8630 log K(AN) -0.1497(n=51). The relationship reveals that log D values (+8 to -8) for a large variety of highly hydrophobic and/or hydrophilic compounds can be estimated indirectly from the narrow range of log K(AN) values (+3 to -3) determined using the present method. Furthermore, log K(AN) values for highly polar compounds for which no log D values have been reported, such as amino acids, peptides, proteins, nucleosides, and nucleotides, can be estimated using the present method. The wide-ranging log D values (+5.9 to -7.5) of these molecules were estimated for the first time from their log K(AN) values and the above regression equation. Copyright © 2015 Elsevier B.V. All rights reserved.
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Schoener, Cody A; Curtis-Fisk, Jaime L; Rogers, True L; Tate, Michael P
2016-10-01
Ethylcellulose is commonly dissolved in a solvent or formed into an aqueous dispersion and sprayed onto various dosage forms to form a barrier membrane to provide controlled release in pharmaceutical formulations. Due to the variety of solvents utilized in the pharmaceutical industry and the importance solvent can play on film formation and film strength it is critical to understand how solvent can influence these parameters. To systematically study a variety of solvent blends and how these solvent blends influence ethylcellulose film formation, physical and mechanical film properties and solution properties such as clarity and viscosity. Using high throughput capabilities and evaporation rate modeling, thirty-one different solvent blends composed of ethanol, isopropanol, acetone, methanol, and/or water were formulated, analyzed for viscosity and clarity, and narrowed down to four solvent blends. Brookfield viscosity, film casting, mechanical film testing and water permeation were also completed. High throughput analysis identified isopropanol/water, ethanol, ethanol/water and methanol/acetone/water as solvent blends with unique clarity and viscosity values. Evaporation rate modeling further rank ordered these candidates from excellent to poor interaction with ethylcellulose. Isopropanol/water was identified as the most suitable solvent blend for ethylcellulose due to azeotrope formation during evaporation, which resulted in a solvent-rich phase allowing the ethylcellulose polymer chains to remain maximally extended during film formation. Consequently, the highest clarity and most ductile films were formed. Employing high throughput capabilities paired with evaporation rate modeling allowed strong predictions between solvent interaction with ethylcellulose and mechanical film properties.
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Creasy, Arch; Barker, Gregory; Carta, Giorgio
2017-03-01
A methodology is presented to predict protein elution behavior from an ion exchange column using both individual or combined pH and salt gradients based on high-throughput batch isotherm data. The buffer compositions are first optimized to generate linear pH gradients from pH 5.5 to 7 with defined concentrations of sodium chloride. Next, high-throughput batch isotherm data are collected for a monoclonal antibody on the cation exchange resin POROS XS over a range of protein concentrations, salt concentrations, and solution pH. Finally, a previously developed empirical interpolation (EI) method is extended to describe protein binding as a function of the protein and salt concentration and solution pH without using an explicit isotherm model. The interpolated isotherm data are then used with a lumped kinetic model to predict the protein elution behavior. Experimental results obtained for laboratory scale columns show excellent agreement with the predicted elution curves for both individual or combined pH and salt gradients at protein loads up to 45 mg/mL of column. Numerical studies show that the model predictions are robust as long as the isotherm data cover the range of mobile phase compositions where the protein actually elutes from the column. Copyright © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Sibia, Udai S; Grover, Jennifer; Turcotte, Justin J; Seanger, Michelle L; England, Kimberly A; King, Jennifer L; King, Paul J
2018-04-01
We describe a process for studying and improving baseline postanesthesia care unit (PACU)-to-floor transfer times after total joint replacements. Quality improvement project using lean methodology. Phase I of the investigational process involved collection of baseline data. Phase II involved developing targeted solutions to improve throughput. Phase III involved measured project sustainability. Phase I investigations revealed that patients spent an additional 62 minutes waiting in the PACU after being designated ready for transfer. Five to 16 telephone calls were needed between the PACU and the unit to facilitate each patient transfer. The most common reason for delay was unavailability of the unit nurse who was attending to another patient (58%). Phase II interventions resulted in transfer times decreasing to 13 minutes (79% reduction, P < .001). Phase III recorded sustained transfer times at 30 minutes, a net 52% reduction (P < .001) from baseline. Lean methodology resulted in the immediate decrease of PACU-to-floor transfer times by 79%, with a 52% sustained improvement. Our methods can also be used to improve efficiencies of care at other institutions. Copyright © 2016 American Society of PeriAnesthesia Nurses. Published by Elsevier Inc. All rights reserved.
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Synthesis and binding studies of Alzheimer ligands on solid support.
Rzepecki, Petra; Geib, Nina; Peifer, Manuel; Biesemeier, Frank; Schrader, Thomas
2007-05-11
Aminopyrazole derivatives constitute the first class of nonpeptidic rationally designed beta-sheet ligands. Here we describe a double solid-phase protocol for both synthesis and affinity testing. The presented solid-phase synthesis of four types of hybrid compounds relies on the Fmoc strategy and circumvents subsequent HPLC purification by precipitating the final product from organic solution in pure form. Hexa- and octapeptide pendants with internal di- and tetrapeptide bridges are now amenable in high yields to combinatorial synthesis of compound libraries for high-throughput screening purposes. Solid-phase peptide synthesis (SPPS) on an acid-resistant PAM allows us, after PMB deprotection, to subject the free aminopyrazole binding sites in an immobilized state to on-bead assays with fluorescence-labeled peptides. From the fluorescence emission intensity decrease, individual binding constants can be calculated via reference curves by simple application of the law of mass action. Gratifyingly, host/guest complexation can be monitored quantitatively even for those ligands, which are almost insoluble in water.
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On Maximizing the Throughput of Packet Transmission under Energy Constraints.
Wu, Weiwei; Dai, Guangli; Li, Yan; Shan, Feng
2018-06-23
More and more Internet of Things (IoT) wireless devices have been providing ubiquitous services over the recent years. Since most of these devices are powered by batteries, a fundamental trade-off to be addressed is the depleted energy and the achieved data throughput in wireless data transmission. By exploiting the rate-adaptive capacities of wireless devices, most existing works on energy-efficient data transmission try to design rate-adaptive transmission policies to maximize the amount of transmitted data bits under the energy constraints of devices. Such solutions, however, cannot apply to scenarios where data packets have respective deadlines and only integrally transmitted data packets contribute. Thus, this paper introduces a notion of weighted throughput, which measures how much total value of data packets are successfully and integrally transmitted before their own deadlines. By designing efficient rate-adaptive transmission policies, this paper aims to make the best use of the energy and maximize the weighted throughput. What is more challenging but with practical significance, we consider the fading effect of wireless channels in both offline and online scenarios. In the offline scenario, we develop an optimal algorithm that computes the optimal solution in pseudo-polynomial time, which is the best possible solution as the problem undertaken is NP-hard. In the online scenario, we propose an efficient heuristic algorithm based on optimal properties derived for the optimal offline solution. Simulation results validate the efficiency of the proposed algorithm.
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Bao, James J; Liu, Xiaojing; Zhang, Yong; Li, Youxin
2014-09-15
This paper describes the development of a novel high-throughput hollow fiber membrane solvent microextraction technique for the simultaneous measurement of the octanol/water distribution coefficient (logD) for organic compounds such as drugs. The method is based on a designed system, which consists of a 96-well plate modified with 96 hollow fiber membrane tubes and a matching lid with 96 center holes and 96 side holes distributing in 96 grids. Each center hole was glued with a sealed on one end hollow fiber membrane tube, which is used to separate the aqueous phase from the octanol phase. A needle, such as microsyringe or automatic sampler, can be directly inserted into the membrane tube to deposit octanol as the accepted phase or take out the mixture of the octanol and the drug. Each side hole is filled with aqueous phase and could freely take in/out solvent as the donor phase from the outside of the hollow fiber membranes. The logD can be calculated by measuring the drug concentration in each phase after extraction equilibrium. After a comprehensive comparison, the polytetrafluoroethylene hollow fiber with the thickness of 210 μm, an extraction time of 300 min, a temperature of 25 °C and atmospheric pressure without stirring are selected for the high throughput measurement. The correlation coefficient of the linear fit of the logD values of five drugs determined by our system to reference values is 0.9954, showed a nice accurate. The -8.9% intra-day and -4.4% inter-day precision of logD for metronidazole indicates a good precision. In addition, the logD values of eight drugs were simultaneously and successfully measured, which indicated that the 96 throughput measure method of logD value was accurate, precise, reliable and useful for high throughput screening. Copyright © 2014 Elsevier B.V. All rights reserved.
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NASA Astrophysics Data System (ADS)
McLeod, Euan
2016-03-01
The sizing of individual nanoparticles and the recovery of the distributions of sizes from populations of nanoparticles provide valuable information in virology, exosome analysis, air and water quality monitoring, and nanomaterials synthesis. Conventional approaches for nanoparticle sizing include those based on costly or low-throughput laboratory-scale equipment such as transmission electron microscopy or nanoparticle tracking analysis, as well as those approaches that only provide population-averaged quantities, such as dynamic light scattering. Some of these limitations can be overcome using a new family of alternative approaches based on quantitative phase imaging that combines lensfree holographic on-chip microscopy with self-assembled liquid nanolenses. In these approaches, the particles of interest are deposited onto a glass coverslip and the sample is coated with either pure liquid polyethylene glycol (PEG) or aqueous solutions of PEG. Due to surface tension, the PEG self-assembles into nano-scale lenses around the particles of interest. These nanolenses enhance the scattering signatures of the embedded particles such that individual nanoparticles as small as 40 nm are clearly visible in phase images reconstructed from captured holograms. The magnitude of the phase quantitatively corresponds to particle size with an accuracy of +/-11 nm. This family of approaches can individually size more than 10^5 particles in parallel, can handle a large dynamic range of particle sizes (40 nm - 100s of microns), and can accurately size multi-modal distributions of particles. Furthermore, the entire approach has been implemented in a compact and cost-effective device suitable for use in the field or in low-resource settings.
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High-Throughput Thermodynamic Modeling and Uncertainty Quantification for ICME
NASA Astrophysics Data System (ADS)
Otis, Richard A.; Liu, Zi-Kui
2017-05-01
One foundational component of the integrated computational materials engineering (ICME) and Materials Genome Initiative is the computational thermodynamics based on the calculation of phase diagrams (CALPHAD) method. The CALPHAD method pioneered by Kaufman has enabled the development of thermodynamic, atomic mobility, and molar volume databases of individual phases in the full space of temperature, composition, and sometimes pressure for technologically important multicomponent engineering materials, along with sophisticated computational tools for using the databases. In this article, our recent efforts will be presented in terms of developing new computational tools for high-throughput modeling and uncertainty quantification based on high-throughput, first-principles calculations and the CALPHAD method along with their potential propagations to downstream ICME modeling and simulations.
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Landry, James P; Fei, Yiyan; Zhu, X D
2011-12-01
Small-molecule compounds remain the major source of therapeutic and preventative drugs. Developing new drugs against a protein target often requires screening large collections of compounds with diverse structures for ligands or ligand fragments that exhibit sufficiently affinity and desirable inhibition effect on the target before further optimization and development. Since the number of small molecule compounds is large, high-throughput screening (HTS) methods are needed. Small-molecule microarrays (SMM) on a solid support in combination with a suitable binding assay form a viable HTS platform. We demonstrate that by combining an oblique-incidence reflectivity difference optical scanner with SMM we can screen 10,000 small-molecule compounds on a single glass slide for protein ligands without fluorescence labeling. Furthermore using such a label-free assay platform we can simultaneously acquire binding curves of a solution-phase protein to over 10,000 immobilized compounds, thus enabling full characterization of protein-ligand interactions over a wide range of affinity constants.
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NASA Technical Reports Server (NTRS)
Lee, Jonathan A.
2005-01-01
High-throughput measurement techniques are reviewed for solid phase transformation from materials produced by combinatorial methods, which are highly efficient concepts to fabricate large variety of material libraries with different compositional gradients on a single wafer. Combinatorial methods hold high potential for reducing the time and costs associated with the development of new materials, as compared to time-consuming and labor-intensive conventional methods that test large batches of material, one- composition at a time. These high-throughput techniques can be automated to rapidly capture and analyze data, using the entire material library on a single wafer, thereby accelerating the pace of materials discovery and knowledge generation for solid phase transformations. The review covers experimental techniques that are applicable to inorganic materials such as shape memory alloys, graded materials, metal hydrides, ferric materials, semiconductors and industrial alloys.
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Cheong, Fook Chiong; Wong, Chui Ching; Gao, YunFeng; Nai, Mui Hoon; Cui, Yidan; Park, Sungsu; Kenney, Linda J.; Lim, Chwee Teck
2015-01-01
Tracking fast-swimming bacteria in three dimensions can be extremely challenging with current optical techniques and a microscopic approach that can rapidly acquire volumetric information is required. Here, we introduce phase-contrast holographic video microscopy as a solution for the simultaneous tracking of multiple fast moving cells in three dimensions. This technique uses interference patterns formed between the scattered and the incident field to infer the three-dimensional (3D) position and size of bacteria. Using this optical approach, motility dynamics of multiple bacteria in three dimensions, such as speed and turn angles, can be obtained within minutes. We demonstrated the feasibility of this method by effectively tracking multiple bacteria species, including Escherichia coli, Agrobacterium tumefaciens, and Pseudomonas aeruginosa. In addition, we combined our fast 3D imaging technique with a microfluidic device to present an example of a drug/chemical assay to study effects on bacterial motility. PMID:25762336
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Hattrick-Simpers, Jason R.; Gregoire, John M.; Kusne, A. Gilad
With their ability to rapidly elucidate composition-structure-property relationships, high-throughput experimental studies have revolutionized how materials are discovered, optimized, and commercialized. It is now possible to synthesize and characterize high-throughput libraries that systematically address thousands of individual cuts of fabrication parameter space. An unresolved issue remains transforming structural characterization data into phase mappings. This difficulty is related to the complex information present in diffraction and spectroscopic data and its variation with composition and processing. Here, we review the field of automated phase diagram attribution and discuss the impact that emerging computational approaches will have in the generation of phase diagrams andmore » beyond.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Wang, Yonggang, E-mail: wangyg@ustc.edu.cn; Hui, Cong; Liu, Chong
The contribution of this paper is proposing a new entropy extraction mechanism based on sampling phase jitter in ring oscillators to make a high throughput true random number generator in a field programmable gate array (FPGA) practical. Starting from experimental observation and analysis of the entropy source in FPGA, a multi-phase sampling method is exploited to harvest the clock jitter with a maximum entropy and fast sampling speed. This parametrized design is implemented in a Xilinx Artix-7 FPGA, where the carry chains in the FPGA are explored to realize the precise phase shifting. The generator circuit is simple and resource-saving,more » so that multiple generation channels can run in parallel to scale the output throughput for specific applications. The prototype integrates 64 circuit units in the FPGA to provide a total output throughput of 7.68 Gbps, which meets the requirement of current high-speed quantum key distribution systems. The randomness evaluation, as well as its robustness to ambient temperature, confirms that the new method in a purely digital fashion can provide high-speed high-quality random bit sequences for a variety of embedded applications.« less
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Wang, Yonggang; Hui, Cong; Liu, Chong; Xu, Chao
2016-04-01
The contribution of this paper is proposing a new entropy extraction mechanism based on sampling phase jitter in ring oscillators to make a high throughput true random number generator in a field programmable gate array (FPGA) practical. Starting from experimental observation and analysis of the entropy source in FPGA, a multi-phase sampling method is exploited to harvest the clock jitter with a maximum entropy and fast sampling speed. This parametrized design is implemented in a Xilinx Artix-7 FPGA, where the carry chains in the FPGA are explored to realize the precise phase shifting. The generator circuit is simple and resource-saving, so that multiple generation channels can run in parallel to scale the output throughput for specific applications. The prototype integrates 64 circuit units in the FPGA to provide a total output throughput of 7.68 Gbps, which meets the requirement of current high-speed quantum key distribution systems. The randomness evaluation, as well as its robustness to ambient temperature, confirms that the new method in a purely digital fashion can provide high-speed high-quality random bit sequences for a variety of embedded applications.
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Mistarz, Ulrik H; Brown, Jeffery M; Haselmann, Kim F; Rand, Kasper D
2014-12-02
Gas-phase hydrogen/deuterium exchange (HDX) is a fast and sensitive, yet unharnessed analytical approach for providing information on the structural properties of biomolecules, in a complementary manner to mass analysis. Here, we describe a simple setup for ND3-mediated millisecond gas-phase HDX inside a mass spectrometer immediately after ESI (gas-phase HDX-MS) and show utility for studying the primary and higher-order structure of peptides and proteins. HDX was achieved by passing N2-gas through a container filled with aqueous deuterated ammonia reagent (ND3/D2O) and admitting the saturated gas immediately upstream or downstream of the primary skimmer cone. The approach was implemented on three commercially available mass spectrometers and required no or minor fully reversible reconfiguration of gas-inlets of the ion source. Results from gas-phase HDX-MS of peptides using the aqueous ND3/D2O as HDX reagent indicate that labeling is facilitated exclusively through gaseous ND3, yielding similar results to the infusion of purified ND3-gas, while circumventing the complications associated with the use of hazardous purified gases. Comparison of the solution-phase- and gas-phase deuterium uptake of Leu-Enkephalin and Glu-Fibrinopeptide B, confirmed that this gas-phase HDX-MS approach allows for labeling of sites (heteroatom-bound non-amide hydrogens located on side-chains, N-terminus and C-terminus) not accessed by classical solution-phase HDX-MS. The simple setup is compatible with liquid chromatography and a chip-based automated nanoESI interface, allowing for online gas-phase HDX-MS analysis of peptides and proteins separated on a liquid chromatographic time scale at increased throughput. Furthermore, online gas-phase HDX-MS could be performed in tandem with ion mobility separation or electron transfer dissociation, thus enabling multiple orthogonal analyses of the structural properties of peptides and proteins in a single automated LC-MS workflow.
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Putt, Karson S; Pugh, Randall B
2013-01-01
Peracetic acid is gaining usage in numerous industries who have found a myriad of uses for its antimicrobial activity. However, rapid high throughput quantitation methods for peracetic acid and hydrogen peroxide are lacking. Herein, we describe the development of a high-throughput microtiter plate based assay based upon the well known and trusted titration chemical reactions. The adaptation of these titration chemistries to rapid plate based absorbance methods for the sequential determination of hydrogen peroxide specifically and the total amount of peroxides present in solution are described. The results of these methods were compared to those of a standard titration and found to be in good agreement. Additionally, the utility of the developed method is demonstrated through the generation of degradation curves of both peracetic acid and hydrogen peroxide in a mixed solution.
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Putt, Karson S.; Pugh, Randall B.
2013-01-01
Peracetic acid is gaining usage in numerous industries who have found a myriad of uses for its antimicrobial activity. However, rapid high throughput quantitation methods for peracetic acid and hydrogen peroxide are lacking. Herein, we describe the development of a high-throughput microtiter plate based assay based upon the well known and trusted titration chemical reactions. The adaptation of these titration chemistries to rapid plate based absorbance methods for the sequential determination of hydrogen peroxide specifically and the total amount of peroxides present in solution are described. The results of these methods were compared to those of a standard titration and found to be in good agreement. Additionally, the utility of the developed method is demonstrated through the generation of degradation curves of both peracetic acid and hydrogen peroxide in a mixed solution. PMID:24260173
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An industrial engineering approach to laboratory automation for high throughput screening
Menke, Karl C.
2000-01-01
Across the pharmaceutical industry, there are a variety of approaches to laboratory automation for high throughput screening. At Sphinx Pharmaceuticals, the principles of industrial engineering have been applied to systematically identify and develop those automated solutions that provide the greatest value to the scientists engaged in lead generation. PMID:18924701
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Giri, Anupam; Park, Gyeongbae; Yang, Heeseung; Pal, Monalisa; Kwak, Junghyeok; Jeong, Unyong
2018-04-24
2D metal chalcogenide thin films have recently attracted considerable attention owing to their unique physicochemical properties and great potential in a variety of applications. Synthesis of large-area 2D metal chalcogenide thin films in controllable ways remains a key challenge in this research field. Recently, the solution-based synthesis of 2D metal chalcogenide thin films has emerged as an alternative approach to vacuum-based synthesis because it is relatively simple and easy to scale up for high-throughput production. In addition, solution-based thin films open new opportunities that cannot be achieved from vacuum-based thin films. Here, a comprehensive summary regarding the basic structures and properties of different types of 2D metal chalcogenides, the mechanistic details of the chemical reactions in the synthesis of the metal chalcogenide thin films, recent successes in the synthesis by different reaction approaches, and the applications and potential uses is provided. In the last perspective section, the technical challenges to be overcome and the future research directions in the solution-based synthesis of 2D metal chalcogenides are discussed. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Hydrogel Droplet Microfluidics for High-Throughput Single Molecule/Cell Analysis.
Zhu, Zhi; Yang, Chaoyong James
2017-01-17
Heterogeneity among individual molecules and cells has posed significant challenges to traditional bulk assays, due to the assumption of average behavior, which would lose important biological information in heterogeneity and result in a misleading interpretation. Single molecule/cell analysis has become an important and emerging field in biological and biomedical research for insights into heterogeneity between large populations at high resolution. Compared with the ensemble bulk method, single molecule/cell analysis explores the information on time trajectories, conformational states, and interactions of individual molecules/cells, all key factors in the study of chemical and biological reaction pathways. Various powerful techniques have been developed for single molecule/cell analysis, including flow cytometry, atomic force microscopy, optical and magnetic tweezers, single-molecule fluorescence spectroscopy, and so forth. However, some of them have the low-throughput issue that has to analyze single molecules/cells one by one. Flow cytometry is a widely used high-throughput technique for single cell analysis but lacks the ability for intercellular interaction study and local environment control. Droplet microfluidics becomes attractive for single molecule/cell manipulation because single molecules/cells can be individually encased in monodisperse microdroplets, allowing high-throughput analysis and manipulation with precise control of the local environment. Moreover, hydrogels, cross-linked polymer networks that swell in the presence of water, have been introduced into droplet microfluidic systems as hydrogel droplet microfluidics. By replacing an aqueous phase with a monomer or polymer solution, hydrogel droplets can be generated on microfluidic chips for encapsulation of single molecules/cells according to the Poisson distribution. The sol-gel transition property endows the hydrogel droplets with new functionalities and diversified applications in single molecule/cell analysis. The hydrogel can act as a 3D cell culture matrix to mimic the extracellular environment for long-term single cell culture, which allows further heterogeneity study in proliferation, drug screening, and metastasis at the single-cell level. The sol-gel transition allows reactions in solution to be performed rapidly and efficiently with product storage in the gel for flexible downstream manipulation and analysis. More importantly, controllable sol-gel regulation provides a new way to maintain phenotype-genotype linkages in the hydrogel matrix for high throughput molecular evolution. In this Account, we will review the hydrogel droplet generation on microfluidics, single molecule/cell encapsulation in hydrogel droplets, as well as the progress made by our group and others in the application of hydrogel droplet microfluidics for single molecule/cell analysis, including single cell culture, single molecule/cell detection, single cell sequencing, and molecular evolution.
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High speed all-optical networks
NASA Technical Reports Server (NTRS)
Chlamtac, Imrich
1993-01-01
An inherent problem of conventional point-to-point WAN architectures is that they cannot translate optical transmission bandwidth into comparable user available throughput due to the limiting electronic processing speed of the switching nodes. This report presents the first solution to WDM based WAN networks that overcomes this limitation. The proposed Lightnet architecture takes into account the idiosyncrasies of WDM switching/transmission leading to an efficient and pragmatic solution. The Lightnet architecture trades the ample WDM bandwidth for a reduction in the number of processing stages and a simplification of each switching stage, leading to drastically increased effective network throughputs.
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High throughput computing: a solution for scientific analysis
O'Donnell, M.
2011-01-01
handle job failures due to hardware, software, or network interruptions (obviating the need to manually resubmit the job after each stoppage); be affordable; and most importantly, allow us to complete very large, complex analyses that otherwise would not even be possible. In short, we envisioned a job-management system that would take advantage of unused FORT CPUs within a local area network (LAN) to effectively distribute and run highly complex analytical processes. What we found was a solution that uses High Throughput Computing (HTC) and High Performance Computing (HPC) systems to do exactly that (Figure 1).
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Fluorescent Approaches to High Throughput Crystallography
NASA Technical Reports Server (NTRS)
Pusey, Marc L.; Forsythe, Elizabeth
2005-01-01
X-ray crystallography remains the primary method for determining the structure of macromolecules. The first requirement is to have crystals, and obtaining them is often the rate-limiting step. The numbers of crystallization trials that are set up for any one protein for structural genomics, and the rate at which they are being set up, now overwhelm the ability for strictly human analysis of the results. Automated analysis methods are now being implemented with varying degrees of success, but these typically cannot reliably extract intermediate results. By covalently modifying a subpopulation, 51%, of a macromolecule solution with a fluorescent probe, the labeled material will add to a growing crystal as a microheterogeneous growth unit. Labeling procedures can be readily incorporated into the final stages of purification. The covalently attached probe will concentrate in the crystal relative to the solution, and under fluorescent illumination the crystals show up as bright objects against a dark background. As crystalline packing is more dense than amorphous precipitate, the fluorescence intensity can be used as a guide in distinguishing different types of precipitated phases, even in the absence of obvious crystalline features, widening the available potential lead conditions in the absence of clear hits. Non-protein structures, such as salt crystals, will not incorporate the probe and will not show up under fluorescent illumination. Also, brightly fluorescent crystals are readily found against less fluorescent precipitated phases, which under white light illumination may serve to obscure the crystals. Automated image analysis to find crystals should be greatly facilitated, without having to first define crystallization drop boundaries and by having the protein or protein structures all that show up. The trace fluorescently labeled crystals will also emit with sufficient intensity to aid in the automation of crystal alignment using relatively low cost optics, further increasing throughput at synchrotrons. This presentation will focus on the methodology for fluorescent labeling, the crystallization results, and the effects of the trace labeling on the crystal quality.
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Fluorescent Approaches to High Throughput Crystallography
NASA Technical Reports Server (NTRS)
Minamitani, Elizabeth Forsythe; Pusey, Marc L.
2004-01-01
X-ray crystallography remains the primary method for determining the structure of macromolecules. The first requirement is to have crystals, and obtaining them is often the rate-limiting step. The numbers of crystallization trials that are set up for any one protein for structural genomics, and the rate at which they are being set up, now overwhelm the ability for strictly human analysis of the results. Automated analysis methods are now being implemented with varying degrees of success, but these typically cannot reliably extract intermediate results. By covalently modifying a subpopulation, less than or = 1%, of a macromolecule solution with a fluorescent probe, the labeled material will add to a growing crystal as a microheterogeneous growth unit. Labeling procedures can be readily incorporated into the final stages of a macromolecules purification. The covalently attached probe will concentrate in the crystal relative to the solution, and under fluorescent illumination the crystals will show up as bright objects against a dark background. As crystalline packing is more dense than amorphous precipitate, the fluorescence intensity can be used as a guide in distinguishing different types of precipitated phases, even in the absence of obvious crystalline features, widening the available potential lead conditions in the absence of clear "bits." Non-protein structures, such as salt crystals, will not incorporate the probe and will not show up under fluorescent illumination. Also, brightly fluorescent crystals are readily found against less fluorescent precipitated phases, which under white light illumination may serve to obscure the crystals. Automated image analysis to find crystals should be greatly facilitated, without having to first define crystallization drop boundaries and by having the protein or protein structures all that show up. The trace fluorescently labeled crystals will also emit with sufficient intensity to aid in the automation of crystal alignment using relatively low cost optics, further increasing throughput at synchrotrons. This presentation will focus on the methodology for fluorescent labeling, the crystallization results, and the effects of the trace labeling on the crystal quality.
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Fluorescent Approaches to High Throughput Crystallography
NASA Technical Reports Server (NTRS)
Pusey, Marc L.; Forsythe, Elizabeth; Achari, Amiruddha
2005-01-01
X-ray crystallography remains the primary method for determining the structure of macromolecules. The first requirement is to have crystals, and obtaining them is often the rate-limiting step. The numbers of crystallization trials that are set up for any one protein for structural genomics, and the rate at which they are being set up, now overwhelm the ability for strictly human analysis of the results. Automated analysis methods are now being implemented with varying degrees of success, but these typically cannot reliably extract intermediate results. By covalently modifying a subpopulation, less than or = 1 %, of a macromolecule solution with a fluorescent probe, the labeled material will add to a growing crystal as a microheterogeneous growth unit. Labeling procedures can be readily incorporated into the final stages of purification. The covalently attached probe will concentrate in the crystal relative to the solution, and under fluorescent illumination the crystals show up as bright objects against a dark background. As crystalline packing is more dense than amorphous precipitate, the fluorescence intensity can be used as a guide in distinguishing different types of precipitated phases, even in the absence of obvious crystalline features, widening the available potential lead conditions in the absence of clear "hits." Non-protein structures, such as salt crystals, will not incorporate the probe and will not show up under fluorescent illumination. Also, brightly fluorescent crystals are readily found against less fluorescent precipitated phases, which under white light illumination may serve to obscure the crystals. Automated image analysis to find crystals should be greatly facilitated, without having to first define crystallization drop boundaries and by having the protein or protein structures all that show up. The trace fluorescently labeled crystals will also emit with sufficient intensity to aid in the automation of crystal alignment using relatively low cost optics, further increasing throughput at synchrotrons. Preliminary experiments show that the presence of the fluorescent probe does not affect the nucleation process or the quality of the X-ray data obtained.
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Fluorescent Approaches to High Throughput Crystallography
NASA Technical Reports Server (NTRS)
Pusey, Marc L.; Forsythe, Elizabeth
2004-01-01
X-ray crystallography remains the primary method for determining the structure of macromolecules. The first requirement is to have crystals, and obtaining them is often the rate-limiting step. The numbers of crystallization trials that are set up for any one protein for structural genomics, and the rate at which they are being set up, now overwhelm the ability for strictly human analysis of the results. Automated analysis methods are now being implemented with varying degrees of success, but these typically can not reliably extract intermediate results. By covalently modifying a subpopulation, less than or = 1%, of a macromolecule solution with a fluorescent probe, the labeled material will add to a growing crystal as a microheterogeneous growth unit. Labeling procedures can be readily incorporated into the final stages of purification. The covalently attached probe will concentrate in the crystal relative to the solution, and under fluorescent illumination the crystals show up as bright objects against a dark background. As crystalline packing is more dense than amorphous precipitate, the fluorescence intensity can be used as a guide in distinguishing different types of precipitated phases, even in the absence of obvious crystalline features, widening the available potential lead conditions in the absence of clear "hits." Non-protein structures, such as salt crystals, will not incorporate the probe and will not show up under fluorescent illumination. Also, brightly fluorescent crystals are readily found against less fluorescent precipitated phases, which under white light illumination may serve to obscure the crystals. Automated image analysis to find crystals should be greatly facilitated, without having to first define crystallization drop boundaries and by having the protein or protein structures all that show up. The trace fluorescently labeled crystals will also emit with sufficient intensity to aid in the automation of crystal alignment using relatively low cost optics, further increasing throughput at synchrotrons. This presentation will focus on the methodology for fluorescent labeling, the crystallization results, and the effects of the trace labeling on the crystal quality.
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Monolithic methacrylate packed 96-tips for high throughput bioanalysis.
Altun, Zeki; Skoglund, Christina; Abdel-Rehim, Mohamed
2010-04-16
In the pharmaceutical industry the growing number of samples to be analyzed requires high throughput and fully automated analytical techniques. Commonly used sample-preparation methods are solid-phase extraction (SPE), liquid-liquid extraction (LLE) and protein precipitation. In this paper we will discus a new sample-preparation technique based on SPE for high throughput drug extraction developed and used by our group. This new sample-preparation method is based on monolithic methacrylate polymer as packing sorbent for 96-tip robotic device. Using this device a 96-well plate could be handled in 2-4min. The key aspect of the monolithic phase is that monolithic material can offer both good binding capacity and low back-pressure properties compared to e.g. silica phases. The present paper presents the successful application of monolithic 96-tips and LC-MS/MS by the sample preparation of busulphan, rescovitine, metoprolol, pindolol and local anaesthetics from human plasma samples and cyklophosphamid from mice blood samples. Copyright 2009 Elsevier B.V. All rights reserved.
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Fluorescent Approaches to High Throughput Crystallography
NASA Technical Reports Server (NTRS)
Pusey, Marc L.; Forsythe, Elizabeth; Achari, Aniruddha
2006-01-01
We have shown that by covalently modifying a subpopulation, less than or equal to 1%, of a macromolecule with a fluorescent probe, the labeled material will add to a growing crystal as a microheterogeneous growth unit. Labeling procedures can be readily incorporated into the final stages of purification, and the presence of the probe at low concentrations does not affect the X-ray data quality or the crystallization behavior. The presence of the trace fluorescent label gives a number of advantages when used with high throughput crystallizations. The covalently attached probe will concentrate in the crystal relative to the solution, and under fluorescent illumination crystals show up as bright objects against a dark background. Non-protein structures, such as salt crystals, will not incorporate the probe and will not show up under fluorescent illumination. Brightly fluorescent crystals are readily found against less bright precipitated phases, which under white light illumination may obscure the crystals. Automated image analysis to find crystals should be greatly facilitated, without having to first define crystallization drop boundaries as the protein or protein structures is all that shows up. Fluorescence intensity is a faster search parameter, whether visually or by automated methods, than looking for crystalline features. We are now testing the use of high fluorescence intensity regions, in the absence of clear crystalline features or "hits", as a means for determining potential lead conditions. A working hypothesis is that kinetics leading to non-structured phases may overwhelm and trap more slowly formed ordered assemblies, which subsequently show up as regions of brighter fluorescence intensity. Preliminary experiments with test proteins have resulted in the extraction of a number of crystallization conditions from screening outcomes based solely on the presence of bright fluorescent regions. Subsequent experiments will test this approach using a wider range of proteins. The trace fluorescently labeled crystals will also emit with sufficient intensity to aid in the automation of crystal alignment using relatively low cost optics, further increasing throughput at synchrotrons.
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Experimental Design for Combinatorial and High Throughput Materials Development
NASA Astrophysics Data System (ADS)
Cawse, James N.
2002-12-01
In the past decade, combinatorial and high throughput experimental methods have revolutionized the pharmaceutical industry, allowing researchers to conduct more experiments in a week than was previously possible in a year. Now high throughput experimentation is rapidly spreading from its origins in the pharmaceutical world to larger industrial research establishments such as GE and DuPont, and even to smaller companies and universities. Consequently, researchers need to know the kinds of problems, desired outcomes, and appropriate patterns for these new strategies. Editor James Cawse's far-reaching study identifies and applies, with specific examples, these important new principles and techniques. Experimental Design for Combinatorial and High Throughput Materials Development progresses from methods that are now standard, such as gradient arrays, to mathematical developments that are breaking new ground. The former will be particularly useful to researchers entering the field, while the latter should inspire and challenge advanced practitioners. The book's contents are contributed by leading researchers in their respective fields. Chapters include: -High Throughput Synthetic Approaches for the Investigation of Inorganic Phase Space -Combinatorial Mapping of Polymer Blends Phase Behavior -Split-Plot Designs -Artificial Neural Networks in Catalyst Development -The Monte Carlo Approach to Library Design and Redesign This book also contains over 200 useful charts and drawings. Industrial chemists, chemical engineers, materials scientists, and physicists working in combinatorial and high throughput chemistry will find James Cawse's study to be an invaluable resource.
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Fabrication of wafer-scale nanopatterned sapphire substrate through phase separation lithography
NASA Astrophysics Data System (ADS)
Guo, Xu; Ni, Mengyang; Zhuang, Zhe; Dai, Jiangping; Wu, Feixiang; Cui, Yushuang; Yuan, Changsheng; Ge, Haixiong; Chen, Yanfeng
2016-04-01
A phase separation lithography (PSL) based on polymer blend provides an extremely simple, low-cost, and high-throughput way to fabricate wafer-scale disordered nanopatterns. This method was introduced to fabricate nanopatterned sapphire substrates (NPSSs) for GaN-based light-emitting diodes (LEDs). The PSL process only involved in spin-coating of polystyrene (PS)/polyethylene glycol (PEG) polymer blend on sapphire substrate and followed by a development with deionized water to remove PEG moiety. The PS nanoporous network was facilely obtained, and the structural parameters could be effectively tuned by controlling the PS/PEG weight ratio of the spin-coating solution. 2-in. wafer-scale NPSSs were conveniently achieved through the PS nanoporous network in combination with traditional nanofabrication methods, such as O2 reactive ion etching (RIE), e-beam evaporation deposition, liftoff, and chlorine-based RIE. In order to investigate the performance of such NPSSs, typical blue LEDs with emission wavelengths of ~450 nm were grown on the NPSS and a flat sapphire substrate (FSS) by metal-organic chemical vapor deposition, respectively. The integral photoluminescence (PL) intensity of the NPSS LED was enhanced by 32.3 % compared to that of the FSS-LED. The low relative standard deviation of 4.7 % for PL mappings of NPSS LED indicated the high uniformity of PL data across the whole 2-in. wafer. Extremely simple, low cost, and high throughput of the process and the ability to fabricate at the wafer scale make PSL a potential method for production of nanopatterned sapphire substrates.
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Chen, Ming-Luan; Suo, Li-Li; Gao, Qiang; Feng, Yu-Qi
2011-08-01
Using magnetite/silica/poly(methacrylic acid-co-ethylene glycol dimethacrylate) (Fe(3)O(4)/SiO(2)/poly(MAA-co-EDMA)) magnetic microspheres, a rapid and high-throughput magnetic solid-phase extraction coupled with capillary zone electrophoresis (MSPE-CZE) method was developed for the determination of illegal drugs (ketamine, amphetamines, opiates, and metabolites). The MSPE of target analytes could be completed within 2 min, and the eight target analytes could be baseline separated within 15 min by CZE with 30 mM phosphate buffer solution (PBS, pH 2.0) containing 15% v/v ACN as background electrolyte. Furthermore, hydrodynamic injection with field-amplified sample stacking (FASS) was employed to enhance the sensitivity of this MSPE-CZE method. Under such optimal conditions, the limits of detection for the eight target analytes ranged from 0.015 to 0.105 μg/mL. The application feasibility of MSPE-CZE in illegal drugs monitoring was demonstrated by analyzing urine samples, and the recoveries of target drugs for the spiked sample ranging from 85.4 to 110.1%. The method reproducibility was tested by evaluating the intra- and interday precisions, and relative standard deviations of <10.3 and 12.4%, respectively, were obtained. To increase throughput of the analysis, a home-made MSPE array that has potential application to the treatment of 96 samples simultaneously was used. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Scafaro, Andrew P; Negrini, A Clarissa A; O'Leary, Brendan; Rashid, F Azzahra Ahmad; Hayes, Lucy; Fan, Yuzhen; Zhang, You; Chochois, Vincent; Badger, Murray R; Millar, A Harvey; Atkin, Owen K
2017-01-01
Mitochondrial respiration in the dark ( R dark ) is a critical plant physiological process, and hence a reliable, efficient and high-throughput method of measuring variation in rates of R dark is essential for agronomic and ecological studies. However, currently methods used to measure R dark in plant tissues are typically low throughput. We assessed a high-throughput automated fluorophore system of detecting multiple O 2 consumption rates. The fluorophore technique was compared with O 2 -electrodes, infrared gas analysers (IRGA), and membrane inlet mass spectrometry, to determine accuracy and speed of detecting respiratory fluxes. The high-throughput fluorophore system provided stable measurements of R dark in detached leaf and root tissues over many hours. High-throughput potential was evident in that the fluorophore system was 10 to 26-fold faster per sample measurement than other conventional methods. The versatility of the technique was evident in its enabling: (1) rapid screening of R dark in 138 genotypes of wheat; and, (2) quantification of rarely-assessed whole-plant R dark through dissection and simultaneous measurements of above- and below-ground organs. Variation in absolute R dark was observed between techniques, likely due to variation in sample conditions (i.e. liquid vs. gas-phase, open vs. closed systems), indicating that comparisons between studies using different measuring apparatus may not be feasible. However, the high-throughput protocol we present provided similar values of R dark to the most commonly used IRGA instrument currently employed by plant scientists. Together with the greater than tenfold increase in sample processing speed, we conclude that the high-throughput protocol enables reliable, stable and reproducible measurements of R dark on multiple samples simultaneously, irrespective of plant or tissue type.
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Optimizing Crawler4j using MapReduce Programming Model
NASA Astrophysics Data System (ADS)
Siddesh, G. M.; Suresh, Kavya; Madhuri, K. Y.; Nijagal, Madhushree; Rakshitha, B. R.; Srinivasa, K. G.
2017-06-01
World wide web is a decentralized system that consists of a repository of information on the basis of web pages. These web pages act as a source of information or data in the present analytics world. Web crawlers are used for extracting useful information from web pages for different purposes. Firstly, it is used in web search engines where the web pages are indexed to form a corpus of information and allows the users to query on the web pages. Secondly, it is used for web archiving where the web pages are stored for later analysis phases. Thirdly, it can be used for web mining where the web pages are monitored for copyright purposes. The amount of information processed by the web crawler needs to be improved by using the capabilities of modern parallel processing technologies. In order to solve the problem of parallelism and the throughput of crawling this work proposes to optimize the Crawler4j using the Hadoop MapReduce programming model by parallelizing the processing of large input data. Crawler4j is a web crawler that retrieves useful information about the pages that it visits. The crawler Crawler4j coupled with data and computational parallelism of Hadoop MapReduce programming model improves the throughput and accuracy of web crawling. The experimental results demonstrate that the proposed solution achieves significant improvements with respect to performance and throughput. Hence the proposed approach intends to carve out a new methodology towards optimizing web crawling by achieving significant performance gain.
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Optofluidic time-stretch quantitative phase microscopy.
Guo, Baoshan; Lei, Cheng; Wu, Yi; Kobayashi, Hirofumi; Ito, Takuro; Yalikun, Yaxiaer; Lee, Sangwook; Isozaki, Akihiro; Li, Ming; Jiang, Yiyue; Yasumoto, Atsushi; Di Carlo, Dino; Tanaka, Yo; Yatomi, Yutaka; Ozeki, Yasuyuki; Goda, Keisuke
2018-03-01
Innovations in optical microscopy have opened new windows onto scientific research, industrial quality control, and medical practice over the last few decades. One of such innovations is optofluidic time-stretch quantitative phase microscopy - an emerging method for high-throughput quantitative phase imaging that builds on the interference between temporally stretched signal and reference pulses by using dispersive properties of light in both spatial and temporal domains in an interferometric configuration on a microfluidic platform. It achieves the continuous acquisition of both intensity and phase images with a high throughput of more than 10,000 particles or cells per second by overcoming speed limitations that exist in conventional quantitative phase imaging methods. Applications enabled by such capabilities are versatile and include characterization of cancer cells and microalgal cultures. In this paper, we review the principles and applications of optofluidic time-stretch quantitative phase microscopy and discuss its future perspective. Copyright © 2017 Elsevier Inc. All rights reserved.
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Xiong, Zheng; He, Yinyan; Hattrick-Simpers, Jason R; Hu, Jianjun
2017-03-13
The creation of composition-processing-structure relationships currently represents a key bottleneck for data analysis for high-throughput experimental (HTE) material studies. Here we propose an automated phase diagram attribution algorithm for HTE data analysis that uses a graph-based segmentation algorithm and Delaunay tessellation to create a crystal phase diagram from high throughput libraries of X-ray diffraction (XRD) patterns. We also propose the sample-pair based objective evaluation measures for the phase diagram prediction problem. Our approach was validated using 278 diffraction patterns from a Fe-Ga-Pd composition spread sample with a prediction precision of 0.934 and a Matthews Correlation Coefficient score of 0.823. The algorithm was then applied to the open Ni-Mn-Al thin-film composition spread sample to obtain the first predicted phase diagram mapping for that sample.
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High-throughput screening (HTS) for potential thyroid–disrupting chemicals requires a system of assays to capture multiple molecular-initiating events (MIEs) that converge on perturbed thyroid hormone (TH) homeostasis. Screening for MIEs specific to TH-disrupting pathways is limi...
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Bayat, Pouriya; Rezai, Pouya
2018-05-21
One of the common operations in sample preparation is to separate specific particles (e.g. target cells, embryos or microparticles) from non-target substances (e.g. bacteria) in a fluid and to wash them into clean buffers for further processing like detection (called solution exchange in this paper). For instance, solution exchange is widely needed in preparing fluidic samples for biosensing at the point-of-care and point-of-use, but still conducted via the use of cumbersome and time-consuming off-chip analyte washing and purification techniques. Existing small-scale and handheld active and passive devices for washing particles are often limited to very low throughputs or require external sources of energy. Here, we integrated Dean flow recirculation of two fluids in curved microchannels with selective inertial focusing of target particles to develop a microfluidic centrifuge device that can isolate specific particles (as surrogates for target analytes) from bacteria and wash them into a clean buffer at high throughput and efficiency. We could process micron-size particles at a flow rate of 1 mL min-1 and achieve throughputs higher than 104 particles per second. Our results reveal that the device is capable of singleplex solution exchange of 11 μm and 19 μm particles with efficiencies of 86 ± 2% and 93 ± 0.7%, respectively. A purity of 96 ± 2% was achieved in the duplex experiments where 11 μm particles were isolated from 4 μm particles. Application of our device in biological assays was shown by performing duplex experiments where 11 μm or 19 μm particles were isolated from an Escherichia coli bacterial suspension with purities of 91-98%. We envision that our technique will have applications in point-of-care devices for simultaneous purification and solution exchange of cells and embryos from smaller substances in high-volume suspensions at high throughput and efficiency.
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Designing and defining dynamic protein cage nanoassemblies in solution
DOE Office of Scientific and Technical Information (OSTI.GOV)
Lai, Y. -T.; Hura, G. L.; Dyer, K. N.
Central challenges in the design of large and dynamic macromolecular assemblies for synthetic biology lie in developing effective methods for testing design strategies and their outcomes, including comprehensive assessments of solution behavior. Here, we created and validated an advanced design of a 600-kDa protein homododecamer that self-assembles into a symmetric tetrahedral cage. The monomeric unit is composed of a trimerizing apex-forming domain genetically linked to an edge-forming dimerizing domain. Enhancing the crystallographic results, high-throughput small-angle x-ray scattering (SAXS) comprehensively contrasted our modifications under diverse solution conditions. To generate a phase diagram associating structure and assembly, we developed force plots thatmore » measure dissimilarity among multiple SAXS data sets. These new tools, which provided effective feedback on experimental constructs relative to design, have general applicability in analyzing the solution behavior of heterogeneous nanosystems and have been made available as a web-based application. Specifically, our results probed the influence of solution conditions and symmetry on stability and structural adaptability, identifying the dimeric interface as the weak point in the assembly. Force plots comparing SAXS data sets further reveal more complex and controllable behavior in solution than captured by our crystal structures. Lastly, these methods for objectively and comprehensively comparing SAXS profiles for systems critically affected by solvent conditions and structural heterogeneity provide an enabling technology for advancing the design and bioengineering of nanoscale biological materials.« less
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Designing and defining dynamic protein cage nanoassemblies in solution
Lai, Y. -T.; Hura, G. L.; Dyer, K. N.; ...
2016-12-14
Central challenges in the design of large and dynamic macromolecular assemblies for synthetic biology lie in developing effective methods for testing design strategies and their outcomes, including comprehensive assessments of solution behavior. Here, we created and validated an advanced design of a 600-kDa protein homododecamer that self-assembles into a symmetric tetrahedral cage. The monomeric unit is composed of a trimerizing apex-forming domain genetically linked to an edge-forming dimerizing domain. Enhancing the crystallographic results, high-throughput small-angle x-ray scattering (SAXS) comprehensively contrasted our modifications under diverse solution conditions. To generate a phase diagram associating structure and assembly, we developed force plots thatmore » measure dissimilarity among multiple SAXS data sets. These new tools, which provided effective feedback on experimental constructs relative to design, have general applicability in analyzing the solution behavior of heterogeneous nanosystems and have been made available as a web-based application. Specifically, our results probed the influence of solution conditions and symmetry on stability and structural adaptability, identifying the dimeric interface as the weak point in the assembly. Force plots comparing SAXS data sets further reveal more complex and controllable behavior in solution than captured by our crystal structures. Lastly, these methods for objectively and comprehensively comparing SAXS profiles for systems critically affected by solvent conditions and structural heterogeneity provide an enabling technology for advancing the design and bioengineering of nanoscale biological materials.« less
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High-throughput spectrometer designs in a compact form-factor: principles and applications
NASA Astrophysics Data System (ADS)
Norton, S. M.
2013-05-01
Many compact, portable Raman spectrometers have entered the market in the past few years with applications in narcotics and hazardous material identification, as well as verification applications in pharmaceuticals and security screening. Often, the required compact form-factor has forced designers to sacrifice throughput and sensitivity for portability and low-cost. We will show that a volume phase holographic (VPH)-based spectrometer design can achieve superior throughput and thus sensitivity over conventional Czerny-Turner reflective designs. We will look in depth at the factors influencing throughput and sensitivity and illustrate specific VPH-based spectrometer examples that highlight these design principles.
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Brennan; Biddison; Frauendorf; Schwarcz; Keen; Ecker; Davis; Tinder; Swayze
1998-01-01
An automated, 96-well parallel array synthesizer for solid-phase organic synthesis has been designed and constructed. The instrument employs a unique reagent array delivery format, in which each reagent utilized has a dedicated plumbing system. An inert atmosphere is maintained during all phases of a synthesis, and temperature can be controlled via a thermal transfer plate which holds the injection molded reaction block. The reaction plate assembly slides in the X-axis direction, while eight nozzle blocks holding the reagent lines slide in the Y-axis direction, allowing for the extremely rapid delivery of any of 64 reagents to 96 wells. In addition, there are six banks of fixed nozzle blocks, which deliver the same reagent or solvent to eight wells at once, for a total of 72 possible reagents. The instrument is controlled by software which allows the straightforward programming of the synthesis of a larger number of compounds. This is accomplished by supplying a general synthetic procedure in the form of a command file, which calls upon certain reagents to be added to specific wells via lookup in a sequence file. The bottle position, flow rate, and concentration of each reagent is stored in a separate reagent table file. To demonstrate the utility of the parallel array synthesizer, a small combinatorial library of hydroxamic acids was prepared in high throughput mode for biological screening. Approximately 1300 compounds were prepared on a 10 μmole scale (3-5 mg) in a few weeks. The resulting crude compounds were generally >80% pure, and were utilized directly for high throughput screening in antibacterial assays. Several active wells were found, and the activity was verified by solution-phase synthesis of analytically pure material, indicating that the system described herein is an efficient means for the parallel synthesis of compounds for lead discovery. Copyright 1998 John Wiley & Sons, Inc.
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Xiang, X D
Combinatorial materials synthesis methods and high-throughput evaluation techniques have been developed to accelerate the process of materials discovery and optimization and phase-diagram mapping. Analogous to integrated circuit chips, integrated materials chips containing thousands of discrete different compositions or continuous phase diagrams, often in the form of high-quality epitaxial thin films, can be fabricated and screened for interesting properties. Microspot x-ray method, various optical measurement techniques, and a novel evanescent microwave microscope have been used to characterize the structural, optical, magnetic, and electrical properties of samples on the materials chips. These techniques are routinely used to discover/optimize and map phase diagrams of ferroelectric, dielectric, optical, magnetic, and superconducting materials.
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NASA Astrophysics Data System (ADS)
Watanabe, A.; Furukawa, H.
2018-04-01
The resolution of multichannel Fourier transform (McFT) spectroscopy is insufficient for many applications despite its extreme advantage of high throughput. We propose an improved configuration to realise both performance using a two-dimensional area sensor. For the spectral resolution, we obtained the interferogram of a larger optical path difference by shifting the area sensor without altering any optical components. The non-linear phase error of the interferometer was successfully corrected using a phase-compensation calculation. Warping compensation was also applied to realise a higher throughput to accumulate the signal between vertical pixels. Our approach significantly improved the resolution and signal-to-noise ratio by factors of 1.7 and 34, respectively. This high-resolution and high-sensitivity McFT spectrometer will be useful for detecting weak light signals such as those in non-invasive diagnosis.
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Cai, Long-Fei; Zhu, Ying; Du, Guan-Sheng; Fang, Qun
2012-01-03
We described a microfluidic chip-based system capable of generating droplet array with a large scale concentration gradient by coupling flow injection gradient technique with droplet-based microfluidics. Multiple modules including sample injection, sample dispersion, gradient generation, droplet formation, mixing of sample and reagents, and online reaction within the droplets were integrated into the microchip. In the system, nanoliter-scale sample solution was automatically injected into the chip under valveless flow injection analysis mode. The sample zone was first dispersed in the microchannel to form a concentration gradient along the axial direction of the microchannel and then segmented into a linear array of droplets by immiscible oil phase. With the segmentation and protection of the oil phase, the concentration gradient profile of the sample was preserved in the droplet array with high fidelity. With a single injection of 16 nL of sample solution, an array of droplets with concentration gradient spanning 3-4 orders of magnitude could be generated. The present system was applied in the enzyme inhibition assay of β-galactosidase to preliminarily demonstrate its potential in high throughput drug screening. With a single injection of 16 nL of inhibitor solution, more than 240 in-droplet enzyme inhibition reactions with different inhibitor concentrations could be performed with an analysis time of 2.5 min. Compared with multiwell plate-based screening systems, the inhibitor consumption was reduced 1000-fold. © 2011 American Chemical Society
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Little is known about the developmental toxicity of the expansive chemical landscape in existence today. Significant efforts are being made to apply novel methods to predict developmental activity of chemicals utilizing high-throughput screening (HTS) and high-content screening (...
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The U.S. EPA’s Endocrine Disruptor Screening Program (EDSP) and Office of Research and Development (ORD) are currently developing high throughput assays to screen chemicals that may alter the thyroid hormone pathway. One potential target in this pathway is the sodium iodide...
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High Throughput Prioritization for Integrated Toxicity Testing Based on ToxCast Chemical Profiling
The rational prioritization of chemicals for integrated toxicity testing is a central goal of the U.S. EPA’s ToxCast™ program (http://epa.gov/ncct/toxcast/). ToxCast includes a wide-ranging battery of over 500 in vitro high-throughput screening assays which in Phase I was used to...
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The U.S. EPA’s Endocrine Disruptor Screening Program (EDSP) and Office of Research and Development (ORD) are currently developing high throughput assays to screen chemicals that may alter the thyroid hormone pathway. One potential target in this pathway is the sodium iodide sympo...
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Choosing a CD-ROM Network Solution.
ERIC Educational Resources Information Center
Doering, David
1996-01-01
Discusses issues to consider in selecting a CD-ROM network solution, including throughput (speed of data delivery), security, access, servers, key features, training, jukebox support, documentation, and licenses. Reviews software products offered by Novell, Around Technology, Micro Design, Smart Storage, Microtest, Meridian, CD-Connection,…
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Li, Fumin; Wang, Jun; Jenkins, Rand
2016-05-01
There is an ever-increasing demand for high-throughput LC-MS/MS bioanalytical assays to support drug discovery and development. Matrix effects of sofosbuvir (protonated) and paclitaxel (sodiated) were thoroughly evaluated using high-throughput chromatography (defined as having a run time ≤1 min) under 14 elution conditions with extracts from protein precipitation, liquid-liquid extraction and solid-phase extraction. A slight separation, in terms of retention time, between underlying matrix components and sofosbuvir/paclitaxel can greatly alleviate matrix effects. High-throughput chromatography, with proper optimization, can provide rapid and effective chromatographic separation under 1 min to alleviate matrix effects and enhance assay ruggedness for regulated bioanalysis.
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SACRB-MAC: A High-Capacity MAC Protocol for Cognitive Radio Sensor Networks in Smart Grid
Yang, Zhutian; Shi, Zhenguo; Jin, Chunlin
2016-01-01
The Cognitive Radio Sensor Network (CRSN) is considered as a viable solution to enhance various aspects of the electric power grid and to realize a smart grid. However, several challenges for CRSNs are generated due to the harsh wireless environment in a smart grid. As a result, throughput and reliability become critical issues. On the other hand, the spectrum aggregation technique is expected to play an important role in CRSNs in a smart grid. By using spectrum aggregation, the throughput of CRSNs can be improved efficiently, so as to address the unique challenges of CRSNs in a smart grid. In this regard, we proposed Spectrum Aggregation Cognitive Receiver-Based MAC (SACRB-MAC), which employs the spectrum aggregation technique to improve the throughput performance of CRSNs in a smart grid. Moreover, SACRB-MAC is a receiver-based MAC protocol, which can provide a good reliability performance. Analytical and simulation results demonstrate that SACRB-MAC is a promising solution for CRSNs in a smart grid. PMID:27043573
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SACRB-MAC: A High-Capacity MAC Protocol for Cognitive Radio Sensor Networks in Smart Grid.
Yang, Zhutian; Shi, Zhenguo; Jin, Chunlin
2016-03-31
The Cognitive Radio Sensor Network (CRSN) is considered as a viable solution to enhance various aspects of the electric power grid and to realize a smart grid. However, several challenges for CRSNs are generated due to the harsh wireless environment in a smart grid. As a result, throughput and reliability become critical issues. On the other hand, the spectrum aggregation technique is expected to play an important role in CRSNs in a smart grid. By using spectrum aggregation, the throughput of CRSNs can be improved efficiently, so as to address the unique challenges of CRSNs in a smart grid. In this regard, we proposed Spectrum Aggregation Cognitive Receiver-Based MAC (SACRB-MAC), which employs the spectrum aggregation technique to improve the throughput performance of CRSNs in a smart grid. Moreover, SACRB-MAC is a receiver-based MAC protocol, which can provide a good reliability performance. Analytical and simulation results demonstrate that SACRB-MAC is a promising solution for CRSNs in a smart grid.
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NASA Astrophysics Data System (ADS)
Guo, Baoshan; Lei, Cheng; Ito, Takuro; Yaxiaer, Yalikun; Kobayashi, Hirofumi; Jiang, Yiyue; Tanaka, Yo; Ozeki, Yasuyuki; Goda, Keisuke
2017-02-01
The development of reliable, sustainable, and economical sources of alternative fuels is an important, but challenging goal for the world. As an alternative to liquid fossil fuels, microalgal biofuel is expected to play a key role in reducing the detrimental effects of global warming since microalgae absorb atmospheric CO2 via photosynthesis. Unfortunately, conventional analytical methods only provide population-averaged lipid contents and fail to characterize a diverse population of microalgal cells with single-cell resolution in a noninvasive and interference-free manner. Here we demonstrate high-throughput label-free single-cell screening of lipid-producing microalgal cells with optofluidic time-stretch quantitative phase microscopy. In particular, we use Euglena gracilis - an attractive microalgal species that produces wax esters (suitable for biodiesel and aviation fuel after refinement) within lipid droplets. Our optofluidic time-stretch quantitative phase microscope is based on an integration of a hydrodynamic-focusing microfluidic chip, an optical time-stretch phase-contrast microscope, and a digital image processor equipped with machine learning. As a result, it provides both the opacity and phase contents of every single cell at a high throughput of 10,000 cells/s. We characterize heterogeneous populations of E. gracilis cells under two different culture conditions to evaluate their lipid production efficiency. Our method holds promise as an effective analytical tool for microalgaebased biofuel production.
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Dual-mode ultraflow access networks: a hybrid solution for the access bottleneck
NASA Astrophysics Data System (ADS)
Kazovsky, Leonid G.; Shen, Thomas Shunrong; Dhaini, Ahmad R.; Yin, Shuang; De Leenheer, Marc; Detwiler, Benjamin A.
2013-12-01
Optical Flow Switching (OFS) is a promising solution for large Internet data transfers. In this paper, we introduce UltraFlow Access, a novel optical access network architecture that offers dual-mode service to its end-users: IP and OFS. With UltraFlow Access, we design and implement a new dual-mode control plane and a new dual-mode network stack to ensure efficient connection setup and reliable and optimal data transmission. We study the impact of the UltraFlow system's design on the network throughput. Our experimental results show that with an optimized system design, near optimal (around 10 Gb/s) OFS data throughput can be attained when the line rate is 10Gb/s.
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Shinde, V; Burke, K E; Chakravarty, A; Fleming, M; McDonald, A A; Berger, A; Ecsedy, J; Blakemore, S J; Tirrell, S M; Bowman, D
2014-01-01
Immunohistochemistry-based biomarkers are commonly used to understand target inhibition in key cancer pathways in preclinical models and clinical studies. Automated slide-scanning and advanced high-throughput image analysis software technologies have evolved into a routine methodology for quantitative analysis of immunohistochemistry-based biomarkers. Alongside the traditional pathology H-score based on physical slides, the pathology world is welcoming digital pathology and advanced quantitative image analysis, which have enabled tissue- and cellular-level analysis. An automated workflow was implemented that includes automated staining, slide-scanning, and image analysis methodologies to explore biomarkers involved in 2 cancer targets: Aurora A and NEDD8-activating enzyme (NAE). The 2 workflows highlight the evolution of our immunohistochemistry laboratory and the different needs and requirements of each biological assay. Skin biopsies obtained from MLN8237 (Aurora A inhibitor) phase 1 clinical trials were evaluated for mitotic and apoptotic index, while mitotic index and defects in chromosome alignment and spindles were assessed in tumor biopsies to demonstrate Aurora A inhibition. Additionally, in both preclinical xenograft models and an acute myeloid leukemia phase 1 trial of the NAE inhibitor MLN4924, development of a novel image algorithm enabled measurement of downstream pathway modulation upon NAE inhibition. In the highlighted studies, developing a biomarker strategy based on automated image analysis solutions enabled project teams to confirm target and pathway inhibition and understand downstream outcomes of target inhibition with increased throughput and quantitative accuracy. These case studies demonstrate a strategy that combines a pathologist's expertise with automated image analysis to support oncology drug discovery and development programs.
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Wonczak, Stephan; Thiele, Holger; Nieroda, Lech; Jabbari, Kamel; Borowski, Stefan; Sinha, Vishal; Gunia, Wilfried; Lang, Ulrich; Achter, Viktor; Nürnberg, Peter
2015-01-01
Next generation sequencing (NGS) has been a great success and is now a standard method of research in the life sciences. With this technology, dozens of whole genomes or hundreds of exomes can be sequenced in rather short time, producing huge amounts of data. Complex bioinformatics analyses are required to turn these data into scientific findings. In order to run these analyses fast, automated workflows implemented on high performance computers are state of the art. While providing sufficient compute power and storage to meet the NGS data challenge, high performance computing (HPC) systems require special care when utilized for high throughput processing. This is especially true if the HPC system is shared by different users. Here, stability, robustness and maintainability are as important for automated workflows as speed and throughput. To achieve all of these aims, dedicated solutions have to be developed. In this paper, we present the tricks and twists that we utilized in the implementation of our exome data processing workflow. It may serve as a guideline for other high throughput data analysis projects using a similar infrastructure. The code implementing our solutions is provided in the supporting information files. PMID:25942438
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Valko, K; Du, C M; Bevan, C D; Reynolds, D P; Abraham, M H
2000-08-01
A fast-gradient high-performance liquid chromatographic (HPLC) method has been suggested to characterize the interactions of drugs with an immobilized artificial membrane (IAM). With a set of standards, the gradient retention times can be converted to Chromatographic Hydrophobicity Index values referring to IAM chromatography (CHI(IAM)) that approximates an acetonitrile concentration with which the equal distribution of compound can be achieved between the mobile phase and IAM. The CHI(IAM) values are more suitable for interlaboratory comparison and for high throughput screening of new molecular entities than the log k(IAM) values (isocratic retention factor on IAM). The fast-gradient method has been validated against the isocratic log k(IAM) values using the linear free energy relationship solvation equations based on the data from 48 compounds. The compound set was selected to provide a wide range and the least cross-correlation between the molecular descriptors in the solvation equation: (2) where SP is a solute property (e.g., logarithm of partition coefficients, reversed-phase (RP)-HPLC retention parameters, such as log k, log k(w), etc.) and the explanatory variables are solute descriptors as follows: R(2) is an excess molar refraction that can be obtained from the measured refractive index of a compound, pi(2)(H) is the solute dipolarity/polarizability, summation operatoralpha(2)(H) and summation operatorbeta(2)(0) are the solute overall or effective hydrogen-bond acidity and basicity, respectively, and V(x) is the McGowan characteristic volume (in cm(3)/100 mol) that can be calculated for any solute simply from molecular structure using a table of atomic constants. It was found that the relative constants of the solvation equation were very similar for the CHI(IAM) and for the log k(IAM). The IAM lipophilicity scale was quite similar to the octanol/water lipophilicity scale for neutral compounds. The effect of charge on the interaction with IAM was studied by varying the mobile phase pH. Copyright 2000 Wiley-Liss, Inc.
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Maphutha, Selby; Moothi, Kapil; Meyyappan, M.; Iyuke, Sunny E.
2013-01-01
A carbon nanotube (CNT) integrated polymer composite membrane with a polyvinyl alcohol barrier layer has been prepared to separate oil from water for treatment of oil-containing waste water. The CNTs were synthesised using chemical vapour deposition, and a phase inversion method was employed for the blending of the CNTs in the polymer composite solution for casting of the membrane. Relative to the baseline polymer, an increase of 119% in the tensile strength, 77% in the Young's modulus and 258% in the toughness is seen for a concentration of 7.5% CNTs in the polymer composite. The permeate through the membrane shows oil concentrations below the acceptable 10 mg/L limit with an excellent throughput and oil rejection of over 95%. PMID:23518875
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An Automated High-Throughput System to Fractionate Plant Natural Products for Drug Discovery
Tu, Ying; Jeffries, Cynthia; Ruan, Hong; Nelson, Cynthia; Smithson, David; Shelat, Anang A.; Brown, Kristin M.; Li, Xing-Cong; Hester, John P.; Smillie, Troy; Khan, Ikhlas A.; Walker, Larry; Guy, Kip; Yan, Bing
2010-01-01
The development of an automated, high-throughput fractionation procedure to prepare and analyze natural product libraries for drug discovery screening is described. Natural products obtained from plant materials worldwide were extracted and first prefractionated on polyamide solid-phase extraction cartridges to remove polyphenols, followed by high-throughput automated fractionation, drying, weighing, and reformatting for screening and storage. The analysis of fractions with UPLC coupled with MS, PDA and ELSD detectors provides information that facilitates characterization of compounds in active fractions. Screening of a portion of fractions yielded multiple assay-specific hits in several high-throughput cellular screening assays. This procedure modernizes the traditional natural product fractionation paradigm by seamlessly integrating automation, informatics, and multimodal analytical interrogation capabilities. PMID:20232897
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The use of high-throughput in vitro assays has been proposed to play a significant role in the future of toxicity testing. In this study, rat hepatic metabolic clearance and plasma protein binding were measured for 59 ToxCast phase I chemicals. Computational in vitro-to-in vivo e...
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A high-throughput label-free nanoparticle analyser.
Fraikin, Jean-Luc; Teesalu, Tambet; McKenney, Christopher M; Ruoslahti, Erkki; Cleland, Andrew N
2011-05-01
Synthetic nanoparticles and genetically modified viruses are used in a range of applications, but high-throughput analytical tools for the physical characterization of these objects are needed. Here we present a microfluidic analyser that detects individual nanoparticles and characterizes complex, unlabelled nanoparticle suspensions. We demonstrate the detection, concentration analysis and sizing of individual synthetic nanoparticles in a multicomponent mixture with sufficient throughput to analyse 500,000 particles per second. We also report the rapid size and titre analysis of unlabelled bacteriophage T7 in both salt solution and mouse blood plasma, using just ~1 × 10⁻⁶ l of analyte. Unexpectedly, in the native blood plasma we discover a large background of naturally occurring nanoparticles with a power-law size distribution. The high-throughput detection capability, scalable fabrication and simple electronics of this instrument make it well suited for diverse applications.
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Systematic evaluation of non-animal test methods for skin sensitisation safety assessment.
Reisinger, Kerstin; Hoffmann, Sebastian; Alépée, Nathalie; Ashikaga, Takao; Barroso, Joao; Elcombe, Cliff; Gellatly, Nicola; Galbiati, Valentina; Gibbs, Susan; Groux, Hervé; Hibatallah, Jalila; Keller, Donald; Kern, Petra; Klaric, Martina; Kolle, Susanne; Kuehnl, Jochen; Lambrechts, Nathalie; Lindstedt, Malin; Millet, Marion; Martinozzi-Teissier, Silvia; Natsch, Andreas; Petersohn, Dirk; Pike, Ian; Sakaguchi, Hitoshi; Schepky, Andreas; Tailhardat, Magalie; Templier, Marie; van Vliet, Erwin; Maxwell, Gavin
2015-02-01
The need for non-animal data to assess skin sensitisation properties of substances, especially cosmetics ingredients, has spawned the development of many in vitro methods. As it is widely believed that no single method can provide a solution, the Cosmetics Europe Skin Tolerance Task Force has defined a three-phase framework for the development of a non-animal testing strategy for skin sensitization potency prediction. The results of the first phase – systematic evaluation of 16 test methods – are presented here. This evaluation involved generation of data on a common set of ten substances in all methods and systematic collation of information including the level of standardisation, existing test data,potential for throughput, transferability and accessibility in cooperation with the test method developers.A workshop was held with the test method developers to review the outcome of this evaluation and to discuss the results. The evaluation informed the prioritisation of test methods for the next phase of the non-animal testing strategy development framework. Ultimately, the testing strategy – combined with bioavailability and skin metabolism data and exposure consideration – is envisaged to allow establishment of a data integration approach for skin sensitisation safety assessment of cosmetic ingredients.
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Polymer ligand–induced autonomous sorting and reversible phase separation in binary particle blends
Schmitt, Michael; Zhang, Jianan; Lee, Jaejun; ...
2016-12-23
The tethering of ligands to nanoparticles has emerged as an important strategy to control interactions and organization in particle assembly structures. Here, we demonstrate that ligand interactions in mixtures of polymer-tethered nanoparticles (which are modified with distinct types of polymer chains) can impart upper or lower critical solution temperature (UCST/LCST)–type phase behavior on binary particle mixtures in analogy to the phase behavior of the corresponding linear polymer blends. Therefore, cooling (or heating) of polymer-tethered particle blends with appropriate architecture to temperatures below (or above) the UCST (or LCST) results in the organization of the individual particle constituents into monotype microdomainmore » structures. The shape (bicontinuous or island-type) and lengthscale of particle microdomains can be tuned by variation of the composition and thermal process conditions. Thermal cycling of LCST particle brush blends through the critical temperature enables the reversible growth and dissolution of monoparticle domain structures. The ability to autonomously and reversibly organize multicomponent particle mixtures into monotype microdomain structures could enable transformative advances in the high-throughput fabrication of solid films with tailored and mutable structures and properties that play an important role in a range of nanoparticle-based material technologies.« less
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Polymer ligand–induced autonomous sorting and reversible phase separation in binary particle blends
Schmitt, Michael; Zhang, Jianan; Lee, Jaejun; Lee, Bongjoon; Ning, Xin; Zhang, Ren; Karim, Alamgir; Davis, Robert F.; Matyjaszewski, Krzysztof; Bockstaller, Michael R.
2016-01-01
The tethering of ligands to nanoparticles has emerged as an important strategy to control interactions and organization in particle assembly structures. We demonstrate that ligand interactions in mixtures of polymer-tethered nanoparticles (which are modified with distinct types of polymer chains) can impart upper or lower critical solution temperature (UCST/LCST)–type phase behavior on binary particle mixtures in analogy to the phase behavior of the corresponding linear polymer blends. Therefore, cooling (or heating) of polymer-tethered particle blends with appropriate architecture to temperatures below (or above) the UCST (or LCST) results in the organization of the individual particle constituents into monotype microdomain structures. The shape (bicontinuous or island-type) and lengthscale of particle microdomains can be tuned by variation of the composition and thermal process conditions. Thermal cycling of LCST particle brush blends through the critical temperature enables the reversible growth and dissolution of monoparticle domain structures. The ability to autonomously and reversibly organize multicomponent particle mixtures into monotype microdomain structures could enable transformative advances in the high-throughput fabrication of solid films with tailored and mutable structures and properties that play an important role in a range of nanoparticle-based material technologies. PMID:28028538
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NASA Astrophysics Data System (ADS)
Burrell, Derek J.; Middlebrook, Christopher T.
2017-08-01
Wireless communication systems that employ free-space optical links in place of radio/microwave technologies carry substantial benefits in terms of data throughput, network security and design efficiency. Along with these advantages comes the challenge of counteracting signal degradation caused by atmospheric turbulence in free-space environments. A fully coherent laser source experiences random phase delays along its traversing path in turbulent conditions forming a speckle pattern and lowering the received signal-to-noise ratio upon detection. Preliminary research has shown that receiver-side speckle contrast may be significantly reduced and signal-to-noise ratio increased accordingly through the use of a partially coherent light source. While dynamic diffusers and adaptive optics solutions have been proven effective, they also add expense and complexity to a system that relies on accessibility and robustness for successful implementation. A custom Hadamard diffractive matrix design is used to statically induce partial coherence in a transmitted beam to increase signal-to-noise ratio for experimental turbulence scenarios. Atmospheric phase screens are generated using an open-source software package and subsequently loaded into a spatial light modulator using nematic liquid crystals to modulate the phase.
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Alsenaidy, Mohammad A.; Kim, Jae Hyun; Majumdar, Ranajoy; Weis, David D.; Joshi, Sangeeta B.; Tolbert, Thomas J.; Middaugh, C. Russell; Volkin, David B.
2013-01-01
The structural integrity and conformational stability of an IgG1 monoclonal antibody (mAb), after partial and complete enzymatic removal of the N-linked Fc glycan, was compared to the untreated mAb over a wide range of temperature (10° to 90°C) and solution pH (3 to 8) using circular dichroism, fluorescence spectroscopy, and static light scattering combined with data visualization employing empirical phase diagrams (EPDs). Subtle to larger stability differences between the different glycoforms were observed. Improved detection of physical stability differences was then demonstrated over narrower pH range (4.0-6.0) using smaller temperature increments, especially when combined with an alternative data visualization method (radar plots). Differential scanning calorimetry and differential scanning fluorimetry were then utilized and also showed an improved ability to detect differences in mAb glycoform physical stability. Based on these results, a two-step methodology was used in which mAb glycoform conformational stability is first screened with a wide variety of instruments and environmental stresses, followed by a second evaluation with optimally sensitive experimental conditions, analytical techniques and data visualization methods. With this approach, high-throughput biophysical analysis to assess relatively subtle conformational stability differences in protein glycoforms is demonstrated. PMID:24114789
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Peter W. Carr; K.M. Fuller; D.R. Stoll
A new approach has been developed by modifying a conventional gradient elution liquid chromatograph for the high throughput screening of biological samples to detect the presence of regulated intoxicants. The goal of this work was to improve the speed of a gradient elution screening method over current approaches by optimizing the operational parameters of both the column and the instrument without compromising the reproducibility of the retention times, which are the basis for the identification. Most importantly, the novel instrument configuration substantially reduces the time needed to re-equilibrate the column between gradient runs, thereby reducing the total time for eachmore » analysis. The total analysis time for each gradient elution run is only 2.8 minutes, including 0.3 minutes for column reequilibration between analyses. Retention times standard calibration solutes are reproducible to better than 0.002 minutes in consecutive runs. A corrected retention index was adopted to account for day-to-day and column-to-column variations in retention time. The discriminating power and mean list length were calculated for a library of 47 intoxicants and compared with previous work from other laboratories to evaluate fast gradient elution HPLC as a screening tool.« less
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High-throughput synchronization of mammalian cell cultures by spiral microfluidics.
Lee, Wong Cheng; Bhagat, Ali Asgar S; Lim, Chwee Teck
2014-01-01
The development of mammalian cell cycle synchronization techniques has greatly advanced our understanding of many cellular regulatory events and mechanisms specific to different phases of the cell cycle. In this chapter, we describe a high-throughput microfluidic-based approach for cell cycle synchronization. By exploiting the relationship between cell size and its phase in the cell cycle, large numbers of synchronized cells can be obtained by size fractionation in a spiral microfluidic channel. Protocols for the synchronization of primary cells such as mesenchymal stem cells, and immortal cell lines such as Chinese hamster ovarian cells (CHO-CD36) and HeLa cells are provided as examples.
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Fast and Adaptive Lossless Onboard Hyperspectral Data Compression System
NASA Technical Reports Server (NTRS)
Aranki, Nazeeh I.; Keymeulen, Didier; Kimesh, Matthew A.
2012-01-01
Modern hyperspectral imaging systems are able to acquire far more data than can be downlinked from a spacecraft. Onboard data compression helps to alleviate this problem, but requires a system capable of power efficiency and high throughput. Software solutions have limited throughput performance and are power-hungry. Dedicated hardware solutions can provide both high throughput and power efficiency, while taking the load off of the main processor. Thus a hardware compression system was developed. The implementation uses a field-programmable gate array (FPGA). The implementation is based on the fast lossless (FL) compression algorithm reported in Fast Lossless Compression of Multispectral-Image Data (NPO-42517), NASA Tech Briefs, Vol. 30, No. 8 (August 2006), page 26, which achieves excellent compression performance and has low complexity. This algorithm performs predictive compression using an adaptive filtering method, and uses adaptive Golomb coding. The implementation also packetizes the coded data. The FL algorithm is well suited for implementation in hardware. In the FPGA implementation, one sample is compressed every clock cycle, which makes for a fast and practical realtime solution for space applications. Benefits of this implementation are: 1) The underlying algorithm achieves a combination of low complexity and compression effectiveness that exceeds that of techniques currently in use. 2) The algorithm requires no training data or other specific information about the nature of the spectral bands for a fixed instrument dynamic range. 3) Hardware acceleration provides a throughput improvement of 10 to 100 times vs. the software implementation. A prototype of the compressor is available in software, but it runs at a speed that does not meet spacecraft requirements. The hardware implementation targets the Xilinx Virtex IV FPGAs, and makes the use of this compressor practical for Earth satellites as well as beyond-Earth missions with hyperspectral instruments.
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TCP Throughput Profiles Using Measurements over Dedicated Connections
DOE Office of Scientific and Technical Information (OSTI.GOV)
Rao, Nageswara S.; Liu, Qiang; Sen, Satyabrata
Wide-area data transfers in high-performance computing infrastructures are increasingly being carried over dynamically provisioned dedicated network connections that provide high capacities with no competing traffic. We present extensive TCP throughput measurements and time traces over a suite of physical and emulated 10 Gbps connections with 0-366 ms round-trip times (RTTs). Contrary to the general expectation, they show significant statistical and temporal variations, in addition to the overall dependencies on the congestion control mechanism, buffer size, and the number of parallel streams. We analyze several throughput profiles that have highly desirable concave regions wherein the throughput decreases slowly with RTTs, inmore » stark contrast to the convex profiles predicted by various TCP analytical models. We present a generic throughput model that abstracts the ramp-up and sustainment phases of TCP flows, which provides insights into qualitative trends observed in measurements across TCP variants: (i) slow-start followed by well-sustained throughput leads to concave regions; (ii) large buffers and multiple parallel streams expand the concave regions in addition to improving the throughput; and (iii) stable throughput dynamics, indicated by a smoother Poincare map and smaller Lyapunov exponents, lead to wider concave regions. These measurements and analytical results together enable us to select a TCP variant and its parameters for a given connection to achieve high throughput with statistical guarantees.« less
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Qualitative and quantitative measurement of cannabinoids in cannabis using modified HPLC/DAD method.
Patel, Bhupendra; Wene, Daniel; Fan, Zhihua Tina
2017-11-30
This study presents an accurate and high throughput method for the quantitative determination of various cannabinoids in cannabis plant material using high pressure liquid chromatography (HPLC) with a diode array detector (DAD). Sample extraction and chromatographic analysis conditions for the measurement of cannabinoids in the complex cannabis plant material matrix were optimized. The Agilent Poroshell 120 SB-C18 column provided high resolution for all target analytes with a short run time (10minutes) given the core shell technology. The aqueous buffer mobile phase was optimized with ammonium acetate at pH 4.75. The change in the mobile phase and the new column ensured a separation between cannabidiol (CBD and cannabigerol (CBG) along with cannabigerol and tetrahydrocannabinolic acid (THCA), which were not well separated by previous publications, improved buffering capacity, and provided analytical performance stability. Moreover, baseline drifting was significantly minimized by the use of a low concentration buffer solution (25mM ammonium acetate). In addition, evaporation and reconstitution of the sample residue with a methanol-organic pure (OP) water solution (65:35) significantly reduced the matrix interference. The modified extraction produced good recoveries (>91%) for each of the eight cannabinoids. The optimized method was validated for specificity, linearity, sensitivity, precision, accuracy, and stability. The combined relative standard deviation (%RSD) for intra-day and inter-day precision for all eight analytes varied from 2.5% to 5.2% and 0.28% to 5.5%, respectively. The %RSD for the repeatability study varied from 1.1% to 5.5%. The recoveries from spiked cannabis matrix samples were greater than 90% for all analytes, except delta-8-tetrahydrocannabinol (Δ 8 -THC), which was 80%. The recoveries varied from 81% to 107% with a precision of 0.7-8.1%RSD. Delta-9-tetrahydrocannabinol (Δ 9 -THC) in all of the cannabis samples (n=635) was less than 10%, which is in compliance with the NJ Medicinal Marijuana regulation. Analysis of samples from two cultivars, which included ten individual samples, four composite samples, seven calibration standards, and four quality control standards, can be performed within 24hours by this high throughput method. Published by Elsevier B.V.
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High speed all optical networks
NASA Technical Reports Server (NTRS)
Chlamtac, Imrich; Ganz, Aura
1990-01-01
An inherent problem of conventional point-to-point wide area network (WAN) architectures is that they cannot translate optical transmission bandwidth into comparable user available throughput due to the limiting electronic processing speed of the switching nodes. The first solution to wavelength division multiplexing (WDM) based WAN networks that overcomes this limitation is presented. The proposed Lightnet architecture takes into account the idiosyncrasies of WDM switching/transmission leading to an efficient and pragmatic solution. The Lightnet architecture trades the ample WDM bandwidth for a reduction in the number of processing stages and a simplification of each switching stage, leading to drastically increased effective network throughputs. The principle of the Lightnet architecture is the construction and use of virtual topology networks, embedded in the original network in the wavelength domain. For this construction Lightnets utilize the new concept of lightpaths which constitute the links of the virtual topology. Lightpaths are all-optical, multihop, paths in the network that allow data to be switched through intermediate nodes using high throughput passive optical switches. The use of the virtual topologies and the associated switching design introduce a number of new ideas, which are discussed in detail.
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Guo, Mengzhe; Liang, Junling; Wu, Shihua
2010-08-13
In this work, we have developed a novel hybrid two-dimensional counter-current chromatography and liquid chromatography (2D CCC x LC) system for the continuous purification of arctiin from crude extract of Arctium lappa. The first dimensional CCC column has been designed to fractionalize crude complex extract into pure arctiin effluent using a one-component organic/salt-containing system, and the second dimensional LC column has been packed with macroporous resin for on-line adsorption, desalination and desorption of arctiin which was effluent purified from the first CCC dimension. Thus, the crude arctiin mixture has been purified efficiently and conveniently by on-line CCC x LC in spite of the use of a salt-containing solvent system in CCC separation. As a result, high purity (more than 97%) of arctiin has been isolated by repeated injections both using the ethyl acetate-8% sodium chloride aqueous solution and butanol-1% sodium chloride aqueous solution. By contrast with the traditional CCC processes using multi-component organic/aqueous solvent systems, the present on-line CCC x LC process only used a one-component organic solvent and thus the solvent is easier to recover and regenerate. All of used solvents such as ethyl acetate, n-butanol and NaCl aqueous solution are low toxicity and environment-friendly. Moreover, the lower phase of salt-containing aqueous solution used as mobile phase, only contained minor organic solvent, which will save much organic solvent in continuous separation. In summary, our results indicated that the on-line hybrid 2D CCC x LC system using one-component organic/salt-containing aqueous solution is very promising and powerful tool for high-throughput purification of arctiin from fruits of A. lappa. 2010 Elsevier B.V. All rights reserved.
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The development of a general purpose ARM-based processing unit for the ATLAS TileCal sROD
NASA Astrophysics Data System (ADS)
Cox, M. A.; Reed, R.; Mellado, B.
2015-01-01
After Phase-II upgrades in 2022, the data output from the LHC ATLAS Tile Calorimeter will increase significantly. ARM processors are common in mobile devices due to their low cost, low energy consumption and high performance. It is proposed that a cost-effective, high data throughput Processing Unit (PU) can be developed by using several consumer ARM processors in a cluster configuration to allow aggregated processing performance and data throughput while maintaining minimal software design difficulty for the end-user. This PU could be used for a variety of high-level functions on the high-throughput raw data such as spectral analysis and histograms to detect possible issues in the detector at a low level. High-throughput I/O interfaces are not typical in consumer ARM System on Chips but high data throughput capabilities are feasible via the novel use of PCI-Express as the I/O interface to the ARM processors. An overview of the PU is given and the results for performance and throughput testing of four different ARM Cortex System on Chips are presented.
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Multi-step high-throughput conjugation platform for the development of antibody-drug conjugates.
Andris, Sebastian; Wendeler, Michaela; Wang, Xiangyang; Hubbuch, Jürgen
2018-07-20
Antibody-drug conjugates (ADCs) form a rapidly growing class of biopharmaceuticals which attracts a lot of attention throughout the industry due to its high potential for cancer therapy. They combine the specificity of a monoclonal antibody (mAb) and the cell-killing capacity of highly cytotoxic small molecule drugs. Site-specific conjugation approaches involve a multi-step process for covalent linkage of antibody and drug via a linker. Despite the range of parameters that have to be investigated, high-throughput methods are scarcely used so far in ADC development. In this work an automated high-throughput platform for a site-specific multi-step conjugation process on a liquid-handling station is presented by use of a model conjugation system. A high-throughput solid-phase buffer exchange was successfully incorporated for reagent removal by utilization of a batch cation exchange step. To ensure accurate screening of conjugation parameters, an intermediate UV/Vis-based concentration determination was established including feedback to the process. For conjugate characterization, a high-throughput compatible reversed-phase chromatography method with a runtime of 7 min and no sample preparation was developed. Two case studies illustrate the efficient use for mapping the operating space of a conjugation process. Due to the degree of automation and parallelization, the platform is capable of significantly reducing process development efforts and material demands and shorten development timelines for antibody-drug conjugates. Copyright © 2018 Elsevier B.V. All rights reserved.
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de Loor, Henriette; Poesen, Ruben; De Leger, Wout; Dehaen, Wim; Augustijns, Patrick; Evenepoel, Pieter; Meijers, Björn
2016-09-14
Chronic kidney disease (CKD) is associated with an increased risk of mortality and cardiovascular disease, which is, at least partly, mediated by the accumulation of so-called uremic retention solutes. Although there has been an increasing interest in the behavior of these solutes, derived from both the endogenous and colonic microbial metabolism, methods to simultaneously and accurately measure a broad panel of relevant uremic retention solutes remain scarce. We developed a highly sensitive ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method. A high throughput sample preparation was used with extraction of analytes from 50 μl serum using Ostro plate technology. For most solutes, stable isotopes labelled metabolites were used as internal standards. Chromatography was achieved using an Acquity UPLC CSH Fluoro Phenyl column. The total run time was 8 min, the mobile phase was a gradient of 0.1% formic acid in Milli-Q water and pure methanol at a flow rate of 0.5 ml min(-1). Detection was performed using a tandem mass spectrometer with alternated positive and negative electrospray ionization. Calibration curves were linear for all solutes. Precision was assessed according to the NCCLS EP5-T guideline, being below 15% for all metabolites. Mean recoveries were between 83 and 104% for all metabolites. The validated method was successfully applied in a cohort of 488 patients with CKD. We developed and validated a sensitive and robust UPLC-MS/MS method for quantification of 15 uremic retention solutes derived from endogenous and colonic microbial metabolism. This method allows for studying the behavior and relevance of these solutes in patients with CKD. Copyright © 2016 Elsevier B.V. All rights reserved.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Ebert, Jon Llyod
This Small Business Innovative Research (SBIR) Phase I project will demonstrate the feasibility of an innovative temperature control technology for Metal-Organic Chemical Vapor Deposition (MOCVD) process used in the fabrication of Multi-Quantum Well (MQW) LEDs. The proposed control technology has the strong potential to improve both throughput and performance quality of the manufactured LED. The color of the light emitted by an LED is a strong function of the substrate temperature during the deposition process. Hence, accurate temperature control of the MOCVD process is essential for ensuring that the LED performance matches the design specification. The Gallium Nitride (GaN) epitaxymore » process involves depositing multiple layers at different temperatures. Much of the recipe time is spent ramping from one process temperature to another, adding significant overhead to the production time. To increase throughput, the process temperature must transition over a range of several hundred degrees Centigrade many times with as little overshoot and undershoot as possible, in the face of several sources of process disturbance such as changing emissivities. Any throughput increase achieved by faster ramping must also satisfy the constraint of strict temperature uniformity across the carrier so that yield is not affected. SC Solutions is a leading supplier of embedded real-time temperature control technology for MOCVD systems used in LED manufacturing. SC’s Multiple Input Multiple Output (MIMO) temperature controllers use physics-based models to achieve the performance demanded by our customers. However, to meet DOE’s ambitious goals of cost reduction of LED products, a new generation of temperature controllers has to be developed. SC believes that the proposed control technology will be made feasible by the confluence of mathematical formulation as a convex optimization problem, new efficient and scalable algorithms, and the increase in computational power available for real-time control.« less
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Optimization of throughput in semipreparative chiral liquid chromatography using stacked injection.
Taheri, Mohammadreza; Fotovati, Mohsen; Hosseini, Seyed-Kiumars; Ghassempour, Alireza
2017-10-01
An interesting mode of chromatography for preparation of pure enantiomers from pure samples is the method of stacked injection as a pseudocontinuous procedure. Maximum throughput and minimal production costs can be achieved by the use of total chiral column length in this mode of chromatography. To maximize sample loading, often touching bands of the two enantiomers is automatically achieved. Conventional equations show direct correlation between touching-band loadability and the selectivity factor of two enantiomers. The important question for one who wants to obtain the highest throughput is "How to optimize different factors including selectivity, resolution, run time, and loading of the sample in order to save time without missing the touching-band resolution?" To answer this question, tramadol and propranolol were separated on cellulose 3,5-dimethyl phenyl carbamate, as two pure racemic mixtures with low and high solubilities in mobile phase, respectively. The mobile phase composition consisted of n-hexane solvent with alcohol modifier and diethylamine as the additive. A response surface methodology based on central composite design was used to optimize separation factors against the main responses. According to the stacked injection properties, two processes were investigated for maximizing throughput: one with a poorly soluble and another with a highly soluble racemic mixture. For each case, different optimization possibilities were inspected. It was revealed that resolution is a crucial response for separations of this kind. Peak area and run time are two critical parameters in optimization of stacked injection for binary mixtures which have low solubility in the mobile phase. © 2017 Wiley Periodicals, Inc.
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Vera, C M; Shock, D; Dennis, G R; Farrell, W; Shalliker, R A
2017-04-14
The chiral separation of d- and l- FMOC amino acids was undertaken using the Lux Cellulose-1 polysaccharide based chiral column in HPLC (normal phase and reverse phase) and SFC conditions. This was done to compare the relative selectivity and separation between the three separation modes and to evaluate the potential benefits of SFC separations with regards to resolution, throughput, economic and environmental impact. It was established that the separation of d- and l- FMOC amino acids in SFC displayed behaviours that were similar to both normal phase and reversed phase, rather than distinctly one or the other. Additionally, although reversed phase conditions yielded significantly higher resolution values between enantiomers across the range of amino acids studied, improvements in selectivity in SFC via the introduction of higher concentrations of formic acid in the mobile phase allowed for better resolution per unit of time. Moreover since the SFC mobile phase is composed mostly of recyclable CO 2 , there is a reduction in organic solvent consumption, which minimises the economic and environmental costs. Copyright © 2017. Published by Elsevier B.V.
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Boisvert, Michel; Fayad, Paul B; Sauvé, Sébastien
2012-11-19
A new solid phase extraction (SPE) method coupled to a high throughput sample analysis technique was developed for the simultaneous determination of nine selected emerging contaminants in wastewater (atrazine, desethylatrazine, 17β-estradiol, ethynylestradiol, norethindrone, caffeine, carbamazepine, diclofenac and sulfamethoxazole). We specifically included pharmaceutical compounds from multiple therapeutic classes, as well as pesticides. Sample pre-concentration and clean-up was performed using a mixed-mode SPE cartridge (Strata ABW) having both cation and anion exchange properties, followed by analysis by laser diode thermal desorption atmospheric pressure chemical ionization coupled to tandem mass spectrometry (LDTD-APCI-MS/MS). The LDTD interface is a new high-throughput sample introduction method, which reduces total analysis time to less than 15s per sample as compared to minutes with traditional liquid-chromatography coupled to tandem mass spectrometry (LC-MS/MS). Several SPE parameters were evaluated in order to optimize recovery efficiencies when extracting analytes from wastewater, such as the nature of the stationary phase, the loading flow rate, the extraction pH, the volume and composition of the washing solution and the initial sample volume. The method was successfully applied to real wastewater samples from the primary sedimentation tank of a municipal wastewater treatment plant. Recoveries of target compounds from wastewater ranged from 78% to 106%, the limit of detection ranged from 30 to 122ng L(-1) while the limit of quantification ranged from 90 to 370ng L(-1). Calibration curves in the wastewater matrix showed good linearity (R(2)≥0.991) for all target analytes and the intraday and interday coefficient of variation was below 15%, reflecting a good precision. Copyright © 2012 Elsevier B.V. All rights reserved.
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High Throughput Determination of Tetramine in Drinking ...
Report The sampling and analytical procedure (SAP) presented herein, describes a method for the high throughput determination of tetramethylene disulfotetramine in drinking water by solid phase extraction and isotope dilution gas chromatography/mass spectrometry. This method, which will be included in the SAM, is expected to provide the Water Laboratory Alliance, as part of EPA’s Environmental Response Laboratory Network, with a more reliable and faster means of analyte collection and measurement.
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Chen, LiQin; Wang, Hui; Xu, Zhen; Zhang, QiuYue; Liu, Jia; Shen, Jun; Zhang, WanQi
2018-08-03
In the present study, we developed a simple and high-throughput solid phase extraction (SPE) procedure for selective extraction of catecholamines (CAs) in urine samples. The SPE adsorbents were electrospun composite fibers functionalized with 4-carboxybenzo-18-crown-6 ether modified XAD resin and polystyrene, which were packed into 96-well columns and used for high-throughput selective extraction of CAs in healthy human urine samples. Moreover, the extraction efficiency of packed-fiber SPE (PFSPE) was examined by high performance liquid chromatography coupled with fluorescence detector. The parameters affecting the extraction efficiency and impurity removal efficiency were optimized, and good linearity ranging from 0.5 to 400 ng/mL was obtained with a low limit of detection (LOD, 0.2-0.5 ng/mL) and a good repeatability (2.7%-3.7%, n = 6). The extraction recoveries of three CAs ranged from 70.5% to 119.5%. Furthermore, stable and reliable results obtained by the fluorescence detector were superior to those obtained by the electrochemical detector. Collectively, PFSPE coupled with 96-well columns was a simple, rapid, selective, high-throughput and cost-efficient method, and the proposed method could be applied in clinical chemistry. Copyright © 2018 Elsevier B.V. All rights reserved.
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A Barcoding Strategy Enabling Higher-Throughput Library Screening by Microscopy.
Chen, Robert; Rishi, Harneet S; Potapov, Vladimir; Yamada, Masaki R; Yeh, Vincent J; Chow, Thomas; Cheung, Celia L; Jones, Austin T; Johnson, Terry D; Keating, Amy E; DeLoache, William C; Dueber, John E
2015-11-20
Dramatic progress has been made in the design and build phases of the design-build-test cycle for engineering cells. However, the test phase usually limits throughput, as many outputs of interest are not amenable to rapid analytical measurements. For example, phenotypes such as motility, morphology, and subcellular localization can be readily measured by microscopy, but analysis of these phenotypes is notoriously slow. To increase throughput, we developed microscopy-readable barcodes (MiCodes) composed of fluorescent proteins targeted to discernible organelles. In this system, a unique barcode can be genetically linked to each library member, making possible the parallel analysis of phenotypes of interest via microscopy. As a first demonstration, we MiCoded a set of synthetic coiled-coil leucine zipper proteins to allow an 8 × 8 matrix to be tested for specific interactions in micrographs consisting of mixed populations of cells. A novel microscopy-readable two-hybrid fluorescence localization assay for probing candidate interactions in the cytosol was also developed using a bait protein targeted to the peroxisome and a prey protein tagged with a fluorescent protein. This work introduces a generalizable, scalable platform for making microscopy amenable to higher-throughput library screening experiments, thereby coupling the power of imaging with the utility of combinatorial search paradigms.
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Connolly, Brian D.; Petry, Chris; Yadav, Sandeep; Demeule, Barthélemy; Ciaccio, Natalie; Moore, Jamie M.R.; Shire, Steven J.; Gokarn, Yatin R.
2012-01-01
Weak protein-protein interactions are thought to modulate the viscoelastic properties of concentrated antibody solutions. Predicting the viscoelastic behavior of concentrated antibodies from their dilute solution behavior is of significant interest and remains a challenge. Here, we show that the diffusion interaction parameter (kD), a component of the osmotic second virial coefficient (B2) that is amenable to high-throughput measurement in dilute solutions, correlates well with the viscosity of concentrated monoclonal antibody (mAb) solutions. We measured the kD of 29 different mAbs (IgG1 and IgG4) in four different solvent conditions (low and high ion normality) and found a linear dependence between kD and the exponential coefficient that describes the viscosity concentration profiles (|R| ≥ 0.9). Through experimentally measured effective charge measurements, under low ion normality where the electroviscous effect can dominate, we show that the mAb solution viscosity is poorly correlated with the mAb net charge (|R| ≤ 0.6). With this large data set, our results provide compelling evidence in support of weak intermolecular interactions, in contrast to the notion that the electroviscous effect is important in governing the viscoelastic behavior of concentrated mAb solutions. Our approach is particularly applicable as a screening tool for selecting mAbs with desirable viscosity properties early during lead candidate selection. PMID:22828333
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Accelerating the design of solar thermal fuel materials through high throughput simulations.
Liu, Yun; Grossman, Jeffrey C
2014-12-10
Solar thermal fuels (STF) store the energy of sunlight, which can then be released later in the form of heat, offering an emission-free and renewable solution for both solar energy conversion and storage. However, this approach is currently limited by the lack of low-cost materials with high energy density and high stability. In this Letter, we present an ab initio high-throughput computational approach to accelerate the design process and allow for searches over a broad class of materials. The high-throughput screening platform we have developed can run through large numbers of molecules composed of earth-abundant elements and identifies possible metastable structures of a given material. Corresponding isomerization enthalpies associated with the metastable structures are then computed. Using this high-throughput simulation approach, we have discovered molecular structures with high isomerization enthalpies that have the potential to be new candidates for high-energy density STF. We have also discovered physical principles to guide further STF materials design through structural analysis. More broadly, our results illustrate the potential of using high-throughput ab initio simulations to design materials that undergo targeted structural transitions.
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Plastic straw: future of high-speed signaling
NASA Astrophysics Data System (ADS)
Song, Ha Il; Jin, Huxian; Bae, Hyeon-Min
2015-11-01
The ever-increasing demand for bandwidth triggered by mobile and video Internet traffic requires advanced interconnect solutions satisfying functional and economic constraints. A new interconnect called E-TUBE is proposed as a cost-and-power-effective all-electrical-domain wideband waveguide solution for high-speed high-volume short-reach communication links. The E-TUBE achieves an unprecedented level of performance in terms of bandwidth-per-carrier frequency, power, and density without requiring a precision manufacturing process unlike conventional optical/waveguide solutions. The E-TUBE exhibits a frequency-independent loss-profile of 4 dB/m and has nearly 20-GHz bandwidth over the V band. A single-sideband signal transmission enabled by the inherent frequency response of the E-TUBE renders two-times data throughput without any physical overhead compared to conventional radio frequency communication technologies. This new interconnect scheme would be attractive to parties interested in high throughput links, including but not limited to, 100/400 Gbps chip-to-chip communications.
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Liu, Yang; Cao, Fei; Xiong, Hui; Shen, Yanbing; Wang, Min
2016-01-01
To develop a quick method for the preliminarily screening of mutant strains that can accumulate 9α-hydroxyandrost-4-ene-3,17-dione (9α-OH-AD), a high-throughput screening method was presented by applying the principle that 2,4-dinitrophenylhydrazine (DNPH) can react with ketones to produce precipitation. The optimal color assay conditions were the substrate androst-4-ene-3,17-dione (AD) concentration at 2.0 g/L, the ratio of AD to DNPH solution at 1:4, and the sulfuric acid and ethanol solution percentages in DNPH solution at 2% and 35%, respectively. This method was used to preliminarily screen the mutants of Rhodococcus rhodochrous DSM43269, from which the three ones obtained could produce more 9α-OH-AD. This DNPH color assay method not only broadens screening methods and increases screening efficiency in microbial mutation breeding but also establishes a good foundation for obtaining strains for industrial application. PMID:27706217
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Liu, Yang; Cao, Fei; Xiong, Hui; Shen, Yanbing; Wang, Min
2016-01-01
To develop a quick method for the preliminarily screening of mutant strains that can accumulate 9α-hydroxyandrost-4-ene-3,17-dione (9α-OH-AD), a high-throughput screening method was presented by applying the principle that 2,4-dinitrophenylhydrazine (DNPH) can react with ketones to produce precipitation. The optimal color assay conditions were the substrate androst-4-ene-3,17-dione (AD) concentration at 2.0 g/L, the ratio of AD to DNPH solution at 1:4, and the sulfuric acid and ethanol solution percentages in DNPH solution at 2% and 35%, respectively. This method was used to preliminarily screen the mutants of Rhodococcus rhodochrous DSM43269, from which the three ones obtained could produce more 9α-OH-AD. This DNPH color assay method not only broadens screening methods and increases screening efficiency in microbial mutation breeding but also establishes a good foundation for obtaining strains for industrial application.
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The high-throughput synthesis and phase characterisation of amphiphiles: a sweet case study.
Feast, George C; Hutt, Oliver E; Mulet, Xavier; Conn, Charlotte E; Drummond, Calum J; Savage, G Paul
2014-03-03
A new method for the discovery of amphiphiles by using high-throughput (HT) methods to synthesise and characterise a library of galactose- and glucose-containing amphiphilic compounds is presented. The copper-catalysed azide–alkyne cycloaddition (CuAAC) “click” reaction between azide-tethered simple sugars and alkyne-substituted hydrophobic tails was employed to synthesise a library of compounds with systematic variations in chain length and unsaturation in a 24-vial array format. The liquid–crystalline phase behaviour was characterised in a HT manner by using synchrotron small-angle X-ray scattering (SSAXS). The observed structural variation with respect to chain parameters, including chain length and degree of unsaturation, is discussed, as well as hydration effects and degree of hydrogen bonding between head groups. The validity of our HT screening approach was verified by resynthesising a short-chain glucose amphiphile. A separate phase analysis of this compound confirmed the presence of numerous lyotropic liquid–crystalline phases.
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Direct assembling methodologies for high-throughput bioscreening
Rodríguez-Dévora, Jorge I.; Shi, Zhi-dong; Xu, Tao
2012-01-01
Over the last few decades, high-throughput (HT) bioscreening, a technique that allows rapid screening of biochemical compound libraries against biological targets, has been widely used in drug discovery, stem cell research, development of new biomaterials, and genomics research. To achieve these ambitions, scaffold-free (or direct) assembly of biological entities of interest has become critical. Appropriate assembling methodologies are required to build an efficient HT bioscreening platform. The development of contact and non-contact assembling systems as a practical solution has been driven by a variety of essential attributes of the bioscreening system, such as miniaturization, high throughput, and high precision. The present article reviews recent progress on these assembling technologies utilized for the construction of HT bioscreening platforms. PMID:22021162
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Overcoming bias and systematic errors in next generation sequencing data.
Taub, Margaret A; Corrada Bravo, Hector; Irizarry, Rafael A
2010-12-10
Considerable time and effort has been spent in developing analysis and quality assessment methods to allow the use of microarrays in a clinical setting. As is the case for microarrays and other high-throughput technologies, data from new high-throughput sequencing technologies are subject to technological and biological biases and systematic errors that can impact downstream analyses. Only when these issues can be readily identified and reliably adjusted for will clinical applications of these new technologies be feasible. Although much work remains to be done in this area, we describe consistently observed biases that should be taken into account when analyzing high-throughput sequencing data. In this article, we review current knowledge about these biases, discuss their impact on analysis results, and propose solutions.
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Incorporating High-Throughput Exposure Predictions with ...
We previously integrated dosimetry and exposure with high-throughput screening (HTS) to enhance the utility of ToxCast™ HTS data by translating in vitro bioactivity concentrations to oral equivalent doses (OEDs) required to achieve these levels internally. These OEDs were compared against regulatory exposure estimates, providing an activity-to-exposure ratio (AER) useful for a risk-based ranking strategy. As ToxCast™ efforts expand (i.e., Phase II) beyond food-use pesticides towards a wider chemical domain that lacks exposure and toxicity information, prediction tools become increasingly important. In this study, in vitro hepatic clearance and plasma protein binding were measured to estimate OEDs for a subset of Phase II chemicals. OEDs were compared against high-throughput (HT) exposure predictions generated using probabilistic modeling and Bayesian approaches generated by the U.S. EPA ExpoCast™ program. This approach incorporated chemical-specific use and national production volume data with biomonitoring data to inform the exposure predictions. This HT exposure modeling approach provided predictions for all Phase II chemicals assessed in this study whereas estimates from regulatory sources were available for only 7% of chemicals. Of the 163 chemicals assessed in this study, three or 13 chemicals possessed AERs <1 or <100, respectively. Diverse bioactivities y across a range of assays and concentrations was also noted across the wider chemical space su
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NASA Astrophysics Data System (ADS)
McDonald, S. A.; Marone, F.; Hintermüller, C.; Bensadoun, J.-C.; Aebischer, P.; Stampanoni, M.
2009-09-01
The use of conventional absorption based X-ray microtomography can become limited for samples showing only very weak absorption contrast. However, a wide range of samples studied in biology and materials science can produce significant phase shifts of the X-ray beam, and thus the use of the phase signal can provide substantially increased contrast and therefore new and otherwise inaccessible information. The application of two approaches for high-throughput, high-resolution X-ray phase contrast tomography, both available on the TOMCAT beamline of the SLS, is illustrated. Differential Phase Contrast (DPC) imaging uses a grating interferometer and a phase-stepping technique. It has been integrated into the beamline environment on TOMCAT in terms of the fast acquisition and reconstruction of data and the availability to scan samples within an aqueous environment. The second phase contrast approach is a modified transfer of intensity approach that can yield the 3D distribution of the phase (refractive index) of a weakly absorbing object from a single tomographic dataset. These methods are being used for the evaluation of cell integrity in 3D, with the specific aim of following and analyzing progressive cell degeneration to increase knowledge of the mechanistic events of neurodegenerative disorders such as Parkinson's disease.
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Liao, Jun; Wang, Zhe; Zhang, Zibang; Bian, Zichao; Guo, Kaikai; Nambiar, Aparna; Jiang, Yutong; Jiang, Shaowei; Zhong, Jingang; Choma, Michael; Zheng, Guoan
2018-02-01
We report the development of a multichannel microscopy for whole-slide multiplane, multispectral and phase imaging. We use trinocular heads to split the beam path into 6 independent channels and employ a camera array for parallel data acquisition, achieving a maximum data throughput of approximately 1 gigapixel per second. To perform single-frame rapid autofocusing, we place 2 near-infrared light-emitting diodes (LEDs) at the back focal plane of the condenser lens to illuminate the sample from 2 different incident angles. A hot mirror is used to direct the near-infrared light to an autofocusing camera. For multiplane whole-slide imaging (WSI), we acquire 6 different focal planes of a thick specimen simultaneously. For multispectral WSI, we relay the 6 independent image planes to the same focal position and simultaneously acquire information at 6 spectral bands. For whole-slide phase imaging, we acquire images at 3 focal positions simultaneously and use the transport-of-intensity equation to recover the phase information. We also provide an open-source design to further increase the number of channels from 6 to 15. The reported platform provides a simple solution for multiplexed fluorescence imaging and multimodal WSI. Acquiring an instant focal stack without z-scanning may also enable fast 3-dimensional dynamic tracking of various biological samples. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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A High-Throughput Process for the Solid-Phase Purification of Synthetic DNA Sequences
Grajkowski, Andrzej; Cieślak, Jacek; Beaucage, Serge L.
2017-01-01
An efficient process for the purification of synthetic phosphorothioate and native DNA sequences is presented. The process is based on the use of an aminopropylated silica gel support functionalized with aminooxyalkyl functions to enable capture of DNA sequences through an oximation reaction with the keto function of a linker conjugated to the 5′-terminus of DNA sequences. Deoxyribonucleoside phosphoramidites carrying this linker, as a 5′-hydroxyl protecting group, have been synthesized for incorporation into DNA sequences during the last coupling step of a standard solid-phase synthesis protocol executed on a controlled pore glass (CPG) support. Solid-phase capture of the nucleobase- and phosphate-deprotected DNA sequences released from the CPG support is demonstrated to proceed near quantitatively. Shorter than full-length DNA sequences are first washed away from the capture support; the solid-phase purified DNA sequences are then released from this support upon reaction with tetra-n-butylammonium fluoride in dry dimethylsulfoxide (DMSO) and precipitated in tetrahydrofuran (THF). The purity of solid-phase-purified DNA sequences exceeds 98%. The simulated high-throughput and scalability features of the solid-phase purification process are demonstrated without sacrificing purity of the DNA sequences. PMID:28628204
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Solid-phase reductive amination for glycomic analysis.
Jiang, Kuan; Zhu, He; Xiao, Cong; Liu, Ding; Edmunds, Garrett; Wen, Liuqing; Ma, Cheng; Li, Jing; Wang, Peng George
2017-04-15
Reductive amination is an indispensable method for glycomic analysis, as it tremendously facilitates glycan characterization and quantification by coupling functional tags at the reducing ends of glycans. However, traditional in-solution derivatization based approach for the preparation of reductively aminated glycans is quite tedious and time-consuming. Here, a simpler and more efficient strategy termed solid-phase reductive amination was investigated. The general concept underlying this new approach is to streamline glycan extraction, derivatization, and purification on non-porous graphitized carbon sorbents. Neutral and sialylated standard glycans were utilized to test the feasibility of the solid-phase method. As results, almost complete labeling of those glycans with four common labels of aniline, 2-aminobenzamide (2-AB), 2-aminobenzoic acid (2-AA) and 2-amino-N-(2-aminoethyl)-benzamide (AEAB) was obtained, and negligible desialylation occurred during sample preparation. The labeled glycans derived from glycoproteins showed excellent reproducibility in high performance liquid chromatography (HPLC) and matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis. Direct comparisons based on fluorescent absorbance and relative quantification using isotopic labeling demonstrated that the solid-phase strategy enabled 20-30% increase in sample recovery. In short, the solid-phase strategy is simple, reproducible, efficient, and sensitive for glycan analysis. This method was also successfully applied for N-glycan profiling of HEK 293 cells with MALDI-TOF MS, showing its attractive application in the high-throughput analysis of mammalian glycome. Published by Elsevier B.V.
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Elich, Thomas; Iskra, Timothy; Daniels, William; Morrison, Christopher J
2016-06-01
Effective cleaning of chromatography resin is required to prevent fouling and maximize the number of processing cycles which can be achieved. Optimization of resin cleaning procedures, however, can lead to prohibitive material, labor, and time requirements, even when using milliliter scale chromatography columns. In this work, high throughput (HT) techniques were used to evaluate cleaning agents for a monoclonal antibody (mAb) polishing step utilizing Fractogel(®) EMD TMAE HiCap (M) anion exchange (AEX) resin. For this particular mAb feed stream, the AEX resin could not be fully restored with traditional NaCl and NaOH cleaning solutions, resulting in a loss of impurity capacity with resin cycling. Miniaturized microliter scale chromatography columns and an automated liquid handling system (LHS) were employed to evaluate various experimental cleaning conditions. Cleaning agents were monitored for their ability to maintain resin impurity capacity over multiple processing cycles by analyzing the flowthrough material for turbidity and high molecular weight (HMW) content. HT experiments indicated that a 167 mM acetic acid strip solution followed by a 0.5 M NaOH, 2 M NaCl sanitization provided approximately 90% cleaning improvement over solutions containing solely NaCl and/or NaOH. Results from the microliter scale HT experiments were confirmed in subsequent evaluations at the milliliter scale. These results identify cleaning agents which may restore resin performance for applications involving fouling species in ion exchange systems. In addition, this work demonstrates the use of miniaturized columns operated with an automated LHS for HT evaluation of chromatographic cleaning procedures, effectively decreasing material requirements while simultaneously increasing throughput. Biotechnol. Bioeng. 2016;113: 1251-1259. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.
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A high performance hardware implementation image encryption with AES algorithm
NASA Astrophysics Data System (ADS)
Farmani, Ali; Jafari, Mohamad; Miremadi, Seyed Sohrab
2011-06-01
This paper describes implementation of a high-speed encryption algorithm with high throughput for encrypting the image. Therefore, we select a highly secured symmetric key encryption algorithm AES(Advanced Encryption Standard), in order to increase the speed and throughput using pipeline technique in four stages, control unit based on logic gates, optimal design of multiplier blocks in mixcolumn phase and simultaneous production keys and rounds. Such procedure makes AES suitable for fast image encryption. Implementation of a 128-bit AES on FPGA of Altra company has been done and the results are as follow: throughput, 6 Gbps in 471MHz. The time of encrypting in tested image with 32*32 size is 1.15ms.
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High-speed Fourier ptychographic microscopy based on programmable annular illuminations.
Sun, Jiasong; Zuo, Chao; Zhang, Jialin; Fan, Yao; Chen, Qian
2018-05-16
High-throughput quantitative phase imaging (QPI) is essential to cellular phenotypes characterization as it allows high-content cell analysis and avoids adverse effects of staining reagents on cellular viability and cell signaling. Among different approaches, Fourier ptychographic microscopy (FPM) is probably the most promising technique to realize high-throughput QPI by synthesizing a wide-field, high-resolution complex image from multiple angle-variably illuminated, low-resolution images. However, the large dataset requirement in conventional FPM significantly limits its imaging speed, resulting in low temporal throughput. Moreover, the underlying theoretical mechanism as well as optimum illumination scheme for high-accuracy phase imaging in FPM remains unclear. Herein, we report a high-speed FPM technique based on programmable annular illuminations (AIFPM). The optical-transfer-function (OTF) analysis of FPM reveals that the low-frequency phase information can only be correctly recovered if the LEDs are precisely located at the edge of the objective numerical aperture (NA) in the frequency space. By using only 4 low-resolution images corresponding to 4 tilted illuminations matching a 10×, 0.4 NA objective, we present the high-speed imaging results of in vitro Hela cells mitosis and apoptosis at a frame rate of 25 Hz with a full-pitch resolution of 655 nm at a wavelength of 525 nm (effective NA = 0.8) across a wide field-of-view (FOV) of 1.77 mm 2 , corresponding to a space-bandwidth-time product of 411 megapixels per second. Our work reveals an important capability of FPM towards high-speed high-throughput imaging of in vitro live cells, achieving video-rate QPI performance across a wide range of scales, both spatial and temporal.
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Development and Implementation of High-Throughput SNP Genotyping in Barley
USDA-ARS?s Scientific Manuscript database
Approximately 22,000 SNPs were identified from barley ESTs and sequenced amplicons; 4,596 of them were tested for performance in three pilot phase Illumina GoldenGate assays. Pilot phase data from three barley doubled haploid mapping populations supported the production of an initial consensus map, ...
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The ToxCast Chemical Landscape - Paving the Road to 21st Century Toxicology
The ToxCast high-throughput screening (HTS) program within the U.S. Environmental Protection Agency (EPA) was launched in 2007. Phase I of the program screened 310 chemicals, mostly pesticides, across hundreds of ToxCast assay endpoints. In Phase II, the ToxCast library was exp...
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Alsenaidy, Mohammad A.; Jain, Nishant K.; Kim, Jae H.; Middaugh, C. Russell; Volkin, David B.
2014-01-01
In this review, some of the challenges and opportunities encountered during protein comparability assessments are summarized with an emphasis on developing new analytical approaches to better monitor higher-order protein structures. Several case studies are presented using high throughput biophysical methods to collect protein physical stability data as function of temperature, agitation, ionic strength and/or solution pH. These large data sets were then used to construct empirical phase diagrams (EPDs), radar charts, and comparative signature diagrams (CSDs) for data visualization and structural comparisons between the different proteins. Protein samples with different sizes, post-translational modifications, and inherent stability are presented: acidic fibroblast growth factor (FGF-1) mutants, different glycoforms of an IgG1 mAb prepared by deglycosylation, as well as comparisons of different formulations of an IgG1 mAb and granulocyte colony stimulating factor (GCSF). Using this approach, differences in structural integrity and conformational stability profiles were detected under stress conditions that could not be resolved by using the same techniques under ambient conditions (i.e., no stress). Thus, an evaluation of conformational stability differences may serve as an effective surrogate to monitor differences in higher-order structure between protein samples. These case studies are discussed in the context of potential utility in protein comparability studies. PMID:24659968
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Alsenaidy, Mohammad A; Jain, Nishant K; Kim, Jae H; Middaugh, C Russell; Volkin, David B
2014-01-01
In this review, some of the challenges and opportunities encountered during protein comparability assessments are summarized with an emphasis on developing new analytical approaches to better monitor higher-order protein structures. Several case studies are presented using high throughput biophysical methods to collect protein physical stability data as function of temperature, agitation, ionic strength and/or solution pH. These large data sets were then used to construct empirical phase diagrams (EPDs), radar charts, and comparative signature diagrams (CSDs) for data visualization and structural comparisons between the different proteins. Protein samples with different sizes, post-translational modifications, and inherent stability are presented: acidic fibroblast growth factor (FGF-1) mutants, different glycoforms of an IgG1 mAb prepared by deglycosylation, as well as comparisons of different formulations of an IgG1 mAb and granulocyte colony stimulating factor (GCSF). Using this approach, differences in structural integrity and conformational stability profiles were detected under stress conditions that could not be resolved by using the same techniques under ambient conditions (i.e., no stress). Thus, an evaluation of conformational stability differences may serve as an effective surrogate to monitor differences in higher-order structure between protein samples. These case studies are discussed in the context of potential utility in protein comparability studies.
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The application of the high throughput sequencing technology in the transposable elements.
Liu, Zhen; Xu, Jian-hong
2015-09-01
High throughput sequencing technology has dramatically improved the efficiency of DNA sequencing, and decreased the costs to a great extent. Meanwhile, this technology usually has advantages of better specificity, higher sensitivity and accuracy. Therefore, it has been applied to the research on genetic variations, transcriptomics and epigenomics. Recently, this technology has been widely employed in the studies of transposable elements and has achieved fruitful results. In this review, we summarize the application of high throughput sequencing technology in the fields of transposable elements, including the estimation of transposon content, preference of target sites and distribution, insertion polymorphism and population frequency, identification of rare copies, transposon horizontal transfers as well as transposon tagging. We also briefly introduce the major common sequencing strategies and algorithms, their advantages and disadvantages, and the corresponding solutions. Finally, we envision the developing trends of high throughput sequencing technology, especially the third generation sequencing technology, and its application in transposon studies in the future, hopefully providing a comprehensive understanding and reference for related scientific researchers.
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Study of data I/O performance on distributed disk system in mask data preparation
NASA Astrophysics Data System (ADS)
Ohara, Shuichiro; Odaira, Hiroyuki; Chikanaga, Tomoyuki; Hamaji, Masakazu; Yoshioka, Yasuharu
2010-09-01
Data volume is getting larger every day in Mask Data Preparation (MDP). In the meantime, faster data handling is always required. MDP flow typically introduces Distributed Processing (DP) system to realize the demand because using hundreds of CPU is a reasonable solution. However, even if the number of CPU were increased, the throughput might be saturated because hard disk I/O and network speeds could be bottlenecks. So, MDP needs to invest a lot of money to not only hundreds of CPU but also storage and a network device which make the throughput faster. NCS would like to introduce new distributed processing system which is called "NDE". NDE could be a distributed disk system which makes the throughput faster without investing a lot of money because it is designed to use multiple conventional hard drives appropriately over network. NCS studies I/O performance with OASIS® data format on NDE which contributes to realize the high throughput in this paper.
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Mass Transfer Testing of a 12.5-cm Rotor Centrifugal Contactor
DOE Office of Scientific and Technical Information (OSTI.GOV)
D. H. Meikrantz; T. G. Garn; J. D. Law
2008-09-01
TRUEX mass transfer tests were performed using a single stage commercially available 12.5 cm centrifugal contactor and stable cerium (Ce) and europium (Eu). Test conditions included throughputs ranging from 2.5 to 15 Lpm and rotor speeds of 1750 and 2250 rpm. Ce and Eu extraction forward distribution coefficients ranged from 13 to 19. The first and second stage strip back distributions were 0.5 to 1.4 and .002 to .004, respectively, throughout the dynamic test conditions studied. Visual carryover of aqueous entrainment in all organic phase samples was estimated at < 0.1 % and organic carryover into all aqueous phase samplesmore » was about ten times less. Mass transfer efficiencies of = 98 % for both Ce and Eu in the extraction section were obtained over the entire range of test conditions. The first strip stage mass transfer efficiencies ranged from 75 to 93% trending higher with increasing throughput. Second stage mass transfer was greater than 99% in all cases. Increasing the rotor speed from 1750 to 2250 rpm had no significant effect on efficiency for all throughputs tested.« less
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Guo, Baoshan; Lei, Cheng; Kobayashi, Hirofumi; Ito, Takuro; Yalikun, Yaxiaer; Jiang, Yiyue; Tanaka, Yo; Ozeki, Yasuyuki; Goda, Keisuke
2017-05-01
The development of reliable, sustainable, and economical sources of alternative fuels to petroleum is required to tackle the global energy crisis. One such alternative is microalgal biofuel, which is expected to play a key role in reducing the detrimental effects of global warming as microalgae absorb atmospheric CO 2 via photosynthesis. Unfortunately, conventional analytical methods only provide population-averaged lipid amounts and fail to characterize a diverse population of microalgal cells with single-cell resolution in a non-invasive and interference-free manner. Here high-throughput label-free single-cell screening of lipid-producing microalgal cells with optofluidic time-stretch quantitative phase microscopy was demonstrated. In particular, Euglena gracilis, an attractive microalgal species that produces wax esters (suitable for biodiesel and aviation fuel after refinement), within lipid droplets was investigated. The optofluidic time-stretch quantitative phase microscope is based on an integration of a hydrodynamic-focusing microfluidic chip, an optical time-stretch quantitative phase microscope, and a digital image processor equipped with machine learning. As a result, it provides both the opacity and phase maps of every single cell at a high throughput of 10,000 cells/s, enabling accurate cell classification without the need for fluorescent staining. Specifically, the dataset was used to characterize heterogeneous populations of E. gracilis cells under two different culture conditions (nitrogen-sufficient and nitrogen-deficient) and achieve the cell classification with an error rate of only 2.15%. The method holds promise as an effective analytical tool for microalgae-based biofuel production. © 2017 International Society for Advancement of Cytometry. © 2017 International Society for Advancement of Cytometry.
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NASA Astrophysics Data System (ADS)
Foronda, Augusto; Ohta, Chikara; Tamaki, Hisashi
Dirty paper coding (DPC) is a strategy to achieve the region capacity of multiple input multiple output (MIMO) downlink channels and a DPC scheduler is throughput optimal if users are selected according to their queue states and current rates. However, DPC is difficult to implement in practical systems. One solution, zero-forcing beamforming (ZFBF) strategy has been proposed to achieve the same asymptotic sum rate capacity as that of DPC with an exhaustive search over the entire user set. Some suboptimal user group selection schedulers with reduced complexity based on ZFBF strategy (ZFBF-SUS) and proportional fair (PF) scheduling algorithm (PF-ZFBF) have also been proposed to enhance the throughput and fairness among the users, respectively. However, they are not throughput optimal, fairness and throughput decrease if each user queue length is different due to different users channel quality. Therefore, we propose two different scheduling algorithms: a throughput optimal scheduling algorithm (ZFBF-TO) and a reduced complexity scheduling algorithm (ZFBF-RC). Both are based on ZFBF strategy and, at every time slot, the scheduling algorithms have to select some users based on user channel quality, user queue length and orthogonality among users. Moreover, the proposed algorithms have to produce the rate allocation and power allocation for the selected users based on a modified water filling method. We analyze the schedulers complexity and numerical results show that ZFBF-RC provides throughput and fairness improvements compared to the ZFBF-SUS and PF-ZFBF scheduling algorithms.
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NASA Astrophysics Data System (ADS)
Thobois, Ludovic; Cariou, Jean-Pierre; Cappellazzo, Valerio; Musson, Christian; Treve, Vincent
2018-04-01
Today, the demand for increasing airport capacity is high, in particular for increasing runway throughput from an ATM perspective. Runway capacity is often directly linked with the minima longitudinal separation between aircraft on approach phase or between aircraft on departure. The separation minima are based on surveillance capabilities and on wake turbulence (WT) in order to mitigate respectively collision risk and WT-induced accidents, therefore WT hazard becomes a major concern for ATM. For ten years, many research LIDAR systems have been used for better understanding wake vortices behaviors in the operational environment within large range of wind and turbulence conditions. All these studies[1][2] helped to design new concepts of wake separations between aircrafts thanks to the proven capabilities of LIDAR systems to assess the risks of wake vortex (WV) encounters through the circulation retrievals. The re-categorization project, called RECAT [8], has been launched by a joint EUROCONTROL - FAA initiative in order to renew and optimize the out-of-date currently applied ICAO regulations on distance separation. Nowadays, the first phase of regional RECAT projects, which consists in defining new distance separation matrices composed of six/seven static aircraft categories instead of three, entered the operational phase and is deployed in several airports in United States and Europe. In addition, other concepts like Time-Based Separation have also been studied and deployed in London Heathrow. The airports where these solutions have been deployed obtained significant benefits as increased runway throughput and improved resilience to disruptions. For implementing such new WT solutions at an airport, a local safety assessment before the implementation and a risk monitoring after are usually needed. Before implementation, it may be required to determine for the targeted airport the relative variations of risk of wake vortex encounters, given the local ATM rules, the traffic mix, the weather conditions and their impact on the wake vortex decay. After implementation, the risk monitoring might perform in-depth analysis of wake vortex encounter reported by pilots. For all the mentioned steps, the use of scanning Doppler LIDARs is the only experimental sensor capable of measuring the localization and the circulation of the wake vortices and to provide ground truth wake vortex measurements. Next generation operational LIDARs need to be developed to address in a cost effective way these operational needs. Furthermore, a specific configuration and methodology need to be developed to ensure the accuracy of the wake vortex data. Such a LIDAR based wake vortex solution has been tested at Paris Charles De Gaulle which implemented the RECAT-EU wake separation scheme. The wake vortex circulation, initial spacing and decay measured have been compared to the data collected in London Heathrow by a different LIDAR sensor. The results indicated that the initial circulation, the time to demise, the decay curve evolution and the vortex spacing are very coherent between the two databases.
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Accelerating the Design of Solar Thermal Fuel Materials through High Throughput Simulations
DOE Office of Scientific and Technical Information (OSTI.GOV)
Liu, Y; Grossman, JC
2014-12-01
Solar thermal fuels (STF) store the energy of sunlight, which can then be released later in the form of heat, offering an emission-free and renewable solution for both solar energy conversion and storage. However, this approach is currently limited by the lack of low-cost materials with high energy density and high stability. In this Letter, we present an ab initio high-throughput computational approach to accelerate the design process and allow for searches over a broad class of materials. The high-throughput screening platform we have developed can run through large numbers of molecules composed of earth-abundant elements and identifies possible metastablemore » structures of a given material. Corresponding isomerization enthalpies associated with the metastable structures are then computed. Using this high-throughput simulation approach, we have discovered molecular structures with high isomerization enthalpies that have the potential to be new candidates for high-energy density STF. We have also discovered physical principles to guide further STF materials design through structural analysis. More broadly, our results illustrate the potential of using high-throughput ab initio simulations to design materials that undergo targeted structural transitions.« less
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Throughput Maximization for Sensor-Aided Cognitive Radio Networks with Continuous Energy Arrivals
Nguyen, Thanh-Tung; Koo, Insoo
2015-01-01
We consider a Sensor-Aided Cognitive Radio Network (SACRN) in which sensors capable of harvesting energy are distributed throughout the network to support secondary transmitters for sensing licensed channels in order to improve both energy and spectral efficiency. Harvesting ambient energy is one of the most promising solutions to mitigate energy deficiency, prolong device lifetime, and partly reduce the battery size of devices. So far, many works related to SACRN have considered single secondary users capable of harvesting energy in whole slot as well as short-term throughput. In the paper, we consider two types of energy harvesting sensor nodes (EHSN): Type-I sensor nodes will harvest ambient energy in whole slot duration, whereas type-II sensor nodes will only harvest energy after carrying out spectrum sensing. In the paper, we also investigate long-term throughput in the scheduling window, and formulate the throughput maximization problem by considering energy-neutral operation conditions of type-I and -II sensors and the target detection probability. Through simulations, it is shown that the sensing energy consumption of all sensor nodes can be efficiently managed with the proposed scheme to achieve optimal long-term throughput in the window. PMID:26633393
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Correction of Microplate Data from High-Throughput Screening.
Wang, Yuhong; Huang, Ruili
2016-01-01
High-throughput screening (HTS) makes it possible to collect cellular response data from a large number of cell lines and small molecules in a timely and cost-effective manner. The errors and noises in the microplate-formatted data from HTS have unique characteristics, and they can be generally grouped into three categories: run-wise (temporal, multiple plates), plate-wise (background pattern, single plate), and well-wise (single well). In this chapter, we describe a systematic solution for identifying and correcting such errors and noises, mainly basing on pattern recognition and digital signal processing technologies.
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Round, A. R.; Franke, D.; Moritz, S.; Huchler, R.; Fritsche, M.; Malthan, D.; Klaering, R.; Svergun, D. I.; Roessle, M.
2008-01-01
There is a rapidly increasing interest in the use of synchrotron small-angle X-ray scattering (SAXS) for large-scale studies of biological macromolecules in solution, and this requires an adequate means of automating the experiment. A prototype has been developed of an automated sample changer for solution SAXS, where the solutions are kept in thermostatically controlled well plates allowing for operation with up to 192 samples. The measuring protocol involves controlled loading of protein solutions and matching buffers, followed by cleaning and drying of the cell between measurements. The system was installed and tested at the X33 beamline of the EMBL, at the storage ring DORIS-III (DESY, Hamburg), where it was used by over 50 external groups during 2007. At X33, a throughput of approximately 12 samples per hour, with a failure rate of sample loading of less than 0.5%, was observed. The feedback from users indicates that the ease of use and reliability of the user operation at the beamline were greatly improved compared with the manual filling mode. The changer is controlled by a client–server-based network protocol, locally and remotely. During the testing phase, the changer was operated in an attended mode to assess its reliability and convenience. Full integration with the beamline control software, allowing for automated data collection of all samples loaded into the machine with remote control from the user, is presently being implemented. The approach reported is not limited to synchrotron-based SAXS but can also be used on laboratory and neutron sources. PMID:25484841
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Z2Pack: Numerical implementation of hybrid Wannier centers for identifying topological materials
NASA Astrophysics Data System (ADS)
Gresch, Dominik; Autès, Gabriel; Yazyev, Oleg V.; Troyer, Matthias; Vanderbilt, David; Bernevig, B. Andrei; Soluyanov, Alexey A.
2017-02-01
The intense theoretical and experimental interest in topological insulators and semimetals has established band structure topology as a fundamental material property. Consequently, identifying band topologies has become an important, but often challenging, problem, with no exhaustive solution at the present time. In this work we compile a series of techniques, some previously known, that allow for a solution to this problem for a large set of the possible band topologies. The method is based on tracking hybrid Wannier charge centers computed for relevant Bloch states, and it works at all levels of materials modeling: continuous k .p models, tight-binding models, and ab initio calculations. We apply the method to compute and identify Chern, Z2, and crystalline topological insulators, as well as topological semimetal phases, using real material examples. Moreover, we provide a numerical implementation of this technique (the Z2Pack software package) that is ideally suited for high-throughput screening of materials databases for compounds with nontrivial topologies. We expect that our work will allow researchers to (a) identify topological materials optimal for experimental probes, (b) classify existing compounds, and (c) reveal materials that host novel, not yet described, topological states.
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Vandelle, Elodie; Puttilli, Maria Rita; Chini, Andrea; Devescovi, Giulia; Venturi, Vittorio; Polverari, Annalisa
2017-01-01
The life cycle of bacterial phytopathogens consists of a benign epiphytic phase, during which the bacteria grow in the soil or on the plant surface, and a virulent endophytic phase involving the penetration of host defenses and the colonization of plant tissues. Innovative strategies are urgently required to integrate copper treatments that control the epiphytic phase with complementary tools that control the virulent endophytic phase, thus reducing the quantity of chemicals applied to economically and ecologically acceptable levels. Such strategies include targeted treatments that weaken bacterial pathogens, particularly those inhibiting early infection steps rather than tackling established infections. This chapter describes a reporter gene-based chemical genomic high-throughput screen for the induction of bacterial virulence by plant molecules. Specifically, we describe a chemical genomic screening method to identify agonist and antagonist molecules for the induction of targeted bacterial virulence genes by plant extracts, focusing on the experimental controls required to avoid false positives and thus ensuring the results are reliable and reproducible.
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Diagnosis of breast cancer biopsies using quantitative phase imaging
NASA Astrophysics Data System (ADS)
Majeed, Hassaan; Kandel, Mikhail E.; Han, Kevin; Luo, Zelun; Macias, Virgilia; Tangella, Krishnarao; Balla, Andre; Popescu, Gabriel
2015-03-01
The standard practice in the histopathology of breast cancers is to examine a hematoxylin and eosin (H&E) stained tissue biopsy under a microscope. The pathologist looks at certain morphological features, visible under the stain, to diagnose whether a tumor is benign or malignant. This determination is made based on qualitative inspection making it subject to investigator bias. Furthermore, since this method requires a microscopic examination by the pathologist it suffers from low throughput. A quantitative, label-free and high throughput method for detection of these morphological features from images of tissue biopsies is, hence, highly desirable as it would assist the pathologist in making a quicker and more accurate diagnosis of cancers. We present here preliminary results showing the potential of using quantitative phase imaging for breast cancer screening and help with differential diagnosis. We generated optical path length maps of unstained breast tissue biopsies using Spatial Light Interference Microscopy (SLIM). As a first step towards diagnosis based on quantitative phase imaging, we carried out a qualitative evaluation of the imaging resolution and contrast of our label-free phase images. These images were shown to two pathologists who marked the tumors present in tissue as either benign or malignant. This diagnosis was then compared against the diagnosis of the two pathologists on H&E stained tissue images and the number of agreements were counted. In our experiment, the agreement between SLIM and H&E based diagnosis was measured to be 88%. Our preliminary results demonstrate the potential and promise of SLIM for a push in the future towards quantitative, label-free and high throughput diagnosis.
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Integrated optics prototype beam combiner for long baseline interferometry in the L and M bands
NASA Astrophysics Data System (ADS)
Tepper, J.; Labadie, L.; Diener, R.; Minardi, S.; Pott, J.-U.; Thomson, R.; Nolte, S.
2017-06-01
Context. Optical long baseline interferometry is a unique way to study astronomical objects at milli-arcsecond resolutions not attainable with current single-dish telescopes. Yet, the significance of its scientfic return strongly depends on a dense coverage of the uv-plane and a highly stable transfer function of the interferometric instrument. In the last few years, integrated optics (IO) beam combiners have facilitated the emergence of 4-telescope interferometers such as PIONIER or GRAVITY, boosting the imaging capabilities of the VLTI. However, the spectral range beyond 2.2 μm is not ideally covered by the conventional silica based IO. Here, we consider new laser-written IO prototypes made of gallium lanthanum sulfide (GLS) glass, a material that permits access to the mid-infrared spectral regime. Aims: Our goal is to conduct a full characterization of our mid-IR IO two-telescope coupler in order to measure the performance levels directly relevant for long-baseline interferometry. We focus in particular on the exploitation of the L and M astronomical bands. Methods: We use a dedicated Michelson-interferometer setup to perform Fourier transform spectroscopy on the coupler and measure its broadband interferometric performance. We also analyze the polarization properties of the coupler, the differential dispersion and phase degradation, as well as the modal behavior and the total throughput. Results: We measure broadband interferometric contrasts of 94.9% and 92.1% for unpolarized light in the L and M bands. Spectrally integrated splitting ratios are close to 50%, but show chromatic dependence over the considered bandwidths. Additionally, the phase variation due to the combiner is measured and does not exceed 0.04 rad and 0.07 rad across the L and M band, respectively. The total throughput of the coupler including Fresnel and injection losses from free-space is 25.4%. Furthermore, differential birefringence is low (<0.2 rad), in line with the high contrasts reported for unpolarized light. Conclusions: The laser-written IO GLS prototype combiners prove to be a reliable technological solution with promising performance for mid-infrared long-baseline interferometry. In the next steps, we will consider more advanced optical functions, as well as a fiber-fed input, and we will revise the optical design parameters in order to further enhance the total throughput and achromatic behavior.
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Preparation & characterization of high purity Cu2 ZnSn(SxSe1-x)4 nanoparticles
NASA Astrophysics Data System (ADS)
Negash, Bethlehem G.
Research in thin film solar cells applies novel techniques to synthesize cost effective and highly efficient absorber materials in order to generate electricity directly from solar energy. Of these materials, copper zinc tin sulfoselenide (Cu2ZnSn(SxSe1-x) 4) nanoparticles have shown great promise in solar cell applications due to optimal material properties as well as low cost & relative abundance of materials.1,2 Sulfoselenide nanoparticles have also a broader impact in other industries including electronics3, LED 4, and biomedical research5. Of the many routes of manufacturing these class of semiconductors, colloidal synthesis of Cu 2ZnSn(SxSe1-x)4 offers a scalable, low cost and high-throughput route for manufacturing high efficiency thin-film solar cells. Hydrazine processed Cu2ZnSn(SxSe1-x )4 devices have reached a record power conversion efficiency (PCE) of 12.6%, much higher than the 9.6% reported for physical vapor deposition (PVD) systems.6,7. Despite high efficiencies, wet synthesis of nanoparticles, however, is made more complicated in multi-element, quaternary and quinary systems such as copper zinc tin sulfoselenide (CZTSSe) and copper indium gallium diselenide (CIGSe). One major disadvantage in these systems is growth of the desired quaternary or quinary phase in competition with unwanted binary and ternary phases with low energy of formation.8,9 Moreover, various reaction parameters such as reaction time, temperature, and choice of ligand also affect, chemical as well as physical properties of resulting nanoparticles. Understanding of the formation mechanisms of the particles is necessary in order to address some of these challenges in wet synthesis of CZTSSe nanoparticles. In this study, we investigate synthesis conditions & reaction parameters which yield high purity Cu2ZnSn(SxSe1-x) 4 nanoparticles as well as attempt to understand the growth mechanism of these nanoparticles. This was achieved by manipulating anion precursor preparation routes as well order in which precursors are introduced into a reaction system. We report a new solution based sulfoselenide preparation route which has been used to synthesize high purity Cu2ZnSn(S xSe1-x)4 nanoparticles. Uniform phase Cu 2ZnSn(SxSe1-x)4 nanoparticles were successfully synthesized over a wide range of varying chalcogen ratios. It was found that anion precursor solution plays a key role in determining the morphology & phase purity of the final nanoparticles, as observed from X-ray Diffraction (XRD) and Raman spectroscopy. A uniform sulfoselenide solution is needed to produce high purity Cu2ZnSn(SxSe1-x )4 nanoparticles with narrow phase distribution. Moreover, the relative reactivity of each anion must be balanced in order to yield uniform phase nanoparticles. The findings of this study as well as the reported mixed chalcogen precursor preparation route can be applied in various industries, including photovoltaics to produce uniform phase, solution processed sulfoselenide nanoparticles.
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48-spot single-molecule FRET setup with periodic acceptor excitation
NASA Astrophysics Data System (ADS)
Ingargiola, Antonino; Segal, Maya; Gulinatti, Angelo; Rech, Ivan; Labanca, Ivan; Maccagnani, Piera; Ghioni, Massimo; Weiss, Shimon; Michalet, Xavier
2018-03-01
Single-molecule Förster resonance energy transfer (smFRET) allows measuring distances between donor and acceptor fluorophores on the 3-10 nm range. Solution-based smFRET allows measurement of binding-unbinding events or conformational changes of dye-labeled biomolecules without ensemble averaging and free from surface perturbations. When employing dual (or multi) laser excitation, smFRET allows resolving the number of fluorescent labels on each molecule, greatly enhancing the ability to study heterogeneous samples. A major drawback to solution-based smFRET is the low throughput, which renders repetitive measurements expensive and hinders the ability to study kinetic phenomena in real-time. Here we demonstrate a high-throughput smFRET system that multiplexes acquisition by using 48 excitation spots and two 48-pixel single-photon avalanche diode array detectors. The system employs two excitation lasers allowing separation of species with one or two active fluorophores. The performance of the system is demonstrated on a set of doubly labeled double-stranded DNA oligonucleotides with different distances between donor and acceptor dyes along the DNA duplex. We show that the acquisition time for accurate subpopulation identification is reduced from several minutes to seconds, opening the way to high-throughput screening applications and real-time kinetics studies of enzymatic reactions such as DNA transcription by bacterial RNA polymerase.
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A simple and sensitive enzymatic method for cholesterol quantification in macrophages and foam cells
Robinet, Peggy; Wang, Zeneng; Hazen, Stanley L.; Smith, Jonathan D.
2010-01-01
A precise and sensitive method for measuring cellular free and esterified cholesterol is required in order to perform studies of macrophage cholesterol loading, metabolism, storage, and efflux. Until now, the use of an enzymatic cholesterol assay, commonly used for aqueous phase plasma cholesterol assays, has not been optimized for use with solid phase samples such as cells, due to inefficient solubilization of total cholesterol in enzyme compatible solvents. We present an efficient solubilization protocol compatible with an enzymatic cholesterol assay that does not require chemical saponification or chromatographic separation. Another issue with enzyme compatible solvents is the presence of endogenous peroxides that interfere with the enzymatic cholesterol assay. We overcame this obstacle by pretreatment of the reaction solution with the enzyme catalase, which consumed endogenous peroxides resulting in reduced background and increased sensitivity in our method. Finally, we demonstrated that this method for cholesterol quantification in macrophages yields results that are comparable to those measured by stable isotope dilution gas chromatography with mass spectrometry detection. In conclusion, we describe a sensitive, simple, and high-throughput enzymatic method to quantify cholesterol in complex matrices such as cells. PMID:20688754
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Zhong, Zhixiong; Li, Gongke; Wu, Rong; Zhu, Binghui; Luo, Zhibin
2014-08-01
A simple and reliable ultrasound-assisted solid-phase dispersion extraction coupled with ion chromatography was developed for the determination of aminophenols and phenol. The highly viscous hair colorant was dispersed in solvents using anhydrous sodium sulfite having dual functions of dispersant and antioxidant. The use of anhydrous sodium sulfite did not change the sample volume because it could completely dissolve in solution after matrix dispersion. The extraction and cleanup were combined in one single step for simplifying operation. The extraction process could be rapidly accomplished within 9 min with high sample throughput under the synergistic effects of vibration, ultrasound, and heating. Satisfactory linearity was observed with correlation coefficients higher than 0.9992, and the limits of detection varied from 0.02 to 0.09 mg/L. The applicability of the proposed method was demonstrated by measuring the concentrations of aminophenols and phenol in 32 different commercial hair color products. The recoveries ranged from 86.4-101.2% with the relative standard deviations in the range of 0.52-4.3%. The method offers an attractive alternative for the analysis of trace phenols in complex matrices. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Mudanyali, Onur; Erlinger, Anthony; Seo, Sungkyu; Su, Ting-Wei; Tseng, Derek; Ozcan, Aydogan
2009-12-14
Conventional optical microscopes image cells by use of objective lenses that work together with other lenses and optical components. While quite effective, this classical approach has certain limitations for miniaturization of the imaging platform to make it compatible with the advanced state of the art in microfluidics. In this report, we introduce experimental details of a lensless on-chip imaging concept termed LUCAS (Lensless Ultra-wide field-of-view Cell monitoring Array platform based on Shadow imaging) that does not require any microscope objectives or other bulky optical components to image a heterogeneous cell solution over an ultra-wide field of view that can span as large as approximately 18 cm(2). Moreover, unlike conventional microscopes, LUCAS can image a heterogeneous cell solution of interest over a depth-of-field of approximately 5 mm without the need for refocusing which corresponds to up to approximately 9 mL sample volume. This imaging platform records the shadows (i.e., lensless digital holograms) of each cell of interest within its field of view, and automated digital processing of these cell shadows can determine the type, the count and the relative positions of cells within the solution. Because it does not require any bulky optical components or mechanical scanning stages it offers a significantly miniaturized platform that at the same time reduces the cost, which is quite important for especially point of care diagnostic tools. Furthermore, the imaging throughput of this platform is orders of magnitude better than conventional optical microscopes, which could be exceedingly valuable for high-throughput cell-biology experiments.
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Mudanyali, Onur; Erlinger, Anthony; Seo, Sungkyu; Su, Ting-Wei; Tseng, Derek; Ozcan, Aydogan
2009-01-01
Conventional optical microscopes image cells by use of objective lenses that work together with other lenses and optical components. While quite effective, this classical approach has certain limitations for miniaturization of the imaging platform to make it compatible with the advanced state of the art in microfluidics. In this report, we introduce experimental details of a lensless on-chip imaging concept termed LUCAS (Lensless Ultra-wide field-of-view Cell monitoring Array platform based on Shadow imaging) that does not require any microscope objectives or other bulky optical components to image a heterogeneous cell solution over an ultra-wide field of view that can span as large as ~18 cm2. Moreover, unlike conventional microscopes, LUCAS can image a heterogeneous cell solution of interest over a depth-of-field of ~5 mm without the need for refocusing which corresponds to up to ~9 mL sample volume. This imaging platform records the shadows (i.e., lensless digital holograms) of each cell of interest within its field of view, and automated digital processing of these cell shadows can determine the type, the count and the relative positions of cells within the solution. Because it does not require any bulky optical components or mechanical scanning stages it offers a significantly miniaturized platform that at the same time reduces the cost, which is quite important for especially point of care diagnostic tools. Furthermore, the imaging throughput of this platform is orders of magnitude better than conventional optical microscopes, which could be exceedingly valuable for high-throughput cell-biology experiments. PMID:20010542
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Kusne, Aaron Gilad; Gao, Tieren; Mehta, Apurva; Ke, Liqin; Nguyen, Manh Cuong; Ho, Kai-Ming; Antropov, Vladimir; Wang, Cai-Zhuang; Kramer, Matthew J.; Long, Christian; Takeuchi, Ichiro
2014-01-01
Advanced materials characterization techniques with ever-growing data acquisition speed and storage capabilities represent a challenge in modern materials science, and new procedures to quickly assess and analyze the data are needed. Machine learning approaches are effective in reducing the complexity of data and rapidly homing in on the underlying trend in multi-dimensional data. Here, we show that by employing an algorithm called the mean shift theory to a large amount of diffraction data in high-throughput experimentation, one can streamline the process of delineating the structural evolution across compositional variations mapped on combinatorial libraries with minimal computational cost. Data collected at a synchrotron beamline are analyzed on the fly, and by integrating experimental data with the inorganic crystal structure database (ICSD), we can substantially enhance the accuracy in classifying the structural phases across ternary phase spaces. We have used this approach to identify a novel magnetic phase with enhanced magnetic anisotropy which is a candidate for rare-earth free permanent magnet. PMID:25220062
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Marsillac, Sylvain
2015-11-30
The main objective of this proposal was to use several pathways to reduce the production cost of Cu(In,Ga)Se 2 (CIGS) PV modules and therefore the levelized cost of energy (LCOE) associated with this technology. Three high cost drivers were identified, nominally: 1) Materials cost and availability; 2) Large scale uniformity; 3) Improved throughput These three cost drivers were targeted using the following pathways: 1) Reducing the thickness of the CIGS layer while enhancing materials quality; 2) Developing and applying enhanced in-situ metrology via real time spectroscopic ellipsometry; 3) Looking into alternative heterojunction partner, back contact and anti-reflection (AR) coating Elevenmore » main Tasks were then defined to achieve these goals (5 in Phase 1 and 6 in Phase 2), with 11 Milestones and 2 Go/No-go decision points at the end of Phase 1. The key results are summarized below« less
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Evaluation of the Current Status of the Combinatorial Approach for the Study of Phase Diagrams
Wong-Ng, W.
2012-01-01
This paper provides an evaluation of the effectiveness of using the high throughput combinatorial approach for preparing phase diagrams of thin film and bulk materials. Our evaluation is based primarily on examples of combinatorial phase diagrams that have been reported in the literature as well as based on our own laboratory experiments. Various factors that affect the construction of these phase diagrams are examined. Instrumentation and analytical approaches needed to improve data acquisition and data analysis are summarized. PMID:26900530
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Akbani, Rehan; Becker, Karl-Friedrich; Carragher, Neil; Goldstein, Ted; de Koning, Leanne; Korf, Ulrike; Liotta, Lance; Mills, Gordon B; Nishizuka, Satoshi S; Pawlak, Michael; Petricoin, Emanuel F; Pollard, Harvey B; Serrels, Bryan; Zhu, Jingchun
2014-07-01
Reverse phase protein array (RPPA) technology introduced a miniaturized "antigen-down" or "dot-blot" immunoassay suitable for quantifying the relative, semi-quantitative or quantitative (if a well-accepted reference standard exists) abundance of total protein levels and post-translational modifications across a variety of biological samples including cultured cells, tissues, and body fluids. The recent evolution of RPPA combined with more sophisticated sample handling, optical detection, quality control, and better quality affinity reagents provides exquisite sensitivity and high sample throughput at a reasonable cost per sample. This facilitates large-scale multiplex analysis of multiple post-translational markers across samples from in vitro, preclinical, or clinical samples. The technical power of RPPA is stimulating the application and widespread adoption of RPPA methods within academic, clinical, and industrial research laboratories. Advances in RPPA technology now offer scientists the opportunity to quantify protein analytes with high precision, sensitivity, throughput, and robustness. As a result, adopters of RPPA technology have recognized critical success factors for useful and maximum exploitation of RPPA technologies, including the following: preservation and optimization of pre-analytical sample quality, application of validated high-affinity and specific antibody (or other protein affinity) detection reagents, dedicated informatics solutions to ensure accurate and robust quantification of protein analytes, and quality-assured procedures and data analysis workflows compatible with application within regulated clinical environments. In 2011, 2012, and 2013, the first three Global RPPA workshops were held in the United States, Europe, and Japan, respectively. These workshops provided an opportunity for RPPA laboratories, vendors, and users to share and discuss results, the latest technology platforms, best practices, and future challenges and opportunities. The outcomes of the workshops included a number of key opportunities to advance the RPPA field and provide added benefit to existing and future participants in the RPPA research community. The purpose of this report is to share and disseminate, as a community, current knowledge and future directions of the RPPA technology. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.
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Cellular automata models for diffusion of information and highway traffic flow
NASA Astrophysics Data System (ADS)
Fuks, Henryk
In the first part of this work we study a family of deterministic models for highway traffic flow which generalize cellular automaton rule 184. This family is parameterized by the speed limit m and another parameter k that represents degree of 'anticipatory driving'. We compare two driving strategies with identical maximum throughput: 'conservative' driving with high speed limit and 'anticipatory' driving with low speed limit. Those two strategies are evaluated in terms of accident probability. We also discuss fundamental diagrams of generalized traffic rules and examine limitations of maximum achievable throughput. Possible modifications of the model are considered. For rule 184, we present exact calculations of the order parameter in a transition from the moving phase to the jammed phase using the method of preimage counting, and use this result to construct a solution to the density classification problem. In the second part we propose a probabilistic cellular automaton model for the spread of innovations, rumors, news, etc., in a social system. We start from simple deterministic models, for which exact expressions for the density of adopters are derived. For a more realistic model, based on probabilistic cellular automata, we study the influence of a range of interaction R on the shape of the adoption curve. When the probability of adoption is proportional to the local density of adopters, and individuals can drop the innovation with some probability p, the system exhibits a second order phase transition. Critical line separating regions of parameter space in which asymptotic density of adopters is positive from the region where it is equal to zero converges toward the mean-field line when the range of the interaction increases. In a region between R=1 critical line and the mean-field line asymptotic density of adopters depends on R, becoming zero if R is too small (smaller than some critical value). This result demonstrates the importance of connectivity in diffusion of information. We also define a new class of automata networks which incorporates non-local interactions, and discuss its applicability in modeling of diffusion of innovations.
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High throughput screening of CO2 solubility in aqueous monoamine solutions.
Porcheron, Fabien; Gibert, Alexandre; Mougin, Pascal; Wender, Aurélie
2011-03-15
Post-combustion Carbon Capture and Storage technology (CCS) is viewed as an efficient solution to reduce CO(2) emissions of coal-fired power stations. In CCS, an aqueous amine solution is commonly used as a solvent to selectively capture CO(2) from the flue gas. However, this process generates additional costs, mostly from the reboiler heat duty required to release the carbon dioxide from the loaded solvent solution. In this work, we present thermodynamic results of CO(2) solubility in aqueous amine solutions from a 6-reactor High Throughput Screening (HTS) experimental device. This device is fully automated and designed to perform sequential injections of CO(2) within stirred-cell reactors containing the solvent solutions. The gas pressure within each reactor is monitored as a function of time, and the resulting transient pressure curves are transformed into CO(2) absorption isotherms. Solubility measurements are first performed on monoethanolamine, diethanolamine, and methyldiethanolamine aqueous solutions at T = 313.15 K. Experimental results are compared with existing data in the literature to validate the HTS device. In addition, a comprehensive thermodynamic model is used to represent CO(2) solubility variations in different classes of amine structures upon a wide range of thermodynamic conditions. This model is used to fit the experimental data and to calculate the cyclic capacity, which is a key parameter for CO(2) process design. Solubility measurements are then performed on a set of 50 monoamines and cyclic capacities are extracted using the thermodynamic model, to asses the potential of these molecules for CO(2) capture.
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Brown, Colby R; McCalla, Eric; Watson, Cody; Dahn, J R
2015-06-08
Combinatorial synthesis has proven extremely effective in screening for new battery materials for Li-ion battery electrodes. Here, a study in the Li-Ni-Mn-Co-O system is presented, wherein samples with nearly 800 distinct compositions were prepared using a combinatorial and high-throughput method to screen for single-phase materials of high interest as next generation positive electrode materials. X-ray diffraction is used to determine the crystal structure of each sample. The Gibbs' pyramid representing the pseudoquaternary system was studied by making samples within three distinct pseudoternary planes defined at fractional cobalt metal contents of 10%, 20%, and 30% within the Li-Ni-Mn-Co-O system. Two large single-phase regions were observed in the system: the layered region (ordered rocksalt) and cubic spinel region; both of which are of interest for next-generation positive electrodes in lithium-ion batteries. These regions were each found to stretch over a wide range of compositions within the Li-Ni-Mn-Co-O pseudoquaternary system and had complex coexistence regions existing between them. The sample cooling rate was found to have a significant effect on the position of the phase boundaries of the single-phase regions. The results of this work are intended to guide further research by narrowing the composition ranges worthy of study and to illustrate the broad range of applications where solution-based combinatorial synthesis can have significant impact.
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Reyon, Deepak; Maeder, Morgan L; Khayter, Cyd; Tsai, Shengdar Q; Foley, Jonathan E; Sander, Jeffry D; Joung, J Keith
2013-07-01
Customized DNA-binding domains made using transcription activator-like effector (TALE) repeats are rapidly growing in importance as widely applicable research tools. TALE nucleases (TALENs), composed of an engineered array of TALE repeats fused to the FokI nuclease domain, have been used successfully for directed genome editing in various organisms and cell types. TALE transcription factors (TALE-TFs), consisting of engineered TALE repeat arrays linked to a transcriptional regulatory domain, have been used to up- or downregulate expression of endogenous genes in human cells and plants. This unit describes a detailed protocol for the recently described fast ligation-based automatable solid-phase high-throughput (FLASH) assembly method. FLASH enables automated high-throughput construction of engineered TALE repeats using an automated liquid handling robot or manually using a multichannel pipet. Using the automated approach, a single researcher can construct up to 96 DNA fragments encoding TALE repeat arrays of various lengths in a single day, and then clone these to construct sequence-verified TALEN or TALE-TF expression plasmids in a week or less. Plasmids required for FLASH are available by request from the Joung lab (http://eGenome.org). This unit also describes improvements to the Zinc Finger and TALE Targeter (ZiFiT Targeter) web server (http://ZiFiT.partners.org) that facilitate the design and construction of FLASH TALE repeat arrays in high throughput. © 2013 by John Wiley & Sons, Inc.
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Reyon, Deepak; Maeder, Morgan L.; Khayter, Cyd; Tsai, Shengdar Q.; Foley, Jonathan E.; Sander, Jeffry D.; Joung, J. Keith
2013-01-01
Customized DNA-binding domains made using Transcription Activator-Like Effector (TALE) repeats are rapidly growing in importance as widely applicable research tools. TALE nucleases (TALENs), composed of an engineered array of TALE repeats fused to the FokI nuclease domain, have been used successfully for directed genome editing in multiple different organisms and cell types. TALE transcription factors (TALE-TFs), consisting of engineered TALE repeat arrays linked to a transcriptional regulatory domain, have been used to up- or down-regulate expression of endogenous genes in human cells and plants. Here we describe a detailed protocol for practicing the recently described Fast Ligation-based Automatable Solid-phase High-throughput (FLASH) assembly method. FLASH enables automated high-throughput construction of engineered TALE repeats using an automated liquid handling robot or manually using a multi-channel pipet. With the automated version of FLASH, a single researcher can construct up to 96 DNA fragments encoding various length TALE repeat arrays in one day and then clone these to construct sequence-verified TALEN or TALE-TF expression plasmids in one week or less. Plas-mids required to practice FLASH are available by request from the Joung Lab (http://www.jounglab.org/). We also describe here improvements to the Zinc Finger and TALE Targeter (ZiFiT Targeter) webserver (http://ZiFiTBeta.partners.org) that facilitate the design and construction of FLASH TALE repeat arrays in high-throughput. PMID:23821439
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Beyond Atomic Sizes and Hume-Rothery Rules: Understanding and Predicting High-Entropy Alloys
Troparevsky, M. Claudia; Morris, James R.; Daene, Markus; ...
2015-09-03
High-entropy alloys constitute a new class of materials that provide an excellent combination of strength, ductility, thermal stability, and oxidation resistance. Although they have attracted extensive attention due to their potential applications, little is known about why these compounds are stable or how to predict which combination of elements will form a single phase. Here, we present a review of the latest research done on these alloys focusing on the theoretical models devised during the last decade. We discuss semiempirical methods based on the Hume-Rothery rules and stability criteria based on enthalpies of mixing and size mismatch. To provide insightsmore » into the electronic and magnetic properties of high-entropy alloys, we show the results of first-principles calculations of the electronic structure of the disordered solid-solution phase based on both Korringa Kohn Rostoker coherent potential approximation and large supercell models of example face-centered cubic and body-centered cubic systems. Furthermore, we discuss in detail a model based on enthalpy considerations that can predict which elemental combinations are most likely to form a single-phase high-entropy alloy. The enthalpies are evaluated via first-principles high-throughput density functional theory calculations of the energies of formation of binary compounds, and therefore it requires no experimental or empirically derived input. Finally, the model correctly accounts for the specific combinations of metallic elements that are known to form single-phase alloys while rejecting similar combinations that have been tried and shown not to be single phase.« less
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Luu, Van; Jona, Janan; Stanton, Mary K; Peterson, Matthew L; Morrison, Henry G; Nagapudi, Karthik; Tan, Helming
2013-01-30
A 96-well high-throughput cocrystal screening workflow has been developed consisting of solvent-mediated sonic blending synthesis and on-plate solid/solution stability characterization by XRPD. A strategy of cocrystallization screening in selected blend solvents including water mixtures is proposed to not only manipulate solubility of the cocrystal components but also differentiate physical stability of the cocrystal products. Caffeine-oxalic acid and theophylline-oxalic acid cocrystals were prepared and evaluated in relation to saturation levels of the cocrystal components and stability of the cocrystal products in anhydrous and hydrous solvents. AMG 517 was screened with a number of coformers, and solid/solution stability of the resulting cocrystals on the 96-well plate was investigated. A stability trend was observed and confirmed that cocrystals comprised of lower aqueous solubility coformers tended to be more stable in water. Furthermore, cocrystals which could be isolated under hydrous solvent blending condition exhibited superior physical stability to those which could only be obtained under anhydrous condition. This integrated HTS workflow provides an efficient route in an API-sparing approach to screen and identify cocrystal candidates with proper solubility and solid/solution stability properties. Copyright © 2012 Elsevier B.V. All rights reserved.
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NASA Astrophysics Data System (ADS)
Lagus, Todd P.; Edd, Jon F.
2013-03-01
Most cell biology experiments are performed in bulk cell suspensions where cell secretions become diluted and mixed in a contiguous sample. Confinement of single cells to small, picoliter-sized droplets within a continuous phase of oil provides chemical isolation of each cell, creating individual microreactors where rare cell qualities are highlighted and otherwise undetectable signals can be concentrated to measurable levels. Recent work in microfluidics has yielded methods for the encapsulation of cells in aqueous droplets and hydrogels at kilohertz rates, creating the potential for millions of parallel single-cell experiments. However, commercial applications of high-throughput microdroplet generation and downstream sensing and actuation methods are still emerging for cells. Using fluorescence-activated cell sorting (FACS) as a benchmark for commercially available high-throughput screening, this focused review discusses the fluid physics of droplet formation, methods for cell encapsulation in liquids and hydrogels, sensors and actuators and notable biological applications of high-throughput single-cell droplet microfluidics.
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An improved high-throughput lipid extraction method for the analysis of human brain lipids.
Abbott, Sarah K; Jenner, Andrew M; Mitchell, Todd W; Brown, Simon H J; Halliday, Glenda M; Garner, Brett
2013-03-01
We have developed a protocol suitable for high-throughput lipidomic analysis of human brain samples. The traditional Folch extraction (using chloroform and glass-glass homogenization) was compared to a high-throughput method combining methyl-tert-butyl ether (MTBE) extraction with mechanical homogenization utilizing ceramic beads. This high-throughput method significantly reduced sample handling time and increased efficiency compared to glass-glass homogenizing. Furthermore, replacing chloroform with MTBE is safer (less carcinogenic/toxic), with lipids dissolving in the upper phase, allowing for easier pipetting and the potential for automation (i.e., robotics). Both methods were applied to the analysis of human occipital cortex. Lipid species (including ceramides, sphingomyelins, choline glycerophospholipids, ethanolamine glycerophospholipids and phosphatidylserines) were analyzed via electrospray ionization mass spectrometry and sterol species were analyzed using gas chromatography mass spectrometry. No differences in lipid species composition were evident when the lipid extraction protocols were compared, indicating that MTBE extraction with mechanical bead homogenization provides an improved method for the lipidomic profiling of human brain tissue.
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The U.S. EPA’s ToxCast research project was developed to address the need for high-throughput testing of chemicals and a pathway-based approach to hazard screening. Phase I of ToxCast tested over 300 unique compounds (mostly pesticides and antimicrobials). With the addition of Ph...
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Breast cancer diagnosis using spatial light interference microscopy
NASA Astrophysics Data System (ADS)
Majeed, Hassaan; Kandel, Mikhail E.; Han, Kevin; Luo, Zelun; Macias, Virgilia; Tangella, Krishnarao; Balla, Andre; Popescu, Gabriel
2015-11-01
The standard practice in histopathology of breast cancers is to examine a hematoxylin and eosin (H&E) stained tissue biopsy under a microscope to diagnose whether a lesion is benign or malignant. This determination is made based on a manual, qualitative inspection, making it subject to investigator bias and resulting in low throughput. Hence, a quantitative, label-free, and high-throughput diagnosis method is highly desirable. We present here preliminary results showing the potential of quantitative phase imaging for breast cancer screening and help with differential diagnosis. We generated phase maps of unstained breast tissue biopsies using spatial light interference microscopy (SLIM). As a first step toward quantitative diagnosis based on SLIM, we carried out a qualitative evaluation of our label-free images. These images were shown to two pathologists who classified each case as either benign or malignant. This diagnosis was then compared against the diagnosis of the two pathologists on corresponding H&E stained tissue images and the number of agreements were counted. The agreement between SLIM and H&E based diagnosis was 88% for the first pathologist and 87% for the second. Our results demonstrate the potential and promise of SLIM for quantitative, label-free, and high-throughput diagnosis.
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High-throughput NGL electron-beam direct-write lithography system
NASA Astrophysics Data System (ADS)
Parker, N. William; Brodie, Alan D.; McCoy, John H.
2000-07-01
Electron beam lithography systems have historically had low throughput. The only practical solution to this limitation is an approach using many beams writing simultaneously. For single-column multi-beam systems, including projection optics (SCALPELR and PREVAIL) and blanked aperture arrays, throughput and resolution are limited by space-charge effects. Multibeam micro-column (one beam per column) systems are limited by the need for low voltage operation, electrical connection density and fabrication complexities. In this paper, we discuss a new multi-beam concept employing multiple columns each with multiple beams to generate a very large total number of parallel writing beams. This overcomes the limitations of space-charge interactions and low voltage operation. We also discuss a rationale leading to the optimum number of columns and beams per column. Using this approach we show how production throughputs >= 60 wafers per hour can be achieved at CDs
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Handheld Fluorescence Microscopy based Flow Analyzer.
Saxena, Manish; Jayakumar, Nitin; Gorthi, Sai Siva
2016-03-01
Fluorescence microscopy has the intrinsic advantages of favourable contrast characteristics and high degree of specificity. Consequently, it has been a mainstay in modern biological inquiry and clinical diagnostics. Despite its reliable nature, fluorescence based clinical microscopy and diagnostics is a manual, labour intensive and time consuming procedure. The article outlines a cost-effective, high throughput alternative to conventional fluorescence imaging techniques. With system level integration of custom-designed microfluidics and optics, we demonstrate fluorescence microscopy based imaging flow analyzer. Using this system we have imaged more than 2900 FITC labeled fluorescent beads per minute. This demonstrates high-throughput characteristics of our flow analyzer in comparison to conventional fluorescence microscopy. The issue of motion blur at high flow rates limits the achievable throughput in image based flow analyzers. Here we address the issue by computationally deblurring the images and show that this restores the morphological features otherwise affected by motion blur. By further optimizing concentration of the sample solution and flow speeds, along with imaging multiple channels simultaneously, the system is capable of providing throughput of about 480 beads per second.
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Ion channel drug discovery and research: the automated Nano-Patch-Clamp technology.
Brueggemann, A; George, M; Klau, M; Beckler, M; Steindl, J; Behrends, J C; Fertig, N
2004-01-01
Unlike the genomics revolution, which was largely enabled by a single technological advance (high throughput sequencing), rapid advancement in proteomics will require a broader effort to increase the throughput of a number of key tools for functional analysis of different types of proteins. In the case of ion channels -a class of (membrane) proteins of great physiological importance and potential as drug targets- the lack of adequate assay technologies is felt particularly strongly. The available, indirect, high throughput screening methods for ion channels clearly generate insufficient information. The best technology to study ion channel function and screen for compound interaction is the patch clamp technique, but patch clamping suffers from low throughput, which is not acceptable for drug screening. A first step towards a solution is presented here. The nano patch clamp technology, which is based on a planar, microstructured glass chip, enables automatic whole cell patch clamp measurements. The Port-a-Patch is an automated electrophysiology workstation, which uses planar patch clamp chips. This approach enables high quality and high content ion channel and compound evaluation on a one-cell-at-a-time basis. The presented automation of the patch process and its scalability to an array format are the prerequisites for any higher throughput electrophysiology instruments.
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Immobilization methods for the rapid total chemical synthesis of proteins on microtiter plates.
Zitterbart, Robert; Krumrey, Michael; Seitz, Oliver
2017-07-01
The chemical synthesis of proteins typically involves the solid-phase peptide synthesis of unprotected peptide fragments that are stitched together in solution by native chemical ligation (NCL). The process is slow, and throughput is limited because of the need for repeated high performance liquid chromatography purification steps after both solid-phase peptide synthesis and NCL. With an aim to provide faster access to functional proteins and to accelerate the functional analysis of synthetic proteins by parallelization, we developed a method for the high performance liquid chromatography-free synthesis of proteins on the surface of microtiter plates. The method relies on solid-phase synthesis of unprotected peptide fragments, immobilization of the C-terminal fragment and on-surface NCL with an unprotected peptide thioester in crude form. Herein, we describe the development of a suitable immobilization chemistry. We compared (i) formation of nickel(II)-oligohistidine complexes, (ii) Cu-based [2 + 3] alkine-azide cycloaddition and (iii) hydrazone ligation. The comparative study identified the hydrazone ligation as most suitable. The sequence of immobilization via hydrazone ligation, on-surface NCL and radical desulfurization furnished the targeted SH3 domains in near quantitative yield. The synthetic proteins were functional as demonstrated by an on-surface fluorescence-based saturation binding analysis. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.
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Sediment management alternatives for the port of Gulfport, Mississippi.
DOT National Transportation Integrated Search
2010-02-01
The objective of the project is to develop solutions to reduce sediment problems within the Port of Gulfport, MS and to introduce a working : simulation model to reinforce the importance of throughput within the Port of Gulfport. Sediment deposition ...
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Automated solar cell assembly team process research
NASA Astrophysics Data System (ADS)
Nowlan, M. J.; Hogan, S. J.; Darkazalli, G.; Breen, W. F.; Murach, J. M.; Sutherland, S. F.; Patterson, J. S.
1994-06-01
This report describes work done under the Photovoltaic Manufacturing Technology (PVMaT) project, Phase 3A, which addresses problems that are generic to the photovoltaic (PV) industry. Spire's objective during Phase 3A was to use its light soldering technology and experience to design and fabricate solar cell tabbing and interconnecting equipment to develop new, high-yield, high-throughput, fully automated processes for tabbing and interconnecting thin cells. Areas that were addressed include processing rates, process control, yield, throughput, material utilization efficiency, and increased use of automation. Spire teamed with Solec International, a PV module manufacturer, and the University of Massachusetts at Lowell's Center for Productivity Enhancement (CPE), automation specialists, who are lower-tier subcontractors. A number of other PV manufacturers, including Siemens Solar, Mobil Solar, Solar Web, and Texas instruments, agreed to evaluate the processes developed under this program.
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AI-augmented time stretch microscopy
NASA Astrophysics Data System (ADS)
Mahjoubfar, Ata; Chen, Claire L.; Lin, Jiahao; Jalali, Bahram
2017-02-01
Cell reagents used in biomedical analysis often change behavior of the cells that they are attached to, inhibiting their native signaling. On the other hand, label-free cell analysis techniques have long been viewed as challenging either due to insufficient accuracy by limited features, or because of low throughput as a sacrifice of improved precision. We present a recently developed artificial-intelligence augmented microscope, which builds upon high-throughput time stretch quantitative phase imaging (TS-QPI) and deep learning to perform label-free cell classification with record high-accuracy. Our system captures quantitative optical phase and intensity images simultaneously by frequency multiplexing, extracts multiple biophysical features of the individual cells from these images fused, and feeds these features into a supervised machine learning model for classification. The enhanced performance of our system compared to other label-free assays is demonstrated by classification of white blood T-cells versus colon cancer cells and lipid accumulating algal strains for biofuel production, which is as much as five-fold reduction in inaccuracy. This system obtains the accuracy required in practical applications such as personalized drug development, while the cells remain intact and the throughput is not sacrificed. Here, we introduce a data acquisition scheme based on quadrature phase demodulation that enables interruptionless storage of TS-QPI cell images. Our proof of principle demonstration is capable of saving 40 TB of cell images in about four hours, i.e. pictures of every single cell in 10 mL of a sample.
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Computational Particle Dynamic Simulations on Multicore Processors (CPDMu) Final Report Phase I
DOE Office of Scientific and Technical Information (OSTI.GOV)
Schmalz, Mark S
2011-07-24
Statement of Problem - Department of Energy has many legacy codes for simulation of computational particle dynamics and computational fluid dynamics applications that are designed to run on sequential processors and are not easily parallelized. Emerging high-performance computing architectures employ massively parallel multicore architectures (e.g., graphics processing units) to increase throughput. Parallelization of legacy simulation codes is a high priority, to achieve compatibility, efficiency, accuracy, and extensibility. General Statement of Solution - A legacy simulation application designed for implementation on mainly-sequential processors has been represented as a graph G. Mathematical transformations, applied to G, produce a graph representation {und G}more » for a high-performance architecture. Key computational and data movement kernels of the application were analyzed/optimized for parallel execution using the mapping G {yields} {und G}, which can be performed semi-automatically. This approach is widely applicable to many types of high-performance computing systems, such as graphics processing units or clusters comprised of nodes that contain one or more such units. Phase I Accomplishments - Phase I research decomposed/profiled computational particle dynamics simulation code for rocket fuel combustion into low and high computational cost regions (respectively, mainly sequential and mainly parallel kernels), with analysis of space and time complexity. Using the research team's expertise in algorithm-to-architecture mappings, the high-cost kernels were transformed, parallelized, and implemented on Nvidia Fermi GPUs. Measured speedups (GPU with respect to single-core CPU) were approximately 20-32X for realistic model parameters, without final optimization. Error analysis showed no loss of computational accuracy. Commercial Applications and Other Benefits - The proposed research will constitute a breakthrough in solution of problems related to efficient parallel computation of particle and fluid dynamics simulations. These problems occur throughout DOE, military and commercial sectors: the potential payoff is high. We plan to license or sell the solution to contractors for military and domestic applications such as disaster simulation (aerodynamic and hydrodynamic), Government agencies (hydrological and environmental simulations), and medical applications (e.g., in tomographic image reconstruction). Keywords - High-performance Computing, Graphic Processing Unit, Fluid/Particle Simulation. Summary for Members of Congress - Department of Energy has many simulation codes that must compute faster, to be effective. The Phase I research parallelized particle/fluid simulations for rocket combustion, for high-performance computing systems.« less
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High-throughput quantitative analysis by desorption electrospray ionization mass spectrometry.
Manicke, Nicholas E; Kistler, Thomas; Ifa, Demian R; Cooks, R Graham; Ouyang, Zheng
2009-02-01
A newly developed high-throughput desorption electrospray ionization (DESI) source was characterized in terms of its performance in quantitative analysis. A 96-sample array, containing pharmaceuticals in various matrices, was analyzed in a single run with a total analysis time of 3 min. These solution-phase samples were examined from a hydrophobic PTFE ink printed on glass. The quantitative accuracy, precision, and limit of detection (LOD) were characterized. Chemical background-free samples of propranolol (PRN) with PRN-d(7) as internal standard (IS) and carbamazepine (CBZ) with CBZ-d(10) as IS were examined. So were two other sample sets consisting of PRN/PRN-d(7) at varying concentration in a biological milieu of 10% urine or porcine brain total lipid extract, total lipid concentration 250 ng/microL. The background-free samples, examined in a total analysis time of 1.5 s/sample, showed good quantitative accuracy and precision, with a relative error (RE) and relative standard deviation (RSD) generally less than 3% and 5%, respectively. The samples in urine and the lipid extract required a longer analysis time (2.5 s/sample) and showed RSD values of around 10% for the samples in urine and 4% for the lipid extract samples and RE values of less than 3% for both sets. The LOD for PRN and CBZ when analyzed without chemical background was 10 and 30 fmol, respectively. The LOD of PRN increased to 400 fmol analyzed in 10% urine, and 200 fmol when analyzed in the brain lipid extract.
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Baek, Hyoung Gee; Liu, Ruiwu; Lam, Kit S
2009-01-01
The one-bead one-compound (OBOC) combinatorial library method enables the rapid generation and screening of millions of discrete chemical compounds on beads. Most of the OBOC screening methods require the library compounds to remain tethered to the bead during screening process. Methods have also been developed to release library compounds from immobilized beads for in situ solution phase or "lawn" assays. However, this latter approach, while extremely powerful, is severely limited by the lack of suitable solid supports for such assays. Here, we report on the development of a novel hydrogel TentaGel shell-core (HTSC) bead in which hydrogel is grafted onto the polystyrene-based TentaGel (TG) bead as an outer shell (5-80 mum thick) via free radical surface-initiated polymerization. This novel shell-core bilayer resin enables the preparation of encoded OBOC combinatorial small molecule libraries, such that the library compounds reside on the highly hydrophilic outer layer and the coding tags reside in the polystyrene-based TG core. Using fluorescein as a model small molecule compound, we have demonstrated that fluorescein molecules that have been linked covalently to the hydrogel shell via a disulfide bond could readily diffuse out of the hydrogel layer into the bead surrounding after reduction with dithiothreitol. In contrast, under identical condition, the released fluorescein molecules remained bound to unmodified TG bead. We have prepared an encoded OBOC small molecule library on the novel shell-core beads and demonstrated that the beads can be readily decoded.
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Multispot single-molecule FRET: High-throughput analysis of freely diffusing molecules
Panzeri, Francesco
2017-01-01
We describe an 8-spot confocal setup for high-throughput smFRET assays and illustrate its performance with two characteristic experiments. First, measurements on a series of freely diffusing doubly-labeled dsDNA samples allow us to demonstrate that data acquired in multiple spots in parallel can be properly corrected and result in measured sample characteristics consistent with those obtained with a standard single-spot setup. We then take advantage of the higher throughput provided by parallel acquisition to address an outstanding question about the kinetics of the initial steps of bacterial RNA transcription. Our real-time kinetic analysis of promoter escape by bacterial RNA polymerase confirms results obtained by a more indirect route, shedding additional light on the initial steps of transcription. Finally, we discuss the advantages of our multispot setup, while pointing potential limitations of the current single laser excitation design, as well as analysis challenges and their solutions. PMID:28419142
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History, applications, and challenges of immune repertoire research.
Liu, Xiao; Wu, Jinghua
2018-02-27
The diversity of T and B cells in terms of their receptor sequences is huge in the vertebrate's immune system and provides broad protection against the vast diversity of pathogens. Immune repertoire is defined as the sum of T cell receptors and B cell receptors (also named immunoglobulin) that makes the organism's adaptive immune system. Before the emergence of high-throughput sequencing, the studies on immune repertoire were limited by the underdeveloped methodologies, since it was impossible to capture the whole picture by the low-throughput tools. The massive paralleled sequencing technology suits perfectly the researches on immune repertoire. In this article, we review the history of immune repertoire studies, in terms of technologies and research applications. Particularly, we discuss several aspects of challenges in this field and highlight the efforts to develop potential solutions, in the era of high-throughput sequencing of the immune repertoire.
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High-speed zero-copy data transfer for DAQ applications
NASA Astrophysics Data System (ADS)
Pisani, Flavio; Cámpora Pérez, Daniel Hugo; Neufeld, Niko
2015-05-01
The LHCb Data Acquisition (DAQ) will be upgraded in 2020 to a trigger-free readout. In order to achieve this goal we will need to connect around 500 nodes with a total network capacity of 32 Tb/s. To get such an high network capacity we are testing zero-copy technology in order to maximize the theoretical link throughput without adding excessive CPU and memory bandwidth overhead, leaving free resources for data processing resulting in less power, space and money used for the same result. We develop a modular test application which can be used with different transport layers. For the zero-copy implementation we choose the OFED IBVerbs API because it can provide low level access and high throughput. We present throughput and CPU usage measurements of 40 GbE solutions using Remote Direct Memory Access (RDMA), for several network configurations to test the scalability of the system.
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Ye, Haoyu; Ignatova, Svetlana; Peng, Aihua; Chen, Lijuan; Sutherland, Ian
2009-06-26
This paper builds on previous modelling research with short single layer columns to develop rapid methods for optimising high-performance counter-current chromatography at constant stationary phase retention. Benzyl alcohol and p-cresol are used as model compounds to rapidly optimise first flow and then rotational speed operating conditions at a preparative scale with long columns for a given phase system using a Dynamic Extractions Midi-DE centrifuge. The transfer to a high value extract such as the crude ethanol extract of Chinese herbal medicine Millettia pachycarpa Benth. is then demonstrated and validated using the same phase system. The results show that constant stationary phase modelling of flow and speed with long multilayer columns works well as a cheap, quick and effective method of optimising operating conditions for the chosen phase system-hexane-ethyl acetate-methanol-water (1:0.8:1:0.6, v/v). Optimum conditions for resolution were a flow of 20 ml/min and speed of 1200 rpm, but for throughput were 80 ml/min at the same speed. The results show that 80 ml/min gave the best throughputs for tephrosin (518 mg/h), pyranoisoflavone (47.2 mg/h) and dehydrodeguelin (10.4 mg/h), whereas for deguelin (100.5 mg/h), the best flow rate was 40 ml/min.
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Solution processing of chalcogenide materials using thiol-amine "alkahest" solvent systems.
McCarthy, Carrie L; Brutchey, Richard L
2017-05-02
Macroelectronics is a major focus in electronics research and is driven by large area applications such as flat panel displays and thin film solar cells. Innovations for these technologies, such as flexible substrates and mass production, will require efficient and affordable semiconductor processing. Low-temperature solution processing offers mild deposition methods, inexpensive processing equipment, and the possibility of high-throughput processing. In recent years, the discovery that binary "alkahest" mixtures of ethylenediamine and short chain thiols possess the ability to dissolve bulk inorganic materials to yield molecular inks has lead to the wide study of such systems and the straightforward recovery of phase pure crystalline chalcogenide thin films upon solution processing and mild annealing of the inks. In this review, we recount the work that has been done toward elucidating the scope of this method for the solution processing of inorganic materials for use in applications such as photovoltaic devices, electrocatalysts, photodetectors, thermoelectrics, and nanocrystal ligand exchange. We also take stock of the wide range of bulk materials that can be used as soluble precursors, and discuss the work that has been done to reveal the nature of the dissolved species. This method has provided a vast toolbox of over 65 bulk precursors, which can be utilized to develop new routes to functional chalcogenide materials. Future studies in this area should work toward a better understanding of the mechanisms involved in the dissolution and recovery of bulk materials, as well as broadening the scope of soluble precursors and recoverable functional materials for innovative applications.
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Closed-form solutions of performability. [in computer systems
NASA Technical Reports Server (NTRS)
Meyer, J. F.
1982-01-01
It is noted that if computing system performance is degradable then system evaluation must deal simultaneously with aspects of both performance and reliability. One approach is the evaluation of a system's performability which, relative to a specified performance variable Y, generally requires solution of the probability distribution function of Y. The feasibility of closed-form solutions of performability when Y is continuous are examined. In particular, the modeling of a degradable buffer/multiprocessor system is considered whose performance Y is the (normalized) average throughput rate realized during a bounded interval of time. Employing an approximate decomposition of the model, it is shown that a closed-form solution can indeed be obtained.
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Ramakumar, Adarsh; Subramanian, Uma; Prasanna, Pataje G S
2015-11-01
High-throughput individual diagnostic dose assessment is essential for medical management of radiation-exposed subjects after a mass casualty. Cytogenetic assays such as the Dicentric Chromosome Assay (DCA) are recognized as the gold standard by international regulatory authorities. DCA is a multi-step and multi-day bioassay. DCA, as described in the IAEA manual, can be used to assess dose up to 4-6 weeks post-exposure quite accurately but throughput is still a major issue and automation is very essential. The throughput is limited, both in terms of sample preparation as well as analysis of chromosome aberrations. Thus, there is a need to design and develop novel solutions that could utilize extensive laboratory automation for sample preparation, and bioinformatics approaches for chromosome-aberration analysis to overcome throughput issues. We have transitioned the bench-based cytogenetic DCA to a coherent process performing high-throughput automated biodosimetry for individual dose assessment ensuring quality control (QC) and quality assurance (QA) aspects in accordance with international harmonized protocols. A Laboratory Information Management System (LIMS) is designed, implemented and adapted to manage increased sample processing capacity, develop and maintain standard operating procedures (SOP) for robotic instruments, avoid data transcription errors during processing, and automate analysis of chromosome-aberrations using an image analysis platform. Our efforts described in this paper intend to bridge the current technological gaps and enhance the potential application of DCA for a dose-based stratification of subjects following a mass casualty. This paper describes one such potential integrated automated laboratory system and functional evolution of the classical DCA towards increasing critically needed throughput. Published by Elsevier B.V.
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Evaluation of Argonne 9-cm and 10-cm Annular Centrifugal Contactors for SHINE Solution Processing
DOE Office of Scientific and Technical Information (OSTI.GOV)
Wardle, Kent E.; Pereira, Candido; Vandegrift, George
2015-02-01
Work is in progress to evaluate the SHINE Medical Technologies process for producing Mo-99 for medical use from the fission of dissolved low-enriched uranium (LEU). This report addresses the use of Argonne annular centrifugal contactors for periodic treatment of the process solution. In a letter report from FY 2013, Pereira and Vandegrift compared the throughput and physical footprint for the two contactor options available from CINC Industries: the V-02 and V-05, which have rotor diameters of 5 cm and 12.7 cm, respectively. They suggested that an intermediately sized “Goldilocks” contactor might provide a better balance between throughput and footprint tomore » meet the processing needs for the uranium extraction (UREX) processing of the SHINE solution to remove undesired fission products. Included with the submission of this letter report are the assembly drawings for two Argonne-design contactors that are in this intermediate range—9-cm and 10-cm rotors, respectively. The 9-cm contactor (drawing number CE-D6973A, stamped February 15, 1978) was designed as a single-stage unit and built and tested in the late 1970s along with other size units, both smaller and larger. In subsequent years, a significant effort to developed annular centrifugal contactors was undertaken to support work at Hanford implementing the transuranic extraction (TRUEX) process. These contactors had a 10-cm rotor diameter and were fully designed as multistage units with four stages per assembly (drawing number CMT-E1104, stamped March 14, 1990). From a technology readiness perspective, these 10-cm units are much farther ahead in the design progression and, therefore, would require significantly less re-working to make them ready for UREX deployment. Additionally, the overall maximum throughput of ~12 L/min is similar to that of the 9-cm unit (10 L/min), and the former could be efficiently operated over much of the same range of throughput. As a result, only the 10-cm units are considered here, though drawings are provided for the 9-cm unit for reference.« less
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He, Ji; Dai, Xinbin; Zhao, Xuechun
2007-02-09
BLAST searches are widely used for sequence alignment. The search results are commonly adopted for various functional and comparative genomics tasks such as annotating unknown sequences, investigating gene models and comparing two sequence sets. Advances in sequencing technologies pose challenges for high-throughput analysis of large-scale sequence data. A number of programs and hardware solutions exist for efficient BLAST searching, but there is a lack of generic software solutions for mining and personalized management of the results. Systematically reviewing the results and identifying information of interest remains tedious and time-consuming. Personal BLAST Navigator (PLAN) is a versatile web platform that helps users to carry out various personalized pre- and post-BLAST tasks, including: (1) query and target sequence database management, (2) automated high-throughput BLAST searching, (3) indexing and searching of results, (4) filtering results online, (5) managing results of personal interest in favorite categories, (6) automated sequence annotation (such as NCBI NR and ontology-based annotation). PLAN integrates, by default, the Decypher hardware-based BLAST solution provided by Active Motif Inc. with a greatly improved efficiency over conventional BLAST software. BLAST results are visualized by spreadsheets and graphs and are full-text searchable. BLAST results and sequence annotations can be exported, in part or in full, in various formats including Microsoft Excel and FASTA. Sequences and BLAST results are organized in projects, the data publication levels of which are controlled by the registered project owners. In addition, all analytical functions are provided to public users without registration. PLAN has proved a valuable addition to the community for automated high-throughput BLAST searches, and, more importantly, for knowledge discovery, management and sharing based on sequence alignment results. The PLAN web interface is platform-independent, easily configurable and capable of comprehensive expansion, and user-intuitive. PLAN is freely available to academic users at http://bioinfo.noble.org/plan/. The source code for local deployment is provided under free license. Full support on system utilization, installation, configuration and customization are provided to academic users.
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He, Ji; Dai, Xinbin; Zhao, Xuechun
2007-01-01
Background BLAST searches are widely used for sequence alignment. The search results are commonly adopted for various functional and comparative genomics tasks such as annotating unknown sequences, investigating gene models and comparing two sequence sets. Advances in sequencing technologies pose challenges for high-throughput analysis of large-scale sequence data. A number of programs and hardware solutions exist for efficient BLAST searching, but there is a lack of generic software solutions for mining and personalized management of the results. Systematically reviewing the results and identifying information of interest remains tedious and time-consuming. Results Personal BLAST Navigator (PLAN) is a versatile web platform that helps users to carry out various personalized pre- and post-BLAST tasks, including: (1) query and target sequence database management, (2) automated high-throughput BLAST searching, (3) indexing and searching of results, (4) filtering results online, (5) managing results of personal interest in favorite categories, (6) automated sequence annotation (such as NCBI NR and ontology-based annotation). PLAN integrates, by default, the Decypher hardware-based BLAST solution provided by Active Motif Inc. with a greatly improved efficiency over conventional BLAST software. BLAST results are visualized by spreadsheets and graphs and are full-text searchable. BLAST results and sequence annotations can be exported, in part or in full, in various formats including Microsoft Excel and FASTA. Sequences and BLAST results are organized in projects, the data publication levels of which are controlled by the registered project owners. In addition, all analytical functions are provided to public users without registration. Conclusion PLAN has proved a valuable addition to the community for automated high-throughput BLAST searches, and, more importantly, for knowledge discovery, management and sharing based on sequence alignment results. The PLAN web interface is platform-independent, easily configurable and capable of comprehensive expansion, and user-intuitive. PLAN is freely available to academic users at . The source code for local deployment is provided under free license. Full support on system utilization, installation, configuration and customization are provided to academic users. PMID:17291345
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Performance Comparison of SDN Solutions for Switching Dedicated Long-Haul Connections
DOE Office of Scientific and Technical Information (OSTI.GOV)
Rao, Nageswara S
2016-01-01
We consider scenarios with two sites connected over a dedicated, long-haul connection that must quickly fail-over in response to degradations in host-to-host application performance. We present two methods for path fail-over using OpenFlowenabled switches: (a) a light-weight method that utilizes host scripts to monitor the application performance and dpctl API for switching, and (b) a generic method that uses two OpenDaylight (ODL) controllers and REST interfaces. The restoration dynamics of the application contain significant statistical variations due to the controllers, north interfaces and switches; in addition, the variety of vendor implementations further complicates the choice between different solutions. We presentmore » the impulse-response method to estimate the regressions of performance parameters, which enables a rigorous and objective comparison of different solutions. We describe testing results of the two methods, using TCP throughput and connection rtt as main parameters, over a testbed consisting of HP and Cisco switches connected over longhaul connections emulated in hardware by ANUE devices. The combination of analytical and experimental results demonstrates that dpctl method responds seconds faster than ODL method on average, while both methods restore TCP throughput.« less
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Breeding to adapt agriculture to climate change: affordable phenotyping solutions.
Araus, José L; Kefauver, Shawn C
2018-05-28
Breeding is one of the central pillars of adaptation of crops to climate change. However, phenotyping is a key bottleneck that is limiting breeding efficiency. The awareness of phenotyping as a breeding limitation is not only sustained by the lack of adequate approaches, but also by the perception that phenotyping is an expensive activity. Phenotyping is not just dependent on the choice of appropriate traits and tools (e.g. sensors) but relies on how these tools are deployed on their carrying platforms, the speed and volume of data extraction and analysis (throughput), the handling of spatial variability and characterization of environmental conditions, and finally how all the information is integrated and processed. Affordable high throughput phenotyping aims to achieve reasonably priced solutions for all the components comprising the phenotyping pipeline. This mini-review will cover current and imminent solutions for all these components, from the increasing use of conventional digital RGB cameras, within the category of sensors, to open-access cloud-structured data processing and the use of smartphones. Emphasis will be placed on field phenotyping, which is really the main application for day-to-day phenotyping. Copyright © 2018 Elsevier Ltd. All rights reserved.
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SDN solutions for switching dedicated long-haul connections: Measurements and comparative analysis
Rao, Nageswara S. V.
2016-01-01
We consider a scenario of two sites connected over a dedicated, long-haul connection that must quickly fail-over in response to degradations in host-to-host application performance. The traditional layer-2/3 hot stand-by fail-over solutions do not adequately address the variety of application degradations, and more recent single controller Software Defined Networks (SDN) solutions are not effective for long-haul connections. We present two methods for such a path fail-over using OpenFlow enabled switches: (a) a light-weight method that utilizes host scripts to monitor application performance and dpctl API for switching, and (b) a generic method that uses two OpenDaylight (ODL) controllers and RESTmore » interfaces. For both methods, the restoration dynamics of applications contain significant statistical variations due to the complexities of controllers, north bound interfaces and switches; they, together with the wide variety of vendor implementations, complicate the choice among such solutions. We develop the impulse-response method based on regression functions of performance parameters to provide a rigorous and objective comparison of different solutions. We describe testing results of the two proposed methods, using TCP throughput and connection rtt as main parameters, over a testbed consisting of HP and Cisco switches connected over longhaul connections emulated in hardware by ANUE devices. Lastly, the combination of analytical and experimental results demonstrate that the dpctl method responds seconds faster than the ODL method on average, even though both methods eventually restore original TCP throughput.« less
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NASA Technical Reports Server (NTRS)
Lee, Paul U.; Smith, Nancy M.; Bienert, Nancy; Brasil, Connie; Buckley, Nathan; Chevalley, Eric; Homola, Jeffrey; Omar, Faisal; Parke, Bonny; Yoo, Hyo-Sang
2016-01-01
LaGuardia (LGA) departure delay was identified by the stakeholders and subject matter experts as a significant bottleneck in the New York metropolitan area. Departure delay at LGA is primarily due to dependency between LGA's arrival and departure runways: LGA departures cannot begin takeoff until arrivals have cleared the runway intersection. If one-in one-out operations are not maintained and a significant arrival-to-departure imbalance occurs, the departure backup can persist through the rest of the day. At NASA Ames Research Center, a solution called "Departure-sensitive Arrival Spacing" (DSAS) was developed to maximize the departure throughput without creating significant delays in the arrival traffic. The concept leverages a Terminal Sequencing and Spacing (TSS) operations that create and manage the arrival schedule to the runway threshold and added an interface enhancement to the traffic manager's timeline to provide the ability to manually adjust inter-arrival spacing to build precise gaps for multiple departures between arrivals. A more complete solution would include a TSS algorithm enhancement that could automatically build these multi-departure gaps. With this set of capabilities, inter-arrival spacing could be controlled for optimal departure throughput. The concept was prototyped in a human-in-the- loop (HITL) simulation environment so that operational requirements such as coordination procedures, timing and magnitude of TSS schedule adjustments, and display features for Tower, TRACON and Traffic Management Unit could be determined. A HITL simulation was conducted in August 2014 to evaluate the concept in terms of feasibility, controller workload impact, and potential benefits. Three conditions were tested, namely a Baseline condition without scheduling, TSS condition that schedules the arrivals to the runway threshold, and TSS+DSAS condition that adjusts the arrival schedule to maximize the departure throughput. The results showed that during high arrival demand period, departure throughput could be incrementally increased under TSS and TSS+DSAS conditions without compromising the arrival throughput. The concept, operational procedures, and summary results were originally published in ATM20151 but detailed results were omitted. This paper expands on the earlier paper to provide the detailed results on throughput, conformance, safety, flight time/distance, etc. that provide extra insights into the feasibility and the potential benefits on the concept.
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Lee, Hangyeore; Mun, Dong-Gi; Bae, Jingi; Kim, Hokeun; Oh, Se Yeon; Park, Young Soo; Lee, Jae-Hyuk; Lee, Sang-Won
2015-08-21
We report a new and simple design of a fully automated dual-online ultra-high pressure liquid chromatography system. The system employs only two nano-volume switching valves (a two-position four port valve and a two-position ten port valve) that direct solvent flows from two binary nano-pumps for parallel operation of two analytical columns and two solid phase extraction (SPE) columns. Despite the simple design, the sDO-UHPLC offers many advantageous features that include high duty cycle, back flushing sample injection for fast and narrow zone sample injection, online desalting, high separation resolution and high intra/inter-column reproducibility. This system was applied to analyze proteome samples not only in high throughput deep proteome profiling experiments but also in high throughput MRM experiments.
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NASA Astrophysics Data System (ADS)
Ruane, Garreth; Mawet, Dimitri; Mennesson, Bertrand; Jewell, Jeffrey; Shaklan, Stuart
2018-01-01
The Habitable Exoplanet Imaging Mission concept requires an optical coronagraph that provides deep starlight suppression over a broad spectral bandwidth, high throughput for point sources at small angular separation, and insensitivity to temporally varying, low-order aberrations. Vortex coronagraphs are a promising solution that performs optimally on off-axis, monolithic telescopes and may also be designed for segmented telescopes with minor losses in performance. We describe the key advantages of vortex coronagraphs on off-axis telescopes such as (1) unwanted diffraction due to aberrations is passively rejected in several low-order Zernike modes relaxing the wavefront stability requirements for imaging Earth-like planets from <10 to >100 pm rms, (2) stars with angular diameters >0.1 λ / D may be sufficiently suppressed, (3) the absolute planet throughput is >10 % , even for unfavorable telescope architectures, and (4) broadband solutions (Δλ / λ > 0.1) are readily available for both monolithic and segmented apertures. The latter make use of grayscale apodizers in an upstream pupil plane to provide suppression of diffracted light from amplitude discontinuities in the telescope pupil without inducing additional stroke on the deformable mirrors. We set wavefront stability requirements on the telescope, based on a stellar irradiance threshold set at an angular separation of 3 ± 0.5λ / D from the star, and discuss how some requirements may be relaxed by trading robustness to aberrations for planet throughput.
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Ethoscopes: An open platform for high-throughput ethomics.
Geissmann, Quentin; Garcia Rodriguez, Luis; Beckwith, Esteban J; French, Alice S; Jamasb, Arian R; Gilestro, Giorgio F
2017-10-01
Here, we present the use of ethoscopes, which are machines for high-throughput analysis of behavior in Drosophila and other animals. Ethoscopes provide a software and hardware solution that is reproducible and easily scalable. They perform, in real-time, tracking and profiling of behavior by using a supervised machine learning algorithm, are able to deliver behaviorally triggered stimuli to flies in a feedback-loop mode, and are highly customizable and open source. Ethoscopes can be built easily by using 3D printing technology and rely on Raspberry Pi microcomputers and Arduino boards to provide affordable and flexible hardware. All software and construction specifications are available at http://lab.gilest.ro/ethoscope.
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Thousands of untested chemicals in the environment require efficient characterization of carcinogenic potential in humans. A proposed solution is rapid testing of chemicals using in vitro high-throughput screening (HTS) assays for targets in pathways linked to disease processes ...
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Microfabricated Patch Clamp Electrodes for Improved Ion Channel Protein Measurements
NASA Astrophysics Data System (ADS)
Klemic, James; Klemic, Kathryn; Reed, Mark; Sigworth, Frederick
2002-03-01
Ion channels are trans-membrane proteins that underlie many cell functions including hormone and neurotransmitter release, muscle contraction and cell signaling cascades. Ion channel proteins are commonly characterized via the patch clamp method in which an extruded glass tube containing ionic solution, manipulated by an expert technician, is brought into contact with a living cell to record ionic current through the cell membrane. Microfabricated planar patch electrodes, micromolded in the silicone elastomer poly-dimethylsiloxane (PDMS) from microlithographically patterned structures, have been developed that improve on this method. Microfabrication techniques allow arrays of patch electrodes to be fabricated, increasing the throughput of the measurement technique. Planar patch electrodes readily allow the automation of cell sealing, further increasing throughput. Microfabricated electrode arrays may be readily integrated with microfluidic structures to allow fast, in situ solution exchange. Miniaturization of the electrode geometry should increase both the signal to noise and the bandwidth of the measurement. Microfabricated patch electrode arrays have been fabricated and measurements have been taken.
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20180312 - US EPA-Unilever Collaborative Partnership: Accomplishments and Next Steps (SOT)
Reiterating the goals of the partnership, this summarizes the accomplishments and progress made so far in the collaboration, and announces a two phase extension focused on further development of high-throughput transcriptomic platform
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PIZZA: a phase-induced zonal Zernike apodization designed for stellar coronagraphy
NASA Astrophysics Data System (ADS)
Martinache, Frantz
2004-08-01
I explore here the possibilities offered by the general formalism of coronagraphy for the very special case of phase contrast. This technique, invented by Zernike, is commonly used in microscopy, to see phase objects such as micro-organisms, and in strioscopy, to control the quality of optics polishing. It may find application in telescope pupil apodization with significant advantages over classical pupil apodization techniques, including high throughput and no off-axis resolution loss, which is essential for exoplanet imaging.
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Multiple-mouse MRI with multiple arrays of receive coils.
Ramirez, Marc S; Esparza-Coss, Emilio; Bankson, James A
2010-03-01
Compared to traditional single-animal imaging methods, multiple-mouse MRI has been shown to dramatically improve imaging throughput and reduce the potentially prohibitive cost for instrument access. To date, up to a single radiofrequency coil has been dedicated to each animal being simultaneously scanned, thus limiting the sensitivity, flexibility, and ultimate throughput. The purpose of this study was to investigate the feasibility of multiple-mouse MRI with a phased-array coil dedicated to each animal. A dual-mouse imaging system, consisting of a pair of two-element phased-array coils, was developed and used to achieve acceleration factors greater than the number of animals scanned at once. By simultaneously scanning two mice with a retrospectively gated cardiac cine MRI sequence, a 3-fold acceleration was achieved with signal-to-noise ratio in the heart that is equivalent to that achieved with an unaccelerated scan using a commercial mouse birdcage coil. (c) 2010 Wiley-Liss, Inc.
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Polarization masks: concept and initial assessment
NASA Astrophysics Data System (ADS)
Lam, Michael; Neureuther, Andrew R.
2002-07-01
Polarization from photomasks can be used as a new lever to improve lithographic performance in both binary and phase-shifting masks (PSMs). While PSMs manipulate the phase of light to control the temporal addition of electric field vectors, polarization masks manipulate the vector direction of electric field vectors to control the spatial addition of electric field components. This paper explores the theoretical possibilities of polarization masks, showing that it is possible to use bar structures within openings on the mask itself to polarize incident radiation. Rigorous electromagnetic scattering simulations using TEMPEST and imaging with SPLAT are used to give an initial assessment on the functionality of polarization masks, discussing the polarization quality and throughputs achieved with the masks. Openings between 1/8 and 1/3 of a wavelength provide both a low polarization ratio and good transmission. A final overall throughput of 33% - 40% is achievable, corresponding to a dose hit of 2.5x - 3x.
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Phase imaging of mechanical properties of live cells (Conference Presentation)
NASA Astrophysics Data System (ADS)
Wax, Adam
2017-02-01
The mechanisms by which cells respond to mechanical stimuli are essential for cell function yet not well understood. Many rheological tools have been developed to characterize cellular viscoelastic properties but these typically require direct mechanical contact, limiting their throughput. We have developed a new approach for characterizing the organization of subcellular structures using a label free, noncontact, single-shot phase imaging method that correlates to measured cellular mechanical stiffness. The new analysis approach measures refractive index variance and relates it to disorder strength. These measurements are compared to cellular stiffness, measured using the same imaging tool to visualize nanoscale responses to flow shear stimulus. The utility of the technique is shown by comparing shear stiffness and phase disorder strength across five cellular populations with varying mechanical properties. An inverse relationship between disorder strength and shear stiffness is shown, suggesting that cell mechanical properties can be assessed in a format amenable to high throughput studies using this novel, non-contact technique. Further studies will be presented which include examination of mechanical stiffness in early carcinogenic events and investigation of the role of specific cellular structural proteins in mechanotransduction.
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High-throughput continuous hydrothermal synthesis of an entire nanoceramic phase diagram.
Weng, Xiaole; Cockcroft, Jeremy K; Hyett, Geoffrey; Vickers, Martin; Boldrin, Paul; Tang, Chiu C; Thompson, Stephen P; Parker, Julia E; Knowles, Jonathan C; Rehman, Ihtesham; Parkin, Ivan; Evans, Julian R G; Darr, Jawwad A
2009-01-01
A novel High-Throughput Continuous Hydrothermal (HiTCH) flow synthesis reactor was used to make directly and rapidly a 66-sample nanoparticle library (entire phase diagram) of nanocrystalline Ce(x)Zr(y)Y(z)O(2-delta) in less than 12 h. High resolution PXRD data were obtained for the entire heat-treated library (at 1000 degrees C/1 h) in less than a day using the new robotic beamline I11, located at Diamond Light Source (DLS). This allowed Rietveld-quality powder X-ray diffraction (PXRD) data collection of the entire 66-sample library in <1 day. Consequently, the authors rapidly mapped out phase behavior and sintering behaviors for the entire library. Out of the entire 66-sample heat-treated library, the PXRD data suggests that 43 possess the fluorite structure, of which 30 (out of 36) are ternary compositions. The speed, quantity and quality of data obtained by our new approach, offers an exciting new development which will allow structure-property relationships to be accessed for nanoceramics in much shorter time periods.
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Shih, Tsung-Ting; Hsieh, Cheng-Chuan; Luo, Yu-Ting; Su, Yi-An; Chen, Ping-Hung; Chuang, Yu-Chen; Sun, Yuh-Chang
2016-04-15
Herein, a hyphenated system combining a high-throughput solid-phase extraction (htSPE) microchip with inductively coupled plasma-mass spectrometry (ICP-MS) for rapid determination of trace heavy metals was developed. Rather than performing multiple analyses in parallel for the enhancement of analytical throughput, we improved the processing speed for individual samples by increasing the operation flow rate during SPE procedures. To this end, an innovative device combining a micromixer and a multi-channeled extraction unit was designed. Furthermore, a programmable valve manifold was used to interface the developed microchip and ICP-MS instrumentation in order to fully automate the system, leading to a dramatic reduction in operation time and human error. Under the optimized operation conditions for the established system, detection limits of 1.64-42.54 ng L(-1) for the analyte ions were achieved. Validation procedures demonstrated that the developed method could be satisfactorily applied to the determination of trace heavy metals in natural water. Each analysis could be readily accomplished within just 186 s using the established system. This represents, to the best of our knowledge, an unprecedented speed for the analysis of trace heavy metal ions. Copyright © 2016 Elsevier B.V. All rights reserved.
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High throughput electrospinning of high-quality nanofibers via an aluminum disk spinneret
NASA Astrophysics Data System (ADS)
Zheng, Guokuo
In this work, a simple and efficient needleless high throughput electrospinning process using an aluminum disk spinneret with 24 holes is described. Electrospun mats produced by this setup consisted of fine fibers (nano-sized) of the highest quality while the productivity (yield) was many times that obtained from conventional single-needle electrospinning. The goal was to produce scaled-up amounts of the same or better quality nanofibers under variable concentration, voltage, and the working distance than those produced with the single needle lab setting. The fiber mats produced were either polymer or ceramic (such as molybdenum trioxide nanofibers). Through experimentation the optimum process conditions were defined to be: 24 kilovolt, a distance to collector of 15cm. More diluted solutions resulted in smaller diameter fibers. Comparing the morphologies of the nanofibers of MoO3 produced by both the traditional and the high throughput set up it was found that they were very similar. Moreover, the nanofibers production rate is nearly 10 times than that of traditional needle electrospinning. Thus, the high throughput process has the potential to become an industrial nanomanufacturing process and the materials processed by it may be used as filtration devices, in tissue engineering, and as sensors.
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Novel Acoustic Loading of a Mass Spectrometer: Toward Next-Generation High-Throughput MS Screening.
Sinclair, Ian; Stearns, Rick; Pringle, Steven; Wingfield, Jonathan; Datwani, Sammy; Hall, Eric; Ghislain, Luke; Majlof, Lars; Bachman, Martin
2016-02-01
High-throughput, direct measurement of substrate-to-product conversion by label-free detection, without the need for engineered substrates or secondary assays, could be considered the "holy grail" of drug discovery screening. Mass spectrometry (MS) has the potential to be part of this ultimate screening solution, but is constrained by the limitations of existing MS sample introduction modes that cannot meet the throughput requirements of high-throughput screening (HTS). Here we report data from a prototype system (Echo-MS) that uses acoustic droplet ejection (ADE) to transfer femtoliter-scale droplets in a rapid, precise, and accurate fashion directly into the MS. The acoustic source can load samples into the MS from a microtiter plate at a rate of up to three samples per second. The resulting MS signal displays a very sharp attack profile and ions are detected within 50 ms of activation of the acoustic transducer. Additionally, we show that the system is capable of generating multiply charged ion species from simple peptides and large proteins. The combination of high speed and low sample volume has significant potential within not only drug discovery, but also other areas of the industry. © 2015 Society for Laboratory Automation and Screening.
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George, Iniga S; Fennell, Anne Y; Haynes, Paul A
2015-09-01
Protein sample preparation optimisation is critical for establishing reproducible high throughput proteomic analysis. In this study, two different fractionation sample preparation techniques (in-gel digestion and in-solution digestion) for shotgun proteomics were used to quantitatively compare proteins identified in Vitis riparia leaf samples. The total number of proteins and peptides identified were compared between filter aided sample preparation (FASP) coupled with gas phase fractionation (GPF) and SDS-PAGE methods. There was a 24% increase in the total number of reproducibly identified proteins when FASP-GPF was used. FASP-GPF is more reproducible, less expensive and a better method than SDS-PAGE for shotgun proteomics of grapevine samples as it significantly increases protein identification across biological replicates. Total peptide and protein information from the two fractionation techniques is available in PRIDE with the identifier PXD001399 (http://proteomecentral.proteomexchange.org/dataset/PXD001399). © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
McCann, Billy W.; Silva, Nuwan De; Windus, Theresa L.
Computer-aided molecular design and high-throughput screening of viable host architectures can significantly reduce the efforts in the design of novel ligands for efficient extraction of rare earth elements. This paper presents a computational approach to the deliberate design of bis-phosphine oxide host architectures that are structurally organized for complexation of trivalent lanthanides. Molecule building software, HostDesigner, was interfaced with molecular mechanics software, PCModel, providing a tool for generating and screening millions of potential R 2(O)P-link-P(O)R 2 ligand geometries. The molecular mechanics ranking of ligand structures is consistent with both the solution-phase free energies of complexation obtained with density functional theorymore » and the performance of known bis-phosphine oxide extractants. For the case where link is -CH 2-, evaluation of the ligand geometry provides the first characterization of a steric origin for the ‘anomalous aryl strengthening’ effect. The design approach has identified a number of novel bis-phosphine oxide ligands that are better organized for lanthanide complexation than previously studied examples.« less
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Optical critical dimension metrology for directed self-assembly assisted contact hole shrink
NASA Astrophysics Data System (ADS)
Dixit, Dhairya; Green, Avery; Hosler, Erik R.; Kamineni, Vimal; Preil, Moshe E.; Keller, Nick; Race, Joseph; Chun, Jun Sung; O'Sullivan, Michael; Khare, Prasanna; Montgomery, Warren; Diebold, Alain C.
2016-01-01
Directed self-assembly (DSA) is a potential patterning solution for future generations of integrated circuits. Its main advantages are high pattern resolution (˜10 nm), high throughput, no requirement of high-resolution mask, and compatibility with standard fab-equipment and processes. The application of Mueller matrix (MM) spectroscopic ellipsometry-based scatterometry to optically characterize DSA patterned contact hole structures fabricated with phase-separated polystyrene-b-polymethylmethacrylate (PS-b-PMMA) is described. A regression-based approach is used to calculate the guide critical dimension (CD), DSA CD, height of the PS column, thicknesses of underlying layers, and contact edge roughness of the post PMMA etch DSA contact hole sample. Scanning electron microscopy and imaging analysis is conducted as a comparative metric for scatterometry. In addition, optical model-based simulations are used to investigate MM elements' sensitivity to various DSA-based contact hole structures, predict sensitivity to dimensional changes, and its limits to characterize DSA-induced defects, such as hole placement inaccuracy, missing vias, and profile inaccuracy of the PMMA cylinder.
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Synthesis and Characterization of Phase-pure Copper Zinc Tin Sulfide (Cu2ZnSnS4) Nanoparticles
NASA Astrophysics Data System (ADS)
Monahan, Bradley Michael
Semiconductor nanoparticles have been an important area of research in many different disciplines. A substantial amount of this work has been put toward advancing the field of photovoltaics. However, current p-type photovoltaic materials can not sustain the large scale production needed for future energy demands due to their low elemental abundance. Therefore, Earth abundant semiconductor materials have become of great interest to the photovoltaic community especially, the material copper zinc tin sulfide (CZTS), also known by its mineral name kesterite. CZTS exhibits desirable properties for photovoltaics, such as elemental abundance, high absorption coefficient (~104 cm-1 ), high carrier concentration, and optimum direct band gap (1.5 eV). To date, solution based approaches for making CZTS have yielded the most promising conversion efficiencies in solar cells. To that end, the motivation of nanoparticle based inks that can be used in high throughput production are an attractive route for large scale deployment. This has driven the need to make high quality CZTS nanoparticles that possess the properties of the pure kesterite phase with high monodispersity that can be deposited into dense thin films. The inherent challenge of making a quaternary compound of a single phase has made this a difficult task; however, some of those fundamental problems are addressed in this thesis. This had resulted in the synthesis of phase-pure k-CZTS confirmed by powder X-ray diffraction, Raman spectroscopy, UV-visible absorption spectroscopy and energy dispersive x-ray spectroscopy. Furthermore, ultra-fast laser spectroscopy was done on CZTS thin films made from phase-pure kesterite nanoparticles synthesized in this work. This thesis provides new data that directly probes the lifetime of photogenerated free carriers in kesterite CZTS (k-CZTS) thin films.
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Zhang, Wei; Huang, Guangming
2015-11-15
Approaches for analyte screening have been used to aid in the fine-tuning of chemical reactions. Herein, we present a simple and straightforward analyte screening method for chemical reactions via reactive low-temperature plasma ionization mass spectrometry (reactive LTP-MS). Solution-phase reagents deposited on sample substrates were desorbed into the vapor phase by action of the LTP and by thermal desorption. Treated with LTP, both reagents reacted through a vapor phase ion/molecule reaction to generate the product. Finally, protonated reagents and products were identified by LTP-MS. Reaction products from imine formation reaction, Eschweiler-Clarke methylation and the Eberlin reaction were detected via reactive LTP-MS. Products from the imine formation reaction with reagents substituted with different functional groups (26 out of 28 trials) were successfully screened in a time of 30 s each. Besides, two short-lived reactive intermediates of Eschweiler-Clarke methylation were also detected. LTP in this study serves both as an ambient ionization source for analyte identification (including reagents, intermediates and products) and as a means to produce reagent ions to assist gas-phase ion/molecule reactions. The present reactive LTP-MS method enables fast screening for several analytes from several chemical reactions, which possesses good reagent compatibility and the potential to perform high-throughput analyte screening. In addition, with the detection of various reactive intermediates (intermediates I and II of Eschweiler-Clarke methylation), the present method would also contribute to revealing and elucidating reaction mechanisms. Copyright © 2015 John Wiley & Sons, Ltd.
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Wetmore, Barbara A.; Wambaugh, John F.; Allen, Brittany; Ferguson, Stephen S.; Sochaski, Mark A.; Setzer, R. Woodrow; Houck, Keith A.; Strope, Cory L.; Cantwell, Katherine; Judson, Richard S.; LeCluyse, Edward; Clewell, Harvey J.; Thomas, Russell S.; Andersen, Melvin E.
2015-01-01
We previously integrated dosimetry and exposure with high-throughput screening (HTS) to enhance the utility of ToxCast HTS data by translating in vitro bioactivity concentrations to oral equivalent doses (OEDs) required to achieve these levels internally. These OEDs were compared against regulatory exposure estimates, providing an activity-to-exposure ratio (AER) useful for a risk-based ranking strategy. As ToxCast efforts expand (ie, Phase II) beyond food-use pesticides toward a wider chemical domain that lacks exposure and toxicity information, prediction tools become increasingly important. In this study, in vitro hepatic clearance and plasma protein binding were measured to estimate OEDs for a subset of Phase II chemicals. OEDs were compared against high-throughput (HT) exposure predictions generated using probabilistic modeling and Bayesian approaches generated by the U.S. Environmental Protection Agency (EPA) ExpoCast program. This approach incorporated chemical-specific use and national production volume data with biomonitoring data to inform the exposure predictions. This HT exposure modeling approach provided predictions for all Phase II chemicals assessed in this study whereas estimates from regulatory sources were available for only 7% of chemicals. Of the 163 chemicals assessed in this study, 3 or 13 chemicals possessed AERs < 1 or < 100, respectively. Diverse bioactivities across a range of assays and concentrations were also noted across the wider chemical space surveyed. The availability of HT exposure estimation and bioactivity screening tools provides an opportunity to incorporate a risk-based strategy for use in testing prioritization. PMID:26251325
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Opportunities for bead-based multiplex assays in veterinary diagnostic laboratories
USDA-ARS?s Scientific Manuscript database
Bead based multiplex assays (BBMA) also referred to as Luminex, MultiAnalyte Profiling or cytometric bead array (CBA) assays, are applicable for high throughput, simultaneous detection of multiple analytes in solution (from several, up to 50-500 analytes within a single, small sample volume). Curren...
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Van Duren, Jeroen K; Koch, Carl; Luo, Alan
The primary limitation of today’s lightweight structural alloys is that specific yield strengths (SYS) higher than 200MPa x cc/g (typical value for titanium alloys) are extremely difficult to achieve. This holds true especially at a cost lower than 5dollars/kg (typical value for magnesium alloys). Recently, high-entropy alloys (HEA) have shown promising SYS, yet the large composition space of HEA makes screening compositions complex and time-consuming. Over the course of this 2-year project we started from 150 billion compositions and reduced the number of potential low-density (<5g/cc), low-cost (<5dollars/kg) high-entropy alloy (LDHEA) candidates that are single-phase, disordered, solid-solution (SPSS) to amore » few thousand compositions. This was accomplished by means of machine learning to guide design for SPSS LDHEA based on a combination of recursive partitioning, an extensive, experimental HEA database compiled from 24 literature sources, and 91 calculated parameters serving as phenomenological selection rules. Machine learning shows an accuracy of 82% in identifying which compositions of a separate, smaller, experimental HEA database are SPSS HEA. Calculation of Phase Diagrams (CALPHAD) shows an accuracy of 71-77% for the alloys supported by the CALPHAD database, where 30% of the compiled HEA database is not supported by CALPHAD. In addition to machine learning, and CALPHAD, a third tool was developed to aid design of SPSS LDHEA. Phase diagrams were calculated by constructing the Gibbs-free energy convex hull based on easily accessible enthalpy and entropy terms. Surprisingly, accuracy was 78%. Pursuing these LDHEA candidates by high-throughput experimental methods resulted in SPSS LDHEA composed of transition metals (e.g. Cr, Mn, Fe, Ni, Cu) alloyed with Al, yet the high concentration of Al, necessary to bring the mass density below 5.0g/cc, makes these materials hard and brittle, body-centered-cubic (BCC) alloys. A related, yet multi-phase BCC alloy, based on Al-Cr-Fe-Ni, shows compressive strain >10% and specific compressive yield strength of 229 MPa x cc/g, yet does not show ductility in tensile tests due to cleavage. When replacing Cr in Al-Cr-Fe-based 4- and 5-element LDHEA with Mn, hardness drops 2x. Combined with compression test results, including those on the ternaries Al-Cr-Fe and Al-Mn-Fe suggest that Al-Mn-Fe-based LDHEA are still worth pursuing. These initial results only represent one compressive stress-strain curve per composition without any property optimization. As such, reproducibility needs to be followed by optimization to show their full potential. When including Li, Mg, and Zn, single-phase Li-Mg-Al-Ti-Zn LDHEA has been found with a specific ultimate compressive strength of 289MPa x cc/g. Al-Ti-Mn-Zn showed a specific ultimate compressive strength of 73MPa x cc/g. These initial results after hot isostatic pressing (HIP) of the ball-milled powders represent the lower end of what is possible, since no secondary processing (e.g. extrusion) has been performed to optimize strength and ductility. Compositions for multi-phase (e.g. dual-phase) LDHEA were identified largely by automated searches through CALPHAD databases, while screening for large face-centered-cubic (FCC) volume fractions, followed by experimental verification. This resulted in several new alloys. Li-Mg-Al-Mn-Fe and Mg-Mn-Fe-Co ball-milled powders upon HIP show specific ultimate compressive strengths of 198MPa x cc/g and 45MPa x cc/g, respectively. Several malleable quarternary Al-Zn-based alloys have been found upon arc/induction melting, yet with limited specific compressive yield strength (<75 MPa x cc/g). These initial results are all without any optimization for strength and/or ductility. High-throughput experimentation allowed us to triple the existing experimental HEA database as published in the past 10 years in less than 2 years which happened at a rate 10x higher than previous methods. Furthermore, we showed that high-throughput thin-film combinatorial methods can be used to get insight in isothermal phase diagram slices. Although it is straightforward to map hardness as a function of composition for sputtered, thin-film, compositional gradients by nano-indentation and compare the results to micro-indentation on bulk samples, the simultaneous impact of composition, roughness, film density, and microstructure on hardness requires monitoring all these properties as a function of location on the compositional gradient, including dissecting the impact of these 4 factors on the hardness map. These additional efforts impact throughput significantly. This work shows that a lot of progress has been made over the years in predicting phase formation that aids the discovery of new alloys, yet that a lot of work needs to be done to predict phases more accurately for LDHEA, whether done by CALPHAD or by other means. More importantly, more work needs to be done to predict mechanical properties of novel alloys, like yield strength, and ductility. Furthermore, this work shows that there is a need for the generation of an empirical alloy database covering strategic points in a multi-dimensional composition space to allow for faster and more accurate predictive interpolations to identify the oasis in the dessert more quickly. Finally, this work suggests that it is worth pursuing a ductile alloy with a SYS > 300 MPa x cc/g in a mass density range of 6-7 g/cc, since the chances for a single-phase or majority-phase FCC increase significantly. Today’s lightweight steels are in this density range.« less
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"One-sample concept" micro-combinatory for high throughput TEM of binary films.
Sáfrán, György
2018-04-01
Phases of thin films may remarkably differ from that of bulk. Unlike to the comprehensive data files of Binary Phase Diagrams [1] available for bulk, complete phase maps for thin binary layers do not exist. This is due to both the diverse metastable, non-equilibrium or instable phases feasible in thin films and the required volume of characterization work with analytical techniques like TEM, SAED and EDS. The aim of the present work was to develop a method that remarkably facilitates the TEM study of the diverse binary phases of thin films, or the creation of phase maps. A micro-combinatorial method was worked out that enables both preparation and study of a gradient two-component film within a single TEM specimen. For a demonstration of the technique thin Mn x Al 1- x binary samples with evolving concentration from x = 0 to x = 1 have been prepared so that the transition from pure Mn to pure Al covers a 1.5 mm long track within the 3 mm diameter TEM grid. The proposed method enables the preparation and study of thin combinatorial samples including all feasible phases as a function of composition or other deposition parameters. Contrary to known "combinatorial chemistry", in which a series of different samples are deposited in one run, and investigated, one at a time, the present micro-combinatorial method produces a single specimen condensing a complete library of a binary system that can be studied, efficiently, within a single TEM session. That provides extremely high throughput for TEM characterization of composition-dependent phases, exploration of new materials, or the construction of phase diagrams of binary films. Copyright © 2018 Elsevier B.V. All rights reserved.
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High-throughput investigation of catalysts for JP-8 fuel cracking to liquefied petroleum gas.
Bedenbaugh, John E; Kim, Sungtak; Sasmaz, Erdem; Lauterbach, Jochen
2013-09-09
Portable power technologies for military applications necessitate the production of fuels similar to LPG from existing feedstocks. Catalytic cracking of military jet fuel to form a mixture of C₂-C₄ hydrocarbons was investigated using high-throughput experimentation. Cracking experiments were performed in a gas-phase, 16-sample high-throughput reactor. Zeolite ZSM-5 catalysts with low Si/Al ratios (≤25) demonstrated the highest production of C₂-C₄ hydrocarbons at moderate reaction temperatures (623-823 K). ZSM-5 catalysts were optimized for JP-8 cracking activity to LPG through varying reaction temperature and framework Si/Al ratio. The reducing atmosphere required during catalytic cracking resulted in coking of the catalyst and a commensurate decrease in conversion rate. Rare earth metal promoters for ZSM-5 catalysts were screened to reduce coking deactivation rates, while noble metal promoters reduced onset temperatures for coke burnoff regeneration.
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NASA Astrophysics Data System (ADS)
Zhang, Ruizhi; Du, Baoli; Chen, Kan; Reece, Mike; Materials Research Insititute Team
With the increasing computational power and reliable databases, high-throughput screening is playing a more and more important role in the search of new thermoelectric materials. Rather than the well established density functional theory (DFT) calculation based methods, we propose an alternative approach to screen for new TE materials: using crystal structural features as 'descriptors'. We show that a non-distorted transition metal sulphide polyhedral network can be a good descriptor for high power factor according to crystal filed theory. By using Cu/S containing compounds as an example, 1600+ Cu/S containing entries in the Inorganic Crystal Structure Database (ICSD) were screened, and of those 84 phases are identified as promising thermoelectric materials. The screening results are validated by both electronic structure calculations and experimental results from the literature. We also fabricated some new compounds to test our screening results. Another advantage of using crystal structure features as descriptors is that we can easily establish structural relationships between the identified phases. Based on this, two material design approaches are discussed: 1) High-pressure synthesis of metastable phase; 2) In-situ 2-phase composites with coherent interface. This work was supported by a Marie Curie International Incoming Fellowship of the European Community Human Potential Program.
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Boulanger, Jérôme; Muresan, Leila; Tiemann-Boege, Irene
2012-01-01
In spite of the many advances in haplotyping methods, it is still very difficult to characterize rare haplotypes in tissues and different environmental samples or to accurately assess the haplotype diversity in large mixtures. This would require a haplotyping method capable of analyzing the phase of single molecules with an unprecedented throughput. Here we describe such a haplotyping method capable of analyzing in parallel hundreds of thousands single molecules in one experiment. In this method, multiple PCR reactions amplify different polymorphic regions of a single DNA molecule on a magnetic bead compartmentalized in an emulsion drop. The allelic states of the amplified polymorphisms are identified with fluorescently labeled probes that are then decoded from images taken of the arrayed beads by a microscope. This method can evaluate the phase of up to 3 polymorphisms separated by up to 5 kilobases in hundreds of thousands single molecules. We tested the sensitivity of the method by measuring the number of mutant haplotypes synthesized by four different commercially available enzymes: Phusion, Platinum Taq, Titanium Taq, and Phire. The digital nature of the method makes it highly sensitive to detecting haplotype ratios of less than 1:10,000. We also accurately quantified chimera formation during the exponential phase of PCR by different DNA polymerases.
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Cao, Jianmin; Sun, Na; Yu, Weisong; Pang, Xueli; Lin, Yingnan; Kong, Fanyu; Qiu, Jun
2016-12-01
A sensitive and robust multiresidue method for the simultaneous analysis of 114 pesticides in tobacco was developed based on solid-phase extraction coupled with gas chromatography and tandem mass spectrometry. In this strategy, tobacco samples were extracted with acetonitrile and cleaned up with a multilayer solid-phase extraction cartridge Cleanert TPT using acetonitrile/toluene (3:1) as the elution solvent. Two internal standards of different polarity were used to meet simultaneous pesticides quantification demands in the tobacco matrix. Satisfactory linearity in the range of 10-500 ng/mL was obtained for all 114 pesticides with linear regression coefficients higher than 0.994. The limit of detection and limit of quantification values were 0.02-5.27 and 0.06-17.6 ng/g, respectively. For most of the pesticides, acceptable recoveries in the range of 70-120% and repeatabilities (relative standard deviation) of <11% were achieved at spiking levels of 20, 100, and 400 ng/g. Compared with the reported multiresidue analytical method, the proposed method provided a cleaner test solution with smaller amounts of pigments, fatty acids as well as other undesirable interferences. The development and validation of the high sensitivity, high selectivity, easy automation, and high-throughput analytical method meant that it could be successfully used for the determination of pesticides in tobacco samples. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Cheminformatic Analysis of the US EPA ToxCast Chemical Library
The ToxCast project is employing high throughput screening (HTS) technologies, along with chemical descriptors and computational models, to develop approaches for screening and prioritizing environmental chemicals for further toxicity testing. ToxCast Phase I generated HTS data f...
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Mathematical and Computational Modeling in Complex Biological Systems
Li, Wenyang; Zhu, Xiaoliang
2017-01-01
The biological process and molecular functions involved in the cancer progression remain difficult to understand for biologists and clinical doctors. Recent developments in high-throughput technologies urge the systems biology to achieve more precise models for complex diseases. Computational and mathematical models are gradually being used to help us understand the omics data produced by high-throughput experimental techniques. The use of computational models in systems biology allows us to explore the pathogenesis of complex diseases, improve our understanding of the latent molecular mechanisms, and promote treatment strategy optimization and new drug discovery. Currently, it is urgent to bridge the gap between the developments of high-throughput technologies and systemic modeling of the biological process in cancer research. In this review, we firstly studied several typical mathematical modeling approaches of biological systems in different scales and deeply analyzed their characteristics, advantages, applications, and limitations. Next, three potential research directions in systems modeling were summarized. To conclude, this review provides an update of important solutions using computational modeling approaches in systems biology. PMID:28386558
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FPGA cluster for high-performance AO real-time control system
NASA Astrophysics Data System (ADS)
Geng, Deli; Goodsell, Stephen J.; Basden, Alastair G.; Dipper, Nigel A.; Myers, Richard M.; Saunter, Chris D.
2006-06-01
Whilst the high throughput and low latency requirements for the next generation AO real-time control systems have posed a significant challenge to von Neumann architecture processor systems, the Field Programmable Gate Array (FPGA) has emerged as a long term solution with high performance on throughput and excellent predictability on latency. Moreover, FPGA devices have highly capable programmable interfacing, which lead to more highly integrated system. Nevertheless, a single FPGA is still not enough: multiple FPGA devices need to be clustered to perform the required subaperture processing and the reconstruction computation. In an AO real-time control system, the memory bandwidth is often the bottleneck of the system, simply because a vast amount of supporting data, e.g. pixel calibration maps and the reconstruction matrix, need to be accessed within a short period. The cluster, as a general computing architecture, has excellent scalability in processing throughput, memory bandwidth, memory capacity, and communication bandwidth. Problems, such as task distribution, node communication, system verification, are discussed.
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A gas trapping method for high-throughput metabolic experiments.
Krycer, James R; Diskin, Ciana; Nelson, Marin E; Zeng, Xiao-Yi; Fazakerley, Daniel J; James, David E
2018-01-01
Research into cellular metabolism has become more high-throughput, with typical cell-culture experiments being performed in multiwell plates (microplates). This format presents a challenge when trying to collect gaseous products, such as carbon dioxide (CO2), which requires a sealed environment and a vessel separate from the biological sample. To address this limitation, we developed a gas trapping protocol using perforated plastic lids in sealed cell-culture multiwell plates. We used this trap design to measure CO2 production from glucose and fatty acid metabolism, as well as hydrogen sulfide production from cysteine-treated cells. Our data clearly show that this gas trap can be applied to liquid and solid gas-collection media and can be used to study gaseous product generation by both adherent cells and cells in suspension. Since our gas traps can be adapted to multiwell plates of various sizes, they present a convenient, cost-effective solution that can accommodate the trend toward high-throughput measurements in metabolic research.
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Xie, Chen; Tang, Xiaofeng; Berlinghof, Marvin; Langner, Stefan; Chen, Shi; Späth, Andreas; Li, Ning; Fink, Rainer H; Unruh, Tobias; Brabec, Christoph J
2018-06-27
Development of high-quality organic nanoparticle inks is a significant scientific challenge for the industrial production of solution-processed organic photovoltaics (OPVs) with eco-friendly processing methods. In this work, we demonstrate a novel, robot-based, high-throughput procedure performing automatic poly(3-hexylthio-phene-2,5-diyl) and indene-C 60 bisadduct nanoparticle ink synthesis in nontoxic alcohols. A novel methodology to prepare particle dispersions for fully functional OPVs by manipulating the particle size and solvent system was studied in detail. The ethanol dispersion with a particle diameter of around 80-100 nm exhibits reduced degradation, yielding a power conversion efficiency of 4.52%, which is the highest performance reported so far for water/alcohol-processed OPV devices. By successfully deploying the high-throughput robot-based approach for an organic nanoparticle ink preparation, we believe that the findings demonstrated in this work will trigger more research interest and effort on eco-friendly industrial production of OPVs.
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Mathematical and Computational Modeling in Complex Biological Systems.
Ji, Zhiwei; Yan, Ke; Li, Wenyang; Hu, Haigen; Zhu, Xiaoliang
2017-01-01
The biological process and molecular functions involved in the cancer progression remain difficult to understand for biologists and clinical doctors. Recent developments in high-throughput technologies urge the systems biology to achieve more precise models for complex diseases. Computational and mathematical models are gradually being used to help us understand the omics data produced by high-throughput experimental techniques. The use of computational models in systems biology allows us to explore the pathogenesis of complex diseases, improve our understanding of the latent molecular mechanisms, and promote treatment strategy optimization and new drug discovery. Currently, it is urgent to bridge the gap between the developments of high-throughput technologies and systemic modeling of the biological process in cancer research. In this review, we firstly studied several typical mathematical modeling approaches of biological systems in different scales and deeply analyzed their characteristics, advantages, applications, and limitations. Next, three potential research directions in systems modeling were summarized. To conclude, this review provides an update of important solutions using computational modeling approaches in systems biology.
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Burdick, David B; Cavnor, Chris C; Handcock, Jeremy; Killcoyne, Sarah; Lin, Jake; Marzolf, Bruz; Ramsey, Stephen A; Rovira, Hector; Bressler, Ryan; Shmulevich, Ilya; Boyle, John
2010-07-14
High throughput sequencing has become an increasingly important tool for biological research. However, the existing software systems for managing and processing these data have not provided the flexible infrastructure that research requires. Existing software solutions provide static and well-established algorithms in a restrictive package. However as high throughput sequencing is a rapidly evolving field, such static approaches lack the ability to readily adopt the latest advances and techniques which are often required by researchers. We have used a loosely coupled, service-oriented infrastructure to develop SeqAdapt. This system streamlines data management and allows for rapid integration of novel algorithms. Our approach also allows computational biologists to focus on developing and applying new methods instead of writing boilerplate infrastructure code. The system is based around the Addama service architecture and is available at our website as a demonstration web application, an installable single download and as a collection of individual customizable services.
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2010-01-01
Background High throughput sequencing has become an increasingly important tool for biological research. However, the existing software systems for managing and processing these data have not provided the flexible infrastructure that research requires. Results Existing software solutions provide static and well-established algorithms in a restrictive package. However as high throughput sequencing is a rapidly evolving field, such static approaches lack the ability to readily adopt the latest advances and techniques which are often required by researchers. We have used a loosely coupled, service-oriented infrastructure to develop SeqAdapt. This system streamlines data management and allows for rapid integration of novel algorithms. Our approach also allows computational biologists to focus on developing and applying new methods instead of writing boilerplate infrastructure code. Conclusion The system is based around the Addama service architecture and is available at our website as a demonstration web application, an installable single download and as a collection of individual customizable services. PMID:20630057
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Zhao, Miao; Wu, Xiao-Jie; Fan, Ya-Xin; Guo, Bei-Ning; Zhang, Jing
2016-05-30
A rapid ultra high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) assay method was developed for determination of CMS and formed colistin in human plasma and urine. After extraction on a 96-well SPE Supra-Clean Weak Cation Exchange (WCX) plate, the eluents were mixed and injected into the UHPLC-MS/MS system directly. A Phonomenex Kinetex XB-C18 analytical column was employed with a mobile phase consisting of solution "A" (acetonitrile:methanol, 1:1, v/v) and solution "B" (0.1% formic acid in water, v/v). The flow rate was 0.4 mL/min with gradient elution over 3.5 min. Ions were detected in ESI positive ion mode and the precursor-product ion pairs were m/z 390.7/101.3 for colistin A, m/z 386.0/101.2 for colistin B, and m/z 402.3/101.2 for polymyxin B1 (IS), respectively. The lower limit of quantification (LLOQ) was 0.0130 and 0.0251 mg/L for colistin A and colistin B in both plasma and urine with accuracy (relative error, %) <± 12.6% and precision (relative standard deviation, %) <± 10.8%. Stability of CMS was demonstrated in biological samples before and during sample treatment, and in the extract. This new analytical method provides high-throughput treatment and optimized quantification of CMS and colistin, which offers a highly efficient tool for the analysis of a large number of clinical samples as well as routine therapeutic drug monitoring. Copyright © 2016 Elsevier B.V. All rights reserved.
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Closed-form solutions of performability. [modeling of a degradable buffer/multiprocessor system
NASA Technical Reports Server (NTRS)
Meyer, J. F.
1981-01-01
Methods which yield closed form performability solutions for continuous valued variables are developed. The models are similar to those employed in performance modeling (i.e., Markovian queueing models) but are extended so as to account for variations in structure due to faults. In particular, the modeling of a degradable buffer/multiprocessor system is considered whose performance Y is the (normalized) average throughput rate realized during a bounded interval of time. To avoid known difficulties associated with exact transient solutions, an approximate decomposition of the model is employed permitting certain submodels to be solved in equilibrium. These solutions are then incorporated in a model with fewer transient states and by solving the latter, a closed form solution of the system's performability is obtained. In conclusion, some applications of this solution are discussed and illustrated, including an example of design optimization.
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Analysis of data throughput in communication between PLCs and HMI/SCADA systems
NASA Astrophysics Data System (ADS)
Mikolajek, Martin; Koziorek, Jiri
2016-09-01
This paper is focused on Analysis of data throughout in communication between PLCs and HMI/SCADA systems. The first part of paper discusses basic problematic communication between PLC and HMI systems. Next part is about specific types of communications PLC - HMI requests. For those cases paper is talking about response and data throughput1-3 . Subsequent section of this article contains practical parts with various data exchanges between PLC Siemens and HMI. The possibilities of communication that are described in this article are focused on using OPC server for visualization software, custom HMI system and own application created by using .NET with Technology. The last part of this article contains some communication solutions.
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Wireless Networks under a Backoff Attack: A Game Theoretical Perspective.
Parras, Juan; Zazo, Santiago
2018-01-30
We study a wireless sensor network using CSMA/CA in the MAC layer under a backoff attack: some of the sensors of the network are malicious and deviate from the defined contention mechanism. We use Bianchi's network model to study the impact of the malicious sensors on the total network throughput, showing that it causes the throughput to be unfairly distributed among sensors. We model this conflict using game theory tools, where each sensor is a player. We obtain analytical solutions and propose an algorithm, based on Regret Matching, to learn the equilibrium of the game with an arbitrary number of players. Our approach is validated via simulations, showing that our theoretical predictions adjust to reality.
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Ethoscopes: An open platform for high-throughput ethomics
Geissmann, Quentin; Garcia Rodriguez, Luis; Beckwith, Esteban J.; French, Alice S.; Jamasb, Arian R.
2017-01-01
Here, we present the use of ethoscopes, which are machines for high-throughput analysis of behavior in Drosophila and other animals. Ethoscopes provide a software and hardware solution that is reproducible and easily scalable. They perform, in real-time, tracking and profiling of behavior by using a supervised machine learning algorithm, are able to deliver behaviorally triggered stimuli to flies in a feedback-loop mode, and are highly customizable and open source. Ethoscopes can be built easily by using 3D printing technology and rely on Raspberry Pi microcomputers and Arduino boards to provide affordable and flexible hardware. All software and construction specifications are available at http://lab.gilest.ro/ethoscope. PMID:29049280
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Molecular system identification for enzyme directed evolution and design
NASA Astrophysics Data System (ADS)
Guan, Xiangying; Chakrabarti, Raj
2017-09-01
The rational design of chemical catalysts requires methods for the measurement of free energy differences in the catalytic mechanism for any given catalyst Hamiltonian. The scope of experimental learning algorithms that can be applied to catalyst design would also be expanded by the availability of such methods. Methods for catalyst characterization typically either estimate apparent kinetic parameters that do not necessarily correspond to free energy differences in the catalytic mechanism or measure individual free energy differences that are not sufficient for establishing the relationship between the potential energy surface and catalytic activity. Moreover, in order to enhance the duty cycle of catalyst design, statistically efficient methods for the estimation of the complete set of free energy differences relevant to the catalytic activity based on high-throughput measurements are preferred. In this paper, we present a theoretical and algorithmic system identification framework for the optimal estimation of free energy differences in solution phase catalysts, with a focus on one- and two-substrate enzymes. This framework, which can be automated using programmable logic, prescribes a choice of feasible experimental measurements and manipulated input variables that identify the complete set of free energy differences relevant to the catalytic activity and minimize the uncertainty in these free energy estimates for each successive Hamiltonian design. The framework also employs decision-theoretic logic to determine when model reduction can be applied to improve the duty cycle of high-throughput catalyst design. Automation of the algorithm using fluidic control systems is proposed, and applications of the framework to the problem of enzyme design are discussed.
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Delivery of Formulated Industrial Enzymes with Acoustic Technology.
Hwang, Jennifer Dorcas; Ortiz-Maldonado, Mariliz; Paramonov, Sergey
2016-02-01
Industrial enzymes are instrumental in many applications, including carbohydrate processing, fabric and household care, biofuels, food, and animal nutrition, among others. Enzymes have to be active and stable not only in harsh application conditions, but also during shipment and storage. In protein stability studies, formulated concentrated enzyme solutions are frequently diluted gravimetrically prior to enzyme activity measurements, making it challenging to move toward more high-throughput techniques using conventional robotic equipment. Current assay methods pose difficulties when measuring highly concentrated proteins. For example, plastic pipette tips can introduce error because proteins adsorb to the tip surface, despite the presence of detergents, decreasing precision and overall efficiency of protein activity assays. Acoustic liquid handling technology, frequently used for various dilute small-molecule assays, may overcome such problems. Originally shown to effectively deliver dilute solutions of small molecules, this technology is used here as an effective alternative to the aforementioned challenge with viscous concentrated protein solutions. Because the acoustic liquid handler transfers nanoliter quantities of liquids without using pipette tips and without sample loss, it rapidly and uniformly prepares assay plates for enzyme activity measurements within minutes. This increased efficiency transforms the nature of enzyme stability studies toward high precision and throughput. © 2015 Society for Laboratory Automation and Screening.
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Ueda, Keisuke; Higashi, Kenjirou; Moribe, Kunikazu
2017-07-03
We investigated the phase separation behavior and maintenance mechanism of the supersaturated state of poorly water-soluble nifedipine (NIF) in hypromellose (HPMC) derivative solutions. Highly supersaturated NIF formed NIF-rich nanodroplets through phase separation from aqueous solution containing HPMC derivative. Dissolvable NIF concentration in the bulk water phase was limited by the phase separation of NIF from the aqueous solution. HPMC derivatives stabilized the NIF-rich nanodroplets and maintained the NIF supersaturation with phase-separated NIF for several hours. The size of the NIF-rich phase was different depending on the HPMC derivatives dissolved in aqueous solution, although the droplet size had no correlation with the time for which NIF supersaturation was maintained without NIF crystallization. HPMC acetate and HPMC acetate succinate (HPMC-AS) effectively maintained the NIF supersaturation containing phase-separated NIF compared with HPMC. Furthermore, HPMC-AS stabilized NIF supersaturation more effectively in acidic conditions. Solution 1 H NMR measurements of NIF-supersaturated solution revealed that HPMC derivatives distributed into the NIF-rich phase during the phase separation of NIF from the aqueous solution. The hydrophobicity of HPMC derivative strongly affected its distribution into the NIF-rich phase. Moreover, the distribution of HPMC-AS into the NIF-rich phase was promoted at lower pH due to the lower aqueous solubility of HPMC-AS. The distribution of a large amount of HPMC derivatives into NIF-rich phase induced the strong inhibition of NIF crystallization from the NIF-rich phase. Polymer distribution into the drug-rich phase directly monitored by solution NMR technique can be a useful index for the stabilization efficiency of drug-supersaturated solution containing a drug-rich phase.
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Paxman, Rosemary; Stinson, Jake; Dejardin, Anna; McKendry, Rachel A.; Hoogenboom, Bart W.
2012-01-01
Micromechanic resonators provide a small-volume and potentially high-throughput method to determine rheological properties of fluids. Here we explore the accuracy in measuring mass density and viscosity of ethanol-water and glycerol-water model solutions, using a simple and easily implemented model to deduce the hydrodynamic effects on resonating cantilevers of various length-to-width aspect ratios. We next show that these measurements can be extended to determine the alcohol percentage of both model solutions and commercial beverages such as beer, wine and liquor. This demonstrates how micromechanical resonators can be used for quality control of every-day drinks. PMID:22778654
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NASA Technical Reports Server (NTRS)
Wood, Richard J.
1992-01-01
The Architecture for Survivable Systems Processing (ASSP) program is a two phase program whose objective is the derivation, specification, development and validation of an open system architecture capable of supporting advanced processing needs of space, ground, and launch vehicle operations. The output of the first phase is a set of hardware and software standards and specifications defining this architecture at three levels. The second phase will validate these standards and develop the technology necessary to achieve strategic hardness, packaging density, throughput requirements, and interoperability/interchangeability.
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Distributed Channel Allocation and Time Slot Optimization for Green Internet of Things.
Ding, Kaiqi; Zhao, Haitao; Hu, Xiping; Wei, Jibo
2017-10-28
In sustainable smart cities, power saving is a severe challenge in the energy-constrained Internet of Things (IoT). Efficient utilization of limited multiple non-overlap channels and time resources is a promising solution to reduce the network interference and save energy consumption. In this paper, we propose a joint channel allocation and time slot optimization solution for IoT. First, we propose a channel ranking algorithm which enables each node to rank its available channels based on the channel properties. Then, we propose a distributed channel allocation algorithm so that each node can choose a proper channel based on the channel ranking and its own residual energy. Finally, the sleeping duration and spectrum sensing duration are jointly optimized to maximize the normalized throughput and satisfy energy consumption constraints simultaneously. Different from the former approaches, our proposed solution requires no central coordination or any global information that each node can operate based on its own local information in a total distributed manner. Also, theoretical analysis and extensive simulations have validated that when applying our solution in the network of IoT: (i) each node can be allocated to a proper channel based on the residual energy to balance the lifetime; (ii) the network can rapidly converge to a collision-free transmission through each node's learning ability in the process of the distributed channel allocation; and (iii) the network throughput is further improved via the dynamic time slot optimization.
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ExpoCast: Exposure Science for Prioritization and Toxicity Testing (S)
The US EPA is completing the Phase I pilot for a chemical prioritization research program, called ToxCast. Here EPA is developing methods for using computational chemistry, high-throughput screening, and toxicogenomic technologies to predict potential toxicity and prioritize limi...
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ExpoCast: Exposure Science for Prioritization and Toxicity Testing
The US EPA is completing the Phase I pilot for a chemical prioritization research program, called ToxCastTM. Here EPA is developing methods for using computational chemistry, high-throughput screening, and toxicogenomic technologies to predict potential toxicity and prioritize l...
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Phase-Sensitive Surface Plasmon Resonance Sensors: Recent Progress and Future Prospects
Deng, Shijie; Wang, Peng; Yu, Xinglong
2017-01-01
Surface plasmon resonance (SPR) is an optical sensing technique that is capable of performing real-time, label-free and high-sensitivity monitoring of molecular interactions. SPR biosensors can be divided according to their operating principles into angle-, wavelength-, intensity- and phase-interrogated devices. With their complex optical configurations, phase-interrogated SPR sensors generally provide higher sensitivity and throughput, and have thus recently emerged as prominent biosensing devices. To date, several methods have been developed for SPR phase interrogation, including heterodyne detection, polarimetry, shear interferometry, spatial phase modulation interferometry and temporal phase modulation interferometry. This paper summarizes the fundamentals of phase-sensitive SPR sensing, reviews the available methods for phase interrogation of these sensors, and discusses the future prospects for and trends in the development of this technology. PMID:29206182
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In meso in situ serial X-ray crystallography of soluble and membrane proteins
DOE Office of Scientific and Technical Information (OSTI.GOV)
Huang, Chia-Ying; Olieric, Vincent; Ma, Pikyee
A method for performing high-throughput in situ serial X-ray crystallography with soluble and membrane proteins in the lipid cubic phase is described. It works with microgram quantities of protein and lipid (and ligand when present) and is compatible with the most demanding sulfur SAD phasing. The lipid cubic phase (LCP) continues to grow in popularity as a medium in which to generate crystals of membrane (and soluble) proteins for high-resolution X-ray crystallographic structure determination. To date, the PDB includes 227 records attributed to the LCP or in meso method. Among the listings are some of the highest profile membrane proteins,more » including the β{sub 2}-adrenoreceptor–G{sub s} protein complex that figured in the award of the 2012 Nobel Prize in Chemistry to Lefkowitz and Kobilka. The most successful in meso protocol to date uses glass sandwich crystallization plates. Despite their many advantages, glass plates are challenging to harvest crystals from. However, performing in situ X-ray diffraction measurements with these plates is not practical. Here, an alternative approach is described that provides many of the advantages of glass plates and is compatible with high-throughput in situ measurements. The novel in meso in situ serial crystallography (IMISX) method introduced here has been demonstrated with AlgE and PepT (alginate and peptide transporters, respectively) as model integral membrane proteins and with lysozyme as a test soluble protein. Structures were solved by molecular replacement and by experimental phasing using bromine SAD and native sulfur SAD methods to resolutions ranging from 1.8 to 2.8 Å using single-digit microgram quantities of protein. That sulfur SAD phasing worked is testament to the exceptional quality of the IMISX diffraction data. The IMISX method is compatible with readily available, inexpensive materials and equipment, is simple to implement and is compatible with high-throughput in situ serial data collection at macromolecular crystallography synchrotron beamlines worldwide. Because of its simplicity and effectiveness, the IMISX approach is likely to supplant existing in meso crystallization protocols. It should prove particularly attractive in the area of ligand screening for drug discovery and development.« less
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Li, Yongmei; Shin, Young Geun; Yu, Chongwoo; Kosmeder, Jerome W; Hirschelman, Wendy H; Pezzuto, John M; van Breemen, Richard B
2003-12-01
The Caco-2 cell monolayer permeability assay has become a standard model of human intestinal absorption and transport. This paper reviews recent progress in increasing the throughput of Caco-2 cell monolayer assays and in expanding the scope of this assay to include modeling intestinal drug metabolism. The state-of-the-art in Caco-2 cell monolayer permeability assays combines multi-well plates fitted with semi-permeable inserts on which Caco-2 cells have been cultured with liquid chromatography-mass spectrometry (LC-MS) or LC-tandem mass spectrometry (LC-MS-MS) for the quantitative analysis of test compounds and the identification of their intestinal metabolites. After reviewing the progress in increasing the throughput of Caco-2 cell monolayer assays for both modeling human intestinal permeability or transport and the metabolism of xenobiotic compounds, we demonstrate the application of LC-MS and LC-MS-MS to the measurement of resveratrol permeability and metabolism in the Caco-2 model. trans-Resveratrol (trans-3,5,4'-trihydroxystilbene) is a polyphenolic compound occurring in grapes, peanuts and other food sources, that is under investigation as a cancer chemoprevention agent. The apparent permeability coefficient for apical (AP) to basolateral (BL) movement of resveratrol was 2.0 x 10(-5)cm/sec. Resveratrol was not a substrate for P-glycoprotein or the multi-drug resistance associated proteins (MRP). No phase I metabolites were observed, but the phase II conjugates resveratrol-3-glucuronide and resveratrol-3-sulfate was identified based on LC-MS and LC-MS-MS analysis and comparison with synthetic standards. Although these data indicate that resveratrol diffuses rapidly across the intestinal epithelium, extensive phase II metabolism during absorption might reduce resveratrol bioavailability.
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GlycoExtractor: a web-based interface for high throughput processing of HPLC-glycan data.
Artemenko, Natalia V; Campbell, Matthew P; Rudd, Pauline M
2010-04-05
Recently, an automated high-throughput HPLC platform has been developed that can be used to fully sequence and quantify low concentrations of N-linked sugars released from glycoproteins, supported by an experimental database (GlycoBase) and analytical tools (autoGU). However, commercial packages that support the operation of HPLC instruments and data storage lack platforms for the extraction of large volumes of data. The lack of resources and agreed formats in glycomics is now a major limiting factor that restricts the development of bioinformatic tools and automated workflows for high-throughput HPLC data analysis. GlycoExtractor is a web-based tool that interfaces with a commercial HPLC database/software solution to facilitate the extraction of large volumes of processed glycan profile data (peak number, peak areas, and glucose unit values). The tool allows the user to export a series of sample sets to a set of file formats (XML, JSON, and CSV) rather than a collection of disconnected files. This approach not only reduces the amount of manual refinement required to export data into a suitable format for data analysis but also opens the field to new approaches for high-throughput data interpretation and storage, including biomarker discovery and validation and monitoring of online bioprocessing conditions for next generation biotherapeutics.
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Improved routing strategy based on gravitational field theory
NASA Astrophysics Data System (ADS)
Song, Hai-Quan; Guo, Jin
2015-10-01
Routing and path selection are crucial for many communication and logistic applications. We study the interaction between nodes and packets and establish a simple model for describing the attraction of the node to the packet in transmission process by using the gravitational field theory, considering the real and potential congestion of the nodes. On the basis of this model, we propose a gravitational field routing strategy that considers the attractions of all of the nodes on the travel path to the packet. In order to illustrate the efficiency of proposed routing algorithm, we introduce the order parameter to measure the throughput of the network by the critical value of phase transition from a free flow phase to a congested phase, and study the distribution of betweenness centrality and traffic jam. Simulations show that, compared with the shortest path routing strategy, the gravitational field routing strategy considerably enhances the throughput of the network and balances the traffic load, and nearly all of the nodes are used efficiently. Project supported by the Technology and Development Research Project of China Railway Corporation (Grant No. 2012X007-D) and the Key Program of Technology and Development Research Foundation of China Railway Corporation (Grant No. 2012X003-A).
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NASA Astrophysics Data System (ADS)
Fu, Yu-Hang; Bai, Lin; Luo, Kai-Hong; Jin, Yong; Cheng, Yi
2017-04-01
In this work, we propose a general approach for modeling mass transfer and reaction of dilute solute(s) in incompressible three-phase flows by introducing a collision operator in lattice Boltzmann (LB) method. An LB equation was used to simulate the solute dynamics among three different fluids, in which the newly expanded collision operator was used to depict the interface behavior of dilute solute(s). The multiscale analysis showed that the presented model can recover the macroscopic transport equations derived from the Maxwell-Stefan equation for dilute solutes in three-phase systems. Compared with the analytical equation of state of solute and dynamic behavior, these results are proven to constitute a generalized framework to simulate solute distributions in three-phase flows, including compound soluble in one phase, compound adsorbed on single-interface, compound in two phases, and solute soluble in three phases. Moreover, numerical simulations of benchmark cases, such as phase decomposition, multilayered planar interfaces, and liquid lens, were performed to test the stability and efficiency of the model. Finally, the multiphase mass transfer and reaction in Janus droplet transport in a straight microchannel were well reproduced.
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High performance computing environment for multidimensional image analysis
Rao, A Ravishankar; Cecchi, Guillermo A; Magnasco, Marcelo
2007-01-01
Background The processing of images acquired through microscopy is a challenging task due to the large size of datasets (several gigabytes) and the fast turnaround time required. If the throughput of the image processing stage is significantly increased, it can have a major impact in microscopy applications. Results We present a high performance computing (HPC) solution to this problem. This involves decomposing the spatial 3D image into segments that are assigned to unique processors, and matched to the 3D torus architecture of the IBM Blue Gene/L machine. Communication between segments is restricted to the nearest neighbors. When running on a 2 Ghz Intel CPU, the task of 3D median filtering on a typical 256 megabyte dataset takes two and a half hours, whereas by using 1024 nodes of Blue Gene, this task can be performed in 18.8 seconds, a 478× speedup. Conclusion Our parallel solution dramatically improves the performance of image processing, feature extraction and 3D reconstruction tasks. This increased throughput permits biologists to conduct unprecedented large scale experiments with massive datasets. PMID:17634099
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High performance computing environment for multidimensional image analysis.
Rao, A Ravishankar; Cecchi, Guillermo A; Magnasco, Marcelo
2007-07-10
The processing of images acquired through microscopy is a challenging task due to the large size of datasets (several gigabytes) and the fast turnaround time required. If the throughput of the image processing stage is significantly increased, it can have a major impact in microscopy applications. We present a high performance computing (HPC) solution to this problem. This involves decomposing the spatial 3D image into segments that are assigned to unique processors, and matched to the 3D torus architecture of the IBM Blue Gene/L machine. Communication between segments is restricted to the nearest neighbors. When running on a 2 Ghz Intel CPU, the task of 3D median filtering on a typical 256 megabyte dataset takes two and a half hours, whereas by using 1024 nodes of Blue Gene, this task can be performed in 18.8 seconds, a 478x speedup. Our parallel solution dramatically improves the performance of image processing, feature extraction and 3D reconstruction tasks. This increased throughput permits biologists to conduct unprecedented large scale experiments with massive datasets.
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FogEye UV Sensor System : Low Visibility Landing Test (Phase IV Report)
DOT National Transportation Integrated Search
2004-03-01
The potential of FogEye solar blind UV technology to contribute to safe and swift throughput operations at airports has been demonstrated. One application, use of FogEye (Safety Sentry), as an aircraft surface detection sensor has been successfully o...
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Identifying Structural Alerts Based on Zebrafish Developmental Morphological Toxicity (TDS)
Zebrafish constitute a powerful alternative animal model for chemical hazard evaluation. To provide an in vivo complement to high-throughput screening data from the ToxCast program, zebrafish developmental toxicity screens were conducted on the ToxCast Phase I (Padilla et al., 20...
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ToxRefDB: Classifying ToxCast™ Phase I Chemicals Utilizing Structured Toxicity Information
There is an essential need for highly detailed chemicals classifications within the ToxCast™ research program. In order to develop predictive models and biological signatures utilizing high-throughput screening (HTS) and in vitro genomic data, relevant endpoints and toxicities m...
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Understanding potential health risks posed by environmental chemicals is a significant challenge elevated by large numbers of diverse chemicals with generally uncharacterized exposures, mechanisms and toxicities. The present study is a performance evaluation and critical analysis...
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Wide-field optical detection of nanoparticles using on-chip microscopy and self-assembled nanolenses
NASA Astrophysics Data System (ADS)
Mudanyali, Onur; McLeod, Euan; Luo, Wei; Greenbaum, Alon; Coskun, Ahmet F.; Hennequin, Yves; Allier, Cédric P.; Ozcan, Aydogan
2013-03-01
The direct observation of nanoscale objects is a challenging task for optical microscopy because the scattering from an individual nanoparticle is typically weak at optical wavelengths. Electron microscopy therefore remains one of the gold standard visualization methods for nanoparticles, despite its high cost, limited throughput and restricted field-of-view. Here, we describe a high-throughput, on-chip detection scheme that uses biocompatible wetting films to self-assemble aspheric liquid nanolenses around individual nanoparticles to enhance the contrast between the scattered and background light. We model the effect of the nanolens as a spatial phase mask centred on the particle and show that the holographic diffraction pattern of this effective phase mask allows detection of sub-100 nm particles across a large field-of-view of >20 mm2. As a proof-of-concept demonstration, we report on-chip detection of individual polystyrene nanoparticles, adenoviruses and influenza A (H1N1) viral particles.
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Bunn, Jonathan Kenneth; Fang, Randy L; Albing, Mark R; Mehta, Apurva; Kramer, Matthew J; Besser, Matthew F; Hattrick-Simpers, Jason R
2015-07-10
High-temperature alloy coatings that can resist oxidation are urgently needed as nuclear cladding materials to mitigate the danger of hydrogen explosions during meltdown. Here we apply a combination of computationally guided materials synthesis, high-throughput structural characterization and data analysis tools to investigate the feasibility of coatings from the Fe–Cr–Al alloy system. Composition-spread samples were synthesized to cover the region of the phase diagram previous bulk studies have identified as forming protective oxides. The metallurgical and oxide phase evolution were studied via in situ synchrotron glancing incidence x-ray diffraction at temperatures up to 690 K. A composition region with an Al concentration greater than 3.08 at%, and between 20.0 at% and 32.9 at% Cr showed the least overall oxide growth. Subsequently, a series of samples were deposited on stubs and their oxidation behavior at 1373 K was observed. The continued presence of a passivating oxide was confirmed in this region over a period of 6 h.
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Automated solid-phase subcloning based on beads brought into proximity by magnetic force.
Hudson, Elton P; Nikoshkov, Andrej; Uhlen, Mathias; Rockberg, Johan
2012-01-01
In the fields of proteomics, metabolic engineering and synthetic biology there is a need for high-throughput and reliable cloning methods to facilitate construction of expression vectors and genetic pathways. Here, we describe a new approach for solid-phase cloning in which both the vector and the gene are immobilized to separate paramagnetic beads and brought into proximity by magnetic force. Ligation events were directly evaluated using fluorescent-based microscopy and flow cytometry. The highest ligation efficiencies were obtained when gene- and vector-coated beads were brought into close contact by application of a magnet during the ligation step. An automated procedure was developed using a laboratory workstation to transfer genes into various expression vectors and more than 95% correct clones were obtained in a number of various applications. The method presented here is suitable for efficient subcloning in an automated manner to rapidly generate a large number of gene constructs in various vectors intended for high throughput applications.
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The search for new amphiphiles: synthesis of a modular, high-throughput library
Feast, George C; Lepitre, Thomas; Mulet, Xavier; Conn, Charlotte E; Hutt, Oliver E
2014-01-01
Summary Amphiphilic compounds are used in a variety of applications due to their lyotropic liquid-crystalline phase formation, however only a limited number of compounds, in a potentially limitless field, are currently in use. A library of organic amphiphilic compounds was synthesised consisting of glucose, galactose, lactose, xylose and mannose head groups and double and triple-chain hydrophobic tails. A modular, high-throughput approach was developed, whereby head and tail components were conjugated using the copper-catalysed azide–alkyne cycloaddition (CuAAC) reaction. The tails were synthesised from two core alkyne-tethered intermediates, which were subsequently functionalised with hydrocarbon chains varying in length and degree of unsaturation and branching, while the five sugar head groups were selected with ranging substitution patterns and anomeric linkages. A library of 80 amphiphiles was subsequently produced, using a 24-vial array, with the majority formed in very good to excellent yields. A preliminary assessment of the liquid-crystalline phase behaviour is also presented. PMID:25161714
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The search for new amphiphiles: synthesis of a modular, high-throughput library.
Feast, George C; Lepitre, Thomas; Mulet, Xavier; Conn, Charlotte E; Hutt, Oliver E; Savage, G Paul; Drummond, Calum J
2014-01-01
Amphiphilic compounds are used in a variety of applications due to their lyotropic liquid-crystalline phase formation, however only a limited number of compounds, in a potentially limitless field, are currently in use. A library of organic amphiphilic compounds was synthesised consisting of glucose, galactose, lactose, xylose and mannose head groups and double and triple-chain hydrophobic tails. A modular, high-throughput approach was developed, whereby head and tail components were conjugated using the copper-catalysed azide-alkyne cycloaddition (CuAAC) reaction. The tails were synthesised from two core alkyne-tethered intermediates, which were subsequently functionalised with hydrocarbon chains varying in length and degree of unsaturation and branching, while the five sugar head groups were selected with ranging substitution patterns and anomeric linkages. A library of 80 amphiphiles was subsequently produced, using a 24-vial array, with the majority formed in very good to excellent yields. A preliminary assessment of the liquid-crystalline phase behaviour is also presented.
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High-throughput search of ternary chalcogenides for p-type transparent electrodes
Shi, Jingming; Cerqueira, Tiago F. T.; Cui, Wenwen; Nogueira, Fernando; Botti, Silvana; Marques, Miguel A. L.
2017-01-01
Delafossite crystals are fascinating ternary oxides that have demonstrated transparent conductivity and ambipolar doping. Here we use a high-throughput approach based on density functional theory to find delafossite and related layered phases of composition ABX2, where A and B are elements of the periodic table, and X is a chalcogen (O, S, Se, and Te). From the 15 624 compounds studied in the trigonal delafossite prototype structure, 285 are within 50 meV/atom from the convex hull of stability. These compounds are further investigated using global structural prediction methods to obtain their lowest-energy crystal structure. We find 79 systems not present in the materials project database that are thermodynamically stable and crystallize in the delafossite or in closely related structures. These novel phases are then characterized by calculating their band gaps and hole effective masses. This characterization unveils a large diversity of properties, ranging from normal metals, magnetic metals, and some candidate compounds for p-type transparent electrodes. PMID:28266587
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Wide-field optical detection of nanoparticles using on-chip microscopy and self-assembled nanolenses
Mudanyali, Onur; McLeod, Euan; Luo, Wei; Greenbaum, Alon; Coskun, Ahmet F.; Hennequin, Yves; Allier, Cédric P.; Ozcan, Aydogan
2013-01-01
The direct observation of nanoscale objects is a challenging task for optical microscopy because the scattering from an individual nanoparticle is typically weak at optical wavelengths. Electron microscopy therefore remains one of the gold standard visualization methods for nanoparticles, despite its high cost, limited throughput and restricted field-of-view. Here, we describe a high-throughput, on-chip detection scheme that uses biocompatible wetting films to self-assemble aspheric liquid nanolenses around individual nanoparticles to enhance the contrast between the scattered and background light. We model the effect of the nanolens as a spatial phase mask centred on the particle and show that the holographic diffraction pattern of this effective phase mask allows detection of sub-100 nm particles across a large field-of-view of >20 mm2. As a proof-of-concept demonstration, we report on-chip detection of individual polystyrene nanoparticles, adenoviruses and influenza A (H1N1) viral particles. PMID:24358054
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Automated Solid-Phase Subcloning Based on Beads Brought into Proximity by Magnetic Force
Hudson, Elton P.; Nikoshkov, Andrej; Uhlen, Mathias; Rockberg, Johan
2012-01-01
In the fields of proteomics, metabolic engineering and synthetic biology there is a need for high-throughput and reliable cloning methods to facilitate construction of expression vectors and genetic pathways. Here, we describe a new approach for solid-phase cloning in which both the vector and the gene are immobilized to separate paramagnetic beads and brought into proximity by magnetic force. Ligation events were directly evaluated using fluorescent-based microscopy and flow cytometry. The highest ligation efficiencies were obtained when gene- and vector-coated beads were brought into close contact by application of a magnet during the ligation step. An automated procedure was developed using a laboratory workstation to transfer genes into various expression vectors and more than 95% correct clones were obtained in a number of various applications. The method presented here is suitable for efficient subcloning in an automated manner to rapidly generate a large number of gene constructs in various vectors intended for high throughput applications. PMID:22624028
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Sample-Clock Phase-Control Feedback
NASA Technical Reports Server (NTRS)
Quirk, Kevin J.; Gin, Jonathan W.; Nguyen, Danh H.; Nguyen, Huy
2012-01-01
To demodulate a communication signal, a receiver must recover and synchronize to the symbol timing of a received waveform. In a system that utilizes digital sampling, the fidelity of synchronization is limited by the time between the symbol boundary and closest sample time location. To reduce this error, one typically uses a sample clock in excess of the symbol rate in order to provide multiple samples per symbol, thereby lowering the error limit to a fraction of a symbol time. For systems with a large modulation bandwidth, the required sample clock rate is prohibitive due to current technological barriers and processing complexity. With precise control of the phase of the sample clock, one can sample the received signal at times arbitrarily close to the symbol boundary, thus obviating the need, from a synchronization perspective, for multiple samples per symbol. Sample-clock phase-control feedback was developed for use in the demodulation of an optical communication signal, where multi-GHz modulation bandwidths would require prohibitively large sample clock frequencies for rates in excess of the symbol rate. A custom mixedsignal (RF/digital) offset phase-locked loop circuit was developed to control the phase of the 6.4-GHz clock that samples the photon-counting detector output. The offset phase-locked loop is driven by a feedback mechanism that continuously corrects for variation in the symbol time due to motion between the transmitter and receiver as well as oscillator instability. This innovation will allow significant improvements in receiver throughput; for example, the throughput of a pulse-position modulation (PPM) with 16 slots can increase from 188 Mb/s to 1.5 Gb/s.
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Liang, Junling; Meng, Jie; Guo, Mengzhe; Yang, Zhi; Wu, Shihua
2013-05-03
Modern counter-current chromatography (CCC) originated from the helical coil planet centrifuge. Recently, spiral coils were found to possess higher separation efficiency in both the retention of stationary phase and solutes resolution than other CCC coils like the helical and toroidal coils used on type-J CCC and cross-axis CCC. In this work, we built a novel conical coil CCC for the preparative isolation and purification of tanshinones from Salvia miltiorrhiza Bunge. The conical coils were wound on three identical upright tapered holders in head-to-tail and left-handed direction and connected in series. Compared with helical and spiral coil CCC, conical coil CCC not only placed CCC column in a two-dimensional centrifugal field, but also provided a potential centrifugal force gradient both in axial and radial directions. The extra centrifugal gradient made mobile phase move faster and enabled CCC much higher retention of stationary phase and better resolution. As a result, higher efficiency has been obtained with the solvent system of hexane-ethyl acetate-methanol-water (HEMWat) with the volume ratio of 5:5:7:3 by using conical coil CCC apparatus. Four tanshinones, including cryptotanshinone (1), tanshinone I (2), 1,2-dihydrotanshinquinone (3) and tanshinone IIA (4), were well resolved from 500mg to 1g crude samples with high purity. Furthermore, the conical coil CCC can make a much higher solid phase retention, which makes it to be a powerful separation tool with high throughput. This is the first report about conical coil CCC for separation of tanshinones and it may also be an important advancement for natural products isolation. Copyright © 2013 Elsevier B.V. All rights reserved.
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Amrhein, Sven; Schwab, Marie-Luise; Hoffmann, Marc; Hubbuch, Jürgen
2014-11-07
Over the last decade, the use of design of experiment approaches in combination with fully automated high throughput (HTP) compatible screenings supported by robotic liquid handling stations (LHS), adequate fast analytics and data processing has been developed in the biopharmaceutical industry into a strategy of high throughput process development (HTPD) resulting in lower experimental effort, sample reduction and an overall higher degree of process optimization. Apart from HTP technologies, lab-on-a-chip technology has experienced an enormous growth in the last years and allows further reduction of sample consumption. A combination of LHS and lab-on-a-chip technology is highly desirable and realized in the present work to characterize aqueous two phase systems with respect to tie lines. In particular, a new high throughput compatible approach for the characterization of aqueous two phase systems regarding tie lines by exploiting differences in phase densities is presented. Densities were measured by a standalone micro fluidic liquid density sensor, which was integrated into a liquid handling station by means of a developed generic Tip2World interface. This combination of liquid handling stations and lab-on-a-chip technology enables fast, fully automated, and highly accurate density measurements. The presented approach was used to determine the phase diagram of ATPSs composed of potassium phosphate (pH 7) and polyethylene glycol (PEG) with a molecular weight of 300, 400, 600 and 1000 Da respectively in the presence and in the absence of 3% (w/w) sodium chloride. Considering the whole ATPS characterization process, two complete ATPSs could be characterized within 24h, including four runs per ATPS for binodal curve determination (less than 45 min/run), and tie line determination (less than 45 min/run for ATPS preparation and 8h for density determination), which can be performed fully automated over night without requiring man power. The presented methodology provides a cost, time and material effective approach for characterization of ATPS phase diagram on base on highly accurate and comprehensive data. By this means the derived data opens the door for a more detailed description of ATPS towards generating mechanistic based models, since molecular approaches such as MD simulations or molecular descriptions along the line of QSAR heavily rely on accurate and comprehensive data. Copyright © 2014 Elsevier B.V. All rights reserved.
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Software feedback for monochromator tuning at UNICAT (abstract)
NASA Astrophysics Data System (ADS)
Jemian, Pete R.
2002-03-01
Automatic tuning of double-crystal monochromators presents an interesting challenge in software. The goal is to either maximize, or hold constant, the throughput of the monochromator. An additional goal of the software feedback is to disable itself when there is no beam and then, at the user's discretion, re-enable itself when the beam returns. These and other routine goals, such as adherence to limits of travel for positioners, are maintained by software controls. Many solutions exist to lock in and maintain a fixed throughput. Among these include a hardware solution involving a wave form generator, and a lock-in amplifier to autocorrelate the movement of a piezoelectric transducer (PZT) providing fine adjustment of the second crystal Bragg angle. This solution does not work when the positioner is a slow acting device such as a stepping motor. Proportional integral differential (PID) loops have been used to provide feedback through software but additional controls must be provided to maximize the monochromator throughput. Presented here is a software variation of the PID loop which meets the above goals. By using two floating point variables as inputs, representing the intensity of x rays measured before and after the monochromator, it attempts to maximize (or hold constant) the ratio of these two inputs by adjusting an output floating point variable. These floating point variables are connected to hardware channels corresponding to detectors and positioners. When the inputs go out of range, the software will stop making adjustments to the control output. Not limited to monochromator feedback, the software could be used, with beam steering positioners, to maintain a measure of beam position. Advantages of this software feedback are the flexibility of its various components. It has been used with stepping motors and PZTs as positioners. Various devices such as ion chambers, scintillation counters, photodiodes, and photoelectron collectors have been used as detectors. The software provides significant cost savings over hardware feedback methods. Presently implemented in EPICS, the software is sufficiently general to any automated instrument control system.
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Link Analysis of High Throughput Spacecraft Communication Systems for Future Science Missions
NASA Technical Reports Server (NTRS)
Simons, Rainee N.
2015-01-01
NASA's plan to launch several spacecrafts into low Earth Orbit (LEO) to support science missions in the next ten years and beyond requires down link throughput on the order of several terabits per day. The ability to handle such a large volume of data far exceeds the capabilities of current systems. This paper proposes two solutions, first, a high data rate link between the LEO spacecraft and ground via relay satellites in geostationary orbit (GEO). Second, a high data rate direct to ground link from LEO. Next, the paper presents results from computer simulations carried out for both types of links taking into consideration spacecraft transmitter frequency, EIRP, and waveform; elevation angle dependent path loss through Earths atmosphere, and ground station receiver GT.
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Wireless Networks under a Backoff Attack: A Game Theoretical Perspective
Zazo, Santiago
2018-01-01
We study a wireless sensor network using CSMA/CA in the MAC layer under a backoff attack: some of the sensors of the network are malicious and deviate from the defined contention mechanism. We use Bianchi’s network model to study the impact of the malicious sensors on the total network throughput, showing that it causes the throughput to be unfairly distributed among sensors. We model this conflict using game theory tools, where each sensor is a player. We obtain analytical solutions and propose an algorithm, based on Regret Matching, to learn the equilibrium of the game with an arbitrary number of players. Our approach is validated via simulations, showing that our theoretical predictions adjust to reality. PMID:29385752
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Link Analysis of High Throughput Spacecraft Communication Systems for Future Science Missions
NASA Technical Reports Server (NTRS)
Simons, Rainee N.
2015-01-01
NASA's plan to launch several spacecraft into low Earth Orbit (LEO) to support science missions in the next ten years and beyond requires down link throughput on the order of several terabits per day. The ability to handle such a large volume of data far exceeds the capabilities of current systems. This paper proposes two solutions, first, a high data rate link between the LEO spacecraft and ground via relay satellites in geostationary orbit (GEO). Second, a high data rate direct to ground link from LEO. Next, the paper presents results from computer simulations carried out for both types of links taking into consideration spacecraft transmitter frequency, EIRP, and waveform; elevation angle dependent path loss through Earths atmosphere, and ground station receiver GT.
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Printing Proteins as Microarrays for High-Throughput Function Determination
NASA Astrophysics Data System (ADS)
MacBeath, Gavin; Schreiber, Stuart L.
2000-09-01
Systematic efforts are currently under way to construct defined sets of cloned genes for high-throughput expression and purification of recombinant proteins. To facilitate subsequent studies of protein function, we have developed miniaturized assays that accommodate extremely low sample volumes and enable the rapid, simultaneous processing of thousands of proteins. A high-precision robot designed to manufacture complementary DNA microarrays was used to spot proteins onto chemically derivatized glass slides at extremely high spatial densities. The proteins attached covalently to the slide surface yet retained their ability to interact specifically with other proteins, or with small molecules, in solution. Three applications for protein microarrays were demonstrated: screening for protein-protein interactions, identifying the substrates of protein kinases, and identifying the protein targets of small molecules.
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Wang, Saihua; Niu, Hongyun; Cai, Yaqi; Cao, Dong
2018-05-01
High-throughput and rapid detection of hazardous compounds in complicated samples is essential for the solution of environmental problems. We have prepared a "pH-paper-like" chip which can rapidly "indicate" the occurrence of organic contaminants just through dipping the chip in water samples for short time followed by fast analysis with surface-assisted laser desorption/ionization time-of-flight mass spectrometry (SALDI-TOF MS). The chips are composed of polyvinylidene fluoride membrane (PVDFM), polydopamine (PDA) film and Au nanoparticles (Au NPs), which are layer-by-layer assembled according to the adhesion, self-polymerization and reduction property of dopamine. In the Au NPs loaded polydopamine-polyvinylidene fluoride membrane (Au NPs-PDA-PVDFM) chips, PVDFM combined with PDA film are responsible for the enrichment of organic analyte through hydrophobic interactions and π-π stacking; Au NPs serve as effective SALDI matrix for the rapid detection of target analyte. After dipping into water solution for minutes, the Au-PDA-PVDFM chips with enriched organic analytes can be detected directly with SALDI-TOF MS. The good solid-phase extraction performance of the PDA-PVDFM components, remarkable matrix effect of the loaded AuNPs, and sensitivity of the SALDI-TOF MS technique ensure excellent sensitivity and reproducibility for the quantification of trace levels of organic contaminants in environmental water samples. Copyright © 2018 Elsevier B.V. All rights reserved.
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KIM, JAE HYUN; JOSHI, SANGEETA B.; MIDDAUGH, C. RUSSELL; TOLBERT, THOMAS J.; VOLKIN, DAVID B.
2014-01-01
The structural integrity and conformational stability of various IgG1-Fc proteins produced from the yeast Pichia pastoris with different glycosylation site occupancy (di-, mono-, and non- glycosylated) was determined. In addition, the physical stability profiles of three different forms of non-glycosylated Fc molecules (varying amino acid residues at site 297 in the CH2 domain due to point mutations and enzymatic digestion of the Fc glycoforms) were also examined. The physical stability of these IgG1-Fc glycoproteins was examined as a function of pH and temperature by high throughput biophysical analysis using multiple techniques combined with data visualization tools (three index empirical phase diagrams and radar charts). Across the pH range of 4.0 to 6.0, the di- and mono- glycosylated forms of the IgG1-Fc showed the highest and lowest levels of physical stability respectively, with the non-glycosylated forms showing intermediate stability depending on solution pH. In the aglycosylated Fc proteins, the introduction of Asp (D) residues at site 297 (QQ vs. DN vs. DD forms) resulted in more subtle changes in structural integrity and physical stability depending on solution pH. The utility of evaluating the conformational stability profile differences between the various IgG1-Fc glycoproteins is discussed in the context of analytical comparability studies. PMID:24740840
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Luo, Alan A; Zhao, Ji-Cheng; Riggi, Adrienne
The objective of the proposed study is to establish a scientific foundation on kinetic modeling of diffusion, phase precipitation, and casting/solidification, in order to accelerate the design and optimization of cast magnesium (Mg) alloys for weight reduction of U.S. automotive fleet. The team has performed the following tasks: 1) study diffusion kinetics of various Mg-containing binary systems using high-throughput diffusion multiples to establish reliable diffusivity and mobility databases for the Mg-aluminum (Al)-zinc (Zn)-tin (Sn)-calcium (Ca)-strontium (Sr)-manganese (Mn) systems; 2) study the precipitation kinetics (nucleation, growth and coarsening) using both innovative dual-anneal diffusion multiples and cast model alloys to provide largemore » amounts of kinetic data (including interfacial energy) and microstructure atlases to enable implementation of the Kampmann-Wagner numerical model to simulate phase transformation kinetics of non-spherical/non-cuboidal precipitates in Mg alloys; 3) implement a micromodel to take into account back diffusion in the solid phase in order to predict microstructure and microsegregation in multicomponent Mg alloys during dendritic solidification especially under high pressure die-casting (HPDC) conditions; and, 4) widely disseminate the data, knowledge and information using the Materials Genome Initiative infrastructure (http://www.mgidata.org) as well as publications and digital data sharing to enable researchers to identify new pathways/routes to better cast Mg alloys.« less
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Modeling Reproductive Toxicity for Chemical Prioritization into an Integrated Testing Strategy
The EPA ToxCast research program uses a high-throughput screening (HTS) approach for predicting the toxicity of large numbers of chemicals. Phase-I tested 309 well-characterized chemicals in over 500 assays of different molecular targets, cellular responses and cell-states. Of th...
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SEPARATION OF HAFNIUM FROM ZIRCONIUM
Overholser, L.B.; Barton, C.J. Sr.; Ramsey, J.W.
1960-05-31
The separation of hafnium impurities from zirconium can be accomplished by means of organic solvent extraction. The hafnium-containing zirconium feed material is dissolved in an aqueous chloride solution and the resulting solution is contacted with an organic hexone phase, with at least one of the phases containing thiocyanate. The hafnium is extracted into the organic phase while zirconium remains in the aqueous phase. Further recovery of zirconium is effected by stripping the onganic phase with a hydrochloric acid solution and commingling the resulting strip solution with the aqueous feed solution. Hexone is recovered and recycled by means of scrubbing the onganic phase with a sulfuric acid solution to remove the hafnium, and thiocyanate is recovered and recycled by means of neutralizing the effluent streams to obtain ammonium thiocyanate.
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NASA Astrophysics Data System (ADS)
Yan, Zongkai; Zhang, Xiaokun; Li, Guang; Cui, Yuxing; Jiang, Zhaolian; Liu, Wen; Peng, Zhi; Xiang, Yong
2018-01-01
The conventional methods for designing and preparing thin film based on wet process remain a challenge due to disadvantages such as time-consuming and ineffective, which hinders the development of novel materials. Herein, we present a high-throughput combinatorial technique for continuous thin film preparation relied on chemical bath deposition (CBD). The method is ideally used to prepare high-throughput combinatorial material library with low decomposition temperatures and high water- or oxygen-sensitivity at relatively high-temperature. To check this system, a Cu(In, Ga)Se (CIGS) thin films library doped with 0-19.04 at.% of antimony (Sb) was taken as an example to evaluate the regulation of varying Sb doping concentration on the grain growth, structure, morphology and electrical properties of CIGS thin film systemically. Combined with the Energy Dispersive Spectrometer (EDS), X-ray Photoelectron Spectroscopy (XPS), automated X-ray Diffraction (XRD) for rapid screening and Localized Electrochemical Impedance Spectroscopy (LEIS), it was confirmed that this combinatorial high-throughput system could be used to identify the composition with the optimal grain orientation growth, microstructure and electrical properties systematically, through accurately monitoring the doping content and material composition. According to the characterization results, a Sb2Se3 quasi-liquid phase promoted CIGS film-growth model has been put forward. In addition to CIGS thin film reported here, the combinatorial CBD also could be applied to the high-throughput screening of other sulfide thin film material systems.
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Recovery of sugars from ionic liquid biomass liquor by solvent extraction
Brennan, Timothy Charles R.; Holmes, Bradley M.; Simmons, Blake A.; Blanch, Harvey W.
2015-10-13
The present invention provides for a composition comprising a solution comprising (a) an ionic liquid (IL) or ionic liquid-aqueous (ILA) phase and (b) an organic phase, wherein the solution comprises a sugar and a boronic acid. The present invention also provides for a method of removing a sugar from a solution, comprising: (a) providing a solution comprising (i) an IL or ILA phase and (ii) an organic phase, wherein the solution comprises an IL, a sugar and a boronic acid; (b) contacting the sugar with the boronic acid to form a sugar-boronic acid complex, (c) separating the organic phase and the aqueous phase, wherein the organic phase contains the sugar-boronic acid complex, and optionally (d) separating the sugar from the organic phase.
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NASA Astrophysics Data System (ADS)
Goring, S. J.; Richard, S. M.; Williams, J. W.; Dawson, A.
2017-12-01
A broad array of data resources, across disciplines, are needed to study Earth system processes operating at multiple spatial or temporal scales. Data friction frequently delays this integrative and interdisciplinary research, while sustainable solutions may be hampered as a result of academic incentives that penalize technical "tool building" at the expense of research publication. The paleogeosciences, in particular, often integrate data drawn from multiple sub-disciplines and from a range of long-tail and big data sources. Data friction can be lowered and the pace of scientific discovery accelerated through the development and adoption of data standards, both within the paleogeosciences and with allied disciplines. Using the PalEON Project (https://sites.nd.edu/paleonproject/) and the Neotoma Paleoecological Database (https://neotomadb.org) as focal case studies, we first illustrate the advances possible through data standardization. We then focus on new efforts in data standardization and building linkages among paleodata resources underway through the EarthCube-funded Throughput project. A first step underway is to analyze existing standards across paleo-data repositories and identify ways in which the adoption of common standards can promote connectivity, reducing barriers to interdisciplinary research, especially for early career researchers. Experience indicates that standards tend to emerge by necessity and from a mixture of bottom-up and top-down processes. A common pathway is when conventions developed to solve specific problems within a community are extended to address challenges that are more general. The Throughput project will identify, document, and promote such solutions to foster wider adoption of standards for data interchange and reduce data friction in the paleogeosciences.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Milyutin, V.V.; Gelis, V.M.; Penzin, R.A.
1995-12-31
In this paper the results obtained in field tests of decontaminating radioactive natural and industrial solutions of different chemical and radionuclide composition from cesium and strontium radionuclides are reported. Decontamination of industrial reservoir water at the Production Association Mayak (Chelyabinsk Region, Russia) was performed using CMP synthetic zeolite. Efficient decontamination of the feed water is achieved after preliminary precipitation of hardness salts in the form of carbonates. Decontamination of water from the pool for spent fuel element storage from {sup 137}Cs was conducted using NGA ferricyanide sorbent. Decontamination factors with respect to {sup 137}Cs of 400 have been reached, themore » installation throughput being 100,000 by (bed volumes). Decontamination of liquid radwaste at Murmansk Shipping Co was conducted with CFB, CMP synthetic zeolites and NGA ferricyanide sorbent as well. Decontamination of D and D solutions and wastes of the special laundry resulted in decontamination factors within the range of 20--400, 10--100, and 10--30 with respect to {sup 137}Cs, {sup 90}Sr, and total {beta}-activity, respectively. Installation throughput of 3,000--5,000 bv for zeolites and 8,000--10,000 bv for ferrocyanide sorbents has been reached. Results obtained prove the high efficiency of sorption technique for decontaminating solutions from cesium and strontium radionuclides.« less
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Round, Adam; Felisaz, Franck; Fodinger, Lukas; Gobbo, Alexandre; Huet, Julien; Villard, Cyril; Blanchet, Clement E.; Pernot, Petra; McSweeney, Sean; Roessle, Manfred; Svergun, Dmitri I.; Cipriani, Florent
2015-01-01
Small-angle X-ray scattering (SAXS) of macromolecules in solution is in increasing demand by an ever more diverse research community, both academic and industrial. To better serve user needs, and to allow automated and high-throughput operation, a sample changer (BioSAXS Sample Changer) that is able to perform unattended measurements of up to several hundred samples per day has been developed. The Sample Changer is able to handle and expose sample volumes of down to 5 µl with a measurement/cleaning cycle of under 1 min. The samples are stored in standard 96-well plates and the data are collected in a vacuum-mounted capillary with automated positioning of the solution in the X-ray beam. Fast and efficient capillary cleaning avoids cross-contamination and ensures reproducibility of the measurements. Independent temperature control for the well storage and for the measurement capillary allows the samples to be kept cool while still collecting data at physiological temperatures. The Sample Changer has been installed at three major third-generation synchrotrons: on the BM29 beamline at the European Synchrotron Radiation Facility (ESRF), the P12 beamline at the PETRA-III synchrotron (EMBL@PETRA-III) and the I22/B21 beamlines at Diamond Light Source, with the latter being the first commercial unit supplied by Bruker ASC. PMID:25615861
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SVS: data and knowledge integration in computational biology.
Zycinski, Grzegorz; Barla, Annalisa; Verri, Alessandro
2011-01-01
In this paper we present a framework for structured variable selection (SVS). The main concept of the proposed schema is to take a step towards the integration of two different aspects of data mining: database and machine learning perspective. The framework is flexible enough to use not only microarray data, but other high-throughput data of choice (e.g. from mass spectrometry, microarray, next generation sequencing). Moreover, the feature selection phase incorporates prior biological knowledge in a modular way from various repositories and is ready to host different statistical learning techniques. We present a proof of concept of SVS, illustrating some implementation details and describing current results on high-throughput microarray data.
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Assembly and diploid architecture of an individual human genome via single-molecule technologies
Pendleton, Matthew; Sebra, Robert; Pang, Andy Wing Chun; Ummat, Ajay; Franzen, Oscar; Rausch, Tobias; Stütz, Adrian M; Stedman, William; Anantharaman, Thomas; Hastie, Alex; Dai, Heng; Fritz, Markus Hsi-Yang; Cao, Han; Cohain, Ariella; Deikus, Gintaras; Durrett, Russell E; Blanchard, Scott C; Altman, Roger; Chin, Chen-Shan; Guo, Yan; Paxinos, Ellen E; Korbel, Jan O; Darnell, Robert B; McCombie, W Richard; Kwok, Pui-Yan; Mason, Christopher E; Schadt, Eric E; Bashir, Ali
2015-01-01
We present the first comprehensive analysis of a diploid human genome that combines single-molecule sequencing with single-molecule genome maps. Our hybrid assembly markedly improves upon the contiguity observed from traditional shotgun sequencing approaches, with scaffold N50 values approaching 30 Mb, and we identified complex structural variants (SVs) missed by other high-throughput approaches. Furthermore, by combining Illumina short-read data with long reads, we phased both single-nucleotide variants and SVs, generating haplotypes with over 99% consistency with previous trio-based studies. Our work shows that it is now possible to integrate single-molecule and high-throughput sequence data to generate de novo assembled genomes that approach reference quality. PMID:26121404
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2011-11-15
uncle) fcc (uncle) hcp (uncle) phase-diagram Ag Al Al Au Au Bi Bi Ca Ca Cd Cd Ce Ce Co Co Cr Cr Cu Cu Fe Fe Ga Ga Gd Gd Ge Ge Hf...Hf Hg Hg In In Ir Ir La La Li Li Mg Mg Mn Mn Mo Mo Na Na Nb Nb Ni Ni Os Os Pb Pb Pd Pd Pt Pt Rb Rb Re Re Rh Rh Ru Ru Sb Sb Sc...2 S. Curtarolo, A. N. Kolmogorov, and F. H. Cocks, High-throughput ab initio analysis of the Bi-In, Bi- Mg , Bi-Sb, In- Mg , In-Sb, and Mg -Sb systems
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Assembly and diploid architecture of an individual human genome via single-molecule technologies.
Pendleton, Matthew; Sebra, Robert; Pang, Andy Wing Chun; Ummat, Ajay; Franzen, Oscar; Rausch, Tobias; Stütz, Adrian M; Stedman, William; Anantharaman, Thomas; Hastie, Alex; Dai, Heng; Fritz, Markus Hsi-Yang; Cao, Han; Cohain, Ariella; Deikus, Gintaras; Durrett, Russell E; Blanchard, Scott C; Altman, Roger; Chin, Chen-Shan; Guo, Yan; Paxinos, Ellen E; Korbel, Jan O; Darnell, Robert B; McCombie, W Richard; Kwok, Pui-Yan; Mason, Christopher E; Schadt, Eric E; Bashir, Ali
2015-08-01
We present the first comprehensive analysis of a diploid human genome that combines single-molecule sequencing with single-molecule genome maps. Our hybrid assembly markedly improves upon the contiguity observed from traditional shotgun sequencing approaches, with scaffold N50 values approaching 30 Mb, and we identified complex structural variants (SVs) missed by other high-throughput approaches. Furthermore, by combining Illumina short-read data with long reads, we phased both single-nucleotide variants and SVs, generating haplotypes with over 99% consistency with previous trio-based studies. Our work shows that it is now possible to integrate single-molecule and high-throughput sequence data to generate de novo assembled genomes that approach reference quality.
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Ehrenworth, Amy M; Claiborne, Tauris; Peralta-Yahya, Pamela
2017-10-17
Chemical biosensors, for which chemical detection triggers a fluorescent signal, have the potential to accelerate the screening of noncolorimetric chemicals produced by microbes, enabling the high-throughput engineering of enzymes and metabolic pathways. Here, we engineer a G-protein-coupled receptor (GPCR)-based sensor to detect serotonin produced by a producer microbe in the producer microbe's supernatant. Detecting a chemical in the producer microbe's supernatant is nontrivial because of the number of other metabolites and proteins present that could interfere with sensor performance. We validate the two-cell screening system for medium-throughput applications, opening the door to the rapid engineering of microbes for the increased production of serotonin. We focus on serotonin detection as serotonin levels limit the microbial production of hydroxystrictosidine, a modified alkaloid that could accelerate the semisynthesis of camptothecin-derived anticancer pharmaceuticals. This work shows the ease of generating GPCR-based chemical sensors and their ability to detect specific chemicals in complex aqueous solutions, such as microbial spent medium. In addition, this work sets the stage for the rapid engineering of serotonin-producing microbes.
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Arrayed water-in-oil droplet bilayers for membrane transport analysis.
Watanabe, R; Soga, N; Hara, M; Noji, H
2016-08-02
The water-in-oil droplet bilayer is a simple and useful lipid bilayer system for membrane transport analysis. The droplet interface bilayer is readily formed by the contact of two water-in-oil droplets enwrapped by a phospholipid monolayer. However, the size of individual droplets with femtoliter volumes in a high-throughput manner is difficult to control, resulting in low sensitivity and throughput of membrane transport analysis. To overcome this drawback, in this study, we developed a novel micro-device in which a large number of droplet interface bilayers (>500) are formed at a time by using femtoliter-sized droplet arrays immobilized on a hydrophobic/hydrophilic substrate. The droplet volume was controllable from 3.5 to 350 fL by changing the hydrophobic/hydrophilic pattern on the device, allowing high-throughput analysis of membrane transport mechanisms including membrane permeability to solutes (e.g., ions or small molecules) with or without the aid of transport proteins. Thus, this novel platform broadens the versatility of water-in-oil droplet bilayers and will pave the way for novel analytical and pharmacological applications such as drug screening.
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A compact imaging spectroscopic system for biomolecular detections on plasmonic chips.
Lo, Shu-Cheng; Lin, En-Hung; Wei, Pei-Kuen; Tsai, Wan-Shao
2016-10-17
In this study, we demonstrate a compact imaging spectroscopic system for high-throughput detection of biomolecular interactions on plasmonic chips, based on a curved grating as the key element of light diffraction and light focusing. Both the curved grating and the plasmonic chips are fabricated on flexible plastic substrates using a gas-assisted thermal-embossing method. A fiber-coupled broadband light source and a camera are included in the system. Spectral resolution within 1 nm is achieved in sensing environmental index solutions and protein bindings. The detected sensitivities of the plasmonic chip are comparable with a commercial spectrometer. An extra one-dimensional scanning stage enables high-throughput detection of protein binding on a designed plasmonic chip consisting of several nanoslit arrays with different periods. The detected resonance wavelengths match well with the grating equation under an air environment. Wavelength shifts between 1 and 9 nm are detected for antigens of various concentrations binding with antibodies. A simple, mass-productive and cost-effective method has been demonstrated on the imaging spectroscopic system for real-time, label-free, highly sensitive and high-throughput screening of biomolecular interactions.
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Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens.
Morgens, David W; Wainberg, Michael; Boyle, Evan A; Ursu, Oana; Araya, Carlos L; Tsui, C Kimberly; Haney, Michael S; Hess, Gaelen T; Han, Kyuho; Jeng, Edwin E; Li, Amy; Snyder, Michael P; Greenleaf, William J; Kundaje, Anshul; Bassik, Michael C
2017-05-05
CRISPR-Cas9 screens are powerful tools for high-throughput interrogation of genome function, but can be confounded by nuclease-induced toxicity at both on- and off-target sites, likely due to DNA damage. Here, to test potential solutions to this issue, we design and analyse a CRISPR-Cas9 library with 10 variable-length guides per gene and thousands of negative controls targeting non-functional, non-genic regions (termed safe-targeting guides), in addition to non-targeting controls. We find this library has excellent performance in identifying genes affecting growth and sensitivity to the ricin toxin. The safe-targeting guides allow for proper control of toxicity from on-target DNA damage. Using this toxicity as a proxy to measure off-target cutting, we demonstrate with tens of thousands of guides both the nucleotide position-dependent sensitivity to single mismatches and the reduction of off-target cutting using truncated guides. Our results demonstrate a simple strategy for high-throughput evaluation of target specificity and nuclease toxicity in Cas9 screens.
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Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens
Morgens, David W.; Wainberg, Michael; Boyle, Evan A.; Ursu, Oana; Araya, Carlos L.; Tsui, C. Kimberly; Haney, Michael S.; Hess, Gaelen T.; Han, Kyuho; Jeng, Edwin E.; Li, Amy; Snyder, Michael P.; Greenleaf, William J.; Kundaje, Anshul; Bassik, Michael C.
2017-01-01
CRISPR-Cas9 screens are powerful tools for high-throughput interrogation of genome function, but can be confounded by nuclease-induced toxicity at both on- and off-target sites, likely due to DNA damage. Here, to test potential solutions to this issue, we design and analyse a CRISPR-Cas9 library with 10 variable-length guides per gene and thousands of negative controls targeting non-functional, non-genic regions (termed safe-targeting guides), in addition to non-targeting controls. We find this library has excellent performance in identifying genes affecting growth and sensitivity to the ricin toxin. The safe-targeting guides allow for proper control of toxicity from on-target DNA damage. Using this toxicity as a proxy to measure off-target cutting, we demonstrate with tens of thousands of guides both the nucleotide position-dependent sensitivity to single mismatches and the reduction of off-target cutting using truncated guides. Our results demonstrate a simple strategy for high-throughput evaluation of target specificity and nuclease toxicity in Cas9 screens. PMID:28474669
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Yang, Bin; Lamb, Michelle L; Zhang, Tao; Hennessy, Edward J; Grewal, Gurmit; Sha, Li; Zambrowski, Mark; Block, Michael H; Dowling, James E; Su, Nancy; Wu, Jiaquan; Deegan, Tracy; Mikule, Keith; Wang, Wenxian; Kaspera, Rüdiger; Chuaqui, Claudio; Chen, Huawei
2014-12-11
KIFC1 (HSET), a member of the kinesin-14 family of motor proteins, plays an essential role in centrosomal bundling in cancer cells, but its function is not required for normal diploid cell division. To explore the potential of KIFC1 as a therapeutic target for human cancers, a series of potent KIFC1 inhibitors featuring a phenylalanine scaffold was developed from hits identified through high-throughput screening (HTS). Optimization of the initial hits combined both design-synthesis-test cycles and an integrated high-throughput synthesis and biochemical screening method. An important aspect of this integrated method was the utilization of DMSO stock solutions of compounds registered in the corporate compound collection as synthetic reactants. Using this method, over 1500 compounds selected for structural diversity were quickly assembled in assay-ready 384-well plates and were directly tested after the necessary dilutions. Our efforts led to the discovery of a potent KIFC1 inhibitor, AZ82, which demonstrated the desired centrosome declustering mode of action in cell studies.
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NASA Astrophysics Data System (ADS)
Lan, Ding-Hung; Hong, Shao-Huan; Chou, Li-Hui; Wang, Xiao-Feng; Liu, Cheng-Liang
2018-06-01
Organometal halide perovskite materials have demonstrated tremendous advances in the photovoltaic field recently because of their advantageous features of simple fabrication and high power conversion efficiency. To meet the high demand for high throughput and cost-effective, we present a wet process method that enables the probing of the parameters for perovskite layer deposition through two-step sequential ultrasonic spray-coating. This paper describes a detailed investigation on the effects of modification of spray precursor solution (PbI2 and CH3NH3I precursor concentration and solvents used) and post-annealing condition (temperature and time), which can be performed to create optimal film quality as well as improve device efficiency. Through the systematic optimization, the inverted planar perovskite solar cells show the reproducible photovoltaic properties with best power conversion efficiency (PCE) of 10.40% and average PCE of 9.70 ± 0.40%. A continuous spray-coating technique for rapid fabrication of total 16 pieces of perovskite films was demonstrated for providing a viable alternative for the high throughput production of the perovskite solar cells.
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Amsden, Jason J; Herr, Philip J; Landry, David M W; Kim, William; Vyas, Raul; Parker, Charles B; Kirley, Matthew P; Keil, Adam D; Gilchrist, Kristin H; Radauscher, Erich J; Hall, Stephen D; Carlson, James B; Baldasaro, Nicholas; Stokes, David; Di Dona, Shane T; Russell, Zachary E; Grego, Sonia; Edwards, Steven J; Sperline, Roger P; Denton, M Bonner; Stoner, Brian R; Gehm, Michael E; Glass, Jeffrey T
2018-02-01
Despite many potential applications, miniature mass spectrometers have had limited adoption in the field due to the tradeoff between throughput and resolution that limits their performance relative to laboratory instruments. Recently, a solution to this tradeoff has been demonstrated by using spatially coded apertures in magnetic sector mass spectrometers, enabling throughput and signal-to-background improvements of greater than an order of magnitude with no loss of resolution. This paper describes a proof of concept demonstration of a cycloidal coded aperture miniature mass spectrometer (C-CAMMS) demonstrating use of spatially coded apertures in a cycloidal sector mass analyzer for the first time. C-CAMMS also incorporates a miniature carbon nanotube (CNT) field emission electron ionization source and a capacitive transimpedance amplifier (CTIA) ion array detector. Results confirm the cycloidal mass analyzer's compatibility with aperture coding. A >10× increase in throughput was achieved without loss of resolution compared with a single slit instrument. Several areas where additional improvement can be realized are identified. Graphical Abstract ᅟ.
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NASA Astrophysics Data System (ADS)
Amsden, Jason J.; Herr, Philip J.; Landry, David M. W.; Kim, William; Vyas, Raul; Parker, Charles B.; Kirley, Matthew P.; Keil, Adam D.; Gilchrist, Kristin H.; Radauscher, Erich J.; Hall, Stephen D.; Carlson, James B.; Baldasaro, Nicholas; Stokes, David; Di Dona, Shane T.; Russell, Zachary E.; Grego, Sonia; Edwards, Steven J.; Sperline, Roger P.; Denton, M. Bonner; Stoner, Brian R.; Gehm, Michael E.; Glass, Jeffrey T.
2018-02-01
Despite many potential applications, miniature mass spectrometers have had limited adoption in the field due to the tradeoff between throughput and resolution that limits their performance relative to laboratory instruments. Recently, a solution to this tradeoff has been demonstrated by using spatially coded apertures in magnetic sector mass spectrometers, enabling throughput and signal-to-background improvements of greater than an order of magnitude with no loss of resolution. This paper describes a proof of concept demonstration of a cycloidal coded aperture miniature mass spectrometer (C-CAMMS) demonstrating use of spatially coded apertures in a cycloidal sector mass analyzer for the first time. C-CAMMS also incorporates a miniature carbon nanotube (CNT) field emission electron ionization source and a capacitive transimpedance amplifier (CTIA) ion array detector. Results confirm the cycloidal mass analyzer's compatibility with aperture coding. A >10× increase in throughput was achieved without loss of resolution compared with a single slit instrument. Several areas where additional improvement can be realized are identified.
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Lu, Zhi-Yan; Guo, Xiao-Jue; Li, Hui; Huang, Zhong-Zi; Lin, Kuang-Fei; Liu, Yong-Di
2015-01-01
A high-throughput screening system for moderately halophilic phenol-degrading bacteria from various habitats was developed to replace the conventional strain screening owing to its high efficiency. Bacterial enrichments were cultivated in 48 deep well microplates instead of shake flasks or tubes. Measurement of phenol concentrations was performed in 96-well microplates instead of using the conventional spectrophotometric method or high-performance liquid chromatography (HPLC). The high-throughput screening system was used to cultivate forty-three bacterial enrichments and gained a halophilic bacterial community E3 with the best phenol-degrading capability. Halomonas sp. strain 4-5 was isolated from the E3 community. Strain 4-5 was able to degrade more than 94% of the phenol (500 mg·L−1 starting concentration) over a range of 3%–10% NaCl. Additionally, the strain accumulated the compatible solute, ectoine, with increasing salt concentrations. PCR detection of the functional genes suggested that the largest subunit of multicomponent phenol hydroxylase (LmPH) and catechol 1,2-dioxygenase (C12O) were active in the phenol degradation process. PMID:26020478
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NASA Astrophysics Data System (ADS)
Malloy, Matt; Thiel, Brad; Bunday, Benjamin D.; Wurm, Stefan; Mukhtar, Maseeh; Quoi, Kathy; Kemen, Thomas; Zeidler, Dirk; Eberle, Anna Lena; Garbowski, Tomasz; Dellemann, Gregor; Peters, Jan Hendrik
2015-03-01
SEMATECH aims to identify and enable disruptive technologies to meet the ever-increasing demands of semiconductor high volume manufacturing (HVM). As such, a program was initiated in 2012 focused on high-speed e-beam defect inspection as a complement, and eventual successor, to bright field optical patterned defect inspection [1]. The primary goal is to enable a new technology to overcome the key gaps that are limiting modern day inspection in the fab; primarily, throughput and sensitivity to detect ultra-small critical defects. The program specifically targets revolutionary solutions based on massively parallel e-beam technologies, as opposed to incremental improvements to existing e-beam and optical inspection platforms. Wafer inspection is the primary target, but attention is also being paid to next generation mask inspection. During the first phase of the multi-year program multiple technologies were reviewed, a down-selection was made to the top candidates, and evaluations began on proof of concept systems. A champion technology has been selected and as of late 2014 the program has begun to move into the core technology maturation phase in order to enable eventual commercialization of an HVM system. Performance data from early proof of concept systems will be shown along with roadmaps to achieving HVM performance. SEMATECH's vision for moving from early-stage development to commercialization will be shown, including plans for development with industry leading technology providers.
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The U.S. EPA's ToxCast Chemical Screening Program and Predictive Modeling of Toxicity
The ToxCast program was developed by the U.S. EPA's National Center for Computational Toxicology to provide cost-effective high-throughput screening for the potential toxicity of thousands of chemicals. Phase I screened 309 compounds in over 500 assays to evaluate concentration-...
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Gas-Phase Molecular Probe For High Throughput Screening
The U.S. EPA is responsible for evaluating the effects of approximately 80,000 chemicals registered for use in the USA. In addition, approximately 1,000 chemicals are added to this list each year. Due to the vast number of chemicals, it is impossible to conduct traditional toxi...
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The aryl hydrocarbon receptor (AhR) is a transcription factor that mediates adaptive responses to known environmental pollutants, such as aromatic hydrocarbons, through regulation of Phase I and II xenobiotic metabolizing enzymes as well as important growth and differentiation pa...
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USDA-ARS?s Scientific Manuscript database
We describe a suite of software tools for identifying possible functional changes in gene structure that may result from sequence variants. ACE (“Assessing Changes to Exons”) converts phased genotype calls to a collection of explicit haplotype sequences, maps transcript annotations onto them, detect...
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The EPA ToxCast research program uses a high-throughput screening (HTS) approach for predicting the toxicity of large numbers of chemicals. Phase-I tested 309 well-characterized chemicals (mostly pesticides) in over 500 assays of different molecular targets, cellular responses an...
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Momentum has been growing in Toxicology to assess the utility of high-throughput screening (HTS) assays in the determination of chemical testing priorities. However, in vitro potencies determined in these assays do not consider in vivo bioavailability, clearance or exposure estim...
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Gas Phase Probe Molecules for Assessing In vitro Metabolism to Infer an In vivo Response
Efficient and accurate in vitro high-throughput screening (HTS) methods use cellular and molecular based adverse outcome pathways (AOPs) as central elements for exposure assessment and chemical prioritization. However, not all AOPs are based on human or animal systems biology, bu...
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A Dedicated Micro-Tomography Beamline For The Australian Synchrotron
DOE Office of Scientific and Technical Information (OSTI.GOV)
Mayo, Sheridan C.; Stevenson, Andrew W.; Wilkins, Stephen W.
2010-07-23
A dedicated micro-tomography beamline is proposed for the Australian Synchrotron. It will enable high-resolution micro-tomography with resolution below a micron and supporting phase-contrast imaging modes. A key feature of the beamline will be high-throughput/high-speed operation enabling near real-time micro-tomography.
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The EPA ToxCast™ research program uses a high-throughput screening (HTS) approach for predicting the toxicity of large numbers of chemicals. Phase-I contains 309 well-characterized chemicals which are mostly pesticides tested in over 600 assays of different molecular targets, cel...
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Mlinaric, Ana; Milos, Marija; Coen Herak, Désirée; Fucek, Mirjana; Rimac, Vladimira; Zadro, Renata; Rogic, Dunja
2018-02-23
The need to satisfy high-throughput demands for laboratory tests continues to be a challenge. Therefore, we aimed to automate postanalytical phase in hematology and coagulation laboratory by autovalidation of complete blood count (CBC) and routine coagulation test results (prothrombin time [PT], international normalized ratio [PT-INR], activated partial thromboplastin time [APTT], fibrinogen, antithrombin activity [AT] and thrombin time [TT]). Work efficacy and turnaround time (TAT) before and after implementation of automated solutions will be compared. Ordering panels tailored to specific patient populations were implemented. Rerun and reflex testing rules were set in the respective analyzers' software (Coulter DxH Connectivity 1601, Beckman Coulter, FL, USA; AutoAssistant, Siemens Healthcare Diagnostics, Germany), and sample status information was transferred into the laboratory information system. To evaluate if the automation improved TAT and efficacy, data from manually verified results in September and October of 2015 were compared with the corresponding period in 2016 when autovalidation was implemented. Autovalidation rates of 63% for CBC and 65% for routine coagulation test results were achieved. At the TAT of 120 min, the percentage of reported results increased substantially for all analyzed tests, being above 90% for CBC, PT, PT-INR and fibrinogen and 89% for APTT. This output was achieved with three laboratory technicians less compared with the period when the postanalytical phase was not automated. Automation allowed optimized laboratory workflow for specific patient populations, thereby ensuring standardized results reporting. Autovalidation of test results proved to be an efficient tool for improvement of laboratory work efficacy and TAT.
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Modelling Assisted Design and Synthesis of Highly Porous Materials for Chemical Adsorbents
2010-10-01
two phases of crystal, a monoclinic phase within the solution, and after removal from solution a trigonal phase is obtained. The single crystal...days. Single crystal X-ray data showed there existed a monoclinic phase within the solution that, upon removal from solution, rapidly converted to a... monoclinic to trigonal upon desolvation, as the new peak which has emerged matches the simulated PXRD of the trigonal phase. Also, as the sample is
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Hybrid WDM/OCDMA for next generation access network
NASA Astrophysics Data System (ADS)
Wang, Xu; Wada, Naoya; Miyazaki, T.; Cincotti, G.; Kitayama, Ken-ichi
2007-11-01
Hybrid wavelength division multiplexing/optical code division multiple access (WDM/OCDMA) passive optical network (PON), where asynchronous OCDMA traffic transmits over WDM network, can be one potential candidate for gigabit-symmetric fiber-to-the-home (FTTH) services. In a cost-effective WDM/OCDMA network, a large scale multi-port encoder/decoder can be employed in the central office, and a low cost encoder/decoder will be used in optical network unit (ONU). The WDM/OCDMA system could be one promising solution to the symmetric high capacity access network with high spectral efficiency, cost effective, good flexibility and enhanced security. Asynchronous WDM/OCDMA systems have been experimentally demonstrated using superstructured fiber Bragg gratings (SSFBG) and muti-port OCDMA en/decoders. The total throughput has reached above Tera-bit/s with spectral efficiency of about 0.41. The key enabling techniques include ultra-long SSFBG, multi-port E/D with high power contrast ratio, optical thresholding, differential phase shift keying modulation with balanced detection, forward error correction, and etc. Using multi-level modulation formats to carry multi-bit information with single pulse, the total capacity and spectral efficiency could be further enhanced.
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A system architecture for online data interpretation and reduction in fluorescence microscopy
NASA Astrophysics Data System (ADS)
Röder, Thorsten; Geisbauer, Matthias; Chen, Yang; Knoll, Alois; Uhl, Rainer
2010-01-01
In this paper we present a high-throughput sample screening system that enables real-time data analysis and reduction for live cell analysis using fluorescence microscopy. We propose a novel system architecture capable of analyzing a large amount of samples during the experiment and thus greatly minimizing the post-analysis phase that is the common practice today. By utilizing data reduction algorithms, relevant information of the target cells is extracted from the online collected data stream, and then used to adjust the experiment parameters in real-time, allowing the system to dynamically react on changing sample properties and to control the microscope setup accordingly. The proposed system consists of an integrated DSP-FPGA hybrid solution to ensure the required real-time constraints, to execute efficiently the underlying computer vision algorithms and to close the perception-action loop. We demonstrate our approach by addressing the selective imaging of cells with a particular combination of markers. With this novel closed-loop system the amount of superfluous collected data is minimized, while at the same time the information entropy increases.
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Microarray R-based analysis of complex lysate experiments with MIRACLE
List, Markus; Block, Ines; Pedersen, Marlene Lemvig; Christiansen, Helle; Schmidt, Steffen; Thomassen, Mads; Tan, Qihua; Baumbach, Jan; Mollenhauer, Jan
2014-01-01
Motivation: Reverse-phase protein arrays (RPPAs) allow sensitive quantification of relative protein abundance in thousands of samples in parallel. Typical challenges involved in this technology are antibody selection, sample preparation and optimization of staining conditions. The issue of combining effective sample management and data analysis, however, has been widely neglected. Results: This motivated us to develop MIRACLE, a comprehensive and user-friendly web application bridging the gap between spotting and array analysis by conveniently keeping track of sample information. Data processing includes correction of staining bias, estimation of protein concentration from response curves, normalization for total protein amount per sample and statistical evaluation. Established analysis methods have been integrated with MIRACLE, offering experimental scientists an end-to-end solution for sample management and for carrying out data analysis. In addition, experienced users have the possibility to export data to R for more complex analyses. MIRACLE thus has the potential to further spread utilization of RPPAs as an emerging technology for high-throughput protein analysis. Availability: Project URL: http://www.nanocan.org/miracle/ Contact: mlist@health.sdu.dk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25161257
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Microarray R-based analysis of complex lysate experiments with MIRACLE.
List, Markus; Block, Ines; Pedersen, Marlene Lemvig; Christiansen, Helle; Schmidt, Steffen; Thomassen, Mads; Tan, Qihua; Baumbach, Jan; Mollenhauer, Jan
2014-09-01
Reverse-phase protein arrays (RPPAs) allow sensitive quantification of relative protein abundance in thousands of samples in parallel. Typical challenges involved in this technology are antibody selection, sample preparation and optimization of staining conditions. The issue of combining effective sample management and data analysis, however, has been widely neglected. This motivated us to develop MIRACLE, a comprehensive and user-friendly web application bridging the gap between spotting and array analysis by conveniently keeping track of sample information. Data processing includes correction of staining bias, estimation of protein concentration from response curves, normalization for total protein amount per sample and statistical evaluation. Established analysis methods have been integrated with MIRACLE, offering experimental scientists an end-to-end solution for sample management and for carrying out data analysis. In addition, experienced users have the possibility to export data to R for more complex analyses. MIRACLE thus has the potential to further spread utilization of RPPAs as an emerging technology for high-throughput protein analysis. Project URL: http://www.nanocan.org/miracle/. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.
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Computer-Aided Molecular Design of Bis-phosphine Oxide Lanthanide Extractants
McCann, Billy W.; Silva, Nuwan De; Windus, Theresa L.; ...
2016-02-17
Computer-aided molecular design and high-throughput screening of viable host architectures can significantly reduce the efforts in the design of novel ligands for efficient extraction of rare earth elements. This paper presents a computational approach to the deliberate design of bis-phosphine oxide host architectures that are structurally organized for complexation of trivalent lanthanides. Molecule building software, HostDesigner, was interfaced with molecular mechanics software, PCModel, providing a tool for generating and screening millions of potential R 2(O)P-link-P(O)R 2 ligand geometries. The molecular mechanics ranking of ligand structures is consistent with both the solution-phase free energies of complexation obtained with density functional theorymore » and the performance of known bis-phosphine oxide extractants. For the case where link is -CH 2-, evaluation of the ligand geometry provides the first characterization of a steric origin for the ‘anomalous aryl strengthening’ effect. The design approach has identified a number of novel bis-phosphine oxide ligands that are better organized for lanthanide complexation than previously studied examples.« less
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Wagner, Bjoern; Fischer, Holger; Kansy, Manfred; Seelig, Anna; Assmus, Frauke
2015-02-20
Here we present a miniaturized assay, referred to as Carrier-Mediated Distribution System (CAMDIS) for fast and reliable measurement of octanol/water distribution coefficients, log D(oct). By introducing a filter support for octanol, phase separation from water is facilitated and the tendency of emulsion formation (emulsification) at the interface is reduced. A guideline for the best practice of CAMDIS is given, describing a strategy to manage drug adsorption at the filter-supported octanol/buffer interface. We validated the assay on a set of 52 structurally diverse drugs with known shake flask log D(oct) values. Excellent agreement with literature data (r(2) = 0.996, standard error of estimate, SEE = 0.111), high reproducibility (standard deviation, SD < 0.1 log D(oct) units), minimal sample consumption (10 μL of 100 μM DMSO stock solution) and a broad analytical range (log D(oct) range = -0.5 to 4.2) make CAMDIS a valuable tool for the high-throughput assessment of log D(oc)t. Copyright © 2014 Elsevier B.V. All rights reserved.
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Jonke, A.A.
1957-10-01
In improved solvent extraction process is described for the extraction of metal values from highly dilute aqueous solutions. The process comprises contacting an aqueous solution with an organic substantially water-immiscible solvent, whereby metal values are taken up by a solvent extract phase; scrubbing the solvent extract phase with an aqueous scrubbing solution; separating an aqueous solution from the scrubbed solvent extract phase; and contacting the scrubbed solvent phase with an aqueous medium whereby the extracted metal values are removed from the solvent phase and taken up by said medium to form a strip solution containing said metal values, the aqueous scrubbing solution being a mixture of strip solution and an aqueous solution which contains mineral acids anions and is free of the metal values. The process is particularly effective for purifying uranium, where one starts with impure aqueous uranyl nitrate, extracts with tributyl phosphate dissolved in carbon tetrachloride, scrubs with aqueous nitric acid and employs water to strip the uranium from the scrubbed organic phase.
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Solar Power Satellite (SPS) fiber optic link assessment
NASA Technical Reports Server (NTRS)
1980-01-01
A feasibility demonstration of a 980 MHz fiber optic link for the Solar Power Satellite (SPS) phase reference distribution system was accomplished. A dual fiber-optic link suitable for a phase distribution frequency of 980 MHz was built and tested. The major link components include single mode injection laser diodes, avalanche photodiodes, and multimode high bandwidth fibers. Signal throughput was demonstrated to be stable and of high quality in all cases. For a typical SPS link length of 200 meters, the transmitted phase at 980 MHz varies approximately 2.5 degrees for every deg C of fiber temperature change. This rate is acceptable because of the link length compensation feature of the phase control design.
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2013-06-17
of the films without having to fabricate capacitors. In addition, the use of X - ray diffraction (XRD) analysis enabled Chikyow et al.40 to identify an...effects of Al doping and annealing on the thermal stabil- ity of the Y2O3/Si gate stack were studied by X - ray photoemission spectroscopy (XPS) and X - ray ...the major diffraction features in the phase distribution. For a given structural phase, the X - ray peak intensity allows one to track the compositional
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Verdirame, Maria; Veneziano, Maria; Alfieri, Anna; Di Marco, Annalise; Monteagudo, Edith; Bonelli, Fabio
2010-03-11
Turbulent Flow Chromatography (TFC) is a powerful approach for on-line extraction in bioanalytical studies. It improves sensitivity and reduces sample preparation time, two factors that are of primary importance in drug discovery. In this paper the application of the ARIA system to the analytical support of in vivo pharmacokinetics (PK) and in vitro drug metabolism studies is described, with an emphasis in high throughput optimization. For PK studies, a comparison between acetonitrile plasma protein precipitation (APPP) and TFC was carried out. Our optimized TFC methodology gave better S/N ratios and lower limit of quantification (LOQ) than conventional procedures. A robust and high throughput analytical method to support hepatocyte metabolic stability screening of new chemical entities was developed by hyphenation of TFC with mass spectrometry. An in-loop dilution injection procedure was implemented to overcome one of the main issues when using TFC, that is the early elution of hydrophilic compounds that renders low recoveries. A comparison between off-line solid phase extraction (SPE) and TFC was also carried out, and recovery, sensitivity (LOQ), matrix effect and robustness were evaluated. The use of two parallel columns in the configuration of the system provided a further increase of the throughput. Copyright 2009 Elsevier B.V. All rights reserved.
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NASA Astrophysics Data System (ADS)
Hartmann, D.; Sarfert, W.; Meier, S.; Bolink, H.; García Santamaría, S.; Wecker, J.
2010-05-01
Typically high efficient OLED device structures are based on a multitude of stacked thin organic layers prepared by thermal evaporation. For lighting applications these efficient device stacks have to be up-scaled to large areas which is clearly challenging in terms of high through-put processing at low-cost. One promising approach to meet cost-efficiency, high through-put and high light output is the combination of solution and evaporation processing. Moreover, the objective is to substitute as many thermally evaporated layers as possible by solution processing without sacrificing the device performance. Hence, starting from the anode side, evaporated layers of an efficient white light emitting OLED stack are stepwise replaced by solution processable polymer and small molecule layers. In doing so different solutionprocessable hole injection layers (= polymer HILs) are integrated into small molecule devices and evaluated with regard to their electro-optical performance as well as to their planarizing properties, meaning the ability to cover ITO spikes, defects and dust particles. Thereby two approaches are followed whereas in case of the "single HIL" approach only one polymer HIL is coated and in case of the "combined HIL" concept the coated polymer HIL is combined with a thin evaporated HIL. These HIL architectures are studied in unipolar as well as bipolar devices. As a result the combined HIL approach facilitates a better control over the hole current, an improved device stability as well as an improved current and power efficiency compared to a single HIL as well as pure small molecule based OLED stacks. Furthermore, emitting layers based on guest/host small molecules are fabricated from solution and integrated into a white hybrid stack (WHS). Up to three evaporated layers were successfully replaced by solution-processing showing comparable white light emission spectra like an evaporated small molecule reference stack and lifetime values of several 100 h.
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Routing optimization in networks based on traffic gravitational field model
NASA Astrophysics Data System (ADS)
Liu, Longgeng; Luo, Guangchun
2017-04-01
For research on the gravitational field routing mechanism on complex networks, we further analyze the gravitational effect of paths. In this study, we introduce the concept of path confidence degree to evaluate the unblocked reliability of paths that it takes the traffic state of all nodes on the path into account from the overall. On the basis of this, we propose an improved gravitational field routing protocol considering all the nodes’ gravities on the path and the path confidence degree. In order to evaluate the transmission performance of the routing strategy, an order parameter is introduced to measure the network throughput by the critical value of phase transition from a free-flow phase to a jammed phase, and the betweenness centrality is used to evaluate the transmission performance and traffic congestion of the network. Simulation results show that compared with the shortest-path routing strategy and the previous gravitational field routing strategy, the proposed algorithm improves the network throughput considerably and effectively balances the traffic load within the network, and all nodes in the network are utilized high efficiently. As long as γ ≥ α, the transmission performance can reach the maximum and remains unchanged for different α and γ, which ensures that the proposed routing protocol is high efficient and stable.
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Dargó, Gergő; Boros, Krisztina; Péter, László; Malanga, Milo; Sohajda, Tamás; Szente, Lajos; Balogh, György T
2018-05-05
The present study was aimed to develop a medium-throughput screening technique for investigation of cyclodextrin (CD)-active pharmaceutical ingredient (API) complexes. Dual-phase potentiometric lipophilicity measurement, as gold standard technique, was combined with the partition coefficient method (plotting the reciprocal of partition coefficients of APIs as a function of CD concentration). A general equation was derived for determination of stability constants of 1:1 CD-API complexes (K 1:1,CD ) based on solely the changes of partition coefficients (logP o/w N -logP app N ), without measurement of the actual API concentrations. Experimentally determined logP value (-1.64) of 6-deoxy-6[(5/6)-fluoresceinylthioureido]-HPBCD (FITC-NH-HPBCD) was used to estimate the logP value (≈ -2.5 to -3) of (2-hydroxypropyl)-ß-cyclodextrin (HPBCD). The results suggested that the amount of HPBCD can be considered to be inconsequential in the octanol phase. The decrease of octanol volume due to the octanol-CD complexation was considered, thus a corrected octanol-water phase ratio was also introduced. The K 1:1,CD values obtained by this developed method showed a good accordance with the results from other orthogonal methods. Copyright © 2018 Elsevier B.V. All rights reserved.
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High throughput optical scanner
Basiji, David A.; van den Engh, Gerrit J.
2001-01-01
A scanning apparatus is provided to obtain automated, rapid and sensitive scanning of substrate fluorescence, optical density or phosphorescence. The scanner uses a constant path length optical train, which enables the combination of a moving beam for high speed scanning with phase-sensitive detection for noise reduction, comprising a light source, a scanning mirror to receive light from the light source and sweep it across a steering mirror, a steering mirror to receive light from the scanning mirror and reflect it to the substrate, whereby it is swept across the substrate along a scan arc, and a photodetector to receive emitted or scattered light from the substrate, wherein the optical path length from the light source to the photodetector is substantially constant throughout the sweep across the substrate. The optical train can further include a waveguide or mirror to collect emitted or scattered light from the substrate and direct it to the photodetector. For phase-sensitive detection the light source is intensity modulated and the detector is connected to phase-sensitive detection electronics. A scanner using a substrate translator is also provided. For two dimensional imaging the substrate is translated in one dimension while the scanning mirror scans the beam in a second dimension. For a high throughput scanner, stacks of substrates are loaded onto a conveyor belt from a tray feeder.
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Lehotay, Steven J; Han, Lijun; Sapozhnikova, Yelena
2016-01-01
This study demonstrated the application of an automated high-throughput mini-cartridge solid-phase extraction (mini-SPE) cleanup for the rapid low-pressure gas chromatography-tandem mass spectrometry (LPGC-MS/MS) analysis of pesticides and environmental contaminants in QuEChERS extracts of foods. Cleanup efficiencies and breakthrough volumes using different mini-SPE sorbents were compared using avocado, salmon, pork loin, and kale as representative matrices. Optimum extract load volume was 300 µL for the 45 mg mini-cartridges containing 20/12/12/1 (w/w/w/w) anh. MgSO 4 /PSA (primary secondary amine)/C 18 /CarbonX sorbents used in the final method. In method validation to demonstrate high-throughput capabilities and performance results, 230 spiked extracts of 10 different foods (apple, kiwi, carrot, kale, orange, black olive, wheat grain, dried basil, pork, and salmon) underwent automated mini-SPE cleanup and analysis over the course of 5 days. In all, 325 analyses for 54 pesticides and 43 environmental contaminants (3 analyzed together) were conducted using the 10 min LPGC-MS/MS method without changing the liner or retuning the instrument. Merely, 1 mg equivalent sample injected achieved <5 ng g -1 limits of quantification. With the use of internal standards, method validation results showed that 91 of the 94 analytes including pairs achieved satisfactory results (70-120 % recovery and RSD ≤ 25 %) in the 10 tested food matrices ( n = 160). Matrix effects were typically less than ±20 %, mainly due to the use of analyte protectants, and minimal human review of software data processing was needed due to summation function integration of analyte peaks. This study demonstrated that the automated mini-SPE + LPGC-MS/MS method yielded accurate results in rugged, high-throughput operations with minimal labor and data review.
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Shi, Lei; Zhang, Jianjun; Shi, Yi; Ding, Xu; Wei, Zhenchun
2015-01-14
We consider the base station placement problem for wireless sensor networks with successive interference cancellation (SIC) to improve throughput. We build a mathematical model for SIC. Although this model cannot be solved directly, it enables us to identify a necessary condition for SIC on distances from sensor nodes to the base station. Based on this relationship, we propose to divide the feasible region of the base station into small pieces and choose a point within each piece for base station placement. The point with the largest throughput is identified as the solution. The complexity of this algorithm is polynomial. Simulation results show that this algorithm can achieve about 25% improvement compared with the case that the base station is placed at the center of the network coverage area when using SIC.
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L-edge spectroscopy of dilute, radiation-sensitive systems using a transition-edge-sensor array
NASA Astrophysics Data System (ADS)
Titus, Charles J.; Baker, Michael L.; Lee, Sang Jun; Cho, Hsiao-Mei; Doriese, William B.; Fowler, Joseph W.; Gaffney, Kelly; Gard, Johnathon D.; Hilton, Gene C.; Kenney, Chris; Knight, Jason; Li, Dale; Marks, Ronald; Minitti, Michael P.; Morgan, Kelsey M.; O'Neil, Galen C.; Reintsema, Carl D.; Schmidt, Daniel R.; Sokaras, Dimosthenis; Swetz, Daniel S.; Ullom, Joel N.; Weng, Tsu-Chien; Williams, Christopher; Young, Betty A.; Irwin, Kent D.; Solomon, Edward I.; Nordlund, Dennis
2017-12-01
We present X-ray absorption spectroscopy and resonant inelastic X-ray scattering (RIXS) measurements on the iron L-edge of 0.5 mM aqueous ferricyanide. These measurements demonstrate the ability of high-throughput transition-edge-sensor (TES) spectrometers to access the rich soft X-ray (100-2000 eV) spectroscopy regime for dilute and radiation-sensitive samples. Our low-concentration data are in agreement with high-concentration measurements recorded by grating spectrometers. These results show that soft-X-ray RIXS spectroscopy acquired by high-throughput TES spectrometers can be used to study the local electronic structure of dilute metal-centered complexes relevant to biology, chemistry, and catalysis. In particular, TES spectrometers have a unique ability to characterize frozen solutions of radiation- and temperature-sensitive samples.
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Caboche, Ségolène; Audebert, Christophe; Hot, David
2014-01-01
The recent progresses of high-throughput sequencing (HTS) technologies enable easy and cost-reduced access to whole genome sequencing (WGS) or re-sequencing. HTS associated with adapted, automatic and fast bioinformatics solutions for sequencing applications promises an accurate and timely identification and characterization of pathogenic agents. Many studies have demonstrated that data obtained from HTS analysis have allowed genome-based diagnosis, which has been consistent with phenotypic observations. These proofs of concept are probably the first steps toward the future of clinical microbiology. From concept to routine use, many parameters need to be considered to promote HTS as a powerful tool to help physicians and clinicians in microbiological investigations. This review highlights the milestones to be completed toward this purpose. PMID:25437800
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Middleware Evaluation and Benchmarking for Use in Mission Operations Centers
NASA Technical Reports Server (NTRS)
Antonucci, Rob; Waktola, Waka
2005-01-01
Middleware technologies have been promoted as timesaving, cost-cutting alternatives to the point-to-point communication used in traditional mission operations systems. However, missions have been slow to adopt the new technology. The lack of existing middleware-based missions has given rise to uncertainty about middleware's ability to perform in an operational setting. Most mission architects are also unfamiliar with the technology and do not know the benefits and detriments to architectural choices - or even what choices are available. We will present the findings of a study that evaluated several middleware options specifically for use in a mission operations system. We will address some common misconceptions regarding the applicability of middleware-based architectures, and we will identify the design decisions and tradeoffs that must be made when choosing a middleware solution. The Middleware Comparison and Benchmark Study was conducted at NASA Goddard Space Flight Center to comprehensively evaluate candidate middleware products, compare and contrast the performance of middleware solutions with the traditional point- to-point socket approach, and assess data delivery and reliability strategies. The study focused on requirements of the Global Precipitation Measurement (GPM) mission, validating the potential use of middleware in the GPM mission ground system. The study was jointly funded by GPM and the Goddard Mission Services Evolution Center (GMSEC), a virtual organization for providing mission enabling solutions and promoting the use of appropriate new technologies for mission support. The study was broken into two phases. To perform the generic middleware benchmarking and performance analysis, a network was created with data producers and consumers passing data between themselves. The benchmark monitored the delay, throughput, and reliability of the data as the characteristics were changed. Measurements were taken under a variety of topologies, data demands, and data characteristics, using several middleware products. All results were compared to systems using traditional point-to-point socket communication. By comparing performance results under Merent settings, inferences could be made about each middleware's ability to meet certain requirements of the GPM mission. The second phase simulated a middleware-based mission operations center. Actual mission support tools were either used or simulated to create real world demands on the middleware. Network and computer demands were watched closely to verify that no specific idiosyncrasies of mission operations activities would prove unsupportable by the middleware. In our presentation, we will address some commonly accepted misconceptions concerning middleware in mission support architectures. Specifically, we will focus on the perception that middleware solutions are too slow or impose too much overhead for real-time mission operations, and that middleware solutions are too expensive for small
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Isoelectric focusing of proteins and peptides
NASA Technical Reports Server (NTRS)
Egen, N.
1979-01-01
Egg-white solution was chosen as the reference solution in order to assess the effects of operational parameters (voltage, flow rate, ampholine pH range and concentration, and protein concentration) of the RIEF apparatus on protein resolution. Topics of discussion include: (1) comparison of RIEF apparatus to conventional IEF techniques (column and PAG) with respect to resolution and throughput; (2) peptide and protein separation (AHF, Thymosin - Fraction 5, vasoactive peptide, L-asparaginase and ACP); and (3) detection of peptides - dansyl derivatives of amino acids and peptides, post-focusing fluorescent labeling of amino acids, peptides and proteins, and ampholine extraction from focused gels.
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Flexible and evolutionary optical access networks
NASA Astrophysics Data System (ADS)
Hsueh, Yu-Li
Passive optical networks (PONs) are promising solutions that will open the first-mile bottleneck. Current PONs employ time division multiplexing (TDM) to share bandwidth among users, leading to low cost but limited capacity. In the future, wavelength division multiplexing (WDM) technologies will be deployed to achieve high performance. This dissertation describes several advanced technologies to enhance PON systems. A spectral shaping line coding scheme is developed to allow a simple and cost-effective overlay of high data-rate services in existing PONs, leaving field-deployed fibers and existing services untouched. Spectral shapes of coded signals can be manipulated to adapt to different systems. For a specific tolerable interference level, the optimal line code can be found which maximizes the data throughput. Experiments are conducted to demonstrate and compare several optimized line codes. A novel PON employing dynamic wavelength allocation to provide bandwidth sharing across multiple physical PONs is designed and experimentally demonstrated. Tunable lasers, arrayed waveguide gratings, and coarse/fine filtering combine to create a flexible optical access solution. The network's excellent scalability can bridge the gap between conventional TDM PONs and WDM PONs. Scheduling algorithms with quality of service support are also investigated. Simulation results show that the proposed architecture exhibits significant performance gain over conventional PON systems. Streaming video transmission is demonstrated on the prototype experimental testbed. The powerful architecture is a promising candidate for next-generation optical access networks. A new CDR circuit for receiving the bursty traffic in PONs is designed and analyzed. It detects data transition edges upon arrival of the data burst and quickly selects the best clock phase by a control logic circuit. Then, an analog delay-locked loop (DLL) keeps track of data transitions and removes phase errors throughout the burst. The combination of the fast phase detection mechanism and a feedback loop based on DLL allows both fast response and manageable jitter performance in the burst-mode application. A new efficient numerical algorithm is developed to analyze holey optical fibers. The algorithm has been verified against experimental data, and is exploited to design holey optical fibers optimized for the discrete Raman amplification.
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Brabcová, Ivana; Hlaváčková, Markéta; Satínský, Dalibor; Solich, Petr
2013-11-15
A simple and automated HPLC column-switching method with rapid sample pretreatment has been developed for quantitative determination of β-carotene in food supplements. Commercially samples of food supplements were dissolved in chloroform with help of saponification with 1M solution of sodium hydroxide in ultrasound bath. A 20-min sample dissolution/extraction step was necessary before chromatography analysis to transfer β-carotene from solid state of food supplements preparations (capsules,tablets) to chloroform solution. Sample volume - 3μL of chloroform phase was directly injected into the HPLC system. Next on-line sample clean-up was achieved on the pretreatment precolumn Chromolith Guard Cartridge RP-18e (Merck), 10×4.6mm, with a washing mobile phase (methanol:water, 92:8, (v/v)) at a flow rate of 1.5mL/min. Valve switch to analytical column was set at 2.5min in a back-flush mode. After column switching to the analytical column Ascentis Express C-18, 30×4.6mm, particle size 2.7μm (Sigma Aldrich), the separation and determination of β-carotene in food supplements was performed using a mobile phase consisting of 100% methanol, column temperature at 60°C and flow rate 1.5mL/min. The detector was set at 450nm. Under the optimum chromatographic conditions standard calibration curve was measured with good linearity - correlation coefficient for β-carotene (r(2)=0.999014; n=6) between the peak areas and concentration of β-carotene 20-200μg/mL. Accuracy of the method defined as a mean recovery was in the range 96.66-102.40%. The intraday method precision was satisfactory at three concentration levels 20, 125 and 200μg/mL and relative standard deviations were in the range 0.90-1.02%. The chromatography method has shown high sample throughput during column-switching pretreatment process and analysis in one step in short time (6min) of the whole chromatographic analysis. Copyright © 2013 Elsevier Ltd. All rights reserved.
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Supercritical fluid regeneration of adsorbents
NASA Astrophysics Data System (ADS)
Defilippi, R. P.; Robey, R. J.
1983-05-01
The results of a program to perform studies supercritical (fluid) carbon dioxide (SCF CO2) regeneration of adsorbents, using samples of industrial wastewaters from manufacturing pesticides and synthetic solution, and to estimate the economics of the specific wastewater treatment regenerations, based on test data are given. Processing costs for regenerating granular activated carbon GAC) for treating industrial wastewaters depend on stream properties and regeneration throughput.
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Chen, A.; Yarmush, M.L.; Maguire, T.
2014-01-01
There is a large emphasis within the pharmaceutical industry to provide tools that will allow early research and development groups to better predict dose ranges for and metabolic responses of candidate molecules in a high throughput manner, prior to entering clinical trials. These tools incorporate approaches ranging from PBPK, QSAR, and molecular dynamics simulations in the in silico realm, to micro cell culture analogue (CCAs)s in the in vitro realm. This paper will serve to review these areas of high throughput predictive research, and highlight hurdles and potential solutions. In particular we will focus on CCAs, as their incorporation with PBPK modeling has the potential to replace animal testing, with a more predictive assay that can combine multiple organ analogs on one microfluidic platform in physiologically correct volume ratios. While several advantages arise from the current embodiments of CCAS in a microfluidic format that can be exploited for realistic simulations of drug absorption, metabolism and action, we explore some of the concerns with these systems, and provide a potential path forward to realizing animal-free solutions. Furthermore we envision that, together with theoretical modeling, CCAs may produce reliable predictions of the efficacy of newly developed drugs. PMID:22571482
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Internal Structure and Morphology Profile in Optimizing Filter Membrane Performance
NASA Astrophysics Data System (ADS)
Sanaei, Pejman; Cummings, Linda J.
Membrane filters are in widespread use, and manufacturers have considerable interest in improving their performance, in terms of particle retention properties, and total throughput over the filter lifetime. A good question to ask is therefore: what is the optimal configuration of filter membranes, in terms of internal morphology (pore size and shape), to achieve the most efficient filtration? To answer this question, we must first propose a robust measure of filtration performance. As filtration occurs the membrane becomes blocked, or fouled, by the impurities in the feed solution, and any performance measure must take account of this. For example, one performance measure might be the total throughput (the volume of filtered feed solution) at the end of the filtration process, when the membrane is so badly blocked that it is deemed no longer functional. Here we present a simplified mathematical model, which (i) characterizes membrane internal pore structure via pore or permeability profiles in the depth of the membrane; (ii) accounts for various membrane fouling mechanisms (adsorption, blocking and cake formation); and (iv) predicts the optimum pore profile for our chosen performance measure. NSF DMS-1261596 and NSF DMS-1615719.
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IoT for Real-Time Measurement of High-Throughput Liquid Dispensing in Laboratory Environments.
Shumate, Justin; Baillargeon, Pierre; Spicer, Timothy P; Scampavia, Louis
2018-04-01
Critical to maintaining quality control in high-throughput screening is the need for constant monitoring of liquid-dispensing fidelity. Traditional methods involve operator intervention with gravimetric analysis to monitor the gross accuracy of full plate dispenses, visual verification of contents, or dedicated weigh stations on screening platforms that introduce potential bottlenecks and increase the plate-processing cycle time. We present a unique solution using open-source hardware, software, and 3D printing to automate dispenser accuracy determination by providing real-time dispense weight measurements via a network-connected precision balance. This system uses an Arduino microcontroller to connect a precision balance to a local network. By integrating the precision balance as an Internet of Things (IoT) device, it gains the ability to provide real-time gravimetric summaries of dispensing, generate timely alerts when problems are detected, and capture historical dispensing data for future analysis. All collected data can then be accessed via a web interface for reviewing alerts and dispensing information in real time or remotely for timely intervention of dispense errors. The development of this system also leveraged 3D printing to rapidly prototype sensor brackets, mounting solutions, and component enclosures.
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Runway Operations Planning: A Two-Stage Heuristic Algorithm
NASA Technical Reports Server (NTRS)
Anagnostakis, Ioannis; Clarke, John-Paul
2003-01-01
The airport runway is a scarce resource that must be shared by different runway operations (arrivals, departures and runway crossings). Given the possible sequences of runway events, careful Runway Operations Planning (ROP) is required if runway utilization is to be maximized. From the perspective of departures, ROP solutions are aircraft departure schedules developed by optimally allocating runway time for departures given the time required for arrivals and crossings. In addition to the obvious objective of maximizing throughput, other objectives, such as guaranteeing fairness and minimizing environmental impact, can also be incorporated into the ROP solution subject to constraints introduced by Air Traffic Control (ATC) procedures. This paper introduces a two stage heuristic algorithm for solving the Runway Operations Planning (ROP) problem. In the first stage, sequences of departure class slots and runway crossings slots are generated and ranked based on departure runway throughput under stochastic conditions. In the second stage, the departure class slots are populated with specific flights from the pool of available aircraft, by solving an integer program with a Branch & Bound algorithm implementation. Preliminary results from this implementation of the two-stage algorithm on real-world traffic data are presented.
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Future computing platforms for science in a power constrained era
Abdurachmanov, David; Elmer, Peter; Eulisse, Giulio; ...
2015-12-23
Power consumption will be a key constraint on the future growth of Distributed High Throughput Computing (DHTC) as used by High Energy Physics (HEP). This makes performance-per-watt a crucial metric for selecting cost-efficient computing solutions. For this paper, we have done a wide survey of current and emerging architectures becoming available on the market including x86-64 variants, ARMv7 32-bit, ARMv8 64-bit, Many-Core and GPU solutions, as well as newer System-on-Chip (SoC) solutions. We compare performance and energy efficiency using an evolving set of standardized HEP-related benchmarks and power measurement techniques we have been developing. In conclusion, we evaluate the potentialmore » for use of such computing solutions in the context of DHTC systems, such as the Worldwide LHC Computing Grid (WLCG).« less
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Operational Concept for Flight Crews to Participate in Merging and Spacing of Aircraft
NASA Technical Reports Server (NTRS)
Baxley, Brian T.; Barmore, Bryan E.; Abbott, Terence S.; Capron, William R.
2006-01-01
The predicted tripling of air traffic within the next 15 years is expected to cause significant aircraft delays and create a major financial burden for the airline industry unless the capacity of the National Airspace System can be increased. One approach to improve throughput and reduce delay is to develop new ground tools, airborne tools, and procedures to reduce the variance of aircraft delivery to the airport, thereby providing an increase in runway throughput capacity and a reduction in arrival aircraft delay. The first phase of the Merging and Spacing Concept employs a ground based tool used by Air Traffic Control that creates an arrival time to the runway threshold based on the aircraft s current position and speed, then makes minor adjustments to that schedule to accommodate runway throughput constraints such as weather and wake vortex separation criteria. The Merging and Spacing Concept also employs arrival routing that begins at an en route metering fix at altitude and continues to the runway threshold with defined lateral, vertical, and velocity criteria. This allows the desired spacing interval between aircraft at the runway to be translated back in time and space to the metering fix. The tool then calculates a specific speed for each aircraft to fly while enroute to the metering fix based on the adjusted land timing for that aircraft. This speed is data-linked to the crew who fly this speed, causing the aircraft to arrive at the metering fix with the assigned spacing interval behind the previous aircraft in the landing sequence. The second phase of the Merging and Spacing Concept increases the timing precision of the aircraft delivery to the runway threshold by having flight crews using an airborne system make minor speed changes during enroute, descent, and arrival phases of flight. These speed changes are based on broadcast aircraft state data to determine the difference between the actual and assigned time interval between the aircraft pair. The airborne software then calculates a speed adjustment to null that difference over the remaining flight trajectory. Follow-on phases still under development will expand the concept to all types of aircraft, arriving from any direction, merging at different fixes and altitudes, and to any airport. This paper describes the implementation phases of the Merging and Spacing Concept, and provides high-level results of research conducted to date.
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Daniels, Edward J.; Jody, Bassam J.; Bonsignore, Patrick V.
1994-01-01
A process and system for treating aluminum salt cake containing water soluble halide salts by contacting the salt cake with water to dissolve water soluble halide salts forming a saturated brine solution. Transporting a portion of about 25% of the saturated brine solution to a reactor and introducing into the saturated brine solution at least an equal volume of a water-miscible low-boiling organic material such as acetone to precipitate a portion of the dissolved halide salts forming a three-phase mixture of an aqueous-organic-salt solution phase and a precipitated salt phase and an organic rich phase. The precipitated salt phase is separated from the other phases and the organic rich phase is recycled to the reactor. The remainder of the saturated brine solution is sent to a multiple effect evaporator having a plurality of stages with the last stage thereof producing low grade steam which is used to boil off the organic portion of the solution which is recycled.
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Daniels, E.J.; Jody, B.J.; Bonsignore, P.V.
1994-07-19
A process and system are disclosed for treating aluminum salt cake containing water soluble halide salts by contacting the salt cake with water to dissolve water soluble halide salts forming a saturated brine solution. Transporting a portion of about 25% of the saturated brine solution to a reactor and introducing into the saturated brine solution at least an equal volume of a water-miscible low-boiling organic material such as acetone to precipitate a portion of the dissolved halide salts forming a three-phase mixture of an aqueous-organic-salt solution phase and a precipitated salt phase and an organic rich phase. The precipitated salt phase is separated from the other phases and the organic rich phase is recycled to the reactor. The remainder of the saturated brine solution is sent to a multiple effect evaporator having a plurality of stages with the last stage thereof producing low grade steam which is used to boil off the organic portion of the solution which is recycled. 3 figs.
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2-D weighted least-squares phase unwrapping
Ghiglia, Dennis C.; Romero, Louis A.
1995-01-01
Weighted values of interferometric signals are unwrapped by determining the least squares solution of phase unwrapping for unweighted values of the interferometric signals; and then determining the least squares solution of phase unwrapping for weighted values of the interferometric signals by preconditioned conjugate gradient methods using the unweighted solutions as preconditioning values. An output is provided that is representative of the least squares solution of phase unwrapping for weighted values of the interferometric signals.
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2-D weighted least-squares phase unwrapping
Ghiglia, D.C.; Romero, L.A.
1995-06-13
Weighted values of interferometric signals are unwrapped by determining the least squares solution of phase unwrapping for unweighted values of the interferometric signals; and then determining the least squares solution of phase unwrapping for weighted values of the interferometric signals by preconditioned conjugate gradient methods using the unweighted solutions as preconditioning values. An output is provided that is representative of the least squares solution of phase unwrapping for weighted values of the interferometric signals. 6 figs.
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Nakayama, Daichi; Mok, Yeongbong; Noh, Minwoo; Park, Jeongseon; Kang, Sunyoung; Lee, Yan
2014-03-21
Lower critical solution temperature (LCST) phase transition of glycol ether (GE)-water mixtures induces an abrupt change in osmotic pressure driven by a mild temperature change. The temperature-controlled osmotic change was applied for the forward osmosis (FO) desalination. Among three GEs evaluated, di(ethylene glycol) n-hexyl ether (DEH) was selected as a potential FO draw solute. A DEH-water mixture with a high osmotic pressure could draw fresh water from a high-salt feed solution such as seawater through a semipermeable membrane at around 10 °C. The water-drawn DEH-water mixture was phase-separated into a water-rich phase and a DEH-rich phase at around 30 °C. The water-rich phase with a much reduced osmotic pressure released water into a low-salt solution, and the DEH-rich phase was recovered into the initial DEH-water mixture. The phase separation behaviour, the residual GE concentration in the water-rich phase, the osmotic pressure of the DEH-water mixture, and the osmotic flux between the DEH-water mixture and salt solutions were carefully analysed for FO desalination. The liquid-liquid phase separation of the GE-water mixture driven by the mild temperature change between 10 °C and 30 °C is very attractive for the development of an ideal draw solute for future practical FO desalination.
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Hamper, Bruce C; Kesselring, Allen S; Chott, Robert C; Yang, Shengtian
2009-01-01
A solid-phase organic synthesis method has been developed for the preparation of trisubstituted pyrimidin-6-one carboxylic acids 12, which allows elaboration to a 3-dimensional combinatorial library. Three substituents are introduced by initial Knoevenagel condensation of an aldehyde and malonate ester resin 7 to give resin bound 1. Cyclization of 1 with an N-substituted amidine 10, oxidation, and cleavage afforded pyrimidinone 12. The initial solid-phase reaction sequence was followed by gel-phase (19)FNMR and direct-cleavage (1)H NMR of intermediate resins to determine the optimal conditions. The scope of the method for library production was determined by investigation of a 3 x 4 pilot library of twelve compounds. Cyclocondensation of N-methylamidines and 7 followed by CAN oxidation gave mixtures of the resin bound pyrimidin-6-one 11 and the regioisomeric pyrimidin-4-one 15, which after cleavage from the resin afforded a nearly 1:1 mixture of pyrimidin-6-one and pyrimidin-4-one carboxylic acids 12 and 16, respectively. The regiochemical assignment was confirmed by ROESY1D and gHMBC NMR experiments. A library was prepared using 8 aldehydes, 3 nitriles, and 4 amines to give a full combinatorial set of 96 pyrimidinones 12. Confirmation of structural identity and purity was carried out by LCMS using coupled ELS detection and by high-throughput flow (1)H NMR.
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Chatterjee, Anirban; Mirer, Paul L; Zaldivar Santamaria, Elvira; Klapperich, Catherine; Sharon, Andre; Sauer-Budge, Alexis F
2010-06-01
The life science and healthcare communities have been redefining the importance of ribonucleic acid (RNA) through the study of small molecule RNA (in RNAi/siRNA technologies), micro RNA (in cancer research and stem cell research), and mRNA (gene expression analysis for biologic drug targets). Research in this field increasingly requires efficient and high-throughput isolation techniques for RNA. Currently, several commercial kits are available for isolating RNA from cells. Although the quality and quantity of RNA yielded from these kits is sufficiently good for many purposes, limitations exist in terms of extraction efficiency from small cell populations and the ability to automate the extraction process. Traditionally, automating a process decreases the cost and personnel time while simultaneously increasing the throughput and reproducibility. As the RNA field matures, new methods for automating its extraction, especially from low cell numbers and in high throughput, are needed to achieve these improvements. The technology presented in this article is a step toward this goal. The method is based on a solid-phase extraction technology using a porous polymer monolith (PPM). A novel cell lysis approach and a larger binding surface throughout the PPM extraction column ensure a high yield from small starting samples, increasing sensitivity and reducing indirect costs in cell culture and sample storage. The method ensures a fast and simple procedure for RNA isolation from eukaryotic cells, with a high yield both in terms of quality and quantity. The technique is amenable to automation and streamlined workflow integration, with possible miniaturization of the sample handling process making it suitable for high-throughput applications.
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USDA-ARS?s Scientific Manuscript database
High-throughput sequencing of reduced representation genomic libraries has ushered in an era of genotyping-by-sequencing (GBS), where genome-wide genotype data can be obtained for nearly any species. However, there remains a need for imputation-free GBS methods for genotyping large samples taken fr...
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Environmental pollutants that impact critical biological pathways involved in human development and physiology can have unpredictable effects on health. Among these critical pathways, various receptor tyrosine kinases, such as...
EPA’s ToxRefDB contains prenatal guideline study data from rats and rabbits for over 240 chemicals that overlap with the ToxCast in vitro high throughput screening project. A subset of these compounds were tested in Stemina Biomarker Discovery's developmental toxicity platform, a...
Endocrine Profiling and Prioritization of Environmental Chemicals Using ToxCast Data
The prioritization of chemicals for toxicity testing is a primary goal of the U.S. EPA’s ToxCast™ program. Phase I of ToxCast utilized a battery of 467 in vitro, high-throughput screening assays to assess 309 environmental chemicals. One important mode of action leading to toxici...
A predictive model of reproductive toxicity, as observed in rat multigeneration reproductive (MGR) studies, was previously developed using high throughput screening (HTS) data from 36 in vitro assays mapped to 8 genes or gene-sets from Phase I of USEPA ToxCast research program, t...
In support of the Endocrine Disruptor Screening Program (EDSP), the U.S. EPA’s Office of Research and Development (ORD) is currently developing HTPS approaches to identify chemicals that may alter target sites in the thyroid hormone pathway. One target site is the sodium io...
Using high-content imaging data from ToxCast to analyze toxicological tipping points (TDS)
Translating results obtained from high-throughput screening to risk assessment is vital for reducing dependence on animal testing. We studied the effects of 976 chemicals (ToxCast Phase I and II) in HepG2 cells using high-content imaging (HCI) to measure dose and time-depende...
Strategic combinations and tiered application of alternative testing methods to replace or minimize the use of animal models is attracting much attention. With the advancement of high throughput screening (HTS) assays and legacy databases providing in vivo testing results, suffic...
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Feast, George C; Lepitre, Thomas; Tran, Nhiem; Conn, Charlotte E; Hutt, Oliver E; Mulet, Xavier; Drummond, Calum J; Savage, G Paul
2017-03-01
The lyotropic phase behaviour of a library of sugar-based amphiphiles was investigated using high-throughput small-angle X-ray scattering (SAXS). Double unsaturated-chain monosaccharide amphiphiles formed inverse hexagonal and cubic micellar (Fd3m) lyotropic phases under excess water conditions. A galactose-oleyl amphiphile from the library was subsequently formulated into hexosome nanoparticles, which have potential uses as drug delivery vehicles. The nanoparticles were shown to be stable at elevated temperatures and non-cytotoxic up to at least 200μgmL -1 . Crown Copyright © 2016. Published by Elsevier B.V. All rights reserved.
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X-ray scattering data and structural genomics
NASA Astrophysics Data System (ADS)
Doniach, Sebastian
2003-03-01
High throughput structural genomics has the ambitious goal of determining the structure of all, or a very large number of protein folds using the high-resolution techniques of protein crystallography and NMR. However, the program is facing significant bottlenecks in reaching this goal, which include problems of protein expression and crystallization. In this talk, some preliminary results on how the low-resolution technique of small-angle X-ray solution scattering (SAXS) can help ameliorate some of these bottlenecks will be presented. One of the most significant bottlenecks arises from the difficulty of crystallizing integral membrane proteins, where only a handful of structures are available compared to thousands of structures for soluble proteins. By 3-dimensional reconstruction from SAXS data, the size and shape of detergent-solubilized integral membrane proteins can be characterized. This information can then be used to classify membrane proteins which constitute some 25% of all genomes. SAXS may also be used to study the dependence of interparticle interference scattering on solvent conditions so that regions of the protein solution phase diagram which favor crystallization can be elucidated. As a further application, SAXS may be used to provide physical constraints on computational methods for protein structure prediction based on primary sequence information. This in turn can help in identifying structural homologs of a given protein, which can then give clues to its function. D. Walther, F. Cohen and S. Doniach. "Reconstruction of low resolution three-dimensional density maps from one-dimensional small angle x-ray scattering data for biomolecules." J. Appl. Cryst. 33(2):350-363 (2000). Protein structure prediction constrained by solution X-ray scattering data and structural homology identification Zheng WJ, Doniach S JOURNAL OF MOLECULAR BIOLOGY , v. 316(#1) pp. 173-187 FEB 8, 2002
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Changes in apple liquid phase concentration throughout equilibrium in osmotic dehydration.
Barat, J M; Barrera, C; Frías, J M; Fito, P
2007-03-01
Previous results on apple tissue equilibration during osmotic dehydration showed that, at very long processing times, the solute concentrations of the fruit liquid phase and the osmotic solution were the same. In the present study, changes in apple liquid phase composition throughout equilibrium in osmotic dehydration were analyzed and modeled. Results showed that, by the time osmosed samples reached the maximum weight and volume loss, solute concentration of the fruit liquid phase was higher than that of the osmotic solution. The reported overconcentration could be explained in terms of the apple structure shrinkage that occurred during the osmotic dehydration with highly concentrated osmotic solutions due to the elastic response of the food structure to the loss of water and intake of solutes. The fruit liquid phase overconcentration rate was observed to depend on the concentration of the osmotic solution, the processing temperature, the sample size, and shape of the cellular tissue.
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Towards roll-to-roll manufacturing of polymer photonic devices
NASA Astrophysics Data System (ADS)
Subbaraman, Harish; Lin, Xiaohui; Ling, Tao; Guo, L. Jay; Chen, Ray T.
2014-03-01
Traditionally, polymer photonic devices are fabricated using clean-room processes such as photolithography, e-beam lithography, reactive ion etching (RIE) and lift-off methods etc, which leads to long fabrication time, low throughput and high cost. We have utilized a novel process for fabricating polymer photonic devices using a combination of imprinting and ink jet printing methods, which provides high throughput on a variety of rigid and flexible substrates with low cost. We discuss the manufacturing challenges that need to be overcome in order to realize true implementation of roll-to-roll manufacturing of flexible polymer photonic systems. Several metrology and instrumentation challenges involved such as availability of particulate-free high quality substrate, development and implementation of high-speed in-line and off-line inspection and diagnostic tools with adaptive control for patterned and unpatterned material films, development of reliable hardware, etc need to be addressed and overcome in order to realize a successful manufacturing process. Due to extreme resolution requirements compared to print media, the burden of software and hardware tools on the throughput also needs to be carefully determined. Moreover, the effect of web wander and variations in web speed need to accurately be determined in the design of the system hardware and software. In this paper, we show the realization of solutions for few challenges, and utilizing these solutions for developing a high-rate R2R dual stage ink-jet printer that can provide alignment accuracy of <10μm at a web speed of 5m/min. The development of a roll-to-roll manufacturing system for polymer photonic systems opens limitless possibilities for the deployment of high performance components in a variety of applications including communication, sensing, medicine, agriculture, energy, lighting etc.
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Solution of a Complex Least Squares Problem with Constrained Phase.
Bydder, Mark
2010-12-30
The least squares solution of a complex linear equation is in general a complex vector with independent real and imaginary parts. In certain applications in magnetic resonance imaging, a solution is desired such that each element has the same phase. A direct method for obtaining the least squares solution to the phase constrained problem is described.
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Device for two-dimensional gas-phase separation and characterization of ion mixtures
Tang, Keqi [Richland, WA; Shvartsburg, Alexandre A [Richland, WA; Smith, Richard D [Richland, WA
2006-12-12
The present invention relates to a device for separation and characterization of gas-phase ions. The device incorporates an ion source, a field asymmetric waveform ion mobility spectrometry (FAIMS) analyzer, an ion mobility spectrometry (IMS) drift tube, and an ion detector. In one aspect of the invention, FAIMS operating voltages are electrically floated on top of the IMS drift voltage. In the other aspect, the FAIMS/IMS interface is implemented employing an electrodynamic ion funnel, including in particular an hourglass ion funnel. The present invention improves the efficiency (peak capacity) and sensitivity of gas-phase separations; the online FAIMS/IMS coupling creates a fundamentally novel two-dimensional gas-phase separation technology with high peak capacity, specificity, and exceptional throughput.
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CORDIC-based digital signal processing (DSP) element for adaptive signal processing
NASA Astrophysics Data System (ADS)
Bolstad, Gregory D.; Neeld, Kenneth B.
1995-04-01
The High Performance Adaptive Weight Computation (HAWC) processing element is a CORDIC based application specific DSP element that, when connected in a linear array, can perform extremely high throughput (100s of GFLOPS) matrix arithmetic operations on linear systems of equations in real time. In particular, it very efficiently performs the numerically intense computation of optimal least squares solutions for large, over-determined linear systems. Most techniques for computing solutions to these types of problems have used either a hard-wired, non-programmable systolic array approach, or more commonly, programmable DSP or microprocessor approaches. The custom logic methods can be efficient, but are generally inflexible. Approaches using multiple programmable generic DSP devices are very flexible, but suffer from poor efficiency and high computation latencies, primarily due to the large number of DSP devices that must be utilized to achieve the necessary arithmetic throughput. The HAWC processor is implemented as a highly optimized systolic array, yet retains some of the flexibility of a programmable data-flow system, allowing efficient implementation of algorithm variations. This provides flexible matrix processing capabilities that are one to three orders of magnitude less expensive and more dense than the current state of the art, and more importantly, allows a realizable solution to matrix processing problems that were previously considered impractical to physically implement. HAWC has direct applications in RADAR, SONAR, communications, and image processing, as well as in many other types of systems.
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Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing.
Giraud, Mathieu; Salson, Mikaël; Duez, Marc; Villenet, Céline; Quief, Sabine; Caillault, Aurélie; Grardel, Nathalie; Roumier, Christophe; Preudhomme, Claude; Figeac, Martin
2014-05-28
V(D)J recombinations in lymphocytes are essential for immunological diversity. They are also useful markers of pathologies. In leukemia, they are used to quantify the minimal residual disease during patient follow-up. However, the full breadth of lymphocyte diversity is not fully understood. We propose new algorithms that process high-throughput sequencing (HTS) data to extract unnamed V(D)J junctions and gather them into clones for quantification. This analysis is based on a seed heuristic and is fast and scalable because in the first phase, no alignment is performed with germline database sequences. The algorithms were applied to TR γ HTS data from a patient with acute lymphoblastic leukemia, and also on data simulating hypermutations. Our methods identified the main clone, as well as additional clones that were not identified with standard protocols. The proposed algorithms provide new insight into the analysis of high-throughput sequencing data for leukemia, and also to the quantitative assessment of any immunological profile. The methods described here are implemented in a C++ open-source program called Vidjil.
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Wong, Terence T. W.; Lau, Andy K. S.; Ho, Kenneth K. Y.; Tang, Matthew Y. H.; Robles, Joseph D. F.; Wei, Xiaoming; Chan, Antony C. S.; Tang, Anson H. L.; Lam, Edmund Y.; Wong, Kenneth K. Y.; Chan, Godfrey C. F.; Shum, Ho Cheung; Tsia, Kevin K.
2014-01-01
Accelerating imaging speed in optical microscopy is often realized at the expense of image contrast, image resolution, and detection sensitivity – a common predicament for advancing high-speed and high-throughput cellular imaging. We here demonstrate a new imaging approach, called asymmetric-detection time-stretch optical microscopy (ATOM), which can deliver ultrafast label-free high-contrast flow imaging with well delineated cellular morphological resolution and in-line optical image amplification to overcome the compromised imaging sensitivity at high speed. We show that ATOM can separately reveal the enhanced phase-gradient and absorption contrast in microfluidic live-cell imaging at a flow speed as high as ~10 m/s, corresponding to an imaging throughput of ~100,000 cells/sec. ATOM could thus be the enabling platform to meet the pressing need for intercalating optical microscopy in cellular assay, e.g. imaging flow cytometry – permitting high-throughput access to the morphological information of the individual cells simultaneously with a multitude of parameters obtained in the standard assay. PMID:24413677
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Lueangchaichaweng, Warunee; Geukens, Inge; Peeters, Annelies; Jarry, Benjamin; Launay, Franck; Bonardet, Jean-Luc; Jacobs, Pierre A; Pescarmona, Paolo P
2012-02-01
Transition-metal-free oxides were studied as heterogeneous catalysts for the sustainable epoxidation of alkenes with aqueous H₂O₂ by means of high throughput experimentation (HTE) techniques. A full-factorial HTE approach was applied in the various stages of the development of the catalysts: the synthesis of the materials, their screening as heterogeneous catalysts in liquid-phase epoxidation and the optimisation of the reaction conditions. Initially, the chemical composition of transition-metal-free oxides was screened, leading to the discovery of gallium oxide as a novel, active and selective epoxidation catalyst. On the basis of these results, the research line was continued with the study of structured porous aluminosilicates, gallosilicates and silica-gallia composites. In general, the gallium-based materials showed the best catalytic performances. This family of materials represents a promising class of heterogeneous catalysts for the sustainable epoxidation of alkenes and offers a valid alternative to the transition-metal heterogeneous catalysts commonly used in epoxidation. High throughput experimentation played an important role in promoting the development of these catalytic systems.
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Grandjean, Geoffrey; Graham, Ryan; Bartholomeusz, Geoffrey
2011-11-01
In recent years high throughput screening operations have become a critical application in functional and translational research. Although a seemingly unmanageable amount of data is generated by these high-throughput, large-scale techniques, through careful planning, an effective Laboratory Information Management System (LIMS) can be developed and implemented in order to streamline all phases of a workflow. Just as important as data mining and analysis procedures at the end of complex processes is the tracking of individual steps of applications that generate such data. Ultimately, the use of a customized LIMS will enable users to extract meaningful results from large datasets while trusting the robustness of their assays. To illustrate the design of a custom LIMS, this practical example is provided to highlight the important aspects of the design of a LIMS to effectively modulate all aspects of an siRNA screening service. This system incorporates inventory management, control of workflow, data handling and interaction with investigators, statisticians and administrators. All these modules are regulated in a synchronous manner within the LIMS. © 2011 Bentham Science Publishers
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Precipitation in Al–Mg solid solution prepared by solidification under high pressure
DOE Office of Scientific and Technical Information (OSTI.GOV)
Jie, J.C., E-mail: jiejc@dlut.edu.cn; School of Materials Science and Engineering, Harbin Institute of Technology, Harbin 150001; Wang, H.W.
2014-01-15
The precipitation in Al–Mg solid solution containing 21.6 at.% Mg prepared by solidification under 2 GPa was investigated. The results show that the γ-Al{sub 12}Mg{sub 17} phase is formed and the β′ phase cannot be observed in the solid solution during ageing process. The precipitation of γ and β phases takes place in a non-uniform manner during heating process, i.e. the γ and β phases are first formed in the interdendritic region, which is caused by the inhomogeneous distribution of Mg atoms in the solid solution solidified under high pressure. Peak splitting of X-ray diffraction patterns of Al(Mg) solid solutionmore » appears, and then disappears when the samples are aged at 423 K for different times, due to the non-uniform precipitation in Al–Mg solid solution. The direct transformation from the γ to β phase is observed after ageing at 423 K for 24 h. It is considered that the β phase is formed through a peritectoid reaction of α + γ → β which needs the diffusion of Mg atoms across the interface of α/γ phases. - Highlights: • The γ phase is formed and the β′ phase is be observed in Al(Mg) solid solution. • Peak splitting of XRD pattern of Al(Mg) solid solution appears during aged at 150 °C. • The β phase is formed through a peritectoid reaction of α + γ → β.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Bourcier, William L.; Roberts, Sarah K.; Roberts, Jeffery J.
A system for blocking fast flow paths in geological formations includes preparing a solution of colloidal silica having a nonviscous phase and a solid gel phase. The solution of colloidal silica is injected into the geological formations while the solution of colloidal silica is in the nonviscous phase. The solution of colloidal silica is directed into the fast flow paths and reaches the solid gel phase in the fast flow paths thereby blocking flow of fluid in the fast paths.
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Mester, David; Ronin, Yefim; Schnable, Patrick; Aluru, Srinivas; Korol, Abraham
2015-01-01
Our aim was to develop a fast and accurate algorithm for constructing consensus genetic maps for chip-based SNP genotyping data with a high proportion of shared markers between mapping populations. Chip-based genotyping of SNP markers allows producing high-density genetic maps with a relatively standardized set of marker loci for different mapping populations. The availability of a standard high-throughput mapping platform simplifies consensus analysis by ignoring unique markers at the stage of consensus mapping thereby reducing mathematical complicity of the problem and in turn analyzing bigger size mapping data using global optimization criteria instead of local ones. Our three-phase analytical scheme includes automatic selection of ~100-300 of the most informative (resolvable by recombination) markers per linkage group, building a stable skeletal marker order for each data set and its verification using jackknife re-sampling, and consensus mapping analysis based on global optimization criterion. A novel Evolution Strategy optimization algorithm with a global optimization criterion presented in this paper is able to generate high quality, ultra-dense consensus maps, with many thousands of markers per genome. This algorithm utilizes "potentially good orders" in the initial solution and in the new mutation procedures that generate trial solutions, enabling to obtain a consensus order in reasonable time. The developed algorithm, tested on a wide range of simulated data and real world data (Arabidopsis), outperformed two tested state-of-the-art algorithms by mapping accuracy and computation time. PMID:25867943
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Alsenaidy, Mohammad A; Okbazghi, Solomon Z; Kim, Jae Hyun; Joshi, Sangeeta B; Middaugh, C Russell; Tolbert, Thomas J; Volkin, David B
2014-06-01
The structural integrity and conformational stability of various IgG1-Fc proteins produced from the yeast Pichia pastoris with different glycosylation site occupancy (di-, mono-, and nonglycosylated) were determined. In addition, the physical stability profiles of three different forms of nonglycosylated Fc molecules (varying amino-acid residues at site 297 in the CH 2 domain due to the point mutations and enzymatic digestion of the Fc glycoforms) were also examined. The physical stability of these IgG1-Fc glycoproteins was examined as a function of pH and temperature by high-throughput biophysical analysis using multiple techniques combined with data visualization tools (three index empirical phase diagrams and radar charts). Across the pH range of 4.0-6.0, the di- and monoglycosylated forms of the IgG1-Fc showed the highest and lowest levels of physical stability, respectively, with the nonglycosylated forms showing intermediate stability depending on solution pH. In the aglycosylated Fc proteins, the introduction of Asp (D) residues at site 297 (QQ vs. DN vs. DD forms) resulted in more subtle changes in structural integrity and physical stability depending on solution pH. The utility of evaluating the conformational stability profile differences between the various IgG1-Fc glycoproteins is discussed in the context of analytical comparability studies. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.
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METHOD OF INHIBITING CORROSION IN URANYL SULFATE SOLUTIONS
Bohlmann, E.G.; Griess, J.C. Jr.
1960-08-23
A method is given for treating a uranyl sulfate solution to inhibit the corrosiveness of the solution and elevate the phase separation temperature of the solution. Lithium sulfate is added to the solution in an amount ranging from 0.25 to 1.3 times the uranyl sulfate concentration. The corrosiveness of the solution with respect to stainless steel is substantially decreased by this means. This treatment also serves to raise the phase separation temperature of the solution (above 250 deg C), at which time the uranyl sulfate solution separates into two liquid phases of unequal uranium concentration and thus becomes unsuitable as nuclear reactor fuel.
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Boyacı, Ezel; Bojko, Barbara; Reyes-Garcés, Nathaly; Poole, Justen J; Gómez-Ríos, Germán Augusto; Teixeira, Alexandre; Nicol, Beate; Pawliszyn, Janusz
2018-01-18
In vitro high-throughput non-depletive quantitation of chemicals in biofluids is of growing interest in many areas. Some of the challenges facing researchers include the limited volume of biofluids, rapid and high-throughput sampling requirements, and the lack of reliable methods. Coupled to the above, growing interest in the monitoring of kinetics and dynamics of miniaturized biosystems has spurred the demand for development of novel and revolutionary methodologies for analysis of biofluids. The applicability of solid-phase microextraction (SPME) is investigated as a potential technology to fulfill the aforementioned requirements. As analytes with sufficient diversity in their physicochemical features, nicotine, N,N-Diethyl-meta-toluamide, and diclofenac were selected as test compounds for the study. The objective was to develop methodologies that would allow repeated non-depletive sampling from 96-well plates, using 100 µL of sample. Initially, thin film-SPME was investigated. Results revealed substantial depletion and consequent disruption in the system. Therefore, new ultra-thin coated fibers were developed. The applicability of this device to the described sampling scenario was tested by determining the protein binding of the analytes. Results showed good agreement with rapid equilibrium dialysis. The presented method allows high-throughput analysis using small volumes, enabling fast reliable free and total concentration determinations without disruption of system equilibrium.
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Hybrid optoelectronic neural networks using a mutually pumped phase-conjugate mirror
NASA Astrophysics Data System (ADS)
Dunning, G. J.; Owechko, Y.; Soffer, B. H.
1991-06-01
A method is described for interconnecting hybrid optoelectronic neural networks by using a mutually pumped phase conjugate mirror (MP-PCM). In this method, cross talk due to Bragg degeneracies is greatly reduced by storing each weight among many spatially and angularly multiplexed gratings. The effective weight throughput is increased by the parallel updating of weights using outer-product learning. Experiments demonstrated a high degree of interconnectivity between adjacent pixels. A diagram is presented showing the architecture for the optoelectronic neural network using an MP-PCM.
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Uplink Packet-Data Scheduling in DS-CDMA Systems
NASA Astrophysics Data System (ADS)
Choi, Young Woo; Kim, Seong-Lyun
In this letter, we consider the uplink packet scheduling for non-real-time data users in a DS-CDMA system. As an effort to jointly optimize throughput and fairness, we formulate a time-span minimization problem incorporating the time-multiplexing of different simultaneous transmission schemes. Based on simple rules, we propose efficient scheduling algorithms and compare them with the optimal solution obtained by linear programming.
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2013-10-01
silicon-based ultrasonic nozzle to produce high- throughput of monodisperse cobinamide antidote solution for detoxification of CN poisoning in a rabbit...model. Keywords- cyanide poisoning and detoxification, cobinamide antidote, Fourier-horn ultrasonic nozzles , monodisperse aerosol inhaler I...distributions. In contrast, the MHz multiple-Fourier horn ultrasonic nozzle reported recently [8-10] has demonstrated its capability of producing high
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Comparison of actual vs synthesized ternary phase diagrams for solutes of cryobiological interest☆
Kleinhans, F.W.; Mazur, Peter
2009-01-01
Phase diagrams are of great utility in cryobiology, especially those consisting of a cryoprotective agent (CPA) dissolved in a physiological salt solution. These ternary phase diagrams consist of plots of the freezing points of increasing concentrations of solutions of cryoprotective agents (CPA) plus NaCl. Because they are time-consuming to generate, ternary diagrams are only available for a small number of CPA's. We wanted to determine whether accurate ternary phase diagrams could be synthesized by adding together the freezing point depressions of binary solutions of CPA/water and NaCl/water which match the corresponding solute molality concentrations in the ternary solution. We begin with a low concentration of a solution of CPA + salt of given R (CPA/salt) weight ratio. Ice formation in that solution is mimicked by withdrawing water from it which increases the concentrations of both the CPA and the NaCl. We compute the individual solute concentrations, determine their freezing points from published binary phase diagrams, and sum the freezing points. These yield the synthesized ternary phase diagram for a solution of given R. They were compared with published experimental ternary phase diagrams for glycerol, dimethyl sulfoxide (DMSO), sucrose, and ethylene glycol (EG) plus NaCl in water. For the first three, the synthesized and experimental phase diagrams agreed closely, with some divergence occurring as wt % concentrations exceeded 30% for DMSO and 55% for glycerol and sucrose. However, in the case of EG there were substantial differences over nearly the entire range of concentrations which we attribute to systematic errors in the experimental EG data. New experimental EG work will be required to resolve this issue. PMID:17350609
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Comparison of actual vs. synthesized ternary phase diagrams for solutes of cryobiological interest.
Kleinhans, F W; Mazur, Peter
2007-04-01
Phase diagrams are of great utility in cryobiology, especially, those consisting of a cryoprotective agent (CPA) dissolved in a physiological salt solution. These ternary phase diagrams consist of plots of the freezing points of increasing concentrations of solutions of cryoprotective agents (CPA) plus NaCl. Because they are time-consuming to generate, ternary diagrams are only available for a small number of CPAs. We wanted to determine whether accurate ternary phase diagrams could be synthesized by adding together the freezing point depressions of binary solutions of CPA/water and NaCl/water which match the corresponding solute molality concentrations in the ternary solution. We begin with a low concentration of a solution of CPA+salt of given R (CPA/salt) weight ratio. Ice formation in that solution is mimicked by withdrawing water from it which increases the concentrations of both the CPA and the NaCl. We compute the individual solute concentrations, determine their freezing points from published binary phase diagrams, and sum the freezing points. These yield the synthesized ternary phase diagram for a solution of given R. They were compared with published experimental ternary phase diagrams for glycerol, dimethyl sulfoxide (DMSO), sucrose, and ethylene glycol (EG) plus NaCl in water. For the first three, the synthesized and experimental phase diagrams agreed closely, with some divergence occurring as wt% concentrations exceeded 30% for DMSO and 55% for glycerol, and sucrose. However, in the case of EG there were substantial differences over nearly the entire range of concentrations which we attribute to systematic errors in the experimental EG data. New experimental EG work will be required to resolve this issue.
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Vinner, Lasse; Mourier, Tobias; Friis-Nielsen, Jens; Gniadecki, Robert; Dybkaer, Karen; Rosenberg, Jacob; Langhoff, Jill Levin; Cruz, David Flores Santa; Fonager, Jannik; Izarzugaza, Jose M G; Gupta, Ramneek; Sicheritz-Ponten, Thomas; Brunak, Søren; Willerslev, Eske; Nielsen, Lars Peter; Hansen, Anders Johannes
2015-08-19
Although nearly one fifth of all human cancers have an infectious aetiology, the causes for the majority of cancers remain unexplained. Despite the enormous data output from high-throughput shotgun sequencing, viral DNA in a clinical sample typically constitutes a proportion of host DNA that is too small to be detected. Sequence variation among virus genomes complicates application of sequence-specific, and highly sensitive, PCR methods. Therefore, we aimed to develop and characterize a method that permits sensitive detection of sequences despite considerable variation. We demonstrate that our low-stringency in-solution hybridization method enables detection of <100 viral copies. Furthermore, distantly related proviral sequences may be enriched by orders of magnitude, enabling discovery of hitherto unknown viral sequences by high-throughput sequencing. The sensitivity was sufficient to detect retroviral sequences in clinical samples. We used this method to conduct an investigation for novel retrovirus in samples from three cancer types. In accordance with recent studies our investigation revealed no retroviral infections in human B-cell lymphoma cells, cutaneous T-cell lymphoma or colorectal cancer biopsies. Nonetheless, our generally applicable method makes sensitive detection possible and permits sequencing of distantly related sequences from complex material.
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Caraus, Iurie; Alsuwailem, Abdulaziz A; Nadon, Robert; Makarenkov, Vladimir
2015-11-01
Significant efforts have been made recently to improve data throughput and data quality in screening technologies related to drug design. The modern pharmaceutical industry relies heavily on high-throughput screening (HTS) and high-content screening (HCS) technologies, which include small molecule, complementary DNA (cDNA) and RNA interference (RNAi) types of screening. Data generated by these screening technologies are subject to several environmental and procedural systematic biases, which introduce errors into the hit identification process. We first review systematic biases typical of HTS and HCS screens. We highlight that study design issues and the way in which data are generated are crucial for providing unbiased screening results. Considering various data sets, including the publicly available ChemBank data, we assess the rates of systematic bias in experimental HTS by using plate-specific and assay-specific error detection tests. We describe main data normalization and correction techniques and introduce a general data preprocessing protocol. This protocol can be recommended for academic and industrial researchers involved in the analysis of current or next-generation HTS data. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.
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Detection of IgG aggregation by a high throughput method based on extrinsic fluorescence.
He, Feng; Phan, Duke H; Hogan, Sabine; Bailey, Robert; Becker, Gerald W; Narhi, Linda O; Razinkov, Vladimir I
2010-06-01
The utility of extrinsic fluorescence as a tool for high throughput detection of monoclonal antibody aggregates was explored. Several IgG molecules were thermally stressed and the high molecular weight species were fractionated using size-exclusion chromatography (SEC). The isolated aggregates and monomers were studied by following the fluorescence of an extrinsic probe, SYPRO Orange. The dye displayed high sensitivity to structurally altered, aggregated IgG structures compared to the native form, which resulted in very low fluorescence in the presence of the dye. An example of the application is presented here to demonstrate the properties of this detection method. The fluorescence assay was shown to correlate with the SEC method in quantifying IgG aggregates. The fluorescent probe method appears to have potential to detect protein particles that could not be analyzed by SEC. This method may become a powerful high throughput tool to detect IgG aggregates in pharmaceutical solutions and to study other protein properties involving aggregation. It can also be used to study the kinetics of antibody particle formation, and perhaps allow identification of the species, which are the early building blocks of protein particles. (c) 2009 Wiley-Liss, Inc. and the American Pharmacists Association
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Xu, Chun-Xiu; Yin, Xue-Feng
2011-02-04
A chip-based microfluidic system for high-throughput single-cell analysis is described. The system was integrated with continuous introduction of individual cells, rapid dynamic lysis, capillary electrophoretic (CE) separation and laser induced fluorescence (LIF) detection. A cross microfluidic chip with one sheath-flow channel located on each side of the sampling channel was designed. The labeled cells were hydrodynamically focused by sheath-flow streams and sequentially introduced into the cross section of the microchip under hydrostatic pressure generated by adjusting liquid levels in the reservoirs. Combined with the electric field applied on the separation channel, the aligned cells were driven into the separation channel and rapidly lysed within 33ms at the entry of the separation channel by Triton X-100 added in the sheath-flow solution. The maximum rate for introducing individual cells into the separation channel was about 150cells/min. The introduction of sheath-flow streams also significantly reduced the concentration of phosphate-buffered saline (PBS) injected into the separation channel along with single cells, thus reducing Joule heating during electrophoretic separation. The performance of this microfluidic system was evaluated by analysis of reduced glutathione (GSH) and reactive oxygen species (ROS) in single erythrocytes. A throughput of 38cells/min was obtained. The proposed method is simple and robust for high-throughput single-cell analysis, allowing for analysis of cell population with considerable size to generate results with statistical significance. Copyright © 2010 Elsevier B.V. All rights reserved.
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Shi, Lei; Zhang, Jianjun; Shi, Yi; Ding, Xu; Wei, Zhenchun
2015-01-01
We consider the base station placement problem for wireless sensor networks with successive interference cancellation (SIC) to improve throughput. We build a mathematical model for SIC. Although this model cannot be solved directly, it enables us to identify a necessary condition for SIC on distances from sensor nodes to the base station. Based on this relationship, we propose to divide the feasible region of the base station into small pieces and choose a point within each piece for base station placement. The point with the largest throughput is identified as the solution. The complexity of this algorithm is polynomial. Simulation results show that this algorithm can achieve about 25% improvement compared with the case that the base station is placed at the center of the network coverage area when using SIC. PMID:25594600
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Heterogeneous High Throughput Scientific Computing with APM X-Gene and Intel Xeon Phi
NASA Astrophysics Data System (ADS)
Abdurachmanov, David; Bockelman, Brian; Elmer, Peter; Eulisse, Giulio; Knight, Robert; Muzaffar, Shahzad
2015-05-01
Electrical power requirements will be a constraint on the future growth of Distributed High Throughput Computing (DHTC) as used by High Energy Physics. Performance-per-watt is a critical metric for the evaluation of computer architectures for cost- efficient computing. Additionally, future performance growth will come from heterogeneous, many-core, and high computing density platforms with specialized processors. In this paper, we examine the Intel Xeon Phi Many Integrated Cores (MIC) co-processor and Applied Micro X-Gene ARMv8 64-bit low-power server system-on-a-chip (SoC) solutions for scientific computing applications. We report our experience on software porting, performance and energy efficiency and evaluate the potential for use of such technologies in the context of distributed computing systems such as the Worldwide LHC Computing Grid (WLCG).
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[Methods of high-throughput plant phenotyping for large-scale breeding and genetic experiments].
Afonnikov, D A; Genaev, M A; Doroshkov, A V; Komyshev, E G; Pshenichnikova, T A
2016-07-01
Phenomics is a field of science at the junction of biology and informatics which solves the problems of rapid, accurate estimation of the plant phenotype; it was rapidly developed because of the need to analyze phenotypic characteristics in large scale genetic and breeding experiments in plants. It is based on using the methods of computer image analysis and integration of biological data. Owing to automation, new approaches make it possible to considerably accelerate the process of estimating the characteristics of a phenotype, to increase its accuracy, and to remove a subjectivism (inherent to humans). The main technologies of high-throughput plant phenotyping in both controlled and field conditions, their advantages and disadvantages, and also the prospects of their use for the efficient solution of problems of plant genetics and breeding are presented in the review.
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L-edge spectroscopy of dilute, radiation-sensitive systems using a transition-edge-sensor array
DOE Office of Scientific and Technical Information (OSTI.GOV)
Titus, Charles J.; Baker, Michael L.; Lee, Sang Jun
Here, we present X-ray absorption spectroscopy and resonant inelastic X-ray scattering (RIXS) measurements on the iron L-edge of 0.5 mM aqueous ferricyanide. These measurements then demonstrate the ability of high-throughput transition-edge-sensor (TES) spectrometers to access the rich soft X-ray (100–2000 eV) spectroscopy regime for dilute and radiation-sensitive samples. Our low-concentration data are in agreement with high-concentration measurements recorded by grating spectrometers. These results show that soft-X-ray RIXS spectroscopy acquired by high-throughput TES spectrometers can be used to study the local electronic structure of dilute metal-centered complexes relevant to biology, chemistry, and catalysis. In particular, TES spectrometers have a unique abilitymore » to characterize frozen solutions of radiation- and temperature-sensitive samples.« less
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Mercurio, Meagan D; Dambergs, Robert G; Herderich, Markus J; Smith, Paul A
2007-06-13
The methyl cellulose precipitable (MCP) tannin assay and a modified version of the Somers and Evans color assay were adapted to high-throughput (HTP) analysis. To improve efficiency of the MCP tannin assay, a miniaturized 1 mL format and a HTP format using 96 well plates were developed. The Somers color assay was modified to allow the standardization of pH and ethanol concentrations of wine samples in a simple one-step dilution with a buffer solution, thus removing inconsistencies between wine matrices prior to analysis and allowing for its adaptation to a HTP format. Validation studies showed that all new formats were efficient, and results were reproducible and analogous to the original formats.
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L-edge spectroscopy of dilute, radiation-sensitive systems using a transition-edge-sensor array
Titus, Charles J.; Baker, Michael L.; Lee, Sang Jun; ...
2017-12-07
Here, we present X-ray absorption spectroscopy and resonant inelastic X-ray scattering (RIXS) measurements on the iron L-edge of 0.5 mM aqueous ferricyanide. These measurements then demonstrate the ability of high-throughput transition-edge-sensor (TES) spectrometers to access the rich soft X-ray (100–2000 eV) spectroscopy regime for dilute and radiation-sensitive samples. Our low-concentration data are in agreement with high-concentration measurements recorded by grating spectrometers. These results show that soft-X-ray RIXS spectroscopy acquired by high-throughput TES spectrometers can be used to study the local electronic structure of dilute metal-centered complexes relevant to biology, chemistry, and catalysis. In particular, TES spectrometers have a unique abilitymore » to characterize frozen solutions of radiation- and temperature-sensitive samples.« less
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Fibigr, Jakub; Šatínský, Dalibor; Solich, Petr
2016-02-20
A new high-performance liquid chromatography method using fused-core column for fast separation of resveratrol and polydatin has been developed and used for quality control of nutraceuticals with resveratrol and polydatin content. Retention characteristics (log k) were studied under different conditions on C-18, RP-Amide C-18, Phenyl-hexyl, Pentafluorophenyl (F5) and Cyano stationary phases for both compounds. The effect of the volume fraction of acetonitrile on a retention factors log k of resveratrol and polydatin were evaluated. The optimal separation conditions for resveratrol, polydatin and internal standard p-nitrophenol were found on the fused-core column Ascentis Express ES-Cyano (100×3.0mm), particle size 2.7μm, with mobile phase acetonitrile/water solution with 0.5% acetic acid pH 3 (20:80, v/v) at a flow rate of 1.0mL/min and at 60°C. The detection wavelength was set at 305nm. Under the optimal chromatographic conditions, good linearity with regression coefficients in the range (r=0.9992-0.9998; n=10) for both compounds was achieved. Commercial samples of nutraceuticals were extracted with methanol using ultrasound bath for 15min. A 5μL sample volume of the filtered solution was directly injected into the HPLC system. Accuracy of the method defined as a mean recovery was in the range 83.2-107.3% for both nutraceuticals. The intraday method precision was found satisfactory and relative standard deviations of sample analysis were in the range 0.8-4.7%. The developed method has shown high sample throughput during sample preparation process, modern separation approach, and short time (3min) of analysis. The results of study showed that the declared content of resveratrol and polydatin varied widely in different nutraceuticals according the producers (71.50-115.00% of declared content). Copyright © 2015 Elsevier B.V. All rights reserved.
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Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences.
Gao, Song; Sung, Wing-Kin; Nagarajan, Niranjan
2011-11-01
Scaffolding, the problem of ordering and orienting contigs, typically using paired-end reads, is a crucial step in the assembly of high-quality draft genomes. Even as sequencing technologies and mate-pair protocols have improved significantly, scaffolding programs still rely on heuristics, with no guarantees on the quality of the solution. In this work, we explored the feasibility of an exact solution for scaffolding and present a first tractable solution for this problem (Opera). We also describe a graph contraction procedure that allows the solution to scale to large scaffolding problems and demonstrate this by scaffolding several large real and synthetic datasets. In comparisons with existing scaffolders, Opera simultaneously produced longer and more accurate scaffolds demonstrating the utility of an exact approach. Opera also incorporates an exact quadratic programming formulation to precisely compute gap sizes (Availability: http://sourceforge.net/projects/operasf/ ).
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Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences
Gao, Song; Sung, Wing-Kin
2011-01-01
Abstract Scaffolding, the problem of ordering and orienting contigs, typically using paired-end reads, is a crucial step in the assembly of high-quality draft genomes. Even as sequencing technologies and mate-pair protocols have improved significantly, scaffolding programs still rely on heuristics, with no guarantees on the quality of the solution. In this work, we explored the feasibility of an exact solution for scaffolding and present a first tractable solution for this problem (Opera). We also describe a graph contraction procedure that allows the solution to scale to large scaffolding problems and demonstrate this by scaffolding several large real and synthetic datasets. In comparisons with existing scaffolders, Opera simultaneously produced longer and more accurate scaffolds demonstrating the utility of an exact approach. Opera also incorporates an exact quadratic programming formulation to precisely compute gap sizes (Availability: http://sourceforge.net/projects/operasf/). PMID:21929371
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NASA Technical Reports Server (NTRS)
Gerber, C. R.
1972-01-01
The computation and logical functions which are performed by the data processing assembly of the modular space station are defined. The subjects discussed are: (1) requirements analysis, (2) baseline data processing assembly configuration, (3) information flow study, (4) throughput simulation, (5) redundancy study, (6) memory studies, and (7) design requirements specification.
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The US EPA ToxCast program is using in vitro HTS (High-Throughput Screening) methods to profile and model bioactivity of environmental chemicals. The main goals of the ToxCast program are to generate predictive signatures of toxicity, and ultimately provide rapid and cost-effecti...
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The development of multi-well microelectrode array (mwMEA) systems has increased in vitro screening throughput making them an effective method to screen and prioritize large sets of compounds for potential neurotoxicity. In the present experiments, a multiplexed approach was used...
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Liu, Yue; Hu, Jia; Li, Yan; Li, Xiao-Shuang; Wang, Zhong-Liang
2016-10-01
A novel method with high sensitivity for the rapid determination of chrysin, apigenin and luteolin in environment water samples was developed by double-pumps controlled on-line solid-phase extraction (SPE) coupled with high-performance liquid chromatography (HPLC). In the developed technique, metal organic framework MIL-101 was synthesized and applied as a sorbent for SPE. The as-synthesized MIL-101 was characterized by scanning electron microscope, X-ray diffraction spectrometry, thermal gravimetric analysis and micropore physisorption analysis. The MIL-101 behaved as a fast kinetics in the adsorption of chrysin, apigenin and luteolin. On-line SPE of chrysin, apigenin and luteolin was processed by loading a sample solution at a flow rate of 1.0 mL/min for 10 min. The extracted analytes were subsequently eluted into a ZORBAX Bonus-RP analytical column (25 cm long × 4.6 mm i.d.) for HPLC separation under isocratic condition with a mobile phase (MeOH: ACN: 0.02 M H 3 PO 4 = 35:35:30) at a flow rate of 1.0 mL/min. Experimental conditions, including ionic strength, sample pH, sample loading rates, sample loading time and desorption analytes time, were further optimized to obtain efficient preconcentration and high-precision determination of the analytes mentioned above. The method achieved the merits of simplicity, rapidity, sensitivity, wide linear range and high sample throughput. The possible mechanism for the adsorption of flavonoids on MIL-101 was proposed. The developed method has been applied to determine trace chrysin, apigenin and luteolin in a variety of environmental water samples. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Maier-Kiener, Verena; Schuh, Benjamin; George, Easo P.; ...
2016-11-19
The equiatomic high-entropy alloy (HEA), CrMnFeCoNi, has recently been shown to be microstructurally unstable, resulting in a multi-phase microstructure after intermediate-temperature annealing treatments. The decomposition occurs rapidly in the nanocrystalline (NC) state and after longer annealing times in coarse-grained states. To characterize the mechanical properties of differently annealed NC states containing multiple phases, nanoindentation was used in this paper. The results revealed besides drastic changes in hardness, also for the first time significant changes in the Young's modulus and strain rate sensitivity. Finally, nanoindentation of NC HEAs is, therefore, a useful complementary screening tool with high potential as a highmore » throughput approach to detect phase decomposition, which can also be used to qualitatively predict the long-term stability of single-phase HEAs.« less
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Shi, Ya-jun; Shi, Jun-hui; Chen, Shi-bin; Yang, Ming
2015-07-01
Based on the demand of nasal drug delivery high drug loadings, using the unique phase transfer of solute, integrating the phospholipid complex preparation and submicron emulsion molding process of Scutellariae Radix extract, the study obtained the preparation of the high drug loadings submicron emulsion of Scutellariae Radix extract. In the study of drug solution dispersion method, the uniformity of drug dispersed as the evaluation index, the traditional mixing method, grinding, homogenate and solute phase transfer technology were investigated, and the solute phase transfer technology was adopted in the last. With the adoption of new technology, the drug loading capacity reached 1.33% (phospholipid complex was 4%). The drug loading capacity was improved significantly. The transfer of solute method and timing were studied as follows,join the oil phase when the volume of phospholipid complex anhydrous ethanol solution remaining 30%, the solute phase transfer was completed with the continued recycling of anhydrous ethanol. After drug dissolved away to oil phase, the preparation technology of colostrum was determined with the evaluation index of emulsion droplet form. The particle size of submicron emulsion, PDI and stability parameters were used as evaluation index, orthogonal methodology were adopted to optimize the submicron emulsion ingredient and main influential factors of high pressure homogenization technology. The optimized preparation technology of Scutellariae Radix extract nasal submicron emulsion is practical and stable.
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The computation in diagnostics for tokamaks: systems, designs, approaches
NASA Astrophysics Data System (ADS)
Krawczyk, Rafał; Linczuk, Paweł; Czarski, Tomasz; Wojeński, Andrzej; Chernyshova, Maryna; Poźniak, Krzysztof; Kolasiński, Piotr; Kasprowicz, Grzegorz; Zabołotny, Wojciech; Kowalska-Strzeciwilk, Ewa; Malinowski, Karol; Gaska, Michał
2017-08-01
The requirements given for GEM (Gaseous Electron Multiplier) detector based acquisition system for plasma impurities diagnostics triggered a need for the development of a specialized software and hardware architecture. The amount of computations with latency and throughput restrictions cause that an advanced solution is sought for. In order to provide a mechanism fitting the designated tokamaks, an insight into existing solutions was necessary. In the article there is discussed architecture of systems used for plasma diagnostics and in related scientific fields. The developed solution is compared and contrasted with other diagnostic and control systems. Particular attention is payed to specific requirements for plasma impurities diagnostics in tokamak thermal fusion reactor. Subsequently, the details are presented that justified the choice of the system architecture and the discussion on various approaches is given.
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In-Solution SH2 Domain Binding Assay Based on Proximity Ligation.
Machida, Kazuya
2017-01-01
Protein-protein interactions mediated by SH2 domains confer specificity in tyrosine kinase pathways. Traditional assays for assessing interactions between an SH2 domain and its interacting protein such as far-Western and pull-down are inherently low throughput. We developed SH2-PLA, an in-solution SH2 domain binding assay, that takes advantage of the speed and sensitivity of proximity ligation and real-time PCR. SH2-PLA allows for rapid assessment of SH2 domain binding to a target protein using only a few microliters of cell lysate, thereby making it an attractive new tool to study tyrosine kinase signaling.
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Guan, Yue Hugh; Hewitson, Peter; van den Heuvel, Remco N A M; Zhao, Yan; Siebers, Rick P G; Zhuang, Ying-Ping; Sutherland, Ian
2015-12-11
Manufacturing high-value added biotech biopharmaceutical products (e.g. therapeutic proteins) requires quick-to-develop, GMP-compliant, easy-to-scale and cost effective preparatory chromatography technologies. In this work, we describe the construction and testing of a set of 5-mm inner diameter stainless steel toroidal columns for use on commercially available preparatory scale synchronous J-type counter-current chromatography (CCC) machinery. We used a 20.2m long column with an aqueous two-phase system containing 14% (w/w) PEG1000 and 14% (w/w) potassium phosphate at pH 7, and tested a sample loading of 5% column volume and a mobile phase flow rate of 20ml/min. We then satisfactorily demonstrated the potential for a weekly protein separation and preparation throughput of ca. 11g based on a normal weekly routine for separating a pair of model proteins by making five stacked injections on a single portion of stationary phase with no stripping. Compared to our previous 1.6mm bore PTFE toroidal column, the present columns enlarged the nominal column processing throughput by nearly 10. For an ideal model protein injection modality, we observed a scaling up factor of at least 21. The 2 scales of protein separation and purification steps were realized on the same commercial CCC device. Copyright © 2015 Elsevier B.V. All rights reserved.
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Castilhos, Tamara S; Barreto, Fabiano; Meneghini, Leonardo; Bergold, Ana Maria
2016-07-01
A reliable and simple method for the detection and quantification of residues of 14 non-steroidal anti-inflammatory drugs and a metamizole metabolite in swine muscle was developed using liquid chromatography-electrospray ionisation-tandem mass spectrometry (LC-ESI-MS/MS). The samples were extracted with acetonitrile (ACN) in solid-liquid extraction followed by a low-temperature partitioning (LLE-LTP) process at -20 ± 2°C. After evaporation to dryness, the residue was reconstituted with hexane and a mixture of water:acetonitrile (1:1). LC separation was achieved on a reversed-phase (RP18) column with gradient elution using water (phase A) and ACN (phase B) both containing 1 mmol l(-)(1) ammonium acetate (NH4COO) with 0.025% acetic acid. Analysis was carried out on a triple-quadrupole tandem mass spectrometer (LC-MS/MS) in multiple reaction monitoring mode using an electrospray interface in negative and positive mode in a single run. Method validation was performed according to the criteria of Commission Decision No. 2002/657/EC. The matrix effect and linearity were evaluated. Decision limit (CCα), detection capability (CCβ), accuracy and repeatability of the method are also reported. The proposed method proved to be simple, easy and adequate for high-throughput analysis and was applied to routine analysis by the Brazilian Ministry of Agriculture, Livestock and Food Supply.
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Shalia, Kavita; Saranath, Dhananjaya; Rayar, Jaipreet; Shah, Vinod K.; Mashru, Manoj R.; Soneji, Surendra L.
2017-01-01
Background & objectives: Acute myocardial infarction (AMI) is a major health concern in India. The aim of the study was to identify single nucleotide polymorphisms (SNPs) associated with AMI in patients using dedicated chip and validating the identified SNPs on custom-designed chips using high-throughput microarray analysis. Methods: In pilot phase, 48 AMI patients and 48 healthy controls were screened for SNPs using human CVD55K BeadChip with 48,472 SNP probes on Illumina high-throughput microarray platform. The identified SNPs were validated by genotyping additional 160 patients and 179 controls using custom-made Illumina VeraCode GoldenGate Genotyping Assay. Analysis was carried out using PLINK software. Results: From the pilot phase, 98 SNPs present on 94 genes were identified with increased risk of AMI (odds ratio of 1.84-8.85, P=0.04861-0.003337). Five of these SNPs demonstrated association with AMI in the validation phase (P<0.05). Among these, one SNP rs9978223 on interferon gamma receptor 2 [IFNGR2, interferon (IFN)-gamma transducer 1] gene showed a significant association (P=0.00021) with AMI below Bonferroni corrected P value (P=0.00061). IFNGR2 is the second subunit of the receptor for IFN-gamma, an important cytokine in inflammatory reactions. Interpretation & conclusions: The study identified an SNP rs9978223 on IFNGR2 gene, associated with increased risk in AMI patient from India. PMID:29434065
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Li, B O; Liu, Yuan
A phase-field free-energy functional for the solvation of charged molecules (e.g., proteins) in aqueous solvent (i.e., water or salted water) is constructed. The functional consists of the solute volumetric and solute-solvent interfacial energies, the solute-solvent van der Waals interaction energy, and the continuum electrostatic free energy described by the Poisson-Boltzmann theory. All these are expressed in terms of phase fields that, for low free-energy conformations, are close to one value in the solute phase and another in the solvent phase. A key property of the model is that the phase-field interpolation of dielectric coefficient has the vanishing derivative at both solute and solvent phases. The first variation of such an effective free-energy functional is derived. Matched asymptotic analysis is carried out for the resulting relaxation dynamics of the diffused solute-solvent interface. It is shown that the sharp-interface limit is exactly the variational implicit-solvent model that has successfully captured capillary evaporation in hydrophobic confinement and corresponding multiple equilibrium states of underlying biomolecular systems as found in experiment and molecular dynamics simulations. Our phase-field approach and analysis can be used to possibly couple the description of interfacial fluctuations for efficient numerical computations of biomolecular interactions.
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Oliver, Thomas A A; Zhang, Yuyuan; Ashfold, Michael N R; Bradforth, Stephen E
2011-01-01
Gas-phase H (Rydberg) atom photofragment translational spectroscopy and solution-phase femtosecond-pump dispersed-probe transient absorption techniques are applied to explore the excited state dynamics of p-methylthiophenol connecting the short time reactive dynamics in the two phases. The molecule is excited at a range of UV wavelengths from 286 to 193 nm. The experiments clearly demonstrate that photoexcitation results in S-H bond fission--both in the gas phase and in ethanol solution-and that the resulting p-methythiophenoxyl radical fragments are formed with significant vibrational excitation. In the gas phase, the recoil anisotropy of the H atom and the vibrational energy disposal in the p-MePhS radical products formed at the longer excitation wavelengths reveal the operation of two excited state dissociation mechanisms. The prompt excited state dissociation motif appears to map into the condensed phase also. In both phases, radicals are produced in both their ground and first excited electronic states; characteristic signatures for both sets of radical products are already apparent in the condensed phase studies after 50 fs. No evidence is seen for either solute ionisation or proton coupled electron transfer--two alternate mechanisms that have been proposed for similar heteroaromatics in solution. Therefore, at least for prompt S-H bond fissions, the direct observation of the dissociation process in solution confirms that the gas phase photofragmentation studies indeed provide important insights into the early time dynamics that transfer to the condensed phase.
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Ba, Yong; Mao, Yougang; Galdino, Luiz; Günsen, Zorigoo
2013-01-01
The effects of a type I AFP on the bulk melting of frozen AFP solutions and frozen AFP+solute solutions were studied through an NMR microimaging experiment. The solutes studied include sodium chloride and glucose and the amino acids alanine, threonine, arginine, and aspartic acid. We found that the AFP is able to induce the bulk melting of the frozen AFP solutions at temperatures lower than 0 °C and can also keep the ice melted at higher temperatures in the AFP+solute solutions than those in the corresponding solute solutions. The latter shows that the ice phases were in super-heated states in the frozen AFP+solute solutions. We have tried to understand the first experimental phenomenon via the recent theoretical prediction that type I AFP can induce the local melting of ice upon adsorption to ice surfaces. The latter experimental phenomenon was explained with the hypothesis that the adsorption of AFP to ice surfaces introduces a less hydrophilic water-AFP-ice interfacial region, which repels the ionic/hydrophilic solutes. Thus, this interfacial region formed an intermediate chemical potential layer between the water phase and the ice phase, which prevented the transfer of water from the ice phase to the water phase. We have also attempted to understand the significance of the observed melting phenomena to the survival of organisms that express AFPs over cold winters.
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REMOVAL OF CHLORIDE FROM AQUEOUS SOLUTIONS
Schulz, W.W.
1959-08-01
The removal of chlorides from aqueons solutions is described. The process involves contacting the aqueous chloride containing solution with a benzene solution about 0.005 M in phenyl mercuric acetate whereby the chloride anions are taken up by the organic phase and separating the organic phase from the aqueous solutions.
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Song, Xuqin; Xie, Jingmeng; Zhang, Meiyu; Zhang, Yingxia; Li, Jiufeng; Huang, Qiwen; He, Limin
2018-02-15
A high throughput, reliable and reproducible analysis strategy based on high performance liquid chromatography combined to evaporative light scattering detector (HPLC-ELSD) was developed for simultaneous determination of eight cyclopolypeptide antibiotics including vancomycin, polymyxin B (polymyxin B1 and polymyxin B2), polymyxin E (colistin A and colistin B), teicoplanin, bacitracin A, daptomycin and virginiamycin M1 in animal Feed. Feed samples were extracted with methanol-2% formic acid aqueous solution, followed by a solid-phase extraction step using a HLB cartridge. Under the optimum chromatographic conditions and ELSD parameters, target compounds were separated well on a short column filled with biphenyl stationary phase. The method was developed in accordance with pig complete feed and then extended to detect polypeptide antibiotics in piglet premix, pig feed additive, poultry complete feed and fattening pig premix. The results showed that logarithmic calibration curves of eight analytes were linear (r 2 > 0.99) within the concentration range of 5-200 mg mL -1 . The developed method provided good accuracy and precision for quantification of eight polypeptides in five kinds of feeds with recoveries ranging from 72.0% to 105.4% with relative standard deviations <9.5%. The limits of detection ranged from 2 to 5 mg kg -1 . Finally, the method was successfully applied to analyze polypeptide antibiotics in commercial feed. Copyright © 2018 Elsevier B.V. All rights reserved.
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Bloem, Robbert; Garrett-Roe, Sean; Strzalka, Halina; Hamm, Peter; Donaldson, Paul
2010-12-20
We demonstrate how quasi-phase-cycling achieved by sub-cycle delay modulation can be used to replace optical chopping in a box-CARS 2D IR experiment in order to enhance the signal size, and, at the same time, completely eliminate any scattering contamination. Two optical devices are described that can be used for this purpose, a wobbling Brewster window and a photoelastic modulator. They are simple to construct, easy to incorporate into any existing 2D IR setup, and have attractive features such as a high optical throughput and a fast modulation frequency needed to phase cycle on a shot-to-shot basis.
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Kirschner, Nicolas; Dias, Adriana Neves; Budziak, Dilma; da Silveira, Cristian Berto; Merib, Josias; Carasek, Eduardo
2017-12-15
A sustainable approach to TF-SPME is presented using recycled diatomaceous earth, obtained from a beer purification process, as a green sorbent phase for the determination of bisphenol A (BPA), benzophenone (BzP), triclocarban (TCC), 4-methylbenzylidene camphor (4-MBC) and 2-ethylhexyl-p-methoxycinnamate (EHMC) in environmental water samples. TF-SPME was combined with a 96-well plate system allowing for high-throughput analysis due to the simultaneous extraction/desorption up to 96 samples. The proposed sorbent phase exhibited good stability in organic solvents, as well as satisfactory analytical performance. The optimized method consisted of 240 min of extraction at pH 6 with the addition of NaCl (15% w/v). A mixture of MeOH:ACN (50:50 v/v) was used for the desorption the analytes, using a time of 30 min. Limits of detection varied from 1 μg L -1 for BzP and TCC to 8 μg L -1 for the other analytes, and R 2 ranged from 0.9926 for 4-MBC to 0.9988 for BPA. This novel and straightforward approach offers an environmentally-friendly and very promising alternative for routine analysis. . The total sample preparation time per sample was approximately 2.8 min, which is a significant advantage when a large number of analytical run is required. Copyright © 2017 Elsevier B.V. All rights reserved.
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Wills, Lauren P.; Beeson, Gyda C.; Hoover, Douglas B.; Schnellmann, Rick G.; Beeson, Craig C.
2015-01-01
Previous high-throughput screens to identify mitochondrial toxicants used immortalized cell lines and focused on changes in mitochondrial membrane potential, which may not be sufficient and do not identify different types of mitochondrial dysfunction. Primary cultures of renal proximal tubule cells (RPTC) were examined with the Seahorse Extracellular Flux Analyzer to screen 676 compounds (5 μM; 1 h) from the ToxCast Phase II library for mitochondrial toxicants. Of the 676 compounds, 19 were classified as cytotoxicants, 376 were electron transport chain (ETC) inhibitors, and 5 were uncouplers. The remaining 276 compounds were examined after a 5-h exposure to identify slower acting mitochondrial toxicants. This experiment identified 3 cytotoxicants, 110 ETC inhibitors, and 163 compounds with no effect. A subset of the ToxCast Phase II library was also examined in immortalized human renal cells (HK2) to determine differences in susceptibility to mitochondrial toxicity. Of the 131 RPTC ETC inhibitors tested, only 14 were ETC inhibitors in HK2 cells. Of the 5 RPTC uncouplers, 1 compound was an uncoupler in HK2 cells. These results demonstrate that 73% (491/676) of the compounds in the ToxCast Phase II library compounds exhibit RPTC mitochondrial toxicity, overwhelmingly ETC inhibition. In contrast, renal HK2 cells are markedly less sensitive and only identified 6% of the compounds as mitochondrial toxicants. We suggest caution is needed when studying mitochondrial toxicity in immortalized cell lines. This information will provide mechanisms and chemical-based criteria for assessing and predicting mitochondrial liabilities of new drugs, consumer products, and environmental agents. PMID:25926417
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Han, Xu; Liu, Yang; Critser, John K.
2010-01-01
Characterization of the thermodynamic properties of multi-solute aqueous solutions is of critical importance for biological and biochemical research. For example, the phase diagrams of aqueous systems, containing salts, saccharides, and plasma membrane permeating solutes, are indispensible in the field of cryobiology and pharmacology. However, only a few ternary phase diagrams are currently available for these systems. In this study, an auto-sampler differential scanning calorimeter (DSC) was used to determine the quaternary phase diagram of the water-ethylene glycol-sucrose-NaCl system. To improve the accuracy of melting point measurement, a “mass redemption” method was also applied for the DSC technique. Base on the analyses of these experimental data, a comparison was made between the two practical approaches to generate phase diagrams of multi-solute solutions from those of single-solute solutions: the summation of cubic polynomial melting point equations versus the use of osmotic virial equations with cross coefficients. The calculated values of the model standard deviations suggested that both methods are satisfactory for characterizing this quaternary system. PMID:20447385
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Low density microcellular foams
Aubert, J.H.; Clough, R.L.; Curro, J.G.; Quintana, C.A.; Russick, E.M.; Shaw, M.T.
1985-10-02
Low density, microporous polymer foams are provided by a process which comprises forming a solution of polymer and a suitable solvent followed by rapid cooling of the solution to form a phase-separated system and freeze the phase-separated system. The phase-separated system comprises a polymer phase and a solvent phase, each of which is substantially continuous within the other. The morphology of the polymer phase prior to and subsequent to freezing determine the morphology of the resultant foam. Both isotropic and anisotropic foams can be produced. If isotropic foams are produced, the polymer and solvent are tailored such that the solution spontaneously phase-separates prior to the point at which any component freezes. The morphology of the resultant polymer phase determines the morphology of the reusltant foam and the morphology of the polymer phase is retained by cooling the system at a rate sufficient to freeze one or both components of the system before a change in morphology can occur. Anisotropic foams are produced by forming a solution of polymer and solvent that will not phase separate prior to freezing of one or both components of the solution. In such a process, the solvent typically freezes before phase separation occurs. The morphology of the resultant frozen two-phase system determines the morphology of the resultant foam. The process involves subjecting the solution to essentially one-dimensional cooling. Foams having a density of less than 0.1 g/cc and a uniform cell size of less than 10 ..mu..m and a volume such that the foams have a length greater than 1 cm are provided.
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New analytical solutions to the two-phase water faucet problem
Zou, Ling; Zhao, Haihua; Zhang, Hongbin
2016-06-17
Here, the one-dimensional water faucet problem is one of the classical benchmark problems originally proposed by Ransom to study the two-fluid two-phase flow model. With certain simplifications, such as massless gas phase and no wall and interfacial frictions, analytical solutions had been previously obtained for the transient liquid velocity and void fraction distribution. The water faucet problem and its analytical solutions have been widely used for the purposes of code assessment, benchmark and numerical verifications. In our previous study, the Ransom’s solutions were used for the mesh convergence study of a high-resolution spatial discretization scheme. It was found that, atmore » the steady state, an anticipated second-order spatial accuracy could not be achieved, when compared to the existing Ransom’s analytical solutions. A further investigation showed that the existing analytical solutions do not actually satisfy the commonly used two-fluid single-pressure two-phase flow equations. In this work, we present a new set of analytical solutions of the water faucet problem at the steady state, considering the gas phase density’s effect on pressure distribution. This new set of analytical solutions are used for mesh convergence studies, from which anticipated second-order of accuracy is achieved for the 2nd order spatial discretization scheme. In addition, extended Ransom’s transient solutions for the gas phase velocity and pressure are derived, with the assumption of decoupled liquid and gas pressures. Numerical verifications on the extended Ransom’s solutions are also presented.« less
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Traffic-Adaptive, Flow-Specific Medium Access for Wireless Networks
2009-09-01
hybrid, contention and non-contention schemes are shown to be special cases. This work also compares the energy efficiency of centralized and distributed...solutions and proposes an energy efficient version of traffic-adaptive CWS-MAC that includes an adaptive sleep cycle coordinated through the use of...preamble sampling. A preamble sampling probability parameter is introduced to manage the trade-off between energy efficiency and throughput and delay
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Wu, Yupan; Ren, Yukun; Jiang, Hongyuan
2017-01-01
We propose a 3D microfluidic mixer based on the alternating current electrothermal (ACET) flow. The ACET vortex is produced by 3D electrodes embedded in the sidewall of the microchannel and is used to stir the fluidic sample throughout the entire channel depth. An optimized geometrical structure of the proposed 3D micromixer device is obtained based on the enhanced theoretical model of ACET flow and natural convection. We quantitatively analyze the flow field driven by the ACET, and a pattern of electrothermal microvortex is visualized by the micro-particle imaging velocimetry. Then, the mixing experiment is conducted using dye solutions with varying solution conductivities. Mixing efficiency can exceed 90% for electrolytes with 0.2 S/m (1 S/m) when the flow rate is 0.364 μL/min (0.728 μL/min) and the imposed peak-to-peak voltage is 52.5 V (35 V). A critical analysis of our micromixer in comparison with different mixer designs using a comparative mixing index is also performed. The ACET micromixer embedded with sidewall 3D electrodes can achieve a highly effective mixing performance and can generate high throughput in the continuous-flow condition. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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NASA Astrophysics Data System (ADS)
Saptari, Vidi A.; Youcef-Toumi, Kamal; Zhang, John
2004-06-01
A noninvasive blood glucose monitoring device will provide an invaluable tool in the diagnosis and treatment of diabetes. Near infrared (NIR) absorption spectroscopy is one of the most promising optical techniques for in vivo blood glucose sensing to date. Successful realization of such a technology hinges on solving two main problems. First, instrument sensitivity needs to be improved in order to resolve the weak NIR spectral variations due to glucose physiological changes in the blood. Second, interfering signals due to other blood components and tissue changes need to be sufficiently eliminated or compensated for. A simple, low-cost, high-throughput, filter spectrometer optimized for long-wave NIR measurements of biological fluids is developed. The instrument provides noise spectra with a typical rms value of 7 μAU between 2180 nm and 2310 nm with only 5 seconds of data measurement or averaging. Using such an instrument, spectra of aquaeous, synthetic biological solutions containing varying levels of glucose, BSA, triacetin, lactate and urea are obtained. Glucose spectra are isolated, despite the overlapping spectra. Glucose concentrations are predicted with excellent accuracy (SEP<=8.2 mg/dL) using the simple classical least-squares (CLS) and the connonly used partial least-squares (PLS) multivariate techniques.
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Takahashi, Mayumi; Wu, Xiwei; Ho, Michelle; Chomchan, Pritsana; Rossi, John J; Burnett, John C; Zhou, Jiehua
2016-09-22
The systemic evolution of ligands by exponential enrichment (SELEX) technique is a powerful and effective aptamer-selection procedure. However, modifications to the process can dramatically improve selection efficiency and aptamer performance. For example, droplet digital PCR (ddPCR) has been recently incorporated into SELEX selection protocols to putatively reduce the propagation of byproducts and avoid selection bias that result from differences in PCR efficiency of sequences within the random library. However, a detailed, parallel comparison of the efficacy of conventional solution PCR versus the ddPCR modification in the RNA aptamer-selection process is needed to understand effects on overall SELEX performance. In the present study, we took advantage of powerful high throughput sequencing technology and bioinformatics analysis coupled with SELEX (HT-SELEX) to thoroughly investigate the effects of initial library and PCR methods in the RNA aptamer identification. Our analysis revealed that distinct "biased sequences" and nucleotide composition existed in the initial, unselected libraries purchased from two different manufacturers and that the fate of the "biased sequences" was target-dependent during selection. Our comparison of solution PCR- and ddPCR-driven HT-SELEX demonstrated that PCR method affected not only the nucleotide composition of the enriched sequences, but also the overall SELEX efficiency and aptamer efficacy.
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Takahashi, Mayumi; Wu, Xiwei; Ho, Michelle; Chomchan, Pritsana; Rossi, John J.; Burnett, John C.; Zhou, Jiehua
2016-01-01
The systemic evolution of ligands by exponential enrichment (SELEX) technique is a powerful and effective aptamer-selection procedure. However, modifications to the process can dramatically improve selection efficiency and aptamer performance. For example, droplet digital PCR (ddPCR) has been recently incorporated into SELEX selection protocols to putatively reduce the propagation of byproducts and avoid selection bias that result from differences in PCR efficiency of sequences within the random library. However, a detailed, parallel comparison of the efficacy of conventional solution PCR versus the ddPCR modification in the RNA aptamer-selection process is needed to understand effects on overall SELEX performance. In the present study, we took advantage of powerful high throughput sequencing technology and bioinformatics analysis coupled with SELEX (HT-SELEX) to thoroughly investigate the effects of initial library and PCR methods in the RNA aptamer identification. Our analysis revealed that distinct “biased sequences” and nucleotide composition existed in the initial, unselected libraries purchased from two different manufacturers and that the fate of the “biased sequences” was target-dependent during selection. Our comparison of solution PCR- and ddPCR-driven HT-SELEX demonstrated that PCR method affected not only the nucleotide composition of the enriched sequences, but also the overall SELEX efficiency and aptamer efficacy. PMID:27652575
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NASA Astrophysics Data System (ADS)
Bellavista, Paolo; Giannelli, Carlo
The availability of heterogeneous wireless interfaces and of growing computing resources on widespread portable devices pushes for enabling innovative deployment scenarios where mobile nodes dynamically self-organize to offer Internet connectivity to their peers via dynamically established multi-hop multi-path opportunities. We claim the suitability of novel, mobility-aware, and application-layer middleware based on lightweight evaluation indicators to support the complexity of that scenario, involving heterogeneous wireless technologies over differentiated and statically unpredictable execution environments. To validate these claims, we have implemented an innovative middleware that manages the durability/throughput-aware formation and selection of different multi-hop paths simultaneously. This paper specifically focuses on how our middleware effectively exploits Bluetooth for multi-hop multi-path networking, by pointing out the crucial role of i) compliance with standard solutions to favor rapid deployment over off-the-shelf equipment and ii) the reduction of the usual overhead associated with some expensive Bluetooth operations, e.g., device inquiry. In particular, the paper shows how it is possible, on the one hand, to extend JSR-82 to portably access monitoring indicators for lightweight mobility/throughput estimations and, on the other hand, to reduce the time needed to update the set of available Bluetooth-based connectivity opportunities via approximated and lightweight forms of discovery.
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Li, Keyan; Li, Min; Xue, Dongfeng
2012-04-26
By incorporating the solvent effect into the Born effective radius, we have proposed an electronegativity scale of metal ions in aqueous solution with the most common oxidation states and hydration coordination numbers in terms of the effective ionic electrostatic potential. It is found that the metal ions in aqueous solution are poorer electron acceptors compared to those in the gas phase. This solution-phase electronegativity scale shows its efficiency in predicting some important properties of metal ions in aqueous solution such as the aqueous acidities of the metal ions, the stability constants of metal complexes, and the solubility product constants of the metal hydroxides. We have elaborated that the standard reduction potential and the solution-phase electronegativity are two different quantities for describing the processes of metal ions in aqueous solution to soak up electrons with different final states. This work provides a new insight into the chemical behaviors of the metal ions in aqueous solution, indicating a potential application of this electronegativity scale to the design of solution reactions.
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Tankiewicz, Maciej; Fenik, Jolanta; Biziuk, Marek
2011-10-30
The intensification of agriculture means that increasing amounts of toxic organic and inorganic compounds are entering the environment. The pesticides generally applied nowadays are regarded as some of the most dangerous contaminants of the environment. Their presence in the environment, especially in water, is hazardous because they cause human beings to become more susceptible to disease. For these reasons, it is essential to monitor pesticide residues in the environment with the aid of all accessible analytical methods. The analysis of samples for the presence of pesticides is problematic, because of the laborious and time-consuming operations involved in preparing samples for analysis, which themselves may be a source of additional contaminations and errors. To date, it has been standard practice to use large quantities of organic solvents in the sample preparation process; but as these solvents are themselves hazardous, solventless and solvent-minimized techniques are coming into use. This paper discusses the most commonly used over the last 15 years sample preparation techniques for monitoring organophosphorus and organonitrogen pesticides residue in water samples. Furthermore, a significant trend in sample preparation, in accordance with the principles of 'Green Chemistry' is the simplification, miniaturization and automation of analytical techniques. In view of this aspect, several novel techniques are being developed in order to reduce the analysis step, increase the sample throughput and to improve the quality and the sensitivity of analytical methods. The paper describes extraction techniques requiring the use of solvents - liquid-liquid extraction (LLE) and its modifications, membrane extraction techniques, hollow fibre-protected two-phase solvent microextraction, liquid phase microextraction based on the solidification of a floating organic drop (LPME-SFO), solid-phase extraction (SPE) and single-drop microextraction (SDME) - as well as solvent-free techniques - solid phase microextraction (SPME) and stir bar sorptive extraction (SBSE). The advantages and drawbacks of these techniques are also discussed, and some solutions to their limitations are proposed. Copyright © 2011 Elsevier B.V. All rights reserved.
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Phase Separation in Solutions of Monoclonal Antibodies
NASA Astrophysics Data System (ADS)
Benedek, George; Wang, Ying; Lomakin, Aleksey; Latypov, Ramil
2012-02-01
We report the observation of liquid-liquid phase separation (LLPS) in a solution of humanized monoclonal antibodies, IgG2, and the effects of human serum albumin, a major blood protein, on this phase separation. We find a significant reduction of phase separation temperature in the presence of albumin, and a preferential partitioning of the albumin into the antibody-rich phase. We provide a general thermodynamic analysis of the antibody-albumin mixture phase diagram and relate its features to the magnitude of the effective inter-protein interactions. Our analysis suggests that additives (HSA in this report), which have moderate attraction with antibody molecules, may be used to forestall undesirable protein condensation in antibody solutions. Our findings are relevant to understanding the stability of pharmaceutical solutions of antibodies and the mechanisms of cryoglobulinemia.
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Design of an Evolutionary Approach for Intrusion Detection
2013-01-01
A novel evolutionary approach is proposed for effective intrusion detection based on benchmark datasets. The proposed approach can generate a pool of noninferior individual solutions and ensemble solutions thereof. The generated ensembles can be used to detect the intrusions accurately. For intrusion detection problem, the proposed approach could consider conflicting objectives simultaneously like detection rate of each attack class, error rate, accuracy, diversity, and so forth. The proposed approach can generate a pool of noninferior solutions and ensembles thereof having optimized trade-offs values of multiple conflicting objectives. In this paper, a three-phase, approach is proposed to generate solutions to a simple chromosome design in the first phase. In the first phase, a Pareto front of noninferior individual solutions is approximated. In the second phase of the proposed approach, the entire solution set is further refined to determine effective ensemble solutions considering solution interaction. In this phase, another improved Pareto front of ensemble solutions over that of individual solutions is approximated. The ensemble solutions in improved Pareto front reported improved detection results based on benchmark datasets for intrusion detection. In the third phase, a combination method like majority voting method is used to fuse the predictions of individual solutions for determining prediction of ensemble solution. Benchmark datasets, namely, KDD cup 1999 and ISCX 2012 dataset, are used to demonstrate and validate the performance of the proposed approach for intrusion detection. The proposed approach can discover individual solutions and ensemble solutions thereof with a good support and a detection rate from benchmark datasets (in comparison with well-known ensemble methods like bagging and boosting). In addition, the proposed approach is a generalized classification approach that is applicable to the problem of any field having multiple conflicting objectives, and a dataset can be represented in the form of labelled instances in terms of its features. PMID:24376390
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Solid-solution CrCoCuFeNi high-entropy alloy thin films synthesized by sputter deposition
An, Zhinan; Jia, Haoling; Wu, Yueying; ...
2015-05-04
The concept of high configurational entropy requires that the high-entropy alloys (HEAs) yield single-phase solid solutions. However, phase separations are quite common in bulk HEAs. A five-element alloy, CrCoCuFeNi, was deposited via radio frequency magnetron sputtering and confirmed to be a single-phase solid solution through the high-energy synchrotron X-ray diffraction, energy-dispersive spectroscopy, wavelength-dispersive spectroscopy, and transmission electron microscopy. The formation of the solid-solution phase is presumed to be due to the high cooling rate of the sputter-deposition process.
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Pharmaceutical Perspective on Opalescence and Liquid-Liquid Phase Separation in Protein Solutions.
Raut, Ashlesha S; Kalonia, Devendra S
2016-05-02
Opalescence in protein solutions reduces aesthetic appeal of a formulation and can be an indicator of the presence of aggregates or precursor to phase separation in solution signifying reduced product stability. Liquid-liquid phase separation of a protein solution into a protein-rich and a protein-poor phase has been well-documented for globular proteins and recently observed for monoclonal antibody solutions, resulting in physical instability of the formulation. The present review discusses opalescence and liquid-liquid phase separation (LLPS) for therapeutic protein formulations. A brief discussion on theoretical concepts based on thermodynamics, kinetics, and light scattering is presented. This review also discusses theoretical concepts behind intense light scattering in the vicinity of the critical point termed as "critical opalescence". Both opalescence and LLPS are affected by the formulation factors including pH, ionic strength, protein concentration, temperature, and excipients. Literature reports for the effect of these formulation factors on attractive protein-protein interactions in solution as assessed by the second virial coefficient (B2) and the cloud-point temperature (Tcloud) measurements are also presented. The review also highlights pharmaceutical implications of LLPS in protein solutions.
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Carbon-Nanotube-Based Thermoelectric Materials and Devices
DOE Office of Scientific and Technical Information (OSTI.GOV)
Blackburn, Jeffrey L.; Ferguson, Andrew J.; Cho, Chungyeon
Conversion of waste heat to voltage has the potential to significantly reduce the carbon footprint of a number of critical energy sectors, such as the transportation and electricity-generation sectors, and manufacturing processes. Thermal energy is also an abundant low-flux source that can be harnessed to power portable/wearable electronic devices and critical components in remote off-grid locations. As such, a number of different inorganic and organic materials are being explored for their potential in thermoelectric-energy-harvesting devices. Carbon-based thermoelectric materials are particularly attractive due to their use of nontoxic, abundant source-materials, their amenability to high-throughput solution-phase fabrication routes, and the high specificmore » energy (i.e., W g-1) enabled by their low mass. Single-walled carbon nanotubes (SWCNTs) represent a unique 1D carbon allotrope with structural, electrical, and thermal properties that enable efficient thermoelectric-energy conversion. Here, the progress made toward understanding the fundamental thermoelectric properties of SWCNTs, nanotube-based composites, and thermoelectric devices prepared from these materials is reviewed in detail. This progress illuminates the tremendous potential that carbon-nanotube-based materials and composites have for producing high-performance next-generation devices for thermoelectric-energy harvesting.« less
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Carbon-Nanotube-Based Thermoelectric Materials and Devices
Blackburn, Jeffrey L.; Ferguson, Andrew J.; Cho, Chungyeon; ...
2018-01-22
Conversion of waste heat to voltage has the potential to significantly reduce the carbon footprint of a number of critical energy sectors, such as the transportation and electricity-generation sectors, and manufacturing processes. Thermal energy is also an abundant low-flux source that can be harnessed to power portable/wearable electronic devices and critical components in remote off-grid locations. As such, a number of different inorganic and organic materials are being explored for their potential in thermoelectric-energy-harvesting devices. Carbon-based thermoelectric materials are particularly attractive due to their use of nontoxic, abundant source-materials, their amenability to high-throughput solution-phase fabrication routes, and the high specificmore » energy (i.e., W g-1) enabled by their low mass. Single-walled carbon nanotubes (SWCNTs) represent a unique 1D carbon allotrope with structural, electrical, and thermal properties that enable efficient thermoelectric-energy conversion. Here, the progress made toward understanding the fundamental thermoelectric properties of SWCNTs, nanotube-based composites, and thermoelectric devices prepared from these materials is reviewed in detail. This progress illuminates the tremendous potential that carbon-nanotube-based materials and composites have for producing high-performance next-generation devices for thermoelectric-energy harvesting.« less
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Carbon-Nanotube-Based Thermoelectric Materials and Devices.
Blackburn, Jeffrey L; Ferguson, Andrew J; Cho, Chungyeon; Grunlan, Jaime C
2018-03-01
Conversion of waste heat to voltage has the potential to significantly reduce the carbon footprint of a number of critical energy sectors, such as the transportation and electricity-generation sectors, and manufacturing processes. Thermal energy is also an abundant low-flux source that can be harnessed to power portable/wearable electronic devices and critical components in remote off-grid locations. As such, a number of different inorganic and organic materials are being explored for their potential in thermoelectric-energy-harvesting devices. Carbon-based thermoelectric materials are particularly attractive due to their use of nontoxic, abundant source-materials, their amenability to high-throughput solution-phase fabrication routes, and the high specific energy (i.e., W g -1 ) enabled by their low mass. Single-walled carbon nanotubes (SWCNTs) represent a unique 1D carbon allotrope with structural, electrical, and thermal properties that enable efficient thermoelectric-energy conversion. Here, the progress made toward understanding the fundamental thermoelectric properties of SWCNTs, nanotube-based composites, and thermoelectric devices prepared from these materials is reviewed in detail. This progress illuminates the tremendous potential that carbon-nanotube-based materials and composites have for producing high-performance next-generation devices for thermoelectric-energy harvesting. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Polyfluoroalkyl chemicals in house dust
DOE Office of Scientific and Technical Information (OSTI.GOV)
Kato, Kayoko; Calafat, Antonia M., E-mail: acalafat@cdc.gov; Needham, Larry L.
2009-07-15
We developed a high throughput analytical method using on-line solid phase extraction coupled with isotope dilution high-performance liquid chromatography-tandem mass spectrometry (on-line SPE-HPLC-MS/MS) to simultaneously determine the concentrations of 17 polyfluoroalkyl chemicals (PFCs) in house dust. The sample preparation includes dispersion of the dust samples in 0.1 M formic acid:MeOH (1:1), followed by agitation and filtration, addition of the isotope-labeled internal standard solution to the filtrate, and analysis by on-line SPE-HPLC-MS/MS. The limits of quantitation were <4.0 ng/g. The method accuracies ranged between 73.2% and 100.2% for the different analytes at two spike levels. We confirmed the validity of themore » method by analyzing 39 household dust samples collected in 2004. Of the 17 PFCs measured, 6 of them-perfluorobutane sulfonate (PFBuS), N-ethyl-perfluorooctane sulfonamide, 2-(N-ethyl-perfluorooctane sulfonamido) acetic acid (Et-PFOSA-AcOH), 2-(N-methyl-perfluorooctane sulfonamido) ethanol (Me-PFOSA-EtOH), perfluorohexane sulfonate (PFHxS), and perfluorooctane sulfonate (PFOS)-had detection frequencies >70%. We detected PFOS, PFBuS, and PFHxS at the highest median concentration, followed by Et-PFOSA-AcOH and Me-PFOSA-EtOH.« less
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NASA Astrophysics Data System (ADS)
Civitani, M. M.; Hołyszko, J.; Vecchi, G.; Basso, S.; Citterio, O.; Ghigo, M.; Pareschi, G.; Parodi, G.; Incorvaia, S.
2017-09-01
The implementation of an X-ray mission with high imaging capabilities, similar to those achieved with Chandra (< 1 arc second Half Energy Width, HEW), but with a much larger throughput (2.5 m2 effective area @1 keV), represents a compelling request by the scientific community. To this end the Lynx/XRS mission is being studied in USA, with the participation of international partners. In order to figure out the challenging technological task of the mirror fabrication, different approaches are considered, based on monolithic and segmented shells. Starting from the experience done on the glass prototypal shell realized in the past years, the direct polishing of thin (2 mm thick) fused silica monolithic shells is being investigated as a possible solution. A temporary stiffening structure is designed to support the shell during the figuring and polishing operations and to manage the handling up to its integration in the telescope structure. After the grinding and the polishing phases, in order to achieve the required surface accuracy, a final ion beam figuring correction is foreseen. In this paper, we present the technological process and the results achieved so far on a prototypal shell under development.
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The US EPA ToxCast program is using in vitro, high-throughput screening (HTS) to profile and model the bioactivity of environmental chemicals. The main goal of the ToxCast program is to generate predictive signatures of toxicity that ultimately provide rapid and cost-effective me...
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A Crowdsourcing Evaluation of the NIH Chemical Probes
Oprea, Tudor I.; Bologa, Cristian G.; Boyer, Scott; Curpan, Ramona F.; Glen, Robert C.; Hopkins, Andrew L.; Lipinski, Christopher A.; Marshall, Garland R.; Martin, Yvonne C.; Ostopovici-Halip, Liliana; Rishton, Gilbert; Ursu, Oleg; Vaz, Roy J.; Waller, Chris; Waldmann, Herbert; Sklar, Larry A.
2013-01-01
Between 2004 and 2008, the NIH molecular libraries and imaging initiative (MLI) pilot phase funded ten high-throughput Screening Centers, resulting in the deposition of 691 assays into PubChem and the nomination of 64 chemical probes. We crowdsourced the MLI output to 11 experts, who expressed medium or high levels of confidence in 48 of these 64 probes. PMID:19536101
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Li, Yubo; Zhang, Zhenzhu; Liu, Xinyu; Li, Aizhu; Hou, Zhiguo; Wang, Yuming; Zhang, Yanjun
2015-08-28
This study combines solid phase extraction (SPE) using 96-well plates with column-switching technology to construct a rapid and high-throughput method for the simultaneous extraction and non-targeted analysis of small molecules metabolome and lipidome based on ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry. This study first investigated the columns and analytical conditions for small molecules metabolome and lipidome, separated by an HSS T3 and BEH C18 columns, respectively. Next, the loading capacity and actuation duration of SPE were further optimized. Subsequently, SPE and column switching were used together to rapidly and comprehensively analyze the biological samples. The experimental results showed that the new analytical procedure had good precision and maintained sample stability (RSD<15%). The method was then satisfactorily applied to more widely analyze the small molecules metabolome and lipidome to test the throughput. The resulting method represents a new analytical approach for biological samples, and a highly useful tool for researches in metabolomics and lipidomics. Copyright © 2015 Elsevier B.V. All rights reserved.
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High-Throughput Synthesis and Characterization of Eu Doped Ba xSr2- xSiO4 Thin Film Phosphors.
Frost, Sara; Guérin, Samuel; Hayden, Brian E; Soulié, Jean-Philippe; Vian, Chris
2018-06-20
High-throughput techniques have been employed for the synthesis and characterization of thin film phosphors of Eu-doped Ba x Sr 2- x SiO 4 . Direct synthesis from evaporation of the constituent elements under a flux of atomic oxygen on a sapphire substrate at 850 °C was used to directly produce thin film libraries (415 nm thickness) of the crystalline orthosilicate phase with the desired compositional variation (0.24 > x > 1.86). The orthosilicate phase could be synthesized as a pure, or predominantly pure, phase. Annealing the as synthesized library in a reducing atmosphere resulted in the reduction of the Eu while retaining the orthosilicate phase, and resulted in a materials thin film library where fluorescence excited by blue light (450 nm) was observable by the naked eye. Parallel screening of the fluorescence from the combinatorial libraries of Eu doped Ba x Sr 2- x SiO 4 has been implemented by imaging the fluorescent radiation over the library using a monochrome digital camera using a series of color filters. Informatics tools have been developed to allow the 1931 CIE color coordinates and the relative quantum efficiencies of the materials library to be rapidly assessed and mapped against composition, crystal structure and phase purity. The range of compositions gave values of CIE x between 0.17 and 0.52 and CIE y between 0.48 and 0.69 with relative efficiencies in the range 2.0 × 10 -4 -7.6 × 10 -4 . Good agreement was obtained between the thin film phosphors and the fluorescence characteristics of a number of corresponding bulk phosphor powders. The thermal quenching of fluorescence in the thin film libraries was also measured in the temperature range 25-130 °C: The phase purity of the thin film was found to significantly influence both the relative quantum efficiency and the thermal quenching of the fluorescence.
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High-speed cell recognition algorithm for ultrafast flow cytometer imaging system.
Zhao, Wanyue; Wang, Chao; Chen, Hongwei; Chen, Minghua; Yang, Sigang
2018-04-01
An optical time-stretch flow imaging system enables high-throughput examination of cells/particles with unprecedented high speed and resolution. A significant amount of raw image data is produced. A high-speed cell recognition algorithm is, therefore, highly demanded to analyze large amounts of data efficiently. A high-speed cell recognition algorithm consisting of two-stage cascaded detection and Gaussian mixture model (GMM) classification is proposed. The first stage of detection extracts cell regions. The second stage integrates distance transform and the watershed algorithm to separate clustered cells. Finally, the cells detected are classified by GMM. We compared the performance of our algorithm with support vector machine. Results show that our algorithm increases the running speed by over 150% without sacrificing the recognition accuracy. This algorithm provides a promising solution for high-throughput and automated cell imaging and classification in the ultrafast flow cytometer imaging platform. (2018) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).
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Development of a High-Throughput Magnetic Separation Device for Malaria-infected Erythrocytes
Martin, A. Blue; Wu, Wei-Tao; Kameneva, Marina V.; Antaki, James F.
2017-01-01
This study describes a non-dilutive high-gradient magnetic separation (HGMS) device intended to continuously remove malaria-infected red blood cells (iRBCs) from the circulation. A mesoscale prototype device with disposable photo-etched ferromagnetic grid and reusable permanent magnet was designed with a computationally-optimized magnetic force. The prototype device was evaluated in-vitro using a non-pathogenic analog for malaria-infected blood, comprised of 24% healthy RBCs, 6% human methemoglobin RBCs (metRBCs), and 70% phosphate buffer solution (PBS). The device provided a 27.0 ± 2.2% reduction of metRBCs in a single pass at a flow rate of 77 μL min−1. This represents a clearance rate over 380 times greater throughput than microfluidic devices reported previously. These positive results encourage development of a clinical scale system that would economize time and donor blood for treating severe malaria. PMID:28924724
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High-speed cell recognition algorithm for ultrafast flow cytometer imaging system
NASA Astrophysics Data System (ADS)
Zhao, Wanyue; Wang, Chao; Chen, Hongwei; Chen, Minghua; Yang, Sigang
2018-04-01
An optical time-stretch flow imaging system enables high-throughput examination of cells/particles with unprecedented high speed and resolution. A significant amount of raw image data is produced. A high-speed cell recognition algorithm is, therefore, highly demanded to analyze large amounts of data efficiently. A high-speed cell recognition algorithm consisting of two-stage cascaded detection and Gaussian mixture model (GMM) classification is proposed. The first stage of detection extracts cell regions. The second stage integrates distance transform and the watershed algorithm to separate clustered cells. Finally, the cells detected are classified by GMM. We compared the performance of our algorithm with support vector machine. Results show that our algorithm increases the running speed by over 150% without sacrificing the recognition accuracy. This algorithm provides a promising solution for high-throughput and automated cell imaging and classification in the ultrafast flow cytometer imaging platform.
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Raspberry Pi-powered imaging for plant phenotyping.
Tovar, Jose C; Hoyer, J Steen; Lin, Andy; Tielking, Allison; Callen, Steven T; Elizabeth Castillo, S; Miller, Michael; Tessman, Monica; Fahlgren, Noah; Carrington, James C; Nusinow, Dmitri A; Gehan, Malia A
2018-03-01
Image-based phenomics is a powerful approach to capture and quantify plant diversity. However, commercial platforms that make consistent image acquisition easy are often cost-prohibitive. To make high-throughput phenotyping methods more accessible, low-cost microcomputers and cameras can be used to acquire plant image data. We used low-cost Raspberry Pi computers and cameras to manage and capture plant image data. Detailed here are three different applications of Raspberry Pi-controlled imaging platforms for seed and shoot imaging. Images obtained from each platform were suitable for extracting quantifiable plant traits (e.g., shape, area, height, color) en masse using open-source image processing software such as PlantCV. This protocol describes three low-cost platforms for image acquisition that are useful for quantifying plant diversity. When coupled with open-source image processing tools, these imaging platforms provide viable low-cost solutions for incorporating high-throughput phenomics into a wide range of research programs.
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Heterogeneous high throughput scientific computing with APM X-Gene and Intel Xeon Phi
Abdurachmanov, David; Bockelman, Brian; Elmer, Peter; ...
2015-05-22
Electrical power requirements will be a constraint on the future growth of Distributed High Throughput Computing (DHTC) as used by High Energy Physics. Performance-per-watt is a critical metric for the evaluation of computer architectures for cost- efficient computing. Additionally, future performance growth will come from heterogeneous, many-core, and high computing density platforms with specialized processors. In this paper, we examine the Intel Xeon Phi Many Integrated Cores (MIC) co-processor and Applied Micro X-Gene ARMv8 64-bit low-power server system-on-a-chip (SoC) solutions for scientific computing applications. As a result, we report our experience on software porting, performance and energy efficiency and evaluatemore » the potential for use of such technologies in the context of distributed computing systems such as the Worldwide LHC Computing Grid (WLCG).« less
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Library Design-Facilitated High-Throughput Sequencing of Synthetic Peptide Libraries.
Vinogradov, Alexander A; Gates, Zachary P; Zhang, Chi; Quartararo, Anthony J; Halloran, Kathryn H; Pentelute, Bradley L
2017-11-13
A methodology to achieve high-throughput de novo sequencing of synthetic peptide mixtures is reported. The approach leverages shotgun nanoliquid chromatography coupled with tandem mass spectrometry-based de novo sequencing of library mixtures (up to 2000 peptides) as well as automated data analysis protocols to filter away incorrect assignments, noise, and synthetic side-products. For increasing the confidence in the sequencing results, mass spectrometry-friendly library designs were developed that enabled unambiguous decoding of up to 600 peptide sequences per hour while maintaining greater than 85% sequence identification rates in most cases. The reliability of the reported decoding strategy was additionally confirmed by matching fragmentation spectra for select authentic peptides identified from library sequencing samples. The methods reported here are directly applicable to screening techniques that yield mixtures of active compounds, including particle sorting of one-bead one-compound libraries and affinity enrichment of synthetic library mixtures performed in solution.
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Lei, Chunyang; Bie, Hongxia; Fang, Gengfa; Gaura, Elena; Brusey, James; Zhang, Xuekun; Dutkiewicz, Eryk
2016-07-18
Super dense wireless sensor networks (WSNs) have become popular with the development of Internet of Things (IoT), Machine-to-Machine (M2M) communications and Vehicular-to-Vehicular (V2V) networks. While highly-dense wireless networks provide efficient and sustainable solutions to collect precise environmental information, a new channel access scheme is needed to solve the channel collision problem caused by the large number of competing nodes accessing the channel simultaneously. In this paper, we propose a space-time random access method based on a directional data transmission strategy, by which collisions in the wireless channel are significantly decreased and channel utility efficiency is greatly enhanced. Simulation results show that our proposed method can decrease the packet loss rate to less than 2 % in large scale WSNs and in comparison with other channel access schemes for WSNs, the average network throughput can be doubled.
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Targeted post-mortem computed tomography cardiac angiography: proof of concept.
Saunders, Sarah L; Morgan, Bruno; Raj, Vimal; Robinson, Claire E; Rutty, Guy N
2011-07-01
With the increasing use and availability of multi-detector computed tomography and magnetic resonance imaging in autopsy practice, there has been an international push towards the development of the so-called near virtual autopsy. However, currently, a significant obstacle to the consideration as to whether or not near virtual autopsies could one day replace the conventional invasive autopsy is the failure of post-mortem imaging to yield detailed information concerning the coronary arteries. To date, a cost-effective, practical solution to allow high throughput imaging has not been presented within the forensic literature. We present a proof of concept paper describing a simple, quick, cost-effective, manual, targeted in situ post-mortem cardiac angiography method using a minimally invasive approach, to be used with multi-detector computed tomography for high throughput cadaveric imaging which can be used in permanent or temporary mortuaries.
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Development of a High-Throughput Magnetic Separation Device for Malaria-Infected Erythrocytes.
Blue Martin, A; Wu, Wei-Tao; Kameneva, Marina V; Antaki, James F
2017-12-01
This study describes a non-dilutive high-gradient magnetic separation (HGMS) device intended to continuously remove malaria-infected red blood cells (iRBCs) from the circulation. A mesoscale prototype device with disposable photo-etched ferromagnetic grid and reusable permanent magnet was designed with a computationally-optimized magnetic force. The prototype device was evaluated in vitro using a non-pathogenic analog for malaria-infected blood, comprised of 24% healthy RBCs, 6% human methemoglobin RBCs (metRBCs), and 70% phosphate buffer solution (PBS). The device provided a 27.0 ± 2.2% reduction of metRBCs in a single pass at a flow rate of 77 μL min -1 . This represents a clearance rate over 380 times greater throughput than microfluidic devices reported previously. These positive results encourage development of a clinical scale system that would economize time and donor blood for treating severe malaria.
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Use of prior knowledge for the analysis of high-throughput transcriptomics and metabolomics data
2014-01-01
Background High-throughput omics technologies have enabled the measurement of many genes or metabolites simultaneously. The resulting high dimensional experimental data poses significant challenges to transcriptomics and metabolomics data analysis methods, which may lead to spurious instead of biologically relevant results. One strategy to improve the results is the incorporation of prior biological knowledge in the analysis. This strategy is used to reduce the solution space and/or to focus the analysis on biological meaningful regions. In this article, we review a selection of these methods used in transcriptomics and metabolomics. We combine the reviewed methods in three groups based on the underlying mathematical model: exploratory methods, supervised methods and estimation of the covariance matrix. We discuss which prior knowledge has been used, how it is incorporated and how it modifies the mathematical properties of the underlying methods. PMID:25033193
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Xi-cam: a versatile interface for data visualization and analysis
DOE Office of Scientific and Technical Information (OSTI.GOV)
Pandolfi, Ronald J.; Allan, Daniel B.; Arenholz, Elke
Xi-cam is an extensible platform for data management, analysis and visualization.Xi-camaims to provide a flexible and extensible approach to synchrotron data treatment as a solution to rising demands for high-volume/high-throughput processing pipelines. The core ofXi-camis an extensible plugin-based graphical user interface platform which provides users with an interactive interface to processing algorithms. Plugins are available for SAXS/WAXS/GISAXS/GIWAXS, tomography and NEXAFS data. WithXi-cam's `advanced' mode, data processing steps are designed as a graph-based workflow, which can be executed live, locally or remotely. Remote execution utilizes high-performance computing or de-localized resources, allowing for the effective reduction of high-throughput data.Xi-cam's plugin-based architecture targetsmore » cross-facility and cross-technique collaborative development, in support of multi-modal analysis.Xi-camis open-source and cross-platform, and available for download on GitHub.« less
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Xi-cam: a versatile interface for data visualization and analysis
Pandolfi, Ronald J.; Allan, Daniel B.; Arenholz, Elke; ...
2018-05-31
Xi-cam is an extensible platform for data management, analysis and visualization.Xi-camaims to provide a flexible and extensible approach to synchrotron data treatment as a solution to rising demands for high-volume/high-throughput processing pipelines. The core ofXi-camis an extensible plugin-based graphical user interface platform which provides users with an interactive interface to processing algorithms. Plugins are available for SAXS/WAXS/GISAXS/GIWAXS, tomography and NEXAFS data. WithXi-cam's `advanced' mode, data processing steps are designed as a graph-based workflow, which can be executed live, locally or remotely. Remote execution utilizes high-performance computing or de-localized resources, allowing for the effective reduction of high-throughput data.Xi-cam's plugin-based architecture targetsmore » cross-facility and cross-technique collaborative development, in support of multi-modal analysis.Xi-camis open-source and cross-platform, and available for download on GitHub.« less
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Kitaguchi, Koichi; Hanamura, Naoya; Murata, Masaharu; Hashimoto, Masahiko; Tsukagoshi, Kazuhiko
2014-01-01
A fluorocarbon and hydrocarbon organic solvent mixture is known as a temperature-induced phase-separation solution. When a mixed solution of tetradecafluorohexane as a fluorocarbon organic solvent and hexane as a hydrocarbon organic solvent (e.g., 71:29 volume ratio) was delivered in a capillary tube that was controlled at 10°C, the tube radial distribution phenomenon (TRDP) of the solvents was clearly observed through fluorescence images of the dye, perylene, dissolved in the mixed solution. The homogeneous mixed solution (single phase) changed to a heterogeneous solution (two phases) with inner tetradecafluorohexane and outer hexane phases in the tube under laminar flow conditions, generating the dynamic liquid-liquid interface. We also tried to apply TRDP to a separation technique for metal compounds. A model analyte mixture, copper(II) and hematin, was separated through the capillary tube, and detected with a chemiluminescence detector in this order within 4 min.
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Predicting the Fluid-Phase Behavior of Aqueous Solutions of ELP (VPGVG) Sequences Using SAFT-VR.
Zhao, Binwu; Lindeboom, Tom; Benner, Steven; Jackson, George; Galindo, Amparo; Hall, Carol K
2017-10-24
The statistical associating fluid theory for potentials of variable range (SAFT-VR) is used to predict the fluid phase behavior of elastin-like polypeptide (ELP) sequences in aqueous solution with special focus on the loci of lower critical solution temperatures (LCSTs). A SAFT-VR model for these solutions is developed following a coarse-graining approach combining information from atomistic simulations and from previous SAFT models for previously reported relevant systems. Constant-pressure temperature-composition phase diagrams are determined for solutions of (VPGVG) n sequences + water with n = 1 to 300. The SAFT-VR equation of state lends itself to the straightforward calculation of phase boundaries so that complete fluid-phase equilibria can be calculated efficiently. A broad range of thermodynamic conditions of temperature and pressure are considered, and regions of vapor-liquid and liquid-liquid coexistence, including LCSTs, are found. The calculated phase boundaries at low concentrations match those measured experimentally. The temperature-composition phase diagrams of the aqueous ELP solutions at low pressure (0.1 MPa) are similar to those of types V and VI phase behavior in the classification of Scott and van Konynenburg. An analysis of the high-pressure phase behavior confirms, however, that a closed-loop liquid-liquid immiscibility region, separate from the gas-liquid envelope, is present for aqueous solutions of (VPGVG) 30 ; such a phase diagram is typical of type VI phase behavior. ELPs with shorter lengths exhibit both liquid-liquid and gas-liquid regions, both of which become less extensive as the chain length of the ELP is decreased. The strength of the hydrogen-bonding interaction is also found to affect the phase diagram of the (VPGVG) 30 system in that the liquid-liquid and gas-liquid regions expand as the hydrogen-bonding strength is decreased and shrink as it is increased. The LCSTs of the mixtures are seen to decrease as the ELP chain length is increased.
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Phase dependencies of the human baroreceptor reflex
NASA Technical Reports Server (NTRS)
Seidel, H.; Herzel, H.; Eckberg, D. L.
1997-01-01
We studied the influence of respiratory and cardiac phase on responses of the cardiac pacemaker to brief (0.35-s) increases of carotid baroreceptor afferent traffic provoked by neck suction in seven healthy young adult subjects. Cardiac responses to neck suction were measured indirectly from electrocardiographic changes of heart period. Our results show that it is possible to separate the influences of respiratory and cardiac phases at the onset of a neck suction impulse by a product of two factors: one depending only on the respiratory phase and one depending only on the cardiac phase. This result is consistent with the hypothesis that efferent vagal activity is a function of afferent baroreceptor activity, whereas respiratory neurons modulate that medullary throughput independent of the cardiac phase. Furthermore, we have shown that stimulus broadening and stimulus cropping influence the outcome of neck suction experiments in a way that makes it virtually impossible to obtain information on the phase dependency of the cardiac pacemaker's sensitivity to vagal stimulation without accurate knowledge of the functional shape of stimulus broadening.
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Low density microcellular foams
Aubert, James H.; Clough, Roger L.; Curro, John G.; Quintana, Carlos A.; Russick, Edward M.; Shaw, Montgomery T.
1987-01-01
Low density, microporous polymer foams are provided by a process which comprises forming a solution of polymer and a suitable solvent followed by rapid cooling of the solution to form a phase-separated system and freeze the phase-separated system. The phase-separated system comprises a polymer phase and a solvent phase, each of which is substantially continuous within the other. The morphology of the polymer phase prior to and subsequent to freezing determine the morphology of the resultant foam. Both isotropic and anisotropic foams can be produced. If isotropic foams are produced, the polymer and solvent are tailored such that the solution spontaneously phase-separates prior to the point at which any component freezes. The morphology of the resultant polymer phase determines the morphology of the resultant foam and the morphology of the polymer phase is retained by cooling the system at a rate sufficient to freeze one or both components of the system before a change in morphology can occur. Anisotropic foams are produced by forming a solution of polymer and solvent that will not phase separate prior to freezing of one or both components of the solution. In such a process, the solvent typically freezes before phase separation occurs. The morphology of the resultant frozen two-phase system determines the morphology of the resultant foam. The process involves subjecting the solution to essentially one-dimensional cooling. Means for subjecting such a solvent to one-dimensional cooling are also provided. Foams having a density of less than 0.1 g/cc and a uniform cell size of less than 10 .mu.m and a volume such that the foams have a length greater than 1 cm are provided.
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Criteria for predicting the formation of single-phase high-entropy alloys
Troparevsky, M Claudia; Morris, James R..; Kent, Paul R.; ...
2015-03-15
High entropy alloys constitute a new class of materials whose very existence poses fundamental questions. Originally thought to be stabilized by the large entropy of mixing, these alloys have attracted attention due to their potential applications, yet no model capable of robustly predicting which combinations of elements will form a single-phase currently exists. Here we propose a model that, through the use of high-throughput computation of the enthalpies of formation of binary compounds, is able to confirm all known high-entropy alloys while rejecting similar alloys that are known to form multiple phases. Despite the increasing entropy, our model predicts thatmore » the number of potential single-phase multicomponent alloys decreases with an increasing number of components: out of more than two million possible 7-component alloys considered, fewer than twenty single-phase alloys are likely.« less
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Kuo, Wen-Kai; Syu, Siang-He; Lin, Peng-Zhi; Yu, Hsin Her
2016-02-01
This paper reports on a transmitted-type dual-channel guided-mode resonance (GMR) sensor system that uses phase-shifting interferometry (PSI) to achieve tunable phase detection sensitivity. Five interference images are captured for the PSI phase calculation within ∼15 s by using a liquid crystal retarder and a USB web camera. The GMR sensor structure is formed by a nanoimprinting process, and the dual-channel sensor device structure for molding is fabricated using a 3D printer. By changing the rotation angle of the analyzer in front of the camera in the PSI system, the sensor detection sensitivity can be tuned. The proposed system may achieve high throughput as well as high sensitivity. The experimental results show that an optimal detection sensitivity of 6.82×10(-4) RIU can be achieved.
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Watt, Eric D.; Hornung, Michael W.; Hedge, Joan M.; Judson, Richard S.; Crofton, Kevin M.; Houck, Keith A.; Simmons, Steven O.
2016-01-01
High-throughput screening for potential thyroid-disrupting chemicals requires a system of assays to capture multiple molecular-initiating events (MIEs) that converge on perturbed thyroid hormone (TH) homeostasis. Screening for MIEs specific to TH-disrupting pathways is limited in the U.S. Environmental Protection Agency ToxCast screening assay portfolio. To fill 1 critical screening gap, the Amplex UltraRed-thyroperoxidase (AUR-TPO) assay was developed to identify chemicals that inhibit TPO, as decreased TPO activity reduces TH synthesis. The ToxCast phase I and II chemical libraries, comprised of 1074 unique chemicals, were initially screened using a single, high concentration to identify potential TPO inhibitors. Chemicals positive in the single-concentration screen were retested in concentration-response. Due to high false-positive rates typically observed with loss-of-signal assays such as AUR-TPO, we also employed 2 additional assays in parallel to identify possible sources of nonspecific assay signal loss, enabling stratification of roughly 300 putative TPO inhibitors based upon selective AUR-TPO activity. A cell-free luciferase inhibition assay was used to identify nonspecific enzyme inhibition among the putative TPO inhibitors, and a cytotoxicity assay using a human cell line was used to estimate the cellular tolerance limit. Additionally, the TPO inhibition activities of 150 chemicals were compared between the AUR-TPO and an orthogonal peroxidase oxidation assay using guaiacol as a substrate to confirm the activity profiles of putative TPO inhibitors. This effort represents the most extensive TPO inhibition screening campaign to date and illustrates a tiered screening approach that focuses resources, maximizes assay throughput, and reduces animal use. PMID:26884060
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3D imaging of optically cleared tissue using a simplified CLARITY method and on-chip microscopy
Zhang, Yibo; Shin, Yoonjung; Sung, Kevin; Yang, Sam; Chen, Harrison; Wang, Hongda; Teng, Da; Rivenson, Yair; Kulkarni, Rajan P.; Ozcan, Aydogan
2017-01-01
High-throughput sectioning and optical imaging of tissue samples using traditional immunohistochemical techniques can be costly and inaccessible in resource-limited areas. We demonstrate three-dimensional (3D) imaging and phenotyping in optically transparent tissue using lens-free holographic on-chip microscopy as a low-cost, simple, and high-throughput alternative to conventional approaches. The tissue sample is passively cleared using a simplified CLARITY method and stained using 3,3′-diaminobenzidine to target cells of interest, enabling bright-field optical imaging and 3D sectioning of thick samples. The lens-free computational microscope uses pixel super-resolution and multi-height phase recovery algorithms to digitally refocus throughout the cleared tissue and obtain a 3D stack of complex-valued images of the sample, containing both phase and amplitude information. We optimized the tissue-clearing and imaging system by finding the optimal illumination wavelength, tissue thickness, sample preparation parameters, and the number of heights of the lens-free image acquisition and implemented a sparsity-based denoising algorithm to maximize the imaging volume and minimize the amount of the acquired data while also preserving the contrast-to-noise ratio of the reconstructed images. As a proof of concept, we achieved 3D imaging of neurons in a 200-μm-thick cleared mouse brain tissue over a wide field of view of 20.5 mm2. The lens-free microscope also achieved more than an order-of-magnitude reduction in raw data compared to a conventional scanning optical microscope imaging the same sample volume. Being low cost, simple, high-throughput, and data-efficient, we believe that this CLARITY-enabled computational tissue imaging technique could find numerous applications in biomedical diagnosis and research in low-resource settings. PMID:28819645
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Gómez-Ríos, Germán Augusto; Liu, Chang; Tascon, Marcos; Reyes-Garcés, Nathaly; Arnold, Don W; Covey, Thomas R; Pawliszyn, Janusz
2017-04-04
In recent years, the direct coupling of solid phase microextraction (SPME) and mass spectrometry (MS) has shown its great potential to improve limits of quantitation, accelerate analysis throughput, and diminish potential matrix effects when compared to direct injection to MS. In this study, we introduce the open port probe (OPP) as a robust interface to couple biocompatible SPME (Bio-SPME) fibers to MS systems for direct electrospray ionization. The presented design consisted of minimal alterations to the front-end of the instrument and provided better sensitivity, simplicity, speed, wider compound coverage, and high-throughput in comparison to the LC-MS based approach. Quantitative determination of clenbuterol, fentanyl, and buprenorphine was successfully achieved in human urine. Despite the use of short extraction/desorption times (5 min/5 s), limits of quantitation below the minimum required performance levels (MRPL) set by the world antidoping agency (WADA) were obtained with good accuracy (≥90%) and linearity (R 2 > 0.99) over the range evaluated for all analytes using sample volumes of 300 μL. In-line technologies such as multiple reaction monitoring with multistage fragmentation (MRM 3 ) and differential mobility spectrometry (DMS) were used to enhance the selectivity of the method without compromising analysis speed. On the basis of calculations, once coupled to high throughput, this method can potentially yield preparation times as low as 15 s per sample based on the 96-well plate format. Our results demonstrated that Bio-SPME-OPP-MS efficiently integrates sampling/sample cleanup and atmospheric pressure ionization, making it an advantageous configuration for several bioanalytical applications, including doping in sports, in vivo tissue sampling, and therapeutic drug monitoring.
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Advanced digital modulation: Communication techniques and monolithic GaAs technology
NASA Technical Reports Server (NTRS)
Wilson, S. G.; Oliver, J. D., Jr.; Kot, R. C.; Richards, C. R.
1983-01-01
Communications theory and practice are merged with state-of-the-art technology in IC fabrication, especially monolithic GaAs technology, to examine the general feasibility of a number of advanced technology digital transmission systems. Satellite-channel models with (1) superior throughput, perhaps 2 Gbps; (2) attractive weight and cost; and (3) high RF power and spectrum efficiency are discussed. Transmission techniques possessing reasonably simple architectures capable of monolithic fabrication at high speeds were surveyed. This included a review of amplitude/phase shift keying (APSK) techniques and the continuous-phase-modulation (CPM) methods, of which MSK represents the simplest case.
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Rappaz, Benjamin; Cano, Elena; Colomb, Tristan; Kühn, Jonas; Depeursinge, Christian; Simanis, Viesturs; Magistretti, Pierre J; Marquet, Pierre
2009-01-01
Digital holography microscopy (DHM) is an optical technique which provides phase images yielding quantitative information about cell structure and cellular dynamics. Furthermore, the quantitative phase images allow the derivation of other parameters, including dry mass production, density, and spatial distribution. We have applied DHM to study the dry mass production rate and the dry mass surface density in wild-type and mutant fission yeast cells. Our study demonstrates the applicability of DHM as a tool for label-free quantitative analysis of the cell cycle and opens the possibility for its use in high-throughput screening.
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Ma, Vu; Bannon, Anthony W; Baumgartner, Jamie; Hale, Clarence; Hsieh, Faye; Hulme, Christopher; Rorrer, Kirk; Salon, John; van Staden, Carlo; Tempest, Paul
2006-10-01
Melanin-concentrating hormone (MCH) is a cyclic 19 amino acid orexigenic neuropeptide. The action of MCH on feeding is thought to involve the activation of its respective G protein-coupled receptor MCH-R1. Consequently, antagonists that block MCH regulated MCH-R1 activity may provide a viable approach to the treatment of diet-induced obesity. This communication reports the discovery of a novel MCH-R1 receptor antagonist, the biarylether 7, identified through high throughput screening. The solid-phase synthesis and structure-activity relationship of related analogs is described.
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Effect of solution annealing temperature on precipitation in 2205 duplex stainless steel
DOE Office of Scientific and Technical Information (OSTI.GOV)
Kashiwar, A., E-mail: akashiwar@gmail.com; Vennela, N. Phani, E-mail: phanivennela@gmail.com; Kamath, S.L., E-mail: kamath@iitb.ac.in
2012-12-15
In the present study, effect of solution annealing temperature (1050 Degree-Sign C and 1100 Degree-Sign C) and isothermal ageing (700 Degree-Sign C: 15 min to 6 h) on the microstructural changes in 2205 duplex stainless steel has been investigated systematically. Scanning electron microscopy and X-ray diffraction were adopted to follow the microstructural evolution, while an energy dispersive spectrometer attached to scanning electron microscope was used to obtain localised chemical information of various phases. The ferritic matrix of the two phase 2205 duplex stainless steel ({approx} 45% ferrite and {approx} 55% austenite) undergoes a series of metallurgical transformations during ageing-formation ofmore » secondary austenite ({gamma}{sub 2}) and precipitation of Cr and Mo rich intermetallic (chi-{chi} and sigma-{sigma}) phases. For solution annealing at 1050 Degree-Sign C, significant amount of carbides were observed in the ferrite grains after 1 h of ageing at 700 Degree-Sign C. {chi} Phase precipitated after the precipitation of carbides-preferentially at the ferrite-ferrite and also at the ferrite-austenite boundaries. {sigma} Phase was not observed in significant quantity even after 6 h of ageing. The sequence of precipitation in samples solution annealed at 1050 Degree-Sign C was found to be carbides {yields} {chi} {yields} {sigma}. On the contrary, for samples solution annealed at 1100 Degree-Sign C, the precipitation of {chi} phase was negligible. {chi} Phase precipitated before {sigma} phase, preferentially along the ferrite-ferrite grain boundaries and was later consumed in the {sigma} phase precipitation. The {sigma} phase precipitated via the eutectoid transformation of ferrite to yield secondary austenite {gamma}{sub 2} and {sigma} phase in the ferrite and along the ferrite-austenite grain boundaries. An increase in the volume fraction of {gamma}{sub 2} and {sigma} phase with simultaneous decrease in the ferrite was evidenced with ageing. - Highlights: Black-Right-Pointing-Pointer Effect of solution annealing temperature on microstructural evolution is studied. Black-Right-Pointing-Pointer {chi} Phase precipitated preferentially in the samples solution annealed at 1050 Degree-Sign C. Black-Right-Pointing-Pointer {sigma} Phase precipitated preferentially in the samples solution annealed at 1100 Degree-Sign C. Black-Right-Pointing-Pointer For SA at 1050 Degree-Sign C, the sequence of precipitation was carbides {yields} {chi} phase {yields} {sigma} phase. Black-Right-Pointing-Pointer For SA at 1100 Degree-Sign C, {sigma} phase precipitated via the eutectoid reaction: ferrite (F) {yields} {sigma} + {gamma}{sub 2}.« less
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Control and measurement of the phase behavior of aqueous solutions using microfluidics
Shim, Jung-uk; Cristobal, Galder; Link, Darren R.; Thorsen, Todd; Jia, Yanwei; Piattelli, Katie; Fraden, Seth
2008-01-01
A microfluidic device denoted the Phase Chip has been designed to measure and manipulate the phase diagram of multi-component fluid mixtures. The Phase Chip exploits the permeation of water through poly(dimethylsiloxane) (PDMS) in order to controllably vary the concentration of solutes in aqueous nanoliter volume microdrops stored in wells. The permeation of water in the Phase Chip is modeled using the diffusion equation and good agreement between experiment and theory is obtained. The Phase Chip operates by first creating drops of the water/solute mixture whose composition varies sequentially. Next, drops are transported down channels and guided into storage wells using surface tension forces. Finally, the solute concentration of each stored drop is simultaneously varied and measured. Two applications of the Phase Chip are presented. First, the phase diagram of a polymer/salt mixture is measured on-chip and validated off-chip and second, protein crystallization rates are enhanced through the manipulation of the kinetics of nucleation and growth. PMID:17580868
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Glass-liquid phase separation in highly supersaturated aqueous solutions of telaprevir.
Mosquera-Giraldo, Laura I; Taylor, Lynne S
2015-02-02
Amorphous solid dispersions are of great current interest because they can improve the delivery of poorly water-soluble compounds. It has been recently noted that the highly supersaturated solutions generated by dissolution of some ASDs can undergo a phase transition to a colloidal, disordered, drug-rich phase when the concentration exceeds the "amorphous solubility" of the drug. The purpose of this study was to investigate the phase behavior of supersaturated solutions of telaprevir, which is formulated as an amorphous solid dispersion in the commercial product. Different analytical techniques including proton nuclear magnetic resonance spectroscopy (NMR), ultraviolet spectroscopy (UV), fluorescence spectroscopy and flux measurements were used to evaluate the properties of aqueous supersaturated solutions of telaprevir. It was found that highly supersaturated solutions of telaprevir underwent glass-liquid phase separation (GLPS) when the concentration exceeded 90 μg/mL, forming a water-saturated colloidal, amorphous drug-rich phase with a glass transition temperature of 52 °C. From flux measurements, it was observed that the "free" drug concentration reached a maximum at the concentration where GLPS occurred, and did not increase further as the concentration was increased. This phase behavior, which results in a precipitate and a metastable equilibrium between a supersaturated solution and a drug-rich phase, is obviously important in the context of evaluating amorphous solid dispersion formulations and their crystallization routes.
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High-Speed Burst-Mode Clock and Data Recovery Circuits for Multiaccess Networks
NASA Astrophysics Data System (ADS)
Shastri, Bhavin J.
Optical multiaccess networks, and specifically passive optical networks (PONs) are considered to be the most promising technologies for the deployment of fiber-to-the-premises/home/user (FTTx) to solve the problem of limited bandwidth in local area networks with a low-cost solution and a guaranteed quality of service. In a PON, multiple users share the fiber infrastructure in a point-to-multipoint (P2MP) network. This topology introduce optical path delays which inherently cause the data packets to undergo amplitude variations up to 20 dB and phase variations from --2pi to +2pi rad--burst-mode traffic. Consequently, this creates new challenges for the design and test of optical receivers front-ends and clock and data recovery circuits (CDRs), in particular, burst-mode CDRs (BM-CDRs). The research presented in this thesis investigates BM-CDRs, both theoretically and experimentally. We demonstrate two novel BM-CDR architectures. These BM-CDRs achieve error-free operation [bit error rate (BER) <10e--10] while providing instantaneous (0 preamble bit) clock phase acquisition for any phase step (+/-2pi rad) between successive bursts. Instantaneous phase acquisition improves the physical efficiency of upstream PON traffic, and increases the effective throughput of the system by raising the information rate. Our eloquent, scalable BM-CDR architectures leverage the design of low complexity commercial electronics providing a cost-effective solution for PONs. The first BM-CDR (rated at 5 Gb/s) is based on phase-tracking time domain oversampling (semiblind) CDR operated at 2x the bit rate and a clock phase aligner (CPA) that makes use of a phase picking algorithm. The second BM-CDR (rate at 10 Gb/s) is based on semiblind space domain oversampling and employs a phase-tracking CDR with multiphase clocks at the bit rate and a CPA with a novel phase picking algorithm. We experimentally demonstrate these BM-CDRs in optical test beds and study the effect of channel-impairments in: (1) 5 Gb/s time-division multiplexing gigabit PON 20-km uplink; (2) 2.5 Gb/s overlapped subcarrier-multiplexing wavelength-division multiplexed PON 20-km uplink; (3) 1.25 Gb/s 1300-km deployed fiber link spanning Montreal--Quebec City and back; and (4) 622 Mb/s in a 7-user spectral amplitude-coded optical code-division multiple access 20-km PON uplink. We also provide a theoretical framework to model and analyze BM-CDRs. We develop a unified probabilistic theory of BM-CDRs based on semiblind oversampling techniques in either the time or space domain. This theory has also been generalized for conventional CDRs and Nx-oversampling CDRs. Based on this theory, we perform a comprehensive theoretical analysis to quantify the performance of the proposed BM-CDRs in terms of the BER and packet loss ratio to assess the tradeoffs between various parameters, and compare the results experimentally to validate the theoretical model. This analysis coupled with the experimental results will refine theoretical models PONs, and provide input for establishing realistic power budgets.
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2018-01-01
Organic semiconductors (OSCs) are promising materials for cost-effective production of electronic devices because they can be processed from solution employing high-throughput techniques. However, small-molecule OSCs are prone to structural modifications because of the presence of weak van der Waals intermolecular interactions. Hence, controlling the crystallization in these materials is pivotal to achieve high device reproducibility. In this perspective article, we focus on controlling polymorphism and morphology in small-molecule organic semiconducting thin films deposited by solution-shearing techniques compatible with roll-to-roll systems. Special attention is paid to the influence that the different experimental deposition parameters can have on thin films. Further, the main characterization techniques for thin-film structures are reviewed, highlighting the in situ characterization tools that can provide crucial insights into the crystallization mechanisms. PMID:29503976
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Automatic pelvis segmentation from x-ray images of a mouse model
NASA Astrophysics Data System (ADS)
Al Okashi, Omar M.; Du, Hongbo; Al-Assam, Hisham
2017-05-01
The automatic detection and quantification of skeletal structures has a variety of different applications for biological research. Accurate segmentation of the pelvis from X-ray images of mice in a high-throughput project such as the Mouse Genomes Project not only saves time and cost but also helps achieving an unbiased quantitative analysis within the phenotyping pipeline. This paper proposes an automatic solution for pelvis segmentation based on structural and orientation properties of the pelvis in X-ray images. The solution consists of three stages including pre-processing image to extract pelvis area, initial pelvis mask preparation and final pelvis segmentation. Experimental results on a set of 100 X-ray images showed consistent performance of the algorithm. The automated solution overcomes the weaknesses of a manual annotation procedure where intra- and inter-observer variations cannot be avoided.
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Adnan, Mohammed; Marincel, Daniel M; Kleinerman, Olga; Chu, Sang-Hyon; Park, Cheol; Hocker, Samuel J A; Fay, Catharine; Arepalli, Sivaram; Talmon, Yeshayahu; Pasquali, Matteo
2018-03-14
Due to recent advances in high-throughput synthesis, research on boron nitride nanotubes (BNNTs) is moving toward applications. One future goal is the assembly of macroscopic articles of high-aspect-ratio, pristine BNNTs. However, these articles are presently unattainable because of insufficient purification and fabrication methods. We introduce a solution process for extracting BNNTs from synthesis impurities without sonication or the use of surfactants and proceed to convert the extracted BNNTs into thin films. The solution process can also be used to convert as-synthesized material-which contains significant amounts of hexagonal boron nitride ( h-BN)-into mats and aerogels with controllable structure and dimension. The solution extraction method, combined with further advances in synthesis and purification, contributes to the development of all-BNNT macroscopic articles, such as fibers and 3-D structures.
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Phase separation in solutions of monoclonal antibodies and the effect of human serum albumin
Wang, Ying; Lomakin, Aleksey; Latypov, Ramil F.; Benedek, George B.
2011-01-01
We report the observation of liquid-liquid phase separation in a solution of human monoclonal antibody, IgG2, and the effects of human serum albumin, a major blood protein, on this phase separation. We find a significant reduction of phase separation temperature in the presence of albumin, and a preferential partitioning of the albumin into the antibody-rich phase. We provide a general thermodynamic analysis of the antibody-albumin mixture phase diagram and relate its features to the magnitude of the effective interprotein interactions. Our analysis suggests that additives (HSA in this report), which have moderate attraction with antibody molecules, may be used to forestall undesirable proetin condensation in antibody solutions. Our findings are relevant to understanding the stability of pharmaceutical solutions of antibodies and the mechanisms of cryoglobulinemia. PMID:21921237
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A high-throughput media design approach for high performance mammalian fed-batch cultures
Rouiller, Yolande; Périlleux, Arnaud; Collet, Natacha; Jordan, Martin; Stettler, Matthieu; Broly, Hervé
2013-01-01
An innovative high-throughput medium development method based on media blending was successfully used to improve the performance of a Chinese hamster ovary fed-batch medium in shaking 96-deepwell plates. Starting from a proprietary chemically-defined medium, 16 formulations testing 43 of 47 components at 3 different levels were designed. Media blending was performed following a custom-made mixture design of experiments considering binary blends, resulting in 376 different blends that were tested during both cell expansion and fed-batch production phases in one single experiment. Three approaches were chosen to provide the best output of the large amount of data obtained. A simple ranking of conditions was first used as a quick approach to select new formulations with promising features. Then, prediction of the best mixes was done to maximize both growth and titer using the Design Expert software. Finally, a multivariate analysis enabled identification of individual potential critical components for further optimization. Applying this high-throughput method on a fed-batch, rather than on a simple batch, process opens new perspectives for medium and feed development that enables identification of an optimized process in a short time frame. PMID:23563583
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Stanic, Vesna; Broadbent, Charlotte; DiMasi, Elaine
2016-11-14
The interactions of mixtures of anionic and amphoteric surfactants with sugar amphiphiles were studied via high throughput small angle x-ray scattering (SAXS). The sugar amphiphile was composed of Caprate, Caprylate, and Oleate mixed ester of methyl glucoside, MeGCCO. Optimal surfactant interactions are sought which have desirable physical properties, which must be identified in a cost effective manner that can access the large phase space of possible molecular combinations. X-ray scattering patterns obtained via high throughput SAXS can probe a combinatorial sample space and reveal the incorporation of MeGCCO into the micelles and the molecular associations between surfactant molecules. Such datamore » make it possible to efficiently assess the effects of the new amphiphiles in the formulation. A specific finding of this study is that formulations containing comparatively monodisperse and homogeneous surfactant mixtures can be reliably tuned by addition of NaCl, which swells the surfactant micelles with a monotonic dependence on salt concentration. In contrast, the presence of multiple different surfactants destroys clear correlations with NaCl concentration, even in otherwise similar series of formulations.« less
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WIYN bench upgrade: a revitalized spectrograph
NASA Astrophysics Data System (ADS)
Bershady, M.; Barden, S.; Blanche, P.-A.; Blanco, D.; Corson, C.; Crawford, S.; Glaspey, J.; Habraken, S.; Jacoby, G.; Keyes, J.; Knezek, P.; Lemaire, P.; Liang, M.; McDougall, E.; Poczulp, G.; Sawyer, D.; Westfall, K.; Willmarth, D.
2008-07-01
We describe the redesign and upgrade of the versatile fiber-fed Bench Spectrograph on the WIYN 3.5m telescope. The spectrograph is fed by either the Hydra multi-object positioner or integral-field units (IFUs) at two other ports, and can be configured with an adjustable camera-collimator angle to use low-order and echelle gratings. The upgrade, including a new collimator, charge-coupled device (CCD) and modern controller, and volume-phase holographic gratings (VPHG), has high performance-to-cost ratio by combining new technology with a system reconfiguration that optimizes throughput while utilizing as much of the existing instrument as possible. A faster, all-refractive collimator enhances throughput by 60%, nearly eliminates the slit-function due to vignetting, and improves image quality to maintain instrumental resolution. Two VPH gratings deliver twice the diffraction efficiency of existing surface-relief gratings: A 740 l/mm grating (float-glass and post-polished) used in 1st and 2nd-order, and a large 3300 l/mm grating (spectral resolution comparable to the R2 echelle). The combination of collimator, high-quantum efficiency (QE) CCD, and VPH gratings yields throughput gain-factors of up to 3.5.
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Henchoz, Yveline; Guillarme, Davy; Martel, Sophie; Rudaz, Serge; Veuthey, Jean-Luc; Carrupt, Pierre-Alain
2009-08-01
Ultra-high-pressure liquid chromatography (UHPLC) systems able to work with columns packed with sub-2 microm particles offer very fast methods to determine the lipophilicity of new chemical entities. The careful development of the most suitable experimental conditions presented here will help medicinal chemists for high-throughput screening (HTS) log P(oct) measurements. The approach was optimized using a well-balanced set of 38 model compounds and a series of 28 basic compounds such as beta-blockers, local anesthetics, piperazines, clonidine, and derivatives. Different organic modifiers and hybrid stationary phases packed with 1.7-microm particles were evaluated in isocratic as well as gradient modes, and the advantages and limitations of tested conditions pointed out. The UHPLC approach offered a significant enhancement over the classical HPLC methods, by a factor 50 in the lipophilicity determination throughput. The hyphenation of UHPLC with MS detection allowed a further increase in the throughput. Data and results reported herein prove that the UHPLC-MS method can represent a progress in the HTS-measurement of lipophilicity due to its speed (at least a factor of 500 with respect to HPLC approaches) and to an extended field of application.
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NASA Astrophysics Data System (ADS)
Toropova, L. V.; Alexandrov, D. V.
2018-05-01
The directional solidification of a ternary system with an extended phase transition region is theoretically studied. A mathematical model is developed to describe quasi-stationary solidification, and its analytical solution is constructed with allowance for a nonlinear liquids line equation. We demonstrate that the phase diagram nonlinearity leads to substantial changes of analytical solutions.
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NASA Astrophysics Data System (ADS)
Shirayama, Sakae; Uda, Tetsuya
2016-04-01
This research outlines an organic-aqueous-aqueous three-phase solvent extraction method and proposes its use in a new metal separation process for the recycling of manganese (Mn), cobalt (Co), and nickel (Ni) from used lithium ion batteries (LIBs). The three-phase system was formed by mixing xylene organic solution, 50 pct polyethylene glycol (PEG) aqueous solution, and 1 mol L-1 sodium sulfate (Na2SO4) aqueous solution. The xylene organic solution contained 2-ethylhexylphosphonic acid (D2EHPA) as an extractant for Mn ion, and the Na2SO4 aqueous solution contained 1 mol L-1 potassium thiocyanate (KSCN) as an extractant for Co ion. Concentrations of the metal ions were varied by dissolving metal sulfates in the Na2SO4 aqueous solution. As a result of the experiments, Mn, Co, and Ni ions were distributed in the xylene organic phase, PEG-rich aqueous phase, and Na2SO4-rich aqueous phase, respectively. The separation was effective when the pH value was around 4. Numerical simulation was also conducted in order to predict the distribution of metal ions after the multi-stage counter-current extractions.
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Nobrega, R Paul; Brown, Michael; Williams, Cody; Sumner, Chris; Estep, Patricia; Caffry, Isabelle; Yu, Yao; Lynaugh, Heather; Burnina, Irina; Lilov, Asparouh; Desroches, Jordan; Bukowski, John; Sun, Tingwan; Belk, Jonathan P; Johnson, Kirt; Xu, Yingda
2017-10-01
The state-of-the-art industrial drug discovery approach is the empirical interrogation of a library of drug candidates against a target molecule. The advantage of high-throughput kinetic measurements over equilibrium assessments is the ability to measure each of the kinetic components of binding affinity. Although high-throughput capabilities have improved with advances in instrument hardware, three bottlenecks in data processing remain: (1) intrinsic molecular properties that lead to poor biophysical quality in vitro are not accounted for in commercially available analysis models, (2) processing data through a user interface is time-consuming and not amenable to parallelized data collection, and (3) a commercial solution that includes historical kinetic data in the analysis of kinetic competition data does not exist. Herein, we describe a generally applicable method for the automated analysis, storage, and retrieval of kinetic binding data. This analysis can deconvolve poor quality data on-the-fly and store and organize historical data in a queryable format for use in future analyses. Such database-centric strategies afford greater insight into the molecular mechanisms of kinetic competition, allowing for the rapid identification of allosteric effectors and the presentation of kinetic competition data in absolute terms of percent bound to antigen on the biosensor.
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Li, Ben; Li, Yunxiao; Qin, Zhaohui S
2017-06-01
Modern high-throughput biotechnologies such as microarray and next generation sequencing produce a massive amount of information for each sample assayed. However, in a typical high-throughput experiment, only limited amount of data are observed for each individual feature, thus the classical 'large p , small n ' problem. Bayesian hierarchical model, capable of borrowing strength across features within the same dataset, has been recognized as an effective tool in analyzing such data. However, the shrinkage effect, the most prominent feature of hierarchical features, can lead to undesirable over-correction for some features. In this work, we discuss possible causes of the over-correction problem and propose several alternative solutions. Our strategy is rooted in the fact that in the Big Data era, large amount of historical data are available which should be taken advantage of. Our strategy presents a new framework to enhance the Bayesian hierarchical model. Through simulation and real data analysis, we demonstrated superior performance of the proposed strategy. Our new strategy also enables borrowing information across different platforms which could be extremely useful with emergence of new technologies and accumulation of data from different platforms in the Big Data era. Our method has been implemented in R package "adaptiveHM", which is freely available from https://github.com/benliemory/adaptiveHM.
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FMLRC: Hybrid long read error correction using an FM-index.
Wang, Jeremy R; Holt, James; McMillan, Leonard; Jones, Corbin D
2018-02-09
Long read sequencing is changing the landscape of genomic research, especially de novo assembly. Despite the high error rate inherent to long read technologies, increased read lengths dramatically improve the continuity and accuracy of genome assemblies. However, the cost and throughput of these technologies limits their application to complex genomes. One solution is to decrease the cost and time to assemble novel genomes by leveraging "hybrid" assemblies that use long reads for scaffolding and short reads for accuracy. We describe a novel method leveraging a multi-string Burrows-Wheeler Transform with auxiliary FM-index to correct errors in long read sequences using a set of complementary short reads. We demonstrate that our method efficiently produces significantly more high quality corrected sequence than existing hybrid error-correction methods. We also show that our method produces more contiguous assemblies, in many cases, than existing state-of-the-art hybrid and long-read only de novo assembly methods. Our method accurately corrects long read sequence data using complementary short reads. We demonstrate higher total throughput of corrected long reads and a corresponding increase in contiguity of the resulting de novo assemblies. Improved throughput and computational efficiency than existing methods will help better economically utilize emerging long read sequencing technologies.
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Modeling and Simulation Reliable Spacecraft On-Board Computing
NASA Technical Reports Server (NTRS)
Park, Nohpill
1999-01-01
The proposed project will investigate modeling and simulation-driven testing and fault tolerance schemes for Spacecraft On-Board Computing, thereby achieving reliable spacecraft telecommunication. A spacecraft communication system has inherent capabilities of providing multipoint and broadcast transmission, connectivity between any two distant nodes within a wide-area coverage, quick network configuration /reconfiguration, rapid allocation of space segment capacity, and distance-insensitive cost. To realize the capabilities above mentioned, both the size and cost of the ground-station terminals have to be reduced by using reliable, high-throughput, fast and cost-effective on-board computing system which has been known to be a critical contributor to the overall performance of space mission deployment. Controlled vulnerability of mission data (measured in sensitivity), improved performance (measured in throughput and delay) and fault tolerance (measured in reliability) are some of the most important features of these systems. The system should be thoroughly tested and diagnosed before employing a fault tolerance into the system. Testing and fault tolerance strategies should be driven by accurate performance models (i.e. throughput, delay, reliability and sensitivity) to find an optimal solution in terms of reliability and cost. The modeling and simulation tools will be integrated with a system architecture module, a testing module and a module for fault tolerance all of which interacting through a centered graphical user interface.