Site-selective substitutional doping with atomic precision on stepped Al (111) surface by single-atom manipulation.

PubMed

Chen, Chang; Zhang, Jinhu; Dong, Guofeng; Shao, Hezhu; Ning, Bo-Yuan; Zhao, Li; Ning, Xi-Jing; Zhuang, Jun

2014-01-01

In fabrication of nano- and quantum devices, it is sometimes critical to position individual dopants at certain sites precisely to obtain the specific or enhanced functionalities. With first-principles simulations, we propose a method for substitutional doping of individual atom at a certain position on a stepped metal surface by single-atom manipulation. A selected atom at the step of Al (111) surface could be extracted vertically with an Al trimer-apex tip, and then the dopant atom will be positioned to this site. The details of the entire process including potential energy curves are given, which suggests the reliability of the proposed single-atom doping method.

Bilateral step length estimation using a single inertial measurement unit attached to the pelvis

PubMed Central

2012-01-01

Background The estimation of the spatio-temporal gait parameters is of primary importance in both physical activity monitoring and clinical contexts. A method for estimating step length bilaterally, during level walking, using a single inertial measurement unit (IMU) attached to the pelvis is proposed. In contrast to previous studies, based either on a simplified representation of the human gait mechanics or on a general linear regressive model, the proposed method estimates the step length directly from the integration of the acceleration along the direction of progression. Methods The IMU was placed at pelvis level fixed to the subject's belt on the right side. The method was validated using measurements from a stereo-photogrammetric system as a gold standard on nine subjects walking ten laps along a closed loop track of about 25 m, varying their speed. For each loop, only the IMU data recorded in a 4 m long portion of the track included in the calibrated volume of the SP system, were used for the analysis. The method takes advantage of the cyclic nature of gait and it requires an accurate determination of the foot contact instances. A combination of a Kalman filter and of an optimally filtered direct and reverse integration applied to the IMU signals formed a single novel method (Kalman and Optimally filtered Step length Estimation - KOSE method). A correction of the IMU displacement due to the pelvic rotation occurring in gait was implemented to estimate the step length and the traversed distance. Results The step length was estimated for all subjects with less than 3% error. Traversed distance was assessed with less than 2% error. Conclusions The proposed method provided estimates of step length and traversed distance more accurate than any other method applied to measurements obtained from a single IMU that can be found in the literature. In healthy subjects, it is reasonable to expect that, errors in traversed distance estimation during daily monitoring activity would be of the same order of magnitude of those presented. PMID:22316235

Two-step fabrication of single-layer rectangular SnSe flakes

NASA Astrophysics Data System (ADS)

Jiang, Jizhou; Wong, Calvin Pei Yu; Zou, Jing; Li, Shisheng; Wang, Qixing; Chen, Jianyi; Qi, Dianyu; Wang, Hongyu; Eda, Goki; Chua, Daniel H. C.; Shi, Yumeng; Zhang, Wenjing; Thye Shen Wee, Andrew

2017-06-01

Recent findings about ultrahigh thermoelectric performances in SnSe single crystals have stimulated research on this binary semiconductor material. Furthermore, single-layer SnSe is an interesting analogue of phosphorene, with potential applications in two-dimensional (2D) nanoelectronics. Although significant advances in the synthesis of SnSe nanocrystals have been made, fabrication of well-defined large-sized single-layer SnSe flakes in a facile way still remains a challenge. The growth of single-layer rectangular SnSe flakes with a thickness of ~6.8 Å and lateral dimensions of about 30 µm  ×  50 µm is demonstrated by a two-step synthesis method, where bulk rectangular SnSe flakes were synthesized first by a vapor transport deposition method followed by a nitrogen etching technique to fabricate single-layer rectangular SnSe flakes in an atmospheric pressure system. The as-obtained rectangular SnSe flakes exhibited a pure crystalline phase oriented along the a-axis direction. Field-effect transistor devices fabricated on individual single-layer rectangular SnSe flakes using gold electrodes exhibited p-doped ambipolar behavior and a hole mobility of about 0.16 cm2 V-1 s-1. This two-step fabrication method can be helpful for growing other similar 2D large-sized single-layer materials.

Single-step affinity purification for fungal proteomics.

PubMed

Liu, Hui-Lin; Osmani, Aysha H; Ukil, Leena; Son, Sunghun; Markossian, Sarine; Shen, Kuo-Fang; Govindaraghavan, Meera; Varadaraj, Archana; Hashmi, Shahr B; De Souza, Colin P; Osmani, Stephen A

2010-05-01

A single-step protein affinity purification protocol using Aspergillus nidulans is described. Detailed protocols for cell breakage, affinity purification, and depending on the application, methods for protein release from affinity beads are provided. Examples defining the utility of the approaches, which should be widely applicable, are included.

Solubilization of phosphorus from phosphate rocks with Acidithiobacillus thiooxidans following a growing-then-recovery process.

PubMed

Calle-Castañeda, Susana M; Márquez-Godoy, Marco A; Hernández-Ortiz, Juan P

2017-12-29

Phosphorus is an essential nutrient for the synthesis of biomolecules and is particularly important in agriculture, as soils must be constantly supplemented with its inorganic form to ensure high yields and productivity. In this paper, we propose a process to solubilize phosphorus from phosphate rocks, where Acidithiobacillus thiooxidans cultures are pre-cultivated to foster the acidic conditions for bioleaching-two-step "growing-then-recovery"-. Our method solubilizes 100% of phosphorus, whereas the traditional process without pre-cultivation-single-step "growing-and-recovery"-results in a maximum of 56% solubilization. As a proof of principle, we demonstrate that even at low concentrations of the phosphate rock, 1% w/v, the bacterial culture is unviable and biological activity is not observed during the single-step process. On the other hand, in our method, the bacteria are grown without the rock, ensuring high acid production. Once pH levels are below 0.7, the mineral is added to the culture, resulting in high yields of biological solubilization. According to the Fourier Transform Infrared Spectroscopy spectrums, gypsum is the dominant phosphate phase after both the single- and two-step methods. However, calcite and fluorapatite, dominant in the un-treated rock, are still present after the single-step, highlighting the differences between the chemical and the biological methods. Our process opens new avenues for biotechnologies to recover phosphorus in tropical soils and in low-grade phosphate rock reservoirs.

Use of causative variants and SNP weighting in a single-step GBLUP context

USDA-ARS?s Scientific Manuscript database

Much effort has been recently put into identifying causative quantitative trait nucleotides (QTN) in animal breeding, aiming genomic prediction. Among the genomic methods available, single-step GBLUP (ssGBLUP) became the choice because of its simplicity and potentially higher accuracy. When QTN are ...

Inferring subunit stoichiometry from single molecule photobleaching

PubMed Central

2013-01-01

Single molecule photobleaching is a powerful tool for determining the stoichiometry of protein complexes. By attaching fluorophores to proteins of interest, the number of associated subunits in a complex can be deduced by imaging single molecules and counting fluorophore photobleaching steps. Because some bleaching steps might be unobserved, the ensemble of steps will be binomially distributed. In this work, it is shown that inferring the true composition of a complex from such data is nontrivial because binomially distributed observations present an ill-posed inference problem. That is, a unique and optimal estimate of the relevant parameters cannot be extracted from the observations. Because of this, a method has not been firmly established to quantify confidence when using this technique. This paper presents a general inference model for interpreting such data and provides methods for accurately estimating parameter confidence. The formalization and methods presented here provide a rigorous analytical basis for this pervasive experimental tool. PMID:23712552

Procedure for normalization of cDNA libraries

DOEpatents

Bonaldo, Maria DeFatima; Soares, Marcelo Bento

1997-01-01

This invention provides a method to normalize a cDNA library constructed in a vector capable of being converted to single-stranded circles and capable of producing complementary nucleic acid molecules to the single-stranded circles comprising: (a) converting the cDNA library in single-stranded circles; (b) generating complementary nucleic acid molecules to the single-stranded circles; (c) hybridizing the single-stranded circles converted in step (a) with complementary nucleic acid molecules of step (b) to produce partial duplexes to an appropriate Cot; (e) separating the unhybridized single-stranded circles from the hybridized single-stranded circles, thereby generating a normalized cDNA library.

Methods for the continuous production of plastic scintillator materials

DOEpatents

Bross, Alan; Pla-Dalmau, Anna; Mellott, Kerry

1999-10-19

Methods for producing plastic scintillating material employing either two major steps (tumble-mix) or a single major step (inline-coloring or inline-doping). Using the two step method, the polymer pellets are mixed with silicone oil, and the mixture is then tumble mixed with the dopants necessary to yield the proper response from the scintillator material. The mixture is then placed in a compounder and compounded in an inert gas atmosphere. The resultant scintillator material is then extruded and pelletized or formed. When only a single step is employed, the polymer pellets and dopants are metered into an inline-coloring extruding system. The mixture is then processed under a inert gas atmosphere, usually argon or nitrogen, to form plastic scintillator material in the form of either scintillator pellets, for subsequent processing, or as material in the direct formation of the final scintillator shape or form.

Rapid, single-step most-probable-number method for enumerating fecal coliforms in effluents from sewage treatment plants

NASA Technical Reports Server (NTRS)

Munoz, E. F.; Silverman, M. P.

1979-01-01

A single-step most-probable-number method for determining the number of fecal coliform bacteria present in sewage treatment plant effluents is discussed. A single growth medium based on that of Reasoner et al. (1976) and consisting of 5.0 gr. proteose peptone, 3.0 gr. yeast extract, 10.0 gr. lactose, 7.5 gr. NaCl, 0.2 gr. sodium lauryl sulfate, and 0.1 gr. sodium desoxycholate per liter is used. The pH is adjusted to 6.5, and samples are incubated at 44.5 deg C. Bacterial growth is detected either by measuring the increase with time in the electrical impedance ratio between the innoculated sample vial and an uninnoculated reference vial or by visual examination for turbidity. Results obtained by the single-step method for chlorinated and unchlorinated effluent samples are in excellent agreement with those obtained by the standard method. It is suggested that in automated treatment plants impedance ratio data could be automatically matched by computer programs with the appropriate dilution factors and most probable number tables already in the computer memory, with the corresponding result displayed as fecal coliforms per 100 ml of effluent.

Single crystal micromechanical resonator and fabrication methods thereof

DOEpatents

Olsson, Roy H.; Friedmann, Thomas A.; Homeijer, Sara Jensen; Wiwi, Michael; Hattar, Khalid Mikhiel; Clark, Blythe; Bauer, Todd; Van Deusen, Stuart B.

2016-12-20

The present invention relates to a single crystal micromechanical resonator. In particular, the resonator includes a lithium niobate or lithium tantalate suspended plate. Also provided are improved microfabrication methods of making resonators, which does not rely on complicated wafer bonding, layer fracturing, and mechanical polishing steps. Rather, the methods allow the resonator and its components to be formed from a single crystal.

Deferred discrimination algorithm (nibbling) for target filter management

NASA Astrophysics Data System (ADS)

Caulfield, H. John; Johnson, John L.

1999-07-01

A new method of classifying objects is presented. Rather than trying to form the classifier in one step or in one training algorithm, it is done in a series of small steps, or nibbles. This leads to an efficient and versatile system that is trained in series with single one-shot examples but applied in parallel, is implemented with single layer perceptrons, yet maintains its fully sequential hierarchical structure. Based on the nibbling algorithm, a basic new method of target reference filter management is described.

Procedure for normalization of cDNA libraries

DOEpatents

Bonaldo, M.D.; Soares, M.B.

1997-12-30

This invention provides a method to normalize a cDNA library constructed in a vector capable of being converted to single-stranded circles and capable of producing complementary nucleic acid molecules to the single-stranded circles comprising: (a) converting the cDNA library in single-stranded circles; (b) generating complementary nucleic acid molecules to the single-stranded circles; (c) hybridizing the single-stranded circles converted in step (a) with complementary nucleic acid molecules of step (b) to produce partial duplexes to an appropriate Cot; (e) separating the unhybridized single-stranded circles from the hybridized single-stranded circles, thereby generating a normalized cDNA library. 1 fig.

Single step signal group-imidazole labeling of organic phosphate groups under aqueous conditions

DOEpatents

Giese, Roger W.; Wang, Poguang

1996-01-01

Compounds and methods for single step, covalent labeling of the phosphate group of an organic substance under aqueous conditions are described. The labeling compound includes any kind of detectable signal group covalently bound to an imidazole moiety, which can be imidazole or a substituted imidazole. A preferred labeling compound has the formula ##STR1##

A Systems Approach towards an Intelligent and Self-Controlling Platform for Integrated Continuous Reaction Sequences**

PubMed Central

Ingham, Richard J; Battilocchio, Claudio; Fitzpatrick, Daniel E; Sliwinski, Eric; Hawkins, Joel M; Ley, Steven V

2015-01-01

Performing reactions in flow can offer major advantages over batch methods. However, laboratory flow chemistry processes are currently often limited to single steps or short sequences due to the complexity involved with operating a multi-step process. Using new modular components for downstream processing, coupled with control technologies, more advanced multi-step flow sequences can be realized. These tools are applied to the synthesis of 2-aminoadamantane-2-carboxylic acid. A system comprising three chemistry steps and three workup steps was developed, having sufficient autonomy and self-regulation to be managed by a single operator. PMID:25377747

Single-step methods for predicting orbital motion considering its periodic components

NASA Astrophysics Data System (ADS)

Lavrov, K. N.

1989-01-01

Modern numerical methods for integration of ordinary differential equations can provide accurate and universal solutions to celestial mechanics problems. The implicit single sequence algorithms of Everhart and multiple step computational schemes using a priori information on periodic components can be combined to construct implicit single sequence algorithms which combine their advantages. The construction and analysis of the properties of such algorithms are studied, utilizing trigonometric approximation of the solutions of differential equations containing periodic components. The algorithms require 10 percent more machine memory than the Everhart algorithms, but are twice as fast, and yield short term predictions valid for five to ten orbits with good accuracy and five to six times faster than algorithms using other methods.

A Particle Smoother with Sequential Importance Resampling for soil hydraulic parameter estimation: A lysimeter experiment

NASA Astrophysics Data System (ADS)

Montzka, Carsten; Hendricks Franssen, Harrie-Jan; Moradkhani, Hamid; Pütz, Thomas; Han, Xujun; Vereecken, Harry

2013-04-01

An adequate description of soil hydraulic properties is essential for a good performance of hydrological forecasts. So far, several studies showed that data assimilation could reduce the parameter uncertainty by considering soil moisture observations. However, these observations and also the model forcings were recorded with a specific measurement error. It seems a logical step to base state updating and parameter estimation on observations made at multiple time steps, in order to reduce the influence of outliers at single time steps given measurement errors and unknown model forcings. Such outliers could result in erroneous state estimation as well as inadequate parameters. This has been one of the reasons to use a smoothing technique as implemented for Bayesian data assimilation methods such as the Ensemble Kalman Filter (i.e. Ensemble Kalman Smoother). Recently, an ensemble-based smoother has been developed for state update with a SIR particle filter. However, this method has not been used for dual state-parameter estimation. In this contribution we present a Particle Smoother with sequentially smoothing of particle weights for state and parameter resampling within a time window as opposed to the single time step data assimilation used in filtering techniques. This can be seen as an intermediate variant between a parameter estimation technique using global optimization with estimation of single parameter sets valid for the whole period, and sequential Monte Carlo techniques with estimation of parameter sets evolving from one time step to another. The aims are i) to improve the forecast of evaporation and groundwater recharge by estimating hydraulic parameters, and ii) to reduce the impact of single erroneous model inputs/observations by a smoothing method. In order to validate the performance of the proposed method in a real world application, the experiment is conducted in a lysimeter environment.

Single-Camera-Based Method for Step Length Symmetry Measurement in Unconstrained Elderly Home Monitoring.

PubMed

Cai, Xi; Han, Guang; Song, Xin; Wang, Jinkuan

2017-11-01

single-camera-based gait monitoring is unobtrusive, inexpensive, and easy-to-use to monitor daily gait of seniors in their homes. However, most studies require subjects to walk perpendicularly to camera's optical axis or along some specified routes, which limits its application in elderly home monitoring. To build unconstrained monitoring environments, we propose a method to measure step length symmetry ratio (a useful gait parameter representing gait symmetry without significant relationship with age) from unconstrained straight walking using a single camera, without strict restrictions on walking directions or routes. according to projective geometry theory, we first develop a calculation formula of step length ratio for the case of unconstrained straight-line walking. Then, to adapt to general cases, we propose to modify noncollinear footprints, and accordingly provide general procedure for step length ratio extraction from unconstrained straight walking. Our method achieves a mean absolute percentage error (MAPE) of 1.9547% for 15 subjects' normal and abnormal side-view gaits, and also obtains satisfactory MAPEs for non-side-view gaits (2.4026% for 45°-view gaits and 3.9721% for 30°-view gaits). The performance is much better than a well-established monocular gait measurement system suitable only for side-view gaits with a MAPE of 3.5538%. Independently of walking directions, our method can accurately estimate step length ratios from unconstrained straight walking. This demonstrates our method is applicable for elders' daily gait monitoring to provide valuable information for elderly health care, such as abnormal gait recognition, fall risk assessment, etc. single-camera-based gait monitoring is unobtrusive, inexpensive, and easy-to-use to monitor daily gait of seniors in their homes. However, most studies require subjects to walk perpendicularly to camera's optical axis or along some specified routes, which limits its application in elderly home monitoring. To build unconstrained monitoring environments, we propose a method to measure step length symmetry ratio (a useful gait parameter representing gait symmetry without significant relationship with age) from unconstrained straight walking using a single camera, without strict restrictions on walking directions or routes. according to projective geometry theory, we first develop a calculation formula of step length ratio for the case of unconstrained straight-line walking. Then, to adapt to general cases, we propose to modify noncollinear footprints, and accordingly provide general procedure for step length ratio extraction from unconstrained straight walking. Our method achieves a mean absolute percentage error (MAPE) of 1.9547% for 15 subjects' normal and abnormal side-view gaits, and also obtains satisfactory MAPEs for non-side-view gaits (2.4026% for 45°-view gaits and 3.9721% for 30°-view gaits). The performance is much better than a well-established monocular gait measurement system suitable only for side-view gaits with a MAPE of 3.5538%. Independently of walking directions, our method can accurately estimate step length ratios from unconstrained straight walking. This demonstrates our method is applicable for elders' daily gait monitoring to provide valuable information for elderly health care, such as abnormal gait recognition, fall risk assessment, etc.

One-step selection of Vaccinia virus-binding DNA aptamers by MonoLEX

PubMed Central

Nitsche, Andreas; Kurth, Andreas; Dunkhorst, Anna; Pänke, Oliver; Sielaff, Hendrik; Junge, Wolfgang; Muth, Doreen; Scheller, Frieder; Stöcklein, Walter; Dahmen, Claudia; Pauli, Georg; Kage, Andreas

2007-01-01

Background As a new class of therapeutic and diagnostic reagents, more than fifteen years ago RNA and DNA aptamers were identified as binding molecules to numerous small compounds, proteins and rarely even to complete pathogen particles. Most aptamers were isolated from complex libraries of synthetic nucleic acids by a process termed SELEX based on several selection and amplification steps. Here we report the application of a new one-step selection method (MonoLEX) to acquire high-affinity DNA aptamers binding Vaccinia virus used as a model organism for complex target structures. Results The selection against complete Vaccinia virus particles resulted in a 64-base DNA aptamer specifically binding to orthopoxviruses as validated by dot blot analysis, Surface Plasmon Resonance, Fluorescence Correlation Spectroscopy and real-time PCR, following an aptamer blotting assay. The same oligonucleotide showed the ability to inhibit in vitro infection of Vaccinia virus and other orthopoxviruses in a concentration-dependent manner. Conclusion The MonoLEX method is a straightforward procedure as demonstrated here for the identification of a high-affinity DNA aptamer binding Vaccinia virus. MonoLEX comprises a single affinity chromatography step, followed by subsequent physical segmentation of the affinity resin and a single final PCR amplification step of bound aptamers. Therefore, this procedure improves the selection of high affinity aptamers by reducing the competition between aptamers of different affinities during the PCR step, indicating an advantage for the single-round MonoLEX method. PMID:17697378

A two-step leaching method designed based on chemical fraction distribution of the heavy metals for selective leaching of Cd, Zn, Cu, and Pb from metallurgical sludge.

PubMed

Wang, Fen; Yu, Junxia; Xiong, Wanli; Xu, Yuanlai; Chi, Ru-An

2018-01-01

For selective leaching and highly effective recovery of heavy metals from a metallurgical sludge, a two-step leaching method was designed based on the distribution analysis of the chemical fractions of the loaded heavy metal. Hydrochloric acid (HCl) was used as a leaching agent in the first step to leach the relatively labile heavy metals and then ethylenediamine tetraacetic acid (EDTA) was applied to leach the residual metals according to their different fractional distribution. Using the two-step leaching method, 82.89% of Cd, 55.73% of Zn, 10.85% of Cu, and 0.25% of Pb were leached in the first step by 0.7 M HCl at a contact time of 240 min, and the leaching efficiencies for Cd, Zn, Cu, and Pb were elevated up to 99.76, 91.41, 71.85, and 94.06%, by subsequent treatment with 0.2 M EDTA at 480 min, respectively. Furthermore, HCl leaching induced fractional redistribution, which might increase the mobility of the remaining metals and then facilitate the following metal removal by EDTA. The facilitation was further confirmed by the comparison to the one-step leaching method with single HCl or single EDTA, respectively. These results suggested that the designed two-step leaching method by HCl and EDTA could be used for selective leaching and effective recovery of heavy metals from the metallurgical sludge or heavy metal-contaminated solid media.

A modified interval symmetric single step procedure ISS-5D for simultaneous inclusion of polynomial zeros

NASA Astrophysics Data System (ADS)

Sham, Atiyah W. M.; Monsi, Mansor; Hassan, Nasruddin; Suleiman, Mohamed

2013-04-01

The aim of this paper is to present a new modified interval symmetric single-step procedure ISS-5D which is the extension from the previous procedure, ISS1. The ISS-5D method will produce successively smaller intervals that are guaranteed to still contain the zeros. The efficiency of this method is measured on the CPU times and the number of iteration. The procedure is run on five test polynomials and the results obtained are shown in this paper.

Prevalence of gestational diabetes mellitus according to the different criterias

PubMed Central

Akgöl, Evren; Abuşoğlu, Sedat; Gün, Faik Deniz; Ünlü, Ali

2017-01-01

Objective: The two-step approach recommended by the National Diabetes Data Group (NDDG), Carpenter and Coustan (C&C), and O’Sullivan, and the single-step approach recommended by the International Association of Diabetes and Pregnancy Study Group (IADPSG) are used to diagnose gestational diabetes mellitus (GDM). We aimed to determine GDM prevalence and to compare the two-step and single-step approaches used in the southeastern region of Turkey. Materials and Methods: In total, 3048 records of pregnant women screened for GDM between 2008 and 2014 were retrospectively extracted from our laboratory information system. GDM was defined according to the criteria of NDDG, C&C, and O’Sullivan between in 2008 and 2011, and according to those of the IADPSG between 2012 and 2014. Demographic variables were compared using student’s t-test. The linear trends in GDM prevalence with age were calculated using logistic regression. Results: GDM prevalence was found as 4.8%, 8%, and 13.4% using the NDDG, C&C, and O’Sullivan two-step approach, respectively, and 22.3% with the IADPSG single-step approach. GDM prevalence increased with increasing age in both approaches. Conclusion: GDM prevalence was higher using the single-step approach than with the two-step approach. There was a significant increase in GDM prevalence using the IADPSG criteria. PMID:28913130

Single step signal group-imidazole labeling of organic phosphate groups under aqueous conditions

DOEpatents

Giese, R.W.; Wang, P.

1996-04-30

Compounds and methods for single step, covalent labeling of the phosphate group of an organic substance under aqueous conditions are described. The labeling compound includes any kind of detectable signal group covalently bound to an imidazole moiety, which can be imidazole or a substituted imidazole. A preferred labeling compound has the formula shown in the accompanying diagram. 4 figs.

One-step purification of nisin A by immunoaffinity chromatography.

PubMed

Suárez, A M; Azcona, J I; Rodríguez, J M; Sanz, B; Hernández, P E

1997-12-01

The lantibiotic nisin A was purified to homogeneity by a single-step immunoaffinity chromatography method. An immunoadsorption matrix was developed by direct binding of anti-nisin A monoclonal antibodies to N-hydroxysuccinimide-activated Sepharose. The purification procedure was rapid and reproducible and rendered much higher final yields of nisin than any other described method.

Dual initiation strip charge apparatus and methods for making and implementing the same

DOEpatents

Jakaboski, Juan-Carlos [Albuquerque, NM; Todd,; Steven, N [Rio Rancho, NM; Polisar, Stephen [Albuquerque, NM; Hughs, Chance [Tijeras, NM

2011-03-22

A Dual Initiation Strip Charge (DISC) apparatus is initiated by a single initiation source and detonates a strip of explosive charge at two separate contacts. The reflection of explosively induced stresses meet and create a fracture and breach a target along a generally single fracture contour and produce generally fragment-free scattering and no spallation. Methods for making and implementing a DISC apparatus provide numerous advantages over previous methods of creating explosive charges by utilizing steps for rapid prototyping; by implementing efficient steps and designs for metering consistent, repeatable, and controlled amount of high explosive; and by utilizing readily available materials.

Measuring molecular motions inside single cells with improved analysis of single-particle trajectories

NASA Astrophysics Data System (ADS)

Rowland, David J.; Biteen, Julie S.

2017-04-01

Single-molecule super-resolution imaging and tracking can measure molecular motions inside living cells on the scale of the molecules themselves. Diffusion in biological systems commonly exhibits multiple modes of motion, which can be effectively quantified by fitting the cumulative probability distribution of the squared step sizes in a two-step fitting process. Here we combine this two-step fit into a single least-squares minimization; this new method vastly reduces the total number of fitting parameters and increases the precision with which diffusion may be measured. We demonstrate this Global Fit approach on a simulated two-component system as well as on a mixture of diffusing 80 nm and 200 nm gold spheres to show improvements in fitting robustness and localization precision compared to the traditional Local Fit algorithm.

A manual and an automatic TERS based virus discrimination

NASA Astrophysics Data System (ADS)

Olschewski, Konstanze; Kämmer, Evelyn; Stöckel, Stephan; Bocklitz, Thomas; Deckert-Gaudig, Tanja; Zell, Roland; Cialla-May, Dana; Weber, Karina; Deckert, Volker; Popp, Jürgen

2015-02-01

Rapid techniques for virus identification are more relevant today than ever. Conventional virus detection and identification strategies generally rest upon various microbiological methods and genomic approaches, which are not suited for the analysis of single virus particles. In contrast, the highly sensitive spectroscopic technique tip-enhanced Raman spectroscopy (TERS) allows the characterisation of biological nano-structures like virions on a single-particle level. In this study, the feasibility of TERS in combination with chemometrics to discriminate two pathogenic viruses, Varicella-zoster virus (VZV) and Porcine teschovirus (PTV), was investigated. In a first step, chemometric methods transformed the spectral data in such a way that a rapid visual discrimination of the two examined viruses was enabled. In a further step, these methods were utilised to perform an automatic quality rating of the measured spectra. Spectra that passed this test were eventually used to calculate a classification model, through which a successful discrimination of the two viral species based on TERS spectra of single virus particles was also realised with a classification accuracy of 91%.Rapid techniques for virus identification are more relevant today than ever. Conventional virus detection and identification strategies generally rest upon various microbiological methods and genomic approaches, which are not suited for the analysis of single virus particles. In contrast, the highly sensitive spectroscopic technique tip-enhanced Raman spectroscopy (TERS) allows the characterisation of biological nano-structures like virions on a single-particle level. In this study, the feasibility of TERS in combination with chemometrics to discriminate two pathogenic viruses, Varicella-zoster virus (VZV) and Porcine teschovirus (PTV), was investigated. In a first step, chemometric methods transformed the spectral data in such a way that a rapid visual discrimination of the two examined viruses was enabled. In a further step, these methods were utilised to perform an automatic quality rating of the measured spectra. Spectra that passed this test were eventually used to calculate a classification model, through which a successful discrimination of the two viral species based on TERS spectra of single virus particles was also realised with a classification accuracy of 91%. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr07033j

Application of single-step genomic evaluation for crossbred performance in pig.

PubMed

Xiang, T; Nielsen, B; Su, G; Legarra, A; Christensen, O F

2016-03-01

Crossbreding is predominant and intensively used in commercial meat production systems, especially in poultry and swine. Genomic evaluation has been successfully applied for breeding within purebreds but also offers opportunities of selecting purebreds for crossbred performance by combining information from purebreds with information from crossbreds. However, it generally requires that all relevant animals are genotyped, which is costly and presently does not seem to be feasible in practice. Recently, a novel single-step BLUP method for genomic evaluation of both purebred and crossbred performance has been developed that can incorporate marker genotypes into a traditional animal model. This new method has not been validated in real data sets. In this study, we applied this single-step method to analyze data for the maternal trait of total number of piglets born in Danish Landrace, Yorkshire, and two-way crossbred pigs in different scenarios. The genetic correlation between purebred and crossbred performances was investigated first, and then the impact of (crossbred) genomic information on prediction reliability for crossbred performance was explored. The results confirm the existence of a moderate genetic correlation, and it was seen that the standard errors on the estimates were reduced when including genomic information. Models with marker information, especially crossbred genomic information, improved model-based reliabilities for crossbred performance of purebred boars and also improved the predictive ability for crossbred animals and, to some extent, reduced the bias of prediction. We conclude that the new single-step BLUP method is a good tool in the genetic evaluation for crossbred performance in purebred animals.

Simultaneous Measurement of Thermal Conductivity and Specific Heat in a Single TDTR Experiment

NASA Astrophysics Data System (ADS)

Sun, Fangyuan; Wang, Xinwei; Yang, Ming; Chen, Zhe; Zhang, Hang; Tang, Dawei

2018-01-01

Time-domain thermoreflectance (TDTR) technique is a powerful thermal property measurement method, especially for nano-structures and material interfaces. Thermal properties can be obtained by fitting TDTR experimental data with a proper thermal transport model. In a single TDTR experiment, thermal properties with different sensitivity trends can be extracted simultaneously. However, thermal conductivity and volumetric heat capacity usually have similar trends in sensitivity for most materials; it is difficult to measure them simultaneously. In this work, we present a two-step data fitting method to measure the thermal conductivity and volumetric heat capacity simultaneously from a set of TDTR experimental data at single modulation frequency. This method takes full advantage of the information carried by both amplitude and phase signals; it is a more convenient and effective solution compared with the frequency-domain thermoreflectance method. The relative error is lower than 5 % for most cases. A silicon wafer sample was measured by TDTR method to verify the two-step fitting method.

Investigation of correlation classification techniques

NASA Technical Reports Server (NTRS)

Haskell, R. E.

1975-01-01

A two-step classification algorithm for processing multispectral scanner data was developed and tested. The first step is a single pass clustering algorithm that assigns each pixel, based on its spectral signature, to a particular cluster. The output of that step is a cluster tape in which a single integer is associated with each pixel. The cluster tape is used as the input to the second step, where ground truth information is used to classify each cluster using an iterative method of potentials. Once the clusters have been assigned to classes the cluster tape is read pixel-by-pixel and an output tape is produced in which each pixel is assigned to its proper class. In addition to the digital classification programs, a method of using correlation clustering to process multispectral scanner data in real time by means of an interactive color video display is also described.

A Lateral Flow Biosensor for the Detection of Single Nucleotide Polymorphisms.

PubMed

Zeng, Lingwen; Xiao, Zhuo

2017-01-01

A lateral flow biosensor (LFB) is introduced for the detection of single nucleotide polymorphisms (SNPs). The assay is composed of two steps: circular strand displacement reaction and lateral flow biosensor detection. In step 1, the nucleotide at SNP site is recognized by T4 DNA ligase and the signal is amplified by strand displacement DNA polymerase, which can be accomplished at a constant temperature. In step 2, the reaction product of step 1 is detected by a lateral flow biosensor, which is a rapid and cost effective tool for nuclei acid detection. Comparing with conventional methods, it requires no complicated machines. It is suitable for the use of point of care diagnostics. Therefore, this simple, cost effective, robust, and promising LFB detection method of SNP has great potential for the detection of genetic diseases, personalized medicine, cancer related mutations, and drug-resistant mutations of infectious agents.

DAPNe with micro-capillary separatory chemistry-coupled to MALDI-MS for the analysis of polar and non-polar lipid metabolism in one cell

NASA Astrophysics Data System (ADS)

Hamilton, Jason S.; Aguilar, Roberto; Petros, Robby A.; Verbeck, Guido F.

2017-05-01

The cellular metabolome is considered to be a representation of cellular phenotype and cellular response to changes to internal or external events. Methods to expand the coverage of the expansive physiochemical properties that makeup the metabolome currently utilize multi-step extractions and chromatographic separations prior to chemical detection, leading to lengthy analysis times. In this study, a single-step procedure for the extraction and separation of a sample using a micro-capillary as a separatory funnel to achieve analyte partitioning within an organic/aqueous immiscible solvent system is described. The separated analytes are then spotted for MALDI-MS imaging and distribution ratios are calculated. Initially, the method is applied to standard mixtures for proof of partitioning. The extraction of an individual cell is non-reproducible; therefore, a broad chemical analysis of metabolites is necessary and will be illustrated with the one-cell analysis of a single Snu-5 gastric cancer cell taken from a cellular suspension. The method presented here shows a broad partitioning dynamic range as a single-step method for lipid analysis demonstrating a decrease in ion suppression often present in MALDI analysis of lipids.

One-step purification of nisin A by immunoaffinity chromatography.

PubMed Central

Suárez, A M; Azcona, J I; Rodríguez, J M; Sanz, B; Hernández, P E

1997-01-01

The lantibiotic nisin A was purified to homogeneity by a single-step immunoaffinity chromatography method. An immunoadsorption matrix was developed by direct binding of anti-nisin A monoclonal antibodies to N-hydroxysuccinimide-activated Sepharose. The purification procedure was rapid and reproducible and rendered much higher final yields of nisin than any other described method. PMID:9406424

Manipulation of surface morphology of flower-like Ag/ZnO nanorods to enhance photocatalytic performance

NASA Astrophysics Data System (ADS)

U-thaipan, Kasira; Tedsree, Karaked

2018-06-01

The surface morphology of flower-like Ag/ZnO nanorod can be manipulated by adopting different synthetic routes and also loading different levels of Ag in order to alter their surface structures to achieve the maximum photocatalytic efficiency. In a single-step preparation method Ag/ZnO was prepared by heating directly a mixture of Zn2+ and Ag+ precursors in an aqueous NaOH-ethylene glycol solution, while in the two-step preparation method an intermediate of flower-shaped ZnO nanorod was obtained by a hydrothermal process before depositing Ag particles on the ZnO surfaces by chemical reduction. The structure, morphology and optical properties of the synthesized samples were characterized using TEM, SEM, XRD, DRS and PL techniques. The sample prepared by single-step method are characterized with agglomeration of Ag atoms as clusters on the surface of ZnO, whereas in the sample prepared by two-step method Ag atoms are found uniformly dispersed and deposited as discrete Ag nanoparticles on the surface of ZnO. A significant enhancement in the adsorption of visible light was evident for Ag/ZnO samples prepared by two-step method especially with low Ag content (0.5 mol%). The flower-like Ag/ZnO nanorod prepared with 0.5 mol% Ag by two-step process was found to be the most efficient photocatalyst for the degradation of phenol, which can decompose 90% of phenol within 120 min.

Cryo-EM image alignment based on nonuniform fast Fourier transform.

PubMed

Yang, Zhengfan; Penczek, Pawel A

2008-08-01

In single particle analysis, two-dimensional (2-D) alignment is a fundamental step intended to put into register various particle projections of biological macromolecules collected at the electron microscope. The efficiency and quality of three-dimensional (3-D) structure reconstruction largely depends on the computational speed and alignment accuracy of this crucial step. In order to improve the performance of alignment, we introduce a new method that takes advantage of the highly accurate interpolation scheme based on the gridding method, a version of the nonuniform fast Fourier transform, and utilizes a multi-dimensional optimization algorithm for the refinement of the orientation parameters. Using simulated data, we demonstrate that by using less than half of the sample points and taking twice the runtime, our new 2-D alignment method achieves dramatically better alignment accuracy than that based on quadratic interpolation. We also apply our method to image to volume registration, the key step in the single particle EM structure refinement protocol. We find that in this case the accuracy of the method not only surpasses the accuracy of the commonly used real-space implementation, but results are achieved in much shorter time, making gridding-based alignment a perfect candidate for efficient structure determination in single particle analysis.

Cryo-EM Image Alignment Based on Nonuniform Fast Fourier Transform

PubMed Central

Yang, Zhengfan; Penczek, Pawel A.

2008-01-01

In single particle analysis, two-dimensional (2-D) alignment is a fundamental step intended to put into register various particle projections of biological macromolecules collected at the electron microscope. The efficiency and quality of three-dimensional (3-D) structure reconstruction largely depends on the computational speed and alignment accuracy of this crucial step. In order to improve the performance of alignment, we introduce a new method that takes advantage of the highly accurate interpolation scheme based on the gridding method, a version of the nonuniform Fast Fourier Transform, and utilizes a multi-dimensional optimization algorithm for the refinement of the orientation parameters. Using simulated data, we demonstrate that by using less than half of the sample points and taking twice the runtime, our new 2-D alignment method achieves dramatically better alignment accuracy than that based on quadratic interpolation. We also apply our method to image to volume registration, the key step in the single particle EM structure refinement protocol. We find that in this case the accuracy of the method not only surpasses the accuracy of the commonly used real-space implementation, but results are achieved in much shorter time, making gridding-based alignment a perfect candidate for efficient structure determination in single particle analysis. PMID:18499351

General methods for analysis of sequential "n-step" kinetic mechanisms: application to single turnover kinetics of helicase-catalyzed DNA unwinding.

PubMed

Lucius, Aaron L; Maluf, Nasib K; Fischer, Christopher J; Lohman, Timothy M

2003-10-01

Helicase-catalyzed DNA unwinding is often studied using "all or none" assays that detect only the final product of fully unwound DNA. Even using these assays, quantitative analysis of DNA unwinding time courses for DNA duplexes of different lengths, L, using "n-step" sequential mechanisms, can reveal information about the number of intermediates in the unwinding reaction and the "kinetic step size", m, defined as the average number of basepairs unwound between two successive rate limiting steps in the unwinding cycle. Simultaneous nonlinear least-squares analysis using "n-step" sequential mechanisms has previously been limited by an inability to float the number of "unwinding steps", n, and m, in the fitting algorithm. Here we discuss the behavior of single turnover DNA unwinding time courses and describe novel methods for nonlinear least-squares analysis that overcome these problems. Analytic expressions for the time courses, f(ss)(t), when obtainable, can be written using gamma and incomplete gamma functions. When analytic expressions are not obtainable, the numerical solution of the inverse Laplace transform can be used to obtain f(ss)(t). Both methods allow n and m to be continuous fitting parameters. These approaches are generally applicable to enzymes that translocate along a lattice or require repetition of a series of steps before product formation.

A simple and novel method for RNA-seq library preparation of single cell cDNA analysis by hyperactive Tn5 transposase.

PubMed

Brouilette, Scott; Kuersten, Scott; Mein, Charles; Bozek, Monika; Terry, Anna; Dias, Kerith-Rae; Bhaw-Rosun, Leena; Shintani, Yasunori; Coppen, Steven; Ikebe, Chiho; Sawhney, Vinit; Campbell, Niall; Kaneko, Masahiro; Tano, Nobuko; Ishida, Hidekazu; Suzuki, Ken; Yashiro, Kenta

2012-10-01

Deep sequencing of single cell-derived cDNAs offers novel insights into oncogenesis and embryogenesis. However, traditional library preparation for RNA-seq analysis requires multiple steps with consequent sample loss and stochastic variation at each step significantly affecting output. Thus, a simpler and better protocol is desirable. The recently developed hyperactive Tn5-mediated library preparation, which brings high quality libraries, is likely one of the solutions. Here, we tested the applicability of hyperactive Tn5-mediated library preparation to deep sequencing of single cell cDNA, optimized the protocol, and compared it with the conventional method based on sonication. This new technique does not require any expensive or special equipment, which secures wider availability. A library was constructed from only 100 ng of cDNA, which enables the saving of precious specimens. Only a few steps of robust enzymatic reaction resulted in saved time, enabling more specimens to be prepared at once, and with a more reproducible size distribution among the different specimens. The obtained RNA-seq results were comparable to the conventional method. Thus, this Tn5-mediated preparation is applicable for anyone who aims to carry out deep sequencing for single cell cDNAs. Copyright © 2012 Wiley Periodicals, Inc.

Single-step fabrication of quantum funnels via centrifugal colloidal casting of nanoparticle films

PubMed Central

Kim, Jin Young; Adinolfi, Valerio; Sutherland, Brandon R.; Voznyy, Oleksandr; Kwon, S. Joon; Kim, Tae Wu; Kim, Jeongho; Ihee, Hyotcherl; Kemp, Kyle; Adachi, Michael; Yuan, Mingjian; Kramer, Illan; Zhitomirsky, David; Hoogland, Sjoerd; Sargent, Edward H.

2015-01-01

Centrifugal casting of composites and ceramics has been widely employed to improve the mechanical and thermal properties of functional materials. This powerful method has yet to be deployed in the context of nanoparticles—yet size–effect tuning of quantum dots is among their most distinctive and application-relevant features. Here we report the first gradient nanoparticle films to be constructed in a single step. By creating a stable colloid of nanoparticles that are capped with electronic-conduction-compatible ligands we were able to leverage centrifugal casting for thin-films devices. This new method, termed centrifugal colloidal casting, is demonstrated to form films in a bandgap-ordered manner with efficient carrier funnelling towards the lowest energy layer. We constructed the first quantum-gradient photodiode to be formed in a single deposition step and, as a result of the gradient-enhanced electric field, experimentally measured the highest normalized detectivity of any colloidal quantum dot photodetector. PMID:26165185

Activated carbon fibers and engineered forms from renewable resources

DOEpatents

Baker, Frederick S

2013-02-19

A method of producing activated carbon fibers (ACFs) includes the steps of providing a natural carbonaceous precursor fiber material, blending the carbonaceous precursor material with a chemical activation agent to form chemical agent-impregnated precursor fibers, spinning the chemical agent-impregnated precursor material into fibers, and thermally treating the chemical agent-impregnated precursor fibers. The carbonaceous precursor material is both carbonized and activated to form ACFs in a single step. The method produces ACFs exclusive of a step to isolate an intermediate carbon fiber.

Activated carbon fibers and engineered forms from renewable resources

DOEpatents

Baker, Frederick S.

2010-06-01

A method of producing activated carbon fibers (ACFs) includes the steps of providing a natural carbonaceous precursor fiber material, blending the carbonaceous precursor material with a chemical activation agent to form chemical agent-impregnated precursor fibers, spinning the chemical agent-impregnated precursor material into fibers, and thermally treating the chemical agent-impregnated precursor fibers. The carbonaceous precursor material is both carbonized and activated to form ACFs in a single step. The method produces ACFs exclusive of a step to isolate an intermediate carbon fiber.

Estimating Measures of Pass-Fail Reliability from Parallel Half-Tests.

ERIC Educational Resources Information Center

Woodruff, David J.; Sawyer, Richard L.

Two methods for estimating measures of pass-fail reliability are derived, by which both theta and kappa may be estimated from a single test administration. The methods require only a single test administration and are computationally simple. Both are based on the Spearman-Brown formula for estimating stepped-up reliability. The non-distributional…

Motion-induced error reduction by combining Fourier transform profilometry with phase-shifting profilometry.

PubMed

Li, Beiwen; Liu, Ziping; Zhang, Song

2016-10-03

We propose a hybrid computational framework to reduce motion-induced measurement error by combining the Fourier transform profilometry (FTP) and phase-shifting profilometry (PSP). The proposed method is composed of three major steps: Step 1 is to extract continuous relative phase maps for each isolated object with single-shot FTP method and spatial phase unwrapping; Step 2 is to obtain an absolute phase map of the entire scene using PSP method, albeit motion-induced errors exist on the extracted absolute phase map; and Step 3 is to shift the continuous relative phase maps from Step 1 to generate final absolute phase maps for each isolated object by referring to the absolute phase map with error from Step 2. Experiments demonstrate the success of the proposed computational framework for measuring multiple isolated rapidly moving objects.

A WENO-Limited, ADER-DT, Finite-Volume Scheme for Efficient, Robust, and Communication-Avoiding Multi-Dimensional Transport

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

Norman, Matthew R

2014-01-01

The novel ADER-DT time discretization is applied to two-dimensional transport in a quadrature-free, WENO- and FCT-limited, Finite-Volume context. Emphasis is placed on (1) the serial and parallel computational properties of ADER-DT and this framework and (2) the flexibility of ADER-DT and this framework in efficiently balancing accuracy with other constraints important to transport applications. This study demonstrates a range of choices for the user when approaching their specific application while maintaining good parallel properties. In this method, genuine multi-dimensionality, single-step and single-stage time stepping, strict positivity, and a flexible range of limiting are all achieved with only one parallel synchronizationmore » and data exchange per time step. In terms of parallel data transfers per simulated time interval, this improves upon multi-stage time stepping and post-hoc filtering techniques such as hyperdiffusion. This method is evaluated with standard transport test cases over a range of limiting options to demonstrate quantitatively and qualitatively what a user should expect when employing this method in their application.« less

Powder-in-tube and thick-film methods of fabricating high temperature superconductors having enhanced biaxial texture

DOEpatents

Goyal, Amit; Kroeger, Donald M.

2003-11-11

A method for forming an electronically active biaxially textured article includes the steps of providing a substrate having a single crystal metal or metal alloy surface, deforming the substrate to form an elongated substrate surface having biaxial texture and depositing an epitaxial electronically active layer on the biaxially textured surface. The method can include at least one annealing step after the deforming step to produce the biaxially textured substrate surface. The invention can be used to form improved biaxially textured articles, such as superconducting wire and tape articles having improved J.sub.c values.

One Small Step for a Man: Estimation of Gender, Age and Height from Recordings of One Step by a Single Inertial Sensor

PubMed Central

Riaz, Qaiser; Vögele, Anna; Krüger, Björn; Weber, Andreas

2015-01-01

A number of previous works have shown that information about a subject is encoded in sparse kinematic information, such as the one revealed by so-called point light walkers. With the work at hand, we extend these results to classifications of soft biometrics from inertial sensor recordings at a single body location from a single step. We recorded accelerations and angular velocities of 26 subjects using integrated measurement units (IMUs) attached at four locations (chest, lower back, right wrist and left ankle) when performing standardized gait tasks. The collected data were segmented into individual walking steps. We trained random forest classifiers in order to estimate soft biometrics (gender, age and height). We applied two different validation methods to the process, 10-fold cross-validation and subject-wise cross-validation. For all three classification tasks, we achieve high accuracy values for all four sensor locations. From these results, we can conclude that the data of a single walking step (6D: accelerations and angular velocities) allow for a robust estimation of the gender, height and age of a person. PMID:26703601

On Everhart Method

NASA Astrophysics Data System (ADS)

Pârv, Bazil

This paper deals with the Everhart numerical integration method, a well-known method in astronomical research. This method, a single-step one, is widely used for numerical integration of motion equation of celestial bodies. For an integration step, this method uses unequally-spaced substeps, defined by the roots of the so-called generating polynomial of Everhart's method. For this polynomial, this paper proposes and proves new recurrence formulae. The Maple computer algebra system was used to find and prove these formulae. Again, Maple seems to be well suited and easy to use in mathematical research.

Genome-wide base-resolution mapping of DNA methylation in single cells using single-cell bisulfite sequencing (scBS-seq).

PubMed

Clark, Stephen J; Smallwood, Sébastien A; Lee, Heather J; Krueger, Felix; Reik, Wolf; Kelsey, Gavin

2017-03-01

DNA methylation (DNAme) is an important epigenetic mark in diverse species. Our current understanding of DNAme is based on measurements from bulk cell samples, which obscures intercellular differences and prevents analyses of rare cell types. Thus, the ability to measure DNAme in single cells has the potential to make important contributions to the understanding of several key biological processes, such as embryonic development, disease progression and aging. We have recently reported a method for generating genome-wide DNAme maps from single cells, using single-cell bisulfite sequencing (scBS-seq), allowing the quantitative measurement of DNAme at up to 50% of CpG dinucleotides throughout the mouse genome. Here we present a detailed protocol for scBS-seq that includes our most recent developments to optimize recovery of CpGs, mapping efficiency and success rate; reduce hands-on time; and increase sample throughput with the option of using an automated liquid handler. We provide step-by-step instructions for each stage of the method, comprising cell lysis and bisulfite (BS) conversion, preamplification and adaptor tagging, library amplification, sequencing and, lastly, alignment and methylation calling. An individual with relevant molecular biology expertise can complete library preparation within 3 d. Subsequent computational steps require 1-3 d for someone with bioinformatics expertise.

Constructing MnO{sub 2}/single crystalline ZnO nanorod hybrids with enhanced photocatalytic and antibacterial activity

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

Yu, Weiwei; Liu, Tiangui, E-mail: tianguiliu@gmail.com; Cao, Shiyi

In order to improve the photocatalytic and antibacterial activity of ZnO nanorods, ZnO nanorods decorated with MnO{sub 2} nanoparticles (MnO{sub 2}/ZnO nanorod hybrids) were prepared by using microwave assisted coprecipitation method under the influence of hydrogen peroxide, and the structure, photocatalytic activity and antibacterial property of the products were studied. Experimental results indicated that MnO{sub 2} nanoparticles are decorated on the surface of single crystalline ZnO nanorods. Moreover, the resultant MnO{sub 2}/ZnO nanorod hybrids have been proven to possess good photocatalytic and antibacterial activity, which their degradated efficiency for Rhodamin B (RhB) is twice as the pure ZnO nanorods. Enhancementmore » for photocatalytic and antibacterial activity is mainly attributed to the low band gap energy and excellent electrochemical properties of MnO{sub 2} nanoparticles. - Graphical abstract: The MnO{sub 2}/single crystalline ZnO nanorods hybrids, which MnO{sub 2} nanoparticles are loaded on the surface of ZnO nanorods, were prepared by the step-by-step precipitation method under the assistance of ammonia and hydrogen peroxide. Display Omitted - Highlights: • MnO{sub 2}/ZnO nanorod hybrids were prepared by the step-by-step assembly method. • Single crystalline ZnO nanorods can be decorated by MnO{sub 2} nanoparticles. • MnO{sub 2}/ZnO nanorod hybrids possess good photocatalytic and antibacterial activity. • MnO{sub 2} can improve the photocatalytic activity of ZnO nanorods under visible light.« less

Genomic prediction in a nuclear population of layers using single-step models.

PubMed

Yan, Yiyuan; Wu, Guiqin; Liu, Aiqiao; Sun, Congjiao; Han, Wenpeng; Li, Guangqi; Yang, Ning

2018-02-01

Single-step genomic prediction method has been proposed to improve the accuracy of genomic prediction by incorporating information of both genotyped and ungenotyped animals. The objective of this study is to compare the prediction performance of single-step model with a 2-step models and the pedigree-based models in a nuclear population of layers. A total of 1,344 chickens across 4 generations were genotyped by a 600 K SNP chip. Four traits were analyzed, i.e., body weight at 28 wk (BW28), egg weight at 28 wk (EW28), laying rate at 38 wk (LR38), and Haugh unit at 36 wk (HU36). In predicting offsprings, individuals from generation 1 to 3 were used as training data and females from generation 4 were used as validation set. The accuracies of predicted breeding values by pedigree BLUP (PBLUP), genomic BLUP (GBLUP), SSGBLUP and single-step blending (SSBlending) were compared for both genotyped and ungenotyped individuals. For genotyped females, GBLUP performed no better than PBLUP because of the small size of training data, while the 2 single-step models predicted more accurately than the PBLUP model. The average predictive ability of SSGBLUP and SSBlending were 16.0% and 10.8% higher than the PBLUP model across traits, respectively. Furthermore, the predictive abilities for ungenotyped individuals were also enhanced. The average improvements of prediction abilities were 5.9% and 1.5% for SSGBLUP and SSBlending model, respectively. It was concluded that single-step models, especially the SSGBLUP model, can yield more accurate prediction of genetic merits and are preferable for practical implementation of genomic selection in layers. © 2017 Poultry Science Association Inc.

Production of genome-edited pluripotent stem cells and mice by CRISPR/Cas.

PubMed

Horii, Takuro; Hatada, Izuho

2016-01-01

Clustered regularly at interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) nucleases, so-called CRISPR/Cas, was recently developed as an epoch-making genome engineering technology. This system only requires Cas9 nuclease and single-guide RNA complementary to a target locus. CRISPR/Cas enables the generation of knockout cells and animals in a single step. This system can also be used to generate multiple mutations and knockin in a single step, which is not possible using other methods. In this review, we provide an overview of genome editing by CRISPR/Cas in pluripotent stem cells and mice.

Construction of a system for single-cell transgene induction in Caenorhabditis elegans using a pulsed infrared laser

PubMed Central

Churgin, Matthew A.; He, Liping; Murray, John I.; Fang-Yen, Christopher

2014-01-01

The spatial and temporal control of transgene expression is an important tool in C. elegans biology. We previously described a method for evoking gene expression in arbitrary cells by using a focused pulsed infrared laser to induce a heat shock response (Churgin et al 2013). Here we describe detailed methods for building and testing a system for performing single-cell heat shock. Steps include setting up the laser and associated components, coupling the laser beam to a microscope, and testing heat shock protocols. All steps can be carried out using readily available off-the-shelf components. PMID:24835576

Applications of singular value analysis and partial-step algorithm for nonlinear orbit determination

NASA Technical Reports Server (NTRS)

Ryne, Mark S.; Wang, Tseng-Chan

1991-01-01

An adaptive method in which cruise and nonlinear orbit determination problems can be solved using a single program is presented. It involves singular value decomposition augmented with an extended partial step algorithm. The extended partial step algorithm constrains the size of the correction to the spacecraft state and other solve-for parameters. The correction is controlled by an a priori covariance and a user-supplied bounds parameter. The extended partial step method is an extension of the update portion of the singular value decomposition algorithm. It thus preserves the numerical stability of the singular value decomposition method, while extending the region over which it converges. In linear cases, this method reduces to the singular value decomposition algorithm with the full rank solution. Two examples are presented to illustrate the method's utility.

Single-step method for β-galactosidase assays in Escherichia coli using a 96-well microplate reader.

PubMed

Schaefer, Jorrit; Jovanovic, Goran; Kotta-Loizou, Ioly; Buck, Martin

2016-06-15

Historically, the lacZ gene is one of the most universally used reporters of gene expression in molecular biology. Its activity can be quantified using an artificial substrate, o-nitrophenyl-ß-d-galactopyranoside (ONPG). However, the traditional method for measuring LacZ activity (first described by J. H. Miller in 1972) can be challenging for a large number of samples, is prone to variability, and involves hazardous compounds for lysis (e.g., chloroform, toluene). Here we describe a single-step assay using a 96-well microplate reader with a proven alternative cell permeabilization method. This modified protocol reduces handling time by 90%. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

A single-step purification and molecular characterization of functional Shiga toxin 2 variants from pathogenic Escherichia coli

USDA-ARS?s Scientific Manuscript database

Shiga toxin (Stx) 2 variants, Stx2a, Stx2c, Stx2d and Stx2g were purified to homogeneity from bacterial culture supernatants by a one-step monoclonal anti-Stx affinity chromatography method. The method was based on the binding affinity of these Stxs for a monoclonal antibody against the Stx2 A-subun...

Location Prediction Based on Transition Probability Matrices Constructing from Sequential Rules for Spatial-Temporal K-Anonymity Dataset

PubMed Central

Liu, Zhao; Zhu, Yunhong; Wu, Chenxue

2016-01-01

Spatial-temporal k-anonymity has become a mainstream approach among techniques for protection of users’ privacy in location-based services (LBS) applications, and has been applied to several variants such as LBS snapshot queries and continuous queries. Analyzing large-scale spatial-temporal anonymity sets may benefit several LBS applications. In this paper, we propose two location prediction methods based on transition probability matrices constructing from sequential rules for spatial-temporal k-anonymity dataset. First, we define single-step sequential rules mined from sequential spatial-temporal k-anonymity datasets generated from continuous LBS queries for multiple users. We then construct transition probability matrices from mined single-step sequential rules, and normalize the transition probabilities in the transition matrices. Next, we regard a mobility model for an LBS requester as a stationary stochastic process and compute the n-step transition probability matrices by raising the normalized transition probability matrices to the power n. Furthermore, we propose two location prediction methods: rough prediction and accurate prediction. The former achieves the probabilities of arriving at target locations along simple paths those include only current locations, target locations and transition steps. By iteratively combining the probabilities for simple paths with n steps and the probabilities for detailed paths with n-1 steps, the latter method calculates transition probabilities for detailed paths with n steps from current locations to target locations. Finally, we conduct extensive experiments, and correctness and flexibility of our proposed algorithm have been verified. PMID:27508502

Simultaneous determination of PPCPs, EDCs, and artificial sweeteners in environmental water samples using a single-step SPE coupled with HPLC-MS/MS and isotope dilution.

PubMed

Tran, Ngoc Han; Hu, Jiangyong; Ong, Say Leong

2013-09-15

A high-throughput method for the simultaneous determination of 24 pharmaceuticals and personal care products (PPCPs), endocrine disrupting chemicals (EDCs) and artificial sweeteners (ASs) was developed. The method was based on a single-step solid phase extraction (SPE) coupled with high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) and isotope dilution. In this study, a single-step SPE procedure was optimized for simultaneous extraction of all target analytes. Good recoveries (≥ 70%) were observed for all target analytes when extraction was performed using Chromabond(®) HR-X (500 mg, 6 mL) cartridges under acidic condition (pH 2). HPLC-MS/MS parameters were optimized for the simultaneous analysis of 24 PPCPs, EDCs and ASs in a single injection. Quantification was performed by using 13 isotopically labeled internal standards (ILIS), which allows correcting efficiently the loss of the analytes during SPE procedure, matrix effects during HPLC-MS/MS and fluctuation in MS/MS signal intensity due to instrument. Method quantification limit (MQL) for most of the target analytes was below 10 ng/L in all water samples. The method was successfully applied for the simultaneous determination of PPCPs, EDCs and ASs in raw wastewater, surface water and groundwater samples collected in a local catchment area in Singapore. In conclusion, the developed method provided a valuable tool for investigating the occurrence, behavior, transport, and the fate of PPCPs, EDCs and ASs in the aquatic environment. Copyright © 2013 Elsevier B.V. All rights reserved.

A two-step FEM-SEM approach for wave propagation analysis in cable structures

NASA Astrophysics Data System (ADS)

Zhang, Songhan; Shen, Ruili; Wang, Tao; De Roeck, Guido; Lombaert, Geert

2018-02-01

Vibration-based methods are among the most widely studied in structural health monitoring (SHM). It is well known, however, that the low-order modes, characterizing the global dynamic behaviour of structures, are relatively insensitive to local damage. Such local damage may be easier to detect by methods based on wave propagation which involve local high frequency behaviour. The present work considers the numerical analysis of wave propagation in cables. A two-step approach is proposed which allows taking into account the cable sag and the distribution of the axial forces in the wave propagation analysis. In the first step, the static deformation and internal forces are obtained by the finite element method (FEM), taking into account geometric nonlinear effects. In the second step, the results from the static analysis are used to define the initial state of the dynamic analysis which is performed by means of the spectral element method (SEM). The use of the SEM in the second step of the analysis allows for a significant reduction in computational costs as compared to a FE analysis. This methodology is first verified by means of a full FE analysis for a single stretched cable. Next, simulations are made to study the effects of damage in a single stretched cable and a cable-supported truss. The results of the simulations show how damage significantly affects the high frequency response, confirming the potential of wave propagation based methods for SHM.

Acoustic resonator and method of making same

DOEpatents

Kline, Gerald R.; Lakin, Kenneth M.

1985-03-05

A method of fabricating an acoustic wave resonator wherein all processing steps are accomplished from a single side of said substrate. The method involves deposition of a multi-layered Al/AlN structure on a GaAs substrate followed by a series of fabrication steps to define a resonator from said composite. The resulting resonator comprises an AlN layer between two Al layers and another layer of AlN on an exterior of one of said Al layers.

Acoustic resonator and method of making same

DOEpatents

Kline, G.R.; Lakin, K.M.

1983-10-13

A method of fabricating an acoustic wave resonator wherein all processing steps are accomplished from a single side of said substrate. The method involves deposition of a multi-layered Al/AlN structure on a GaAs substrate followed by a series of fabrication steps to define a resonator from said composite. The resulting resonator comprises an AlN layer between two Al layers and another layer of AlN on an exterior of one of said Al layers.

Rapid one-step purification of single-cells encapsulated in alginate microcapsules from oil to aqueous phase using a hydrophobic filter paper: implications for single-cell experiments.

PubMed

Lee, Do-Hyun; Jang, Miran; Park, Je-Kyun

2014-10-01

By virtue of the biocompatibility and physical properties of hydrogel, picoliter-sized hydrogel microcapsules have been considered to be a biometric signature containing several features similar to that of encapsulated single cells, including phenotype, viability, and intracellular content. To maximize the experimental potential of encapsulating cells in hydrogel microcapsules, a method that enables efficient hydrogel microcapsule purification from oil is necessary. Current methods based on centrifugation for the conventional stepwise rinsing of oil, are slow and laborious and decrease the monodispersity and yield of the recovered hydrogel microcapsules. To remedy these shortcomings we have developed a simple one-step method to purify alginate microcapsules, containing a single live cell, from oil to aqueous phase. This method employs oil impregnation using a commercially available hydrophobic filter paper without multistep centrifugal purification and complicated microchannel networks. The oil-suspended alginate microcapsules encapsulating single cells from mammalian cancer cell lines (MCF-7, HepG2, and U937) and microorganisms (Chlorella vulgaris) were successfully exchanged to cell culture media by quick (~10 min) depletion of the surrounding oil phase without coalescence of neighboring microcapsules. Cell proliferation and high integrity of the microcapsules were also demonstrated by long-term incubation of microcapsules containing a single live cell. We expect that this method for the simple and rapid purification of encapsulated single-cell microcapsules will attain widespread adoption, assisting cell biologists and clinicians in the development of single-cell experiments. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Method for distributed agent-based non-expert simulation of manufacturing process behavior

DOEpatents

Ivezic, Nenad; Potok, Thomas E.

2004-11-30

A method for distributed agent based non-expert simulation of manufacturing process behavior on a single-processor computer comprises the steps of: object modeling a manufacturing technique having a plurality of processes; associating a distributed agent with each the process; and, programming each the agent to respond to discrete events corresponding to the manufacturing technique, wherein each discrete event triggers a programmed response. The method can further comprise the step of transmitting the discrete events to each agent in a message loop. In addition, the programming step comprises the step of conditioning each agent to respond to a discrete event selected from the group consisting of a clock tick message, a resources received message, and a request for output production message.

A split-step method to include electron–electron collisions via Monte Carlo in multiple rate equation simulations

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

Huthmacher, Klaus; Molberg, Andreas K.; Rethfeld, Bärbel

2016-10-01

A split-step numerical method for calculating ultrafast free-electron dynamics in dielectrics is introduced. The two split steps, independently programmed in C++11 and FORTRAN 2003, are interfaced via the presented open source wrapper. The first step solves a deterministic extended multi-rate equation for the ionization, electron–phonon collisions, and single photon absorption by free-carriers. The second step is stochastic and models electron–electron collisions using Monte-Carlo techniques. This combination of deterministic and stochastic approaches is a unique and efficient method of calculating the nonlinear dynamics of 3D materials exposed to high intensity ultrashort pulses. Results from simulations solving the proposed model demonstrate howmore » electron–electron scattering relaxes the non-equilibrium electron distribution on the femtosecond time scale.« less

Comparative Analysis of Various Single-tone Frequency Estimation Techniques in High-order Instantaneous Moments Based Phase Estimation Method

NASA Astrophysics Data System (ADS)

Rajshekhar, G.; Gorthi, Sai Siva; Rastogi, Pramod

2010-04-01

For phase estimation in digital holographic interferometry, a high-order instantaneous moments (HIM) based method was recently developed which relies on piecewise polynomial approximation of phase and subsequent evaluation of the polynomial coefficients using the HIM operator. A crucial step in the method is mapping the polynomial coefficient estimation to single-tone frequency determination for which various techniques exist. The paper presents a comparative analysis of the performance of the HIM operator based method in using different single-tone frequency estimation techniques for phase estimation. The analysis is supplemented by simulation results.

Is a multivariate consensus representation of genetic relationships among populations always meaningful?

PubMed Central

Moazami-Goudarzi, K; Laloë, D

2002-01-01

To determine the relationships among closely related populations or species, two methods are commonly used in the literature: phylogenetic reconstruction or multivariate analysis. The aim of this article is to assess the reliability of multivariate analysis. We describe a method that is based on principal component analysis and Mantel correlations, using a two-step process: The first step consists of a single-marker analysis and the second step tests if each marker reveals the same typology concerning population differentiation. We conclude that if single markers are not congruent, the compromise structure is not meaningful. Our model is not based on any particular mutation process and it can be applied to most of the commonly used genetic markers. This method is also useful to determine the contribution of each marker to the typology of populations. We test whether our method is efficient with two real data sets based on microsatellite markers. Our analysis suggests that for closely related populations, it is not always possible to accept the hypothesis that an increase in the number of markers will increase the reliability of the typology analysis. PMID:12242255

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

Isotalo, Aarno

A method referred to as tally nuclides is presented for accurately and efficiently calculating the time-step averages and integrals of any quantities that are weighted sums of atomic densities with constant weights during the step. The method allows all such quantities to be calculated simultaneously as a part of a single depletion solution with existing depletion algorithms. Some examples of the results that can be extracted include step-average atomic densities and macroscopic reaction rates, the total number of fissions during the step, and the amount of energy released during the step. Furthermore, the method should be applicable with several depletionmore » algorithms, and the integrals or averages should be calculated with an accuracy comparable to that reached by the selected algorithm for end-of-step atomic densities. The accuracy of the method is demonstrated in depletion calculations using the Chebyshev rational approximation method. Here, we demonstrate how the ability to calculate energy release in depletion calculations can be used to determine the accuracy of the normalization in a constant-power burnup calculation during the calculation without a need for a reference solution.« less

Calculating Time-Integral Quantities in Depletion Calculations

DOE PAGES

Isotalo, Aarno

2016-06-02

A method referred to as tally nuclides is presented for accurately and efficiently calculating the time-step averages and integrals of any quantities that are weighted sums of atomic densities with constant weights during the step. The method allows all such quantities to be calculated simultaneously as a part of a single depletion solution with existing depletion algorithms. Some examples of the results that can be extracted include step-average atomic densities and macroscopic reaction rates, the total number of fissions during the step, and the amount of energy released during the step. Furthermore, the method should be applicable with several depletionmore » algorithms, and the integrals or averages should be calculated with an accuracy comparable to that reached by the selected algorithm for end-of-step atomic densities. The accuracy of the method is demonstrated in depletion calculations using the Chebyshev rational approximation method. Here, we demonstrate how the ability to calculate energy release in depletion calculations can be used to determine the accuracy of the normalization in a constant-power burnup calculation during the calculation without a need for a reference solution.« less

A high-order positivity-preserving single-stage single-step method for the ideal magnetohydrodynamic equations

NASA Astrophysics Data System (ADS)

Christlieb, Andrew J.; Feng, Xiao; Seal, David C.; Tang, Qi

2016-07-01

We propose a high-order finite difference weighted ENO (WENO) method for the ideal magnetohydrodynamics (MHD) equations. The proposed method is single-stage (i.e., it has no internal stages to store), single-step (i.e., it has no time history that needs to be stored), maintains a discrete divergence-free condition on the magnetic field, and has the capacity to preserve the positivity of the density and pressure. To accomplish this, we use a Taylor discretization of the Picard integral formulation (PIF) of the finite difference WENO method proposed in Christlieb et al. (2015) [23], where the focus is on a high-order discretization of the fluxes (as opposed to the conserved variables). We use the version where fluxes are expanded to third-order accuracy in time, and for the fluid variables space is discretized using the classical fifth-order finite difference WENO discretization. We use constrained transport in order to obtain divergence-free magnetic fields, which means that we simultaneously evolve the magnetohydrodynamic (that has an evolution equation for the magnetic field) and magnetic potential equations alongside each other, and set the magnetic field to be the (discrete) curl of the magnetic potential after each time step. In this work, we compute these derivatives to fourth-order accuracy. In order to retain a single-stage, single-step method, we develop a novel Lax-Wendroff discretization for the evolution of the magnetic potential, where we start with technology used for Hamilton-Jacobi equations in order to construct a non-oscillatory magnetic field. The end result is an algorithm that is similar to our previous work Christlieb et al. (2014) [8], but this time the time stepping is replaced through a Taylor method with the addition of a positivity-preserving limiter. Finally, positivity preservation is realized by introducing a parameterized flux limiter that considers a linear combination of high and low-order numerical fluxes. The choice of the free parameter is then given in such a way that the fluxes are limited towards the low-order solver until positivity is attained. Given the lack of additional degrees of freedom in the system, this positivity limiter lacks energy conservation where the limiter turns on. However, this ingredient can be dropped for problems where the pressure does not become negative. We present two and three dimensional numerical results for several standard test problems including a smooth Alfvén wave (to verify formal order of accuracy), shock tube problems (to test the shock-capturing ability of the scheme), Orszag-Tang, and cloud shock interactions. These results assert the robustness and verify the high-order of accuracy of the proposed scheme.

Single-cell transcriptome conservation in cryopreserved cells and tissues.

PubMed

Guillaumet-Adkins, Amy; Rodríguez-Esteban, Gustavo; Mereu, Elisabetta; Mendez-Lago, Maria; Jaitin, Diego A; Villanueva, Alberto; Vidal, August; Martinez-Marti, Alex; Felip, Enriqueta; Vivancos, Ana; Keren-Shaul, Hadas; Heath, Simon; Gut, Marta; Amit, Ido; Gut, Ivo; Heyn, Holger

2017-03-01

A variety of single-cell RNA preparation procedures have been described. So far, protocols require fresh material, which hinders complex study designs. We describe a sample preservation method that maintains transcripts in viable single cells, allowing one to disconnect time and place of sampling from subsequent processing steps. We sequence single-cell transcriptomes from >1000 fresh and cryopreserved cells using 3'-end and full-length RNA preparation methods. Our results confirm that the conservation process did not alter transcriptional profiles. This substantially broadens the scope of applications in single-cell transcriptomics and could lead to a paradigm shift in future study designs.

Using stepped anvils to make even insulation layers in laser-heated diamond-anvil cell samples

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

Du, Zhixue; Gu, Tingting; Dobrosavljevic, Vasilije

Here, we describe a method to make even insulation layers for high-pressure laser-heated diamond-anvil cell samples using stepped anvils. Moreover, the method works for both single-sided and double-sided laser heating using solid or fluid insulation. The stepped anvils are used as matched pairs or paired with a flat culet anvil to make gasket insulation layers and not actually used at high pressures; thus, their longevity is ensured. We also compare the radial temperature gradients and Soret diffusion of iron between self-insulating samples and samples produced with stepped anvils and find that less pronounced Soret diffusion occurs in samples with evenmore » insulation layers produced by stepped anvils.« less

Using stepped anvils to make even insulation layers in laser-heated diamond-anvil cell samples

DOE PAGES

Du, Zhixue; Gu, Tingting; Dobrosavljevic, Vasilije; ...

2015-09-01

Here, we describe a method to make even insulation layers for high-pressure laser-heated diamond-anvil cell samples using stepped anvils. Moreover, the method works for both single-sided and double-sided laser heating using solid or fluid insulation. The stepped anvils are used as matched pairs or paired with a flat culet anvil to make gasket insulation layers and not actually used at high pressures; thus, their longevity is ensured. We also compare the radial temperature gradients and Soret diffusion of iron between self-insulating samples and samples produced with stepped anvils and find that less pronounced Soret diffusion occurs in samples with evenmore » insulation layers produced by stepped anvils.« less

Off-axis silicon carbide substrates

DOEpatents

Edgar, James; Dudley, Michael; Kuball, Martin; Zhang, Yi; Wang, Guan; Chen, Hui; Zhang, Yu

2014-09-02

A method of epitaxial growth of a material on a crystalline substrate includes selecting a substrate having a crystal plane that includes a plurality of terraces with step risers that join adjacent terraces. Each terrace of the plurality or terraces presents a lattice constant that substantially matches a lattice constant of the material, and each step riser presents a step height and offset that is consistent with portions of the material nucleating on adjacent terraces being in substantial crystalline match at the step riser. The method also includes preparing a substrate by exposing the crystal plane; and epitaxially growing the material on the substrate such that the portions of the material nucleating on adjacent terraces merge into a single crystal lattice without defects at the step risers.

Antibody-Mediated Small Molecule Detection Using Programmable DNA-Switches.

PubMed

Rossetti, Marianna; Ippodrino, Rudy; Marini, Bruna; Palleschi, Giuseppe; Porchetta, Alessandro

2018-06-13

The development of rapid, cost-effective, and single-step methods for the detection of small molecules is crucial for improving the quality and efficiency of many applications ranging from life science to environmental analysis. Unfortunately, current methodologies still require multiple complex, time-consuming washing and incubation steps, which limit their applicability. In this work we present a competitive DNA-based platform that makes use of both programmable DNA-switches and antibodies to detect small target molecules. The strategy exploits both the advantages of proximity-based methods and structure-switching DNA-probes. The platform is modular and versatile and it can potentially be applied for the detection of any small target molecule that can be conjugated to a nucleic acid sequence. Here the rational design of programmable DNA-switches is discussed, and the sensitive, rapid, and single-step detection of different environmentally relevant small target molecules is demonstrated.

Acoustic resonator and method of making same

DOEpatents

Kline, G.R.; Lakin, K.M.

1985-03-05

A method is disclosed of fabricating an acoustic wave resonator wherein all processing steps are accomplished from a single side of said substrate. The method involves deposition of a multi-layered Al/AlN structure on a GaAs substrate followed by a series of fabrication steps to define a resonator from said composite. The resulting resonator comprises an AlN layer between two Al layers and another layer of AlN on an exterior of one of said Al layers. 4 figs.

Direct Sensor Orientation of a Land-Based Mobile Mapping System

PubMed Central

Rau, Jiann-Yeou; Habib, Ayman F.; Kersting, Ana P.; Chiang, Kai-Wei; Bang, Ki-In; Tseng, Yi-Hsing; Li, Yu-Hua

2011-01-01

A land-based mobile mapping system (MMS) is flexible and useful for the acquisition of road environment geospatial information. It integrates a set of imaging sensors and a position and orientation system (POS). The positioning quality of such systems is highly dependent on the accuracy of the utilized POS. This limitation is the major drawback due to the elevated cost associated with high-end GPS/INS units, particularly the inertial system. The potential accuracy of the direct sensor orientation depends on the architecture and quality of the GPS/INS integration process as well as the validity of the system calibration (i.e., calibration of the individual sensors as well as the system mounting parameters). In this paper, a novel single-step procedure using integrated sensor orientation with relative orientation constraint for the estimation of the mounting parameters is introduced. A comparative analysis between the proposed single-step and the traditional two-step procedure is carried out. Moreover, the estimated mounting parameters using the different methods are used in a direct geo-referencing procedure to evaluate their performance and the feasibility of the implemented system. Experimental results show that the proposed system using single-step system calibration method can achieve high 3D positioning accuracy. PMID:22164015

Hydrodynamic and Aerodynamic Tests of Models of Floats for Single-float Seaplanes NACA Models 41-D, 41-E, 61-A, 73, and 73-A

NASA Technical Reports Server (NTRS)

Parkinson, J B; HOUSE R O

1938-01-01

Tests were made in the NACA tank and in the NACA 7 by 10 foot wind tunnel on two models of transverse step floats and three models of pointed step floats considered to be suitable for use with single float seaplanes. The object of the program was the reduction of water resistance and spray of single float seaplanes without reducing the angle of dead rise believed to be necessary for the satisfactory absorption of the shock loads. The results indicated that all the models have less resistance and spray than the model of the Mark V float and that the pointed step floats are somewhat superior to the transverse step floats in these respects. Models 41-D, 61-A, and 73 were tested by the general method over a wide range of loads and speeds. The results are presented in the form of curves and charts for use in design calculations.

A facile one-step fluorescence method for the quantitation of low-content single base deamination impurity in synthetic oligonucleotides.

PubMed

Su, Xiaoye; Liang, Ruiting; Stolee, Jessica A

2018-06-05

Oligonucleotides are being researched and developed as potential drug candidates for the treatment of a broad spectrum of diseases. The characterization of antisense oligonucleotide (ASO) impurities caused by base mutations (e.g. deamination) which are closely related to the target ASO is a significant analytical challenge. Herein, we describe a novel one-step method, utilizing a strategy that combines fluorescence-ON detection with competitive hybridization, to achieve single base mutation quantitation in extensively modified synthetic ASOs. Given that this method is highly specific and sensitive (LoQ = 4 nM), we envision that it will find utility for screening other impurities as well as sequencing modified oligonucleotides. Copyright © 2018 Elsevier B.V. All rights reserved.

The current role of on-line extraction approaches in clinical and forensic toxicology.

PubMed

Mueller, Daniel M

2014-08-01

In today's clinical and forensic toxicological laboratories, automation is of interest because of its ability to optimize processes, to reduce manual workload and handling errors and to minimize exposition to potentially infectious samples. Extraction is usually the most time-consuming step; therefore, automation of this step is reasonable. Currently, from the field of clinical and forensic toxicology, methods using the following on-line extraction techniques have been published: on-line solid-phase extraction, turbulent flow chromatography, solid-phase microextraction, microextraction by packed sorbent, single-drop microextraction and on-line desorption of dried blood spots. Most of these published methods are either single-analyte or multicomponent procedures; methods intended for systematic toxicological analysis are relatively scarce. However, the use of on-line extraction will certainly increase in the near future.

Examinations of the Chemical Step in Enzyme Catalysis.

PubMed

Singh, P; Islam, Z; Kohen, A

2016-01-01

Advances in computational and experimental methods in enzymology have aided comprehension of enzyme-catalyzed chemical reactions. The main difficulty in comparing computational findings to rate measurements is that the first examines a single energy barrier, while the second frequently reflects a combination of many microscopic barriers. We present here intrinsic kinetic isotope effects and their temperature dependence as a useful experimental probe of a single chemical step in a complex kinetic cascade. Computational predictions are tested by this method for two model enzymes: dihydrofolate reductase and thymidylate synthase. The description highlights the significance of collaboration between experimentalists and theoreticians to develop a better understanding of enzyme-catalyzed chemical conversions. © 2016 Elsevier Inc. All rights reserved.

Continuous-Flow Synthesis of N-Succinimidyl 4-[18F]fluorobenzoate Using a Single Microfluidic Chip

PubMed Central

Kimura, Hiroyuki; Tomatsu, Kenji; Saiki, Hidekazu; Arimitsu, Kenji; Ono, Masahiro; Kawashima, Hidekazu; Iwata, Ren; Nakanishi, Hiroaki; Ozeki, Eiichi; Kuge, Yuji; Saji, Hideo

2016-01-01

In the field of positron emission tomography (PET) radiochemistry, compact microreactors provide reliable and reproducible synthesis methods that reduce the use of expensive precursors for radiolabeling and make effective use of the limited space in a hot cell. To develop more compact microreactors for radiosynthesis of 18F-labeled compounds required for the multistep procedure, we attempted radiosynthesis of N-succinimidyl 4-[18F]fluorobenzoate ([18F]SFB) via a three-step procedure using a microreactor. We examined individual steps for [18F]SFB using a batch reactor and microreactor and developed a new continuous-flow synthetic method with a single microfluidic chip to achieve rapid and efficient radiosynthesis of [18F]SFB. In the synthesis of [18F]SFB using this continuous-flow method, the three-step reaction was successfully completed within 6.5 min and the radiochemical yield was 64 ± 2% (n = 5). In addition, it was shown that the quality of [18F]SFB synthesized on this method was equal to that synthesized by conventional methods using a batch reactor in the radiolabeling of bovine serum albumin with [18F]SFB. PMID:27410684

Whole head quantitative susceptibility mapping using a least-norm direct dipole inversion method.

PubMed

Sun, Hongfu; Ma, Yuhan; MacDonald, M Ethan; Pike, G Bruce

2018-06-15

A new dipole field inversion method for whole head quantitative susceptibility mapping (QSM) is proposed. Instead of performing background field removal and local field inversion sequentially, the proposed method performs dipole field inversion directly on the total field map in a single step. To aid this under-determined and ill-posed inversion process and obtain robust QSM images, Tikhonov regularization is implemented to seek the local susceptibility solution with the least-norm (LN) using the L-curve criterion. The proposed LN-QSM does not require brain edge erosion, thereby preserving the cerebral cortex in the final images. This should improve its applicability for QSM-based cortical grey matter measurement, functional imaging and venography of full brain. Furthermore, LN-QSM also enables susceptibility mapping of the entire head without the need for brain extraction, which makes QSM reconstruction more automated and less dependent on intermediate pre-processing methods and their associated parameters. It is shown that the proposed LN-QSM method reduced errors in a numerical phantom simulation, improved accuracy in a gadolinium phantom experiment, and suppressed artefacts in nine subjects, as compared to two-step and other single-step QSM methods. Measurements of deep grey matter and skull susceptibilities from LN-QSM are consistent with established reconstruction methods. Copyright © 2018 Elsevier Inc. All rights reserved.

A rapid, ratiometric, enzyme-free, and sensitive single-step miRNA detection using three-way junction based FRET probes

NASA Astrophysics Data System (ADS)

Luo, Qingying; Liu, Lin; Yang, Cai; Yuan, Jing; Feng, Hongtao; Chen, Yan; Zhao, Peng; Yu, Zhiqiang; Jin, Zongwen

2018-03-01

MicroRNAs (miRNAs) are single stranded endogenous molecules composed of only 18-24 nucleotides which are critical for gene expression regulating the translation of messenger RNAs. Conventional methods based on enzyme-assisted nucleic acid amplification techniques have many problems, such as easy contamination, high cost, susceptibility to false amplification, and tendency to have sequence mismatches. Here we report a rapid, ratiometric, enzyme-free, sensitive, and highly selective single-step miRNA detection using three-way junction assembled (or self-assembled) FRET probes. The developed strategy can be operated within the linear range from subnanomolar to hundred nanomolar concentrations of miRNAs. In comparison with the traditional approaches, our method showed high sensitivity for the miRNA detection and extreme selectivity for the efficient discrimination of single-base mismatches. The results reveal that the strategy paved a new avenue for the design of novel highly specific probes applicable in diagnostics and potentially in microscopic imaging of miRNAs in real biological environments.

Ex Post Facto Monte Carlo Variance Reduction

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

Booth, Thomas E.

The variance in Monte Carlo particle transport calculations is often dominated by a few particles whose importance increases manyfold on a single transport step. This paper describes a novel variance reduction method that uses a large importance change as a trigger to resample the offending transport step. That is, the method is employed only after (ex post facto) a random walk attempts a transport step that would otherwise introduce a large variance in the calculation.Improvements in two Monte Carlo transport calculations are demonstrated empirically using an ex post facto method. First, the method is shown to reduce the variance inmore » a penetration problem with a cross-section window. Second, the method empirically appears to modify a point detector estimator from an infinite variance estimator to a finite variance estimator.« less

A simplified focusing and astigmatism correction method for a scanning electron microscope

NASA Astrophysics Data System (ADS)

Lu, Yihua; Zhang, Xianmin; Li, Hai

2018-01-01

Defocus and astigmatism can lead to blurred images and poor resolution. This paper presents a simplified method for focusing and astigmatism correction of a scanning electron microscope (SEM). The method consists of two steps. In the first step, the fast Fourier transform (FFT) of the SEM image is performed and the FFT is subsequently processed with a threshold to achieve a suitable result. In the second step, the threshold FFT is used for ellipse fitting to determine the presence of defocus and astigmatism. The proposed method clearly provides the relationships between the defocus, the astigmatism and the direction of stretching of the FFT, and it can determine the astigmatism in a single image. Experimental studies are conducted to demonstrate the validity of the proposed method.

Distributed Feedback Laser Based on Single Crystal Perovskite

NASA Astrophysics Data System (ADS)

Sun, Shang; Xiao, Shumin; Song, Qinghai

2017-06-01

We demonstrate a single crystal perovskite based, with grating-structured photoresist on top, highly polarized distributed feedback laser. A lower laser threshold than the Fabry-Perot mode lasers from the same single crystal CH3NH3PbBr3 microplate was obtained. Single crystal CH3NH3PbBr3 microplates was synthesized with one-step solution processed precipitation method. Once the photoresist on top of the microplate was patterned with electron beam, the device was realized. This one-step fabrication process utilized the advantage of single crystal to the greatest extend. The ultra-low defect density in single crystalline microplate offer an opportunity for lower threshold lasing action compare with poly-crystal perovskite films. In the experiment, the lasing action based on the distributed feedback grating design was found with lower threshold and higher intensity than the Fabry-Perot mode lasers supported by the flat facets of the same microplate.

Single-step colony assay for screening antibody libraries.

PubMed

Kato, Mieko; Hanyu, Yoshiro

2017-08-10

We describe a method, single-step colony assay, for simple and rapid screening of single-chain Fv fragment (scFv) libraries. Colonies of Escherichia coli expressing the scFv library are formed on a hydrophilic filter that is positioned in contact with a membrane coated with an antigen. scFv expression is triggered upon treatment of colonies with an induction reagent, following which scFvs are secreted from the cells and diffused to the antigen-coated membrane. scFvs that exhibit binding affinity for the antigen are captured by the membrane-immobilized antigen. Lastly, detection of scFv binding of the antigen on the membrane allows identification of the clones on the filter that express antigen-specific scFvs. We tested this methodology by using an anti-rabbit IgG scFv, scFv(A10B), and a rat immune scFv library. Experiments conducted using scFv(A10B) revealed that this method improves scFv expression during the colony assay. By using our method to screen an immune library of 3×10 3 scFv clones, we established several clones exhibiting affinity for the antigen. Moreover, we tested 7 other antigens, including peptides, and successfully identified positive clones. We believe that this simple procedure and controlled scFv expression of the single-step colony assay could make the antibody screening both rapid and reliable and lead to successful isolation of positive clones from antibody libraries. Copyright © 2017 Elsevier B.V. All rights reserved.

Single-step fabrication of polydimethylsiloxane microwell arrays with long-lasting hydrophilic inner surfaces

NASA Astrophysics Data System (ADS)

Gowa Oyama, Tomoko; Barba, Bin Jeremiah Duenas; Hosaka, Yuji; Taguchi, Mitsumasa

2018-05-01

We propose a single-step fabrication method for polydimethylsiloxane (PDMS) cell-adhesive microwell arrays with long-lasting (>10 months in aqueous medium) hydrophilic inner surfaces without the need for any chemical treatment such as development. Irradiation of a PDMS film with a low-energy electron beam (55 kV) in air generated a ˜40-μm-thick hydrophilic silica-like layer on the PDMS surface, which was the key to the prolonged hydrophilicity. Moreover, the concomitant compaction of the irradiated area produced dozens-of-micrometers-deep concave wells. The hydrophilic microwells generated on the hydrophobic non-irradiated PDMS surface easily trapped nano-/picoliter droplets and cells/single-cells. In addition, the surfaces of the microwells offered stable and favorable cell-adherent environments. The method presented here can realize stable and reliable lab-on-chips and cater to the expanding demand in biological and medical applications.

Single molecule targeted sequencing for cancer gene mutation detection.

PubMed

Gao, Yan; Deng, Liwei; Yan, Qin; Gao, Yongqian; Wu, Zengding; Cai, Jinsen; Ji, Daorui; Li, Gailing; Wu, Ping; Jin, Huan; Zhao, Luyang; Liu, Song; Ge, Liangjin; Deem, Michael W; He, Jiankui

2016-05-19

With the rapid decline in cost of sequencing, it is now affordable to examine multiple genes in a single disease-targeted clinical test using next generation sequencing. Current targeted sequencing methods require a separate step of targeted capture enrichment during sample preparation before sequencing. Although there are fast sample preparation methods available in market, the library preparation process is still relatively complicated for physicians to use routinely. Here, we introduced an amplification-free Single Molecule Targeted Sequencing (SMTS) technology, which combined targeted capture and sequencing in one step. We demonstrated that this technology can detect low-frequency mutations using artificially synthesized DNA sample. SMTS has several potential advantages, including simple sample preparation thus no biases and errors are introduced by PCR reaction. SMTS has the potential to be an easy and quick sequencing technology for clinical diagnosis such as cancer gene mutation detection, infectious disease detection, inherited condition screening and noninvasive prenatal diagnosis.

Single-step preparation of TiO2/MWCNT Nanohybrid materials by laser pyrolysis and application to efficient photovoltaic energy conversion.

PubMed

Wang, Jin; Lin, Yaochen; Pinault, Mathieu; Filoramo, Arianna; Fabert, Marc; Ratier, Bernard; Bouclé, Johann; Herlin-Boime, Nathalie

2015-01-14

This paper presents the continuous-flowand single-step synthesis of a TiO2/MWCNT (multiwall carbon nanotubes) nanohybrid material. The synthesis method allows achieving high coverage and intimate interface between the TiO2particles and MWCNTs, together with a highly homogeneous distribution of nanotubes within the oxide. Such materials used as active layer in theporous photoelectrode of solid-state dye-sensitized solar cells leads to a substantial performance improvement (20%) as compared to reference devices.

A green recyclable SO(3)H-carbon catalyst derived from glycerol for the production of biodiesel from FFA-containing karanja (Pongamia glabra) oil in a single step.

PubMed

Prabhavathi Devi, B L A; Vijai Kumar Reddy, T; Vijaya Lakshmi, K; Prasad, R B N

2014-02-01

Simultaneous esterification and transesterification method is employed for the preparation of biodiesel from 7.5% free fatty acid (FFA) containing karanja (Pongamia glabra) oil using water resistant and reusable carbon-based solid acid catalyst derived from glycerol in a single step. The optimum reaction parameters for obtaining biodiesel in >99% yield by simultaneous esterification and transesterification are: methanol (1:45 mole ratio of oil), catalyst 20wt.% of oil, temperature 160°C and reaction time of 4h. After the reaction, the catalyst was easily recovered by filtration and reused for five times with out any deactivation under optimized conditions. This single-step process could be a potential route for biodiesel production from high FFA containing oils by simplifying the procedure and reducing costs and effluent generation. Copyright © 2013 Elsevier Ltd. All rights reserved.

Considering dominance in reduced single-step genomic evaluations.

PubMed

Ertl, J; Edel, C; Pimentel, E C G; Emmerling, R; Götz, K-U

2018-06-01

Single-step models including dominance can be an enormous computational task and can even be prohibitive for practical application. In this study, we try to answer the question whether a reduced single-step model is able to estimate breeding values of bulls and breeding values, dominance deviations and total genetic values of cows with acceptable quality. Genetic values and phenotypes were simulated (500 repetitions) for a small Fleckvieh pedigree consisting of 371 bulls (180 thereof genotyped) and 553 cows (40 thereof genotyped). This pedigree was virtually extended for 2,407 non-genotyped daughters. Genetic values were estimated with the single-step model and with different reduced single-step models. Including more relatives of genotyped cows in the reduced single-step model resulted in a better agreement of results with the single-step model. Accuracies of genetic values were largest with single-step and smallest with reduced single-step when only the cows genotyped were modelled. The results indicate that a reduced single-step model is suitable to estimate breeding values of bulls and breeding values, dominance deviations and total genetic values of cows with acceptable quality. © 2018 Blackwell Verlag GmbH.

Platelet-rich plasma differs according to preparation method and human variability.

PubMed

Mazzocca, Augustus D; McCarthy, Mary Beth R; Chowaniec, David M; Cote, Mark P; Romeo, Anthony A; Bradley, James P; Arciero, Robert A; Beitzel, Knut

2012-02-15

Varying concentrations of blood components in platelet-rich plasma preparations may contribute to the variable results seen in recently published clinical studies. The purposes of this investigation were (1) to quantify the level of platelets, growth factors, red blood cells, and white blood cells in so-called one-step (clinically used commercial devices) and two-step separation systems and (2) to determine the influence of three separate blood draws on the resulting components of platelet-rich plasma. Three different platelet-rich plasma (PRP) separation methods (on blood samples from eight subjects with a mean age [and standard deviation] of 31.6 ± 10.9 years) were used: two single-spin processes (PRPLP and PRPHP) and a double-spin process (PRPDS) were evaluated for concentrations of platelets, red and white blood cells, and growth factors. Additionally, the effect of three repetitive blood draws on platelet-rich plasma components was evaluated. The content and concentrations of platelets, white blood cells, and growth factors for each method of separation differed significantly. All separation techniques resulted in a significant increase in platelet concentration compared with native blood. Platelet and white blood-cell concentrations of the PRPHP procedure were significantly higher than platelet and white blood-cell concentrations produced by the so-called single-step PRPLP and the so-called two-step PRPDS procedures, although significant differences between PRPLP and PRPDS were not observed. Comparing the results of the three blood draws with regard to the reliability of platelet number and cell counts, wide variations of intra-individual numbers were observed. Single-step procedures are capable of producing sufficient amounts of platelets for clinical usage. Within the evaluated procedures, platelet numbers and numbers of white blood cells differ significantly. The intra-individual results of platelet-rich plasma separations showed wide variations in platelet and cell numbers as well as levels of growth factors regardless of separation method.

Planning energy-efficient bipedal locomotion on patterned terrain

NASA Astrophysics Data System (ADS)

Zamani, Ali; Bhounsule, Pranav A.; Taha, Ahmad

2016-05-01

Energy-efficient bipedal walking is essential in realizing practical bipedal systems. However, current energy-efficient bipedal robots (e.g., passive-dynamics-inspired robots) are limited to walking at a single speed and step length. The objective of this work is to address this gap by developing a method of synthesizing energy-efficient bipedal locomotion on patterned terrain consisting of stepping stones using energy-efficient primitives. A model of Cornell Ranger (a passive-dynamics inspired robot) is utilized to illustrate our technique. First, an energy-optimal trajectory control problem for a single step is formulated and solved. The solution minimizes the Total Cost Of Transport (TCOT is defined as the energy used per unit weight per unit distance travelled) subject to various constraints such as actuator limits, foot scuffing, joint kinematic limits, ground reaction forces. The outcome of the optimization scheme is a table of TCOT values as a function of step length and step velocity. Next, we parameterize the terrain to identify the location of the stepping stones. Finally, the TCOT table is used in conjunction with the parameterized terrain to plan an energy-efficient stepping strategy.

A rapid and efficient newly established method to detect COL1A1-PDGFB gene fusion in dermatofibrosarcoma protuberans

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

Yokoyama, Yoko; Shimizu, Akira; Okada, Etsuko

Highlights: Black-Right-Pointing-Pointer We developed new method to rapidly identify COL1A1-PDGFB fusion in DFSP. Black-Right-Pointing-Pointer New PCR method using a single primer pair detected COL1A1-PDGFB fusion in DFSP. Black-Right-Pointing-Pointer This is the first report of DFSP with a novel COL1A1 breakpoint in exon 5. -- Abstract: The detection of fusion transcripts of the collagen type 1{alpha}1 (COL1A1) and platelet-derived growth factor-BB (PDGFB) genes by genetic analysis has recognized as a reliable and valuable molecular tool for the diagnosis of dermatofibrosarcoma protuberans (DFSP). To detect the COL1A1-PDGFB fusion, almost previous reports performed reverse transcription polymerase chain reaction (RT-PCR) using multiplex forward primersmore » from COL1A1. However, it has possible technical difficulties with respect to the handling of multiple primers and reagents in the procedure. The objective of this study is to establish a rapid, easy, and efficient one-step method of PCR using only a single primer pair to detect the fusion transcripts of the COL1A1 and PDGFB in DFSP. To validate new method, we compared the results of RT-PCR in five patients of DFSP between the previous method using multiplex primers and our established one-step RT-PCR using a single primer pair. In all cases of DFSP, the COL1A1-PDGFB fusion was detected by both previous method and newly established one-step PCR. Importantly, we detected a novel COL1A1 breakpoint in exon 5. The newly developed method is valuable to rapidly identify COL1A1-PDGFB fusion transcripts in DFSP.« less

Improving genetic evaluation of litter size and piglet mortality for both genotyped and nongenotyped individuals using a single-step method.

PubMed

Guo, X; Christensen, O F; Ostersen, T; Wang, Y; Lund, M S; Su, G

2015-02-01

A single-step method allows genetic evaluation using information of phenotypes, pedigree, and markers from genotyped and nongenotyped individuals simultaneously. This paper compared genomic predictions obtained from a single-step BLUP (SSBLUP) method, a genomic BLUP (GBLUP) method, a selection index blending (SELIND) method, and a traditional pedigree-based method (BLUP) for total number of piglets born (TNB), litter size at d 5 after birth (LS5), and mortality rate before d 5 (Mort; including stillbirth) in Danish Landrace and Yorkshire pigs. Data sets of 778,095 litters from 309,362 Landrace sows and 472,001 litters from 190,760 Yorkshire sows were used for the analysis. There were 332,795 Landrace and 207,255 Yorkshire animals in the pedigree data, among which 3,445 Landrace pigs (1,366 boars and 2,079 sows) and 3,372 Yorkshire pigs (1,241 boars and 2,131 sows) were genotyped with the Illumina PorcineSNP60 BeadChip. The results showed that the 3 methods with marker information (SSBLUP, GBLUP, and SELIND) produced more accurate predictions for genotyped animals than the pedigree-based method. For genotyped animals, the average of reliabilities for all traits in both breeds using traditional BLUP was 0.091, which increased to 0.171 w+hen using GBLUP and to 0.179 when using SELIND and further increased to 0.209 when using SSBLUP. Furthermore, the average reliability of EBV for nongenotyped animals was increased from 0.091 for traditional BLUP to 0.105 for the SSBLUP. The results indicate that the SSBLUP is a good approach to practical genomic prediction of litter size and piglet mortality in Danish Landrace and Yorkshire populations.

Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads.

PubMed

Sasagawa, Yohei; Danno, Hiroki; Takada, Hitomi; Ebisawa, Masashi; Tanaka, Kaori; Hayashi, Tetsutaro; Kurisaki, Akira; Nikaido, Itoshi

2018-03-09

High-throughput single-cell RNA-seq methods assign limited unique molecular identifier (UMI) counts as gene expression values to single cells from shallow sequence reads and detect limited gene counts. We thus developed a high-throughput single-cell RNA-seq method, Quartz-Seq2, to overcome these issues. Our improvements in the reaction steps make it possible to effectively convert initial reads to UMI counts, at a rate of 30-50%, and detect more genes. To demonstrate the power of Quartz-Seq2, we analyzed approximately 10,000 transcriptomes from in vitro embryonic stem cells and an in vivo stromal vascular fraction with a limited number of reads.

Morphology of growth of Bi2Sr2CaCu2O8 single crystals

NASA Astrophysics Data System (ADS)

Indenbom, M. V.; van der Beek, C. J.; Berseth, V.; Wolf, Th.; Berger, H.; Benoit, W.

1996-12-01

A good correlation of twins on the basal surface of flux-grown Bi2Sr2CaCu2Ox (BSCCO) single crystals with surface. growth steps is observed, the b-axis being perpendicular to the steps and, thus, parallel to the growth direction. It is found that mono-twin BSCCO single crystals produced by the travelling solvent floating zone method also grow preferentially along b, i.e. nearly perpendicularly to the boule axis, contrary to the common belief. This new understanding of the morphology of growth explains the nature of major defects in these crystals, which considerably change their measured superconducting properties, in a different way.

One-step direct transfer of pristine single-walled carbon nanotubes for functional nanoelectronics.

PubMed

Wu, Chung Chiang; Liu, Chang Hua; Zhong, Zhaohui

2010-03-10

We report a one-step direct transfer technique for the fabrication of functional nanoelectronic devices using pristine single-walled carbon nanotubes (SWNTs). Suspended SWNTs grown by the chemical vapor deposition (CVD) method are aligned and directly transferred onto prepatterned device electrodes at ambient temperature. Using this technique, we successfully fabricated SWNT electromechanical resonators with gate-tunable resonance frequencies. A fully suspended SWNT p-n diode has also been demonstrated with the diode ideality factor equal to 1. Our method eliminates the organic residues on SWNTs resulting from conventional lithography and solution processing. The results open up opportunities for the fundamental study of electron transport physics in ultraclean SWNTs and for room temperature fabrication of novel functional devices based on pristine SWNTs.

Controlled chain polymerisation and chemical soldering for single-molecule electronics.

PubMed

Okawa, Yuji; Akai-Kasaya, Megumi; Kuwahara, Yuji; Mandal, Swapan K; Aono, Masakazu

2012-05-21

Single functional molecules offer great potential for the development of novel nanoelectronic devices with capabilities beyond today's silicon-based devices. To realise single-molecule electronics, the development of a viable method for connecting functional molecules to each other using single conductive polymer chains is required. The method of initiating chain polymerisation using the tip of a scanning tunnelling microscope (STM) is very useful for fabricating single conductive polymer chains at designated positions and thereby wiring single molecules. In this feature article, developments in the controlled chain polymerisation of diacetylene compounds and the properties of polydiacetylene chains are summarised. Recent studies of "chemical soldering", a technique enabling the covalent connection of single polydiacetylene chains to single functional molecules, are also introduced. This represents a key step in advancing the development of single-molecule electronics.

Using string invariants for prediction searching for optimal parameters

NASA Astrophysics Data System (ADS)

Bundzel, Marek; Kasanický, Tomáš; Pinčák, Richard

2016-02-01

We have developed a novel prediction method based on string invariants. The method does not require learning but a small set of parameters must be set to achieve optimal performance. We have implemented an evolutionary algorithm for the parametric optimization. We have tested the performance of the method on artificial and real world data and compared the performance to statistical methods and to a number of artificial intelligence methods. We have used data and the results of a prediction competition as a benchmark. The results show that the method performs well in single step prediction but the method's performance for multiple step prediction needs to be improved. The method works well for a wide range of parameters.

A transition from using multi-step procedures to a fully integrated system for performing extracorporeal photopheresis: A comparison of costs and efficiencies.

PubMed

Azar, Nabih; Leblond, Veronique; Ouzegdouh, Maya; Button, Paul

2017-12-01

The Pitié Salpêtrière Hospital Hemobiotherapy Department, Paris, France, has been providing extracorporeal photopheresis (ECP) since November 2011, and started using the Therakos ® CELLEX ® fully integrated system in 2012. This report summarizes our single-center experience of transitioning from the use of multi-step ECP procedures to the fully integrated ECP system, considering the capacity and cost implications. The total number of ECP procedures performed 2011-2015 was derived from department records. The time taken to complete a single ECP treatment using a multi-step technique and the fully integrated system at our department was assessed. Resource costs (2014€) were obtained for materials and calculated for personnel time required. Time-driven activity-based costing methods were applied to provide a cost comparison. The number of ECP treatments per year increased from 225 (2012) to 727 (2015). The single multi-step procedure took 270 min compared to 120 min for the fully integrated system. The total calculated per-session cost of performing ECP using the multi-step procedure was greater than with the CELLEX ® system (€1,429.37 and €1,264.70 per treatment, respectively). For hospitals considering a transition from multi-step procedures to fully integrated methods for ECP where cost may be a barrier, time-driven activity-based costing should be utilized to gain a more comprehensive understanding the full benefit that such a transition offers. The example from our department confirmed that there were not just cost and time savings, but that the time efficiencies gained with CELLEX ® allow for more patient treatments per year. © 2017 The Authors Journal of Clinical Apheresis Published by Wiley Periodicals, Inc.

Separation and parallel sequencing of the genomes and transcriptomes of single cells using G&T-seq.

PubMed

Macaulay, Iain C; Teng, Mabel J; Haerty, Wilfried; Kumar, Parveen; Ponting, Chris P; Voet, Thierry

2016-11-01

Parallel sequencing of a single cell's genome and transcriptome provides a powerful tool for dissecting genetic variation and its relationship with gene expression. Here we present a detailed protocol for G&T-seq, a method for separation and parallel sequencing of genomic DNA and full-length polyA(+) mRNA from single cells. We provide step-by-step instructions for the isolation and lysis of single cells; the physical separation of polyA(+) mRNA from genomic DNA using a modified oligo-dT bead capture and the respective whole-transcriptome and whole-genome amplifications; and library preparation and sequence analyses of these amplification products. The method allows the detection of thousands of transcripts in parallel with the genetic variants captured by the DNA-seq data from the same single cell. G&T-seq differs from other currently available methods for parallel DNA and RNA sequencing from single cells, as it involves physical separation of the DNA and RNA and does not require bespoke microfluidics platforms. The process can be implemented manually or through automation. When performed manually, paired genome and transcriptome sequencing libraries from eight single cells can be produced in ∼3 d by researchers experienced in molecular laboratory work. For users with experience in the programming and operation of liquid-handling robots, paired DNA and RNA libraries from 96 single cells can be produced in the same time frame. Sequence analysis and integration of single-cell G&T-seq DNA and RNA data requires a high level of bioinformatics expertise and familiarity with a wide range of informatics tools.

Time-resolved, single-cell analysis of induced and programmed cell death via non-invasive propidium iodide and counterstain perfusion.

PubMed

Krämer, Christina E M; Wiechert, Wolfgang; Kohlheyer, Dietrich

2016-09-01

Conventional propidium iodide (PI) staining requires the execution of multiple steps prior to analysis, potentially affecting assay results as well as cell vitality. In this study, this multistep analysis method has been transformed into a single-step, non-toxic, real-time method via live-cell imaging during perfusion with 0.1 μM PI inside a microfluidic cultivation device. Dynamic PI staining was an effective live/dead analytical tool and demonstrated consistent results for single-cell death initiated by direct or indirect triggers. Application of this method for the first time revealed the apparent antibiotic tolerance of wild-type Corynebacterium glutamicum cells, as indicated by the conversion of violet fluorogenic calcein acetoxymethyl ester (CvAM). Additional implementation of this method provided insight into the induced cell lysis of Escherichia coli cells expressing a lytic toxin-antitoxin module, providing evidence for non-lytic cell death and cell resistance to toxin production. Finally, our dynamic PI staining method distinguished necrotic-like and apoptotic-like cell death phenotypes in Saccharomyces cerevisiae among predisposed descendants of nutrient-deprived ancestor cells using PO-PRO-1 or green fluorogenic calcein acetoxymethyl ester (CgAM) as counterstains. The combination of single-cell cultivation, fluorescent time-lapse imaging, and PI perfusion facilitates spatiotemporally resolved observations that deliver new insights into the dynamics of cellular behaviour.

Out of the picture: a study of family drawings by children from step-, single-parent, and non-step families.

PubMed

Dunn, Judy; O'Connor, Thomas G; Levy, Irit

2002-12-01

Investigated the family drawings of 180 children ages 5 to 7 years in various family settings, including stepfather, single-parent, complex stepfamilies, and 2-parent control families. The relations of family type and biological relatedness to omission of family members and grouping of parents were examined. Children from step- and single-parent families were more likely to exclude family members than children from "control" non-step families, and exclusion was predicted from biological relatedness. Children who were biologically related to both resident parents were also more likely to group their parents together. Omission of family members was found to be associated with children's adjustment (specifically more externalizing and internalizing behavior) as reported by teachers and parents. The results indicate that biological relatedness is a salient aspect of very young children's representations of their families. The association between adjustment and exclusion of family members and grouping of parents indicates that family drawings may be useful research and clinical tools, when used in combination with other methods of assessment.

The effect of cane use on the compensatory step following posterior perturbations.

PubMed

Hall, Courtney D; Jensen, Jody L

2004-08-01

The compensatory step is a critical component of the balance response and is impaired in older fallers. The purpose of this research was to examine whether utilization of a cane modified the compensatory step response following external posterior perturbations. Single subject withdrawal design was employed. Single subject statistical analysis--the standard deviation bandwidth-method--supplemented visual analysis of the data. Four older adults (range: 73-83 years) with balance impairment who habitually use a cane completed this study. Subjects received a series of sudden backward pulls that were large enough to elicit compensatory stepping. We examined the following variables both with and without cane use: timing of cane loading relative to step initiation and center of mass acceleration, stability margin, center of mass excursion and velocity, step length and width. No participant loaded the cane prior to initiation of the first compensatory step. There was no effect of cane use on the stability margin, nor was there an effect of cane use on center of mass excursion or velocity, or step length or width. These data suggest that cane use does not necessarily improve balance recovery following an external posterior perturbation when the individual is forced to rely on compensatory stepping. Instead these data suggest that the strongest factor in modifying step characteristics is experience with the perturbation.

Red, green, and blue lasing enabled by single-exciton gain in colloidal quantum dot films

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

Nurmikko, Arto V.; Dang, Cuong

The methods and materials described herein contemplate the use films of colloidal quantum dots as a gain medium in a vertical-cavity surface-emitting laser. The present disclosure demonstrates a laser with single-exciton gain in the red, green, and blue wavelengths. Leveraging this nanocomposite gain, the results realize a significant step toward full-color single-material lasers.

Texture-based segmentation and analysis of emphysema depicted on CT images

NASA Astrophysics Data System (ADS)

Tan, Jun; Zheng, Bin; Wang, Xingwei; Lederman, Dror; Pu, Jiantao; Sciurba, Frank C.; Gur, David; Leader, J. Ken

2011-03-01

In this study we present a texture-based method of emphysema segmentation depicted on CT examination consisting of two steps. Step 1, a fractal dimension based texture feature extraction is used to initially detect base regions of emphysema. A threshold is applied to the texture result image to obtain initial base regions. Step 2, the base regions are evaluated pixel-by-pixel using a method that considers the variance change incurred by adding a pixel to the base in an effort to refine the boundary of the base regions. Visual inspection revealed a reasonable segmentation of the emphysema regions. There was a strong correlation between lung function (FEV1%, FEV1/FVC, and DLCO%) and fraction of emphysema computed using the texture based method, which were -0.433, -.629, and -0.527, respectively. The texture-based method produced more homogeneous emphysematous regions compared to simple thresholding, especially for large bulla, which can appear as speckled regions in the threshold approach. In the texture-based method, single isolated pixels may be considered as emphysema only if neighboring pixels meet certain criteria, which support the idea that single isolated pixels may not be sufficient evidence that emphysema is present. One of the strength of our complex texture-based approach to emphysema segmentation is that it goes beyond existing approaches that typically extract a single or groups texture features and individually analyze the features. We focus on first identifying potential regions of emphysema and then refining the boundary of the detected regions based on texture patterns.

Acoustic resonator with Al electrodes on an AlN layer and using a GaAs substrate

DOEpatents

Kline, Gerald R.; Lakin, Kenneth M.

1985-12-03

A method of fabricating an acoustic wave resonator wherein all processing steps are accomplished from a single side of said substrate. The method involves deposition of a multi-layered Al/AlN structure on a GaAs substrate followed by a series of fabrication steps to define a resonator from said composite. The resulting resonator comprises an AlN layer between two Al layers and another layer of AlN on an exterior of one of said Al layers.

Pre-Steady-State Kinetic Analysis of Single-Nucleotide Incorporation by DNA Polymerases

PubMed Central

Su, Yan; Guengerich, F. Peter

2016-01-01

Pre-steady-state kinetic analysis is a powerful and widely used method to obtain multiple kinetic parameters. This protocol provides a step-by-step procedure for pre-steady-state kinetic analysis of single-nucleotide incorporation by a DNA polymerase. It describes the experimental details of DNA substrate annealing, reaction mixture preparation, handling of the RQF-3 rapid quench-flow instrument, denaturing polyacrylamide DNA gel preparation, electrophoresis, quantitation, and data analysis. The core and unique part of this protocol is the rationale for preparation of the reaction mixture (the ratio of the polymerase to the DNA substrate) and methods for conducting pre-steady-state assays on an RQF-3 rapid quench-flow instrument, as well as data interpretation after analysis. In addition, the methods for the DNA substrate annealing and DNA polyacrylamide gel preparation, electrophoresis, quantitation and analysis are suitable for use in other studies. PMID:27248785

Single incision multiport versus conventional laparoscopic inguinal hernia repair: A matched comparison

PubMed Central

Rajapandian, Subbiah; Bhushan, Chittawadagi; Sabnis, Sandeep C.; Jain, Manish; Raj, Palanivelu Praveen; Parathasarthi, Ramakrishnan; Senthilnathan, Palanisamy; Palanivelu, Chinnusamy

2018-01-01

Background: The popularity of single-incision procedures is on the rise as wound cosmesis is increasingly being seen as an important body image-related outcome. In this study, we assess the potential benefits of single-incision multiport laparoscopic totally extra-peritoneal (S-TEP) without using specialised ports or instruments and compare the same with the conventional laparoscopic TEP (C-TEP) surgery in terms of operative time, post-operative pain, complications, cost and cosmesis. Materials and Methods: This is a prospective case-matched study of the patients undergoing S-TEP versus C-TEP from June 2014 to December 2015. Results: Each group had 36 patients. The two groups were comparable in the clinical characteristics. The mean duration of surgery for a unilateral hernia in C-TEP and S-TEP was 45.13 ± 10.58 min and 72.63 ± 15.23 min, respectively. The mean visual analogue scale (VAS) score for pain was significantly higher in S-TEP group at post-operative day (POD) 0 and 1. However, at POD 7, there was no significant difference between the groups. At 1st and 6-week post-surgery, the cosmetic results were significantly better in S-TEP group as compared to C-TEP, however, at 6 months, the scar was highly acceptable in both treatment groups. Conclusion: S-TEP, using conventional laparoscopic instruments, is safe and feasible even in resource challenged setting. However, there is a need to review the indications and advantages of single-incision laparoscopic surgery, as no difference in cosmetic outcome by VAS score in S-TEP versus conventional laparoscopic arm seen by the end of 1 month. PMID:28695883

Comparison of in situ DGT measurement with ex situ methods for predicting cadmium bioavailability in soils with combined pollution to biotas.

PubMed

Wang, Peifang; Liu, Cui; Yao, Yu; Wang, Chao; Wang, Teng; Yuan, Ye; Hou, Jun

2017-05-01

To assess the capabilities of the different techniques in predicting Cadmium (Cd) bioavailability in Cd-contaminated soils with the addition of Zn, one in situ technique (diffusive gradients in thin films; DGT) was compared with soil solution concentration and four widely used single-step extraction methods (acetic acid, EDTA, sodium acetate and CaCl 2 ). Wheat and maize were selected as tested species. The results demonstrated that single Cd-polluted soils inhibited the growth of wheat and maize significantly compared with control plants; the shoot and root biomasses of the plants both dropped significantly (P < 0.05). The addition of Zn exhibited a strong antagonism to the physiological toxicity induced by Cd. The Pearson correlation coefficient presented positive correlations (P < 0.01, R > 0.9) between Cd concentrations in two plants and Cd bioavailability indicated by each method in soils. Consequently, the results indicated that the DGT technique could be regarded as a good predictor of Cd bioavailability to plants, comparable to soil solution concentration and the four single-step extraction methods. Because the DGT technique can offer in situ data, it is expected to be widely used in more areas.

Automated Discovery of Elementary Chemical Reaction Steps Using Freezing String and Berny Optimization Methods.

PubMed

Suleimanov, Yury V; Green, William H

2015-09-08

We present a simple protocol which allows fully automated discovery of elementary chemical reaction steps using in cooperation double- and single-ended transition-state optimization algorithms--the freezing string and Berny optimization methods, respectively. To demonstrate the utility of the proposed approach, the reactivity of several single-molecule systems of combustion and atmospheric chemistry importance is investigated. The proposed algorithm allowed us to detect without any human intervention not only "known" reaction pathways, manually detected in the previous studies, but also new, previously "unknown", reaction pathways which involve significant atom rearrangements. We believe that applying such a systematic approach to elementary reaction path finding will greatly accelerate the discovery of new chemistry and will lead to more accurate computer simulations of various chemical processes.

A facile single-step synthesis of polyvinylpyrrolidone-silver nanocomposites using a conventional spray dryer

NASA Astrophysics Data System (ADS)

Kim, Byung-Ho; Hyuck Kim, Yoon; Lee, Young Jin; Lee, Mi Jai; Kim, Jin-Ho; Hwang, Jonghee; Jeon, Dae-Woo

2018-01-01

We have developed a facile single-step synthesis of silver nanocomposite using a conventional spray dryer. We investigated the synthetic conditions by controlling the concentrations of the chemical reactants. Further, we confirmed the effect of the molecular weight of polyvinylpyrrolidones, and revealed that the molecular weight significantly affected the properties of the resultant silver nanocomposites. The long-term stability of the silver nanocomposites was tested, and little change was observed, even after storage for three months. Most of all, the simple commercial implementation, in combination with large-scale synthesis, possesses a variety of advantages, compared to conventional complicated and costly dry-process synthesis methods. Thus, our method presents opportunities for further investigation, for both lab-scale studies and large-scale industrial applications.

A data reduction technique and associated computer program for obtaining vehicle attitudes with a single onboard camera

NASA Technical Reports Server (NTRS)

Bendura, R. J.; Renfroe, P. G.

1974-01-01

A detailed discussion of the application of a previously method to determine vehicle flight attitude using a single camera onboard the vehicle is presented with emphasis on the digital computer program format and data reduction techniques. Application requirements include film and earth-related coordinates of at least two landmarks (or features), location of the flight vehicle with respect to the earth, and camera characteristics. Included in this report are a detailed discussion of the program input and output format, a computer program listing, a discussion of modifications made to the initial method, a step-by-step basic data reduction procedure, and several example applications. The computer program is written in FORTRAN 4 language for the Control Data 6000 series digital computer.

Variation of Cats under Domestication: Genetic Assignment of Domestic Cats to Breeds and Worldwide Random Bred Populations

PubMed Central

Kurushima, J. D.; Lipinski, M. J.; Gandolfi, B.; Froenicke, L.; Grahn, J. C.; Grahn, R. A.; Lyons, L. A.

2012-01-01

Summary Both cat breeders and the lay public have interests in the origins of their pets, not only in the genetic identity of the purebred individuals, but also the historical origins of common household cats. The cat fancy is a relatively new institution with over 85% of its 40–50 breeds arising only in the past 75 years, primarily through selection on single-gene aesthetic traits. The short, yet intense cat breed history poses a significant challenge to the development of a genetic marker-based breed identification strategy. Using different breed assignment strategies and methods, 477 cats representing 29 fancy breeds were analysed with 38 short tandem repeats, 148 intergenic and five phenotypic single nucleotide polymorphisms. Results suggest the frequentist method of Paetkau (accuracy single nucleotide polymorphisms = 0.78, short tandem repeats = 0.88) surpasses the Bayesian method of Rannala and Mountain (single nucleotide polymorphisms = 0.56, short tandem repeats = 0.83) for accurate assignment of individuals to the correct breed. Additionally, a post-assignment verification step with the five phenotypic single nucleotide polymorphisms accurately identified between 0.31 and 0.58 of the mis-assigned individuals raising the sensitivity of assignment with the frequentist method to 0.89 and 0.92 single nucleotide polymorphisms and short tandem repeats respectively. This study provides a novel multi-step assignment strategy and suggests that, despite their short breed history and breed family groupings, a majority of cats can be assigned to their proper breed or population of origin, i.e. race. PMID:23171373

Single Cell Total RNA Sequencing through Isothermal Amplification in Picoliter-Droplet Emulsion.

PubMed

Fu, Yusi; Chen, He; Liu, Lu; Huang, Yanyi

2016-11-15

Prevalent single cell RNA amplification and sequencing chemistries mainly focus on polyadenylated RNAs in eukaryotic cells by using oligo(dT) primers for reverse transcription. We develop a new RNA amplification method, "easier-seq", to reverse transcribe and amplify the total RNAs, both with and without polyadenylate tails, from a single cell for transcriptome sequencing with high efficiency, reproducibility, and accuracy. By distributing the reverse transcribed cDNA molecules into 1.5 × 10 5 aqueous droplets in oil, the cDNAs are isothermally amplified using random primers in each of these 65-pL reactors separately. This new method greatly improves the ease of single-cell RNA sequencing by reducing the experimental steps. Meanwhile, with less chance to induce errors, this method can easily maintain the quality of single-cell sequencing. In addition, this polyadenylate-tail-independent method can be seamlessly applied to prokaryotic cell RNA sequencing.

A stepped-plate bi-frequency source for generating a difference frequency sound with a parametric array.

PubMed

Je, Yub; Lee, Haksue; Park, Jongkyu; Moon, Wonkyu

2010-06-01

An ultrasonic radiator is developed to generate a difference frequency sound from two frequencies of ultrasound in air with a parametric array. A design method is proposed for an ultrasonic radiator capable of generating highly directive, high-amplitude ultrasonic sound beams at two different frequencies in air based on a modification of the stepped-plate ultrasonic radiator. The stepped-plate ultrasonic radiator was introduced by Gallego-Juarez et al. [Ultrasonics 16, 267-271 (1978)] in their previous study and can effectively generate highly directive, large-amplitude ultrasonic sounds in air, but only at a single frequency. Because parametric array sources must be able to generate sounds at more than one frequency, a design modification is crucial to the application of a stepped-plate ultrasonic radiator as a parametric array source in air. The aforementioned method was employed to design a parametric radiator for use in air. A prototype of this design was constructed and tested to determine whether it could successfully generate a difference frequency sound with a parametric array. The results confirmed that the proposed single small-area transducer was suitable as a parametric radiator in air.

Testing electroexplosive devices by programmed pulsing techniques

NASA Technical Reports Server (NTRS)

Rosenthal, L. A.; Menichelli, V. J.

1976-01-01

A novel method for testing electroexplosive devices is proposed wherein capacitor discharge pulses, with increasing energy in a step-wise fashion, are delivered to the device under test. The size of the energy increment can be programmed so that firing takes place after many, or after only a few, steps. The testing cycle is automatically terminated upon firing. An energy-firing contour relating the energy required to the programmed step size describes the single-pulse firing energy and the possible sensitization or desensitization of the explosive device.

40 CFR 141.402 - Ground water source microbial monitoring and analytical methods.

Code of Federal Regulations, 2013 CFR

2013-07-01

... for the presence of E. coli, enterococci, or coliphage: Analytical Methods for Source Water Monitoring... Microbiology, 62:3881-3884. 10 EPA Method 1601: Male-specific (F+) and Somatic Coliphage in Water by Two-step... 20460. 11 EPA Method 1602: Male-specific (F+) and Somatic Coliphage in Water by Single Agar Layer (SAL...

40 CFR 141.402 - Ground water source microbial monitoring and analytical methods.

Code of Federal Regulations, 2014 CFR

2014-07-01

... for the presence of E. coli, enterococci, or coliphage: Analytical Methods for Source Water Monitoring... Microbiology, 62:3881-3884. 10 EPA Method 1601: Male-specific (F+) and Somatic Coliphage in Water by Two-step... 20460. 11 EPA Method 1602: Male-specific (F+) and Somatic Coliphage in Water by Single Agar Layer (SAL...

A scalable and accurate method for classifying protein-ligand binding geometries using a MapReduce approach.

PubMed

Estrada, T; Zhang, B; Cicotti, P; Armen, R S; Taufer, M

2012-07-01

We present a scalable and accurate method for classifying protein-ligand binding geometries in molecular docking. Our method is a three-step process: the first step encodes the geometry of a three-dimensional (3D) ligand conformation into a single 3D point in the space; the second step builds an octree by assigning an octant identifier to every single point in the space under consideration; and the third step performs an octree-based clustering on the reduced conformation space and identifies the most dense octant. We adapt our method for MapReduce and implement it in Hadoop. The load-balancing, fault-tolerance, and scalability in MapReduce allow screening of very large conformation spaces not approachable with traditional clustering methods. We analyze results for docking trials for 23 protein-ligand complexes for HIV protease, 21 protein-ligand complexes for Trypsin, and 12 protein-ligand complexes for P38alpha kinase. We also analyze cross docking trials for 24 ligands, each docking into 24 protein conformations of the HIV protease, and receptor ensemble docking trials for 24 ligands, each docking in a pool of HIV protease receptors. Our method demonstrates significant improvement over energy-only scoring for the accurate identification of native ligand geometries in all these docking assessments. The advantages of our clustering approach make it attractive for complex applications in real-world drug design efforts. We demonstrate that our method is particularly useful for clustering docking results using a minimal ensemble of representative protein conformational states (receptor ensemble docking), which is now a common strategy to address protein flexibility in molecular docking. Copyright © 2012 Elsevier Ltd. All rights reserved.

Comparison study on mechanical properties single step and three step artificial aging on duralium

NASA Astrophysics Data System (ADS)

Tsamroh, Dewi Izzatus; Puspitasari, Poppy; Andoko, Sasongko, M. Ilman N.; Yazirin, Cepi

2017-09-01

Duralium is kind of non-ferro alloy that used widely in industrial. That caused its properties such as mild, high ductility, and resistance from corrosion. This study aimed to know mechanical properties of duralium on single step and three step articial aging process. Mechanical properties that discussed in this study focused on toughness value, tensile strength, and microstructure of duralium. Toughness value of single step artificial aging was 0.082 joule/mm2, and toughness value of three step artificial aging was 0,0721 joule/mm2. Duralium tensile strength of single step artificial aging was 32.36 kgf/mm^2, and duralium tensile strength of three step artificial aging was 32,70 kgf/mm^2. Based on microstructure photo of duralium of single step artificial aging showed that precipitate (θ) was not spreading evenly indicated by black spot which increasing the toughness of material. While microstructure photo of duralium that treated by three step artificial aging showed that it had more precipitate (θ) spread evenly compared with duralium that treated by single step artificial aging.

Overlapping MALDI-Mass Spectrometry Imaging for In-Parallel MS and MS/MS Data Acquisition without Sacrificing Spatial Resolution

NASA Astrophysics Data System (ADS)

Hansen, Rebecca L.; Lee, Young Jin

2017-09-01

Metabolomics experiments require chemical identifications, often through MS/MS analysis. In mass spectrometry imaging (MSI), this necessitates running several serial tissue sections or using a multiplex data acquisition method. We have previously developed a multiplex MSI method to obtain MS and MS/MS data in a single experiment to acquire more chemical information in less data acquisition time. In this method, each raster step is composed of several spiral steps and each spiral step is used for a separate scan event (e.g., MS or MS/MS). One main limitation of this method is the loss of spatial resolution as the number of spiral steps increases, limiting its applicability for high-spatial resolution MSI. In this work, we demonstrate multiplex MS imaging is possible without sacrificing spatial resolution by the use of overlapping spiral steps, instead of spatially separated spiral steps as used in the previous work. Significant amounts of matrix and analytes are still left after multiple spectral acquisitions, especially with nanoparticle matrices, so that high quality MS and MS/MS data can be obtained on virtually the same tissue spot. This method was then applied to visualize metabolites and acquire their MS/MS spectra in maize leaf cross-sections at 10 μm spatial resolution. [Figure not available: see fulltext.

Methods for transforming and expression screening of filamentous fungal cells with a DNA library

DOEpatents

Teter, Sarah; Lamsa, Michael; Cherry, Joel; Ward, Connie

2015-06-02

The present invention relates to methods for expression screening of filamentous fungal transformants, comprising: (a) isolating single colony transformants of a DNA library introduced into E. coli; (b) preparing DNA from each of the single colony E. coli transformants; (c) introducing a sample of each of the DNA preparations of step (b) into separate suspensions of protoplasts of a filamentous fungus to obtain transformants thereof, wherein each transformant contains one or more copies of an individual polynucleotide from the DNA library; (d) growing the individual filamentous fungal transformants of step (c) on selective growth medium, thereby permitting growth of the filamentous fungal transformants, while suppressing growth of untransformed filamentous fungi; and (e) measuring activity or a property of each polypeptide encoded by the individual polynucleotides. The present invention also relates to isolated polynucleotides encoding polypeptides of interest obtained by such methods, to nucleic acid constructs, expression vectors, and recombinant host cells comprising the isolated polynucleotides, and to methods of producing the polypeptides encoded by the isolated polynucleotides.

A streamlined workflow for single-cells genome-wide copy-number profiling by low-pass sequencing of LM-PCR whole-genome amplification products.

PubMed

Ferrarini, Alberto; Forcato, Claudio; Buson, Genny; Tononi, Paola; Del Monaco, Valentina; Terracciano, Mario; Bolognesi, Chiara; Fontana, Francesca; Medoro, Gianni; Neves, Rui; Möhlendick, Birte; Rihawi, Karim; Ardizzoni, Andrea; Sumanasuriya, Semini; Flohr, Penny; Lambros, Maryou; de Bono, Johann; Stoecklein, Nikolas H; Manaresi, Nicolò

2018-01-01

Chromosomal instability and associated chromosomal aberrations are hallmarks of cancer and play a critical role in disease progression and development of resistance to drugs. Single-cell genome analysis has gained interest in latest years as a source of biomarkers for targeted-therapy selection and drug resistance, and several methods have been developed to amplify the genomic DNA and to produce libraries suitable for Whole Genome Sequencing (WGS). However, most protocols require several enzymatic and cleanup steps, thus increasing the complexity and length of protocols, while robustness and speed are key factors for clinical applications. To tackle this issue, we developed a single-tube, single-step, streamlined protocol, exploiting ligation mediated PCR (LM-PCR) Whole Genome Amplification (WGA) method, for low-pass genome sequencing with the Ion Torrent™ platform and copy number alterations (CNAs) calling from single cells. The method was evaluated on single cells isolated from 6 aberrant cell lines of the NCI-H series. In addition, to demonstrate the feasibility of the workflow on clinical samples, we analyzed single circulating tumor cells (CTCs) and white blood cells (WBCs) isolated from the blood of patients affected by prostate cancer or lung adenocarcinoma. The results obtained show that the developed workflow generates data accurately representing whole genome absolute copy number profiles of single cell and allows alterations calling at resolutions down to 100 Kbp with as few as 200,000 reads. The presented data demonstrate the feasibility of the Ampli1™ WGA-based low-pass workflow for detection of CNAs in single tumor cells which would be of particular interest for genome-driven targeted therapy selection and for monitoring of disease progression.

A method for using unmanned aerial vehicles for emergency investigation of single geo-hazards and sample applications of this method

NASA Astrophysics Data System (ADS)

Huang, Haifeng; Long, Jingjing; Yi, Wu; Yi, Qinglin; Zhang, Guodong; Lei, Bangjun

2017-11-01

In recent years, unmanned aerial vehicles (UAVs) have become widely used in emergency investigations of major natural hazards over large areas; however, UAVs are less commonly employed to investigate single geo-hazards. Based on a number of successful investigations in the Three Gorges Reservoir area, China, a complete UAV-based method for performing emergency investigations of single geo-hazards is described. First, a customized UAV system that consists of a multi-rotor UAV subsystem, an aerial photography subsystem, a ground control subsystem and a ground surveillance subsystem is described in detail. The implementation process, which includes four steps, i.e., indoor preparation, site investigation, on-site fast processing and application, and indoor comprehensive processing and application, is then elaborated, and two investigation schemes, automatic and manual, that are used in the site investigation step are put forward. Moreover, some key techniques and methods - e.g., the layout and measurement of ground control points (GCPs), route planning, flight control and image collection, and the Structure from Motion (SfM) photogrammetry processing - are explained. Finally, three applications are given. Experience has shown that using UAVs for emergency investigation of single geo-hazards greatly reduces the time, intensity and risks associated with on-site work and provides valuable, high-accuracy, high-resolution information that supports emergency responses.

Surface Structure Spread Single Crystals (S4C): Preparation and characterization

NASA Astrophysics Data System (ADS)

de Alwis, A.; Holsclaw, B.; Pushkarev, V. V.; Reinicker, A.; Lawton, T. J.; Blecher, M. E.; Sykes, E. C. H.; Gellman, A. J.

2013-02-01

A set of six spherically curved Cu single crystals referred to as Surface Structure Spread Single Crystals (S4Cs) has been prepared in such a way that their exposed surfaces collectively span all possible crystallographic surface orientations that can be cleaved from the face centered cubic Cu lattice. The method for preparing these S4Cs and for finding the high symmetry pole point is described. Optical profilometry has been used to determine the true shapes of the S4Cs and show that over the majority of the surface, the shape is extremely close to that of a perfect sphere. The local orientations of the surfaces lie within ± 1° of the orientation expected on the basis of the spherical shape; their orientation is as good as that of many commercially prepared single crystals. STM imaging has been used to characterize the atomic level structure of the Cu(111) ± 11°-S4C. This has shown that the average step densities and the average step orientations match those expected based on the spherical shape. In other words, although there is some distribution of step-step spacing and step orientations, there is no evidence of large scale reconstruction or faceting. The Cu S4Cs have local structures based on the ideal termination of the face centered cubic Cu lattice in the direction of termination. The set of Cu S4Cs will serve as the basis for high throughput investigations of structure sensitive surface chemistry on Cu.

Single-step microwave-assisted hot water extraction of hemicelluloses from selected lignocellulosic materials - A biorefinery approach.

PubMed

Mihiretu, Gezahegn T; Brodin, Malin; Chimphango, Annie F; Øyaas, Karin; Hoff, Bård H; Görgens, Johann F

2017-10-01

The viability of single-step microwave-induced pressurized hot water conditions for co-production of xylan-based biopolymers and bioethanol from aspenwood sawdust and sugarcane trash was investigated. Extraction of hemicelluloses was conducted using microwave-assisted pressurized hot water system. The effects of temperature and time on extraction yield and enzymatic digestibility of resulting solids were determined. Temperatures between 170-200°C for aspenwood and 165-195°C for sugarcane trash; retention times between 8-22min for both feedstocks, were selected for optimization purpose. Maximum xylan extraction yields of 66 and 50%, and highest cellulose digestibilities of 78 and 74%, were attained for aspenwood and sugarcane trash respectively. Monomeric xylose yields for both feedstocks were below 7%, showing that the xylan extracts were predominantly in non-monomeric form. Thus, single-step microwave-assisted hot water method is viable biorefinery approach to extract xylan from lignocelluloses while rendering the solid residues sufficiently digestible for ethanol production. Copyright © 2017 Elsevier Ltd. All rights reserved.

Online hyphenation of extraction, Sephadex LH-20 column chromatography, and high-speed countercurrent chromatography: A highly efficient strategy for the preparative separation of andrographolide from Andrographis paniculata in a single step.

PubMed

Zhang, Ying-Qi; Wang, Shan-Shan; Han, Chao; Xu, Jin-Fang; Luo, Jian-Guang; Kong, Ling-Yi

2017-12-01

A novel isolation strategy, online hyphenation of ultrasonic extraction, Sephadex LH-20 column chromatography combined with high-speed countercurrent chromatography, was developed for pure compounds extraction and purification. Andrographolide from Andrographis paniculata was achieved only in a single step purification protocol via the present strategy. The crude powder was ultrasonic extracted and extraction was pumped into Sephadex LH-20 column directly to cut the nontarget fractions followed by the second-dimensional high-speed countercurrent chromatography, hyphenated by a six-port valve equipped at the post-end of Sephadex LH-20 column, for the final purification. The results yielded andrographolide with the amount of 1.02 mg and a purity of 98.5% in a single step, indicating that the present method is effective to harvest target compound from medicinal plant. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

One-step direct-laser metal writing of sub-100 nm 3D silver nanostructures in a gelatin matrix

NASA Astrophysics Data System (ADS)

Kang, SeungYeon; Vora, Kevin; Mazur, Eric

2015-03-01

Developing an ability to fabricate high-resolution, 3D metal nanostructures in a stretchable 3D matrix is a critical step to realizing novel optoelectronic devices such as tunable bulk metal-dielectric optical devices and THz metamaterial devices that are not feasible with alternative techniques. We report a new chemistry method to fabricate high-resolution, 3D silver nanostructures using a femtosecond-laser direct metal writing technique. Previously, only fabrication of 3D polymeric structures or single-/few-layer metal structures was possible. Our method takes advantage of unique gelatin properties to overcome such previous limitations as limited freedom in 3D material design and short sample lifetime. We fabricate more than 15 layers of 3D silver nanostructures with a resolution of less than 100 nm in a stable dielectric matrix that is flexible and has high large transparency that is well-matched for potential applications in the optical and THz metamaterial regimes. This is a single-step process that does not require any further processing. This work will be of interest to those interested in fabrication methods that utilize nonlinear light-matter interactions and the realization of future metamaterials.

A two steps solution approach to solving large nonlinear models: application to a problem of conjunctive use.

PubMed

Vieira, J; Cunha, M C

2011-01-01

This article describes a solution method of solving large nonlinear problems in two steps. The two steps solution approach takes advantage of handling smaller and simpler models and having better starting points to improve solution efficiency. The set of nonlinear constraints (named as complicating constraints) which makes the solution of the model rather complex and time consuming is eliminated from step one. The complicating constraints are added only in the second step so that a solution of the complete model is then found. The solution method is applied to a large-scale problem of conjunctive use of surface water and groundwater resources. The results obtained are compared with solutions determined with the direct solve of the complete model in one single step. In all examples the two steps solution approach allowed a significant reduction of the computation time. This potential gain of efficiency of the two steps solution approach can be extremely important for work in progress and it can be particularly useful for cases where the computation time would be a critical factor for having an optimized solution in due time.

Very-short-term wind power prediction by a hybrid model with single- and multi-step approaches

NASA Astrophysics Data System (ADS)

Mohammed, E.; Wang, S.; Yu, J.

2017-05-01

Very-short-term wind power prediction (VSTWPP) has played an essential role for the operation of electric power systems. This paper aims at improving and applying a hybrid method of VSTWPP based on historical data. The hybrid method is combined by multiple linear regressions and least square (MLR&LS), which is intended for reducing prediction errors. The predicted values are obtained through two sub-processes:1) transform the time-series data of actual wind power into the power ratio, and then predict the power ratio;2) use the predicted power ratio to predict the wind power. Besides, the proposed method can include two prediction approaches: single-step prediction (SSP) and multi-step prediction (MSP). WPP is tested comparatively by auto-regressive moving average (ARMA) model from the predicted values and errors. The validity of the proposed hybrid method is confirmed in terms of error analysis by using probability density function (PDF), mean absolute percent error (MAPE) and means square error (MSE). Meanwhile, comparison of the correlation coefficients between the actual values and the predicted values for different prediction times and window has confirmed that MSP approach by using the hybrid model is the most accurate while comparing to SSP approach and ARMA. The MLR&LS is accurate and promising for solving problems in WPP.

A transition from using multi‐step procedures to a fully integrated system for performing extracorporeal photopheresis: A comparison of costs and efficiencies

PubMed Central

Leblond, Veronique; Ouzegdouh, Maya; Button, Paul

2017-01-01

Abstract Introduction The Pitié Salpêtrière Hospital Hemobiotherapy Department, Paris, France, has been providing extracorporeal photopheresis (ECP) since November 2011, and started using the Therakos® CELLEX® fully integrated system in 2012. This report summarizes our single‐center experience of transitioning from the use of multi‐step ECP procedures to the fully integrated ECP system, considering the capacity and cost implications. Materials and Methods The total number of ECP procedures performed 2011–2015 was derived from department records. The time taken to complete a single ECP treatment using a multi‐step technique and the fully integrated system at our department was assessed. Resource costs (2014€) were obtained for materials and calculated for personnel time required. Time‐driven activity‐based costing methods were applied to provide a cost comparison. Results The number of ECP treatments per year increased from 225 (2012) to 727 (2015). The single multi‐step procedure took 270 min compared to 120 min for the fully integrated system. The total calculated per‐session cost of performing ECP using the multi‐step procedure was greater than with the CELLEX® system (€1,429.37 and €1,264.70 per treatment, respectively). Conclusions For hospitals considering a transition from multi‐step procedures to fully integrated methods for ECP where cost may be a barrier, time‐driven activity‐based costing should be utilized to gain a more comprehensive understanding the full benefit that such a transition offers. The example from our department confirmed that there were not just cost and time savings, but that the time efficiencies gained with CELLEX® allow for more patient treatments per year. PMID:28419561

Single-cell genomics for the masses

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

Tringe, Susannah G.

In this issue of Nature Biotechnology, Lan et al. describe a new tool in the toolkit for studying uncultivated microbial communities, enabling orders of magnitude higher single cell genome throughput than previous methods. This is achieved by a complex droplet microfluidics workflow encompassing steps from physical cell isolation through genome sequencing, producing tens of thousands of lowcoverage genomes from individual cells.

Single-cell genomics for the masses

DOE PAGES

Tringe, Susannah G.

2017-07-12

In this issue of Nature Biotechnology, Lan et al. describe a new tool in the toolkit for studying uncultivated microbial communities, enabling orders of magnitude higher single cell genome throughput than previous methods. This is achieved by a complex droplet microfluidics workflow encompassing steps from physical cell isolation through genome sequencing, producing tens of thousands of lowcoverage genomes from individual cells.

Microwave pyrolysis using self-generated pyrolysis gas as activating agent: An innovative single-step approach to convert waste palm shell into activated carbon

NASA Astrophysics Data System (ADS)

Yek, Peter Nai Yuh; Keey Liew, Rock; Shahril Osman, Mohammad; Chung Wong, Chee; Lam, Su Shiung

2017-11-01

Waste palm shell (WPS) is a biomass residue largely available from palm oil industries. An innovative microwave pyrolysis method was developed to produce biochar from WPS while the pyrolysis gas generated as another product is simultaneously used as activating agent to transform the biochar into waste palm shell activated carbon (WPSAC), thus allowing carbonization and activation to be performed simultaneously in a single-step approach. The pyrolysis method was investigated over a range of process temperature and feedstock amount with emphasis on the yield and composition of the WPSAC obtained. The WPSAC was tested as dye adsorbent in removing methylene blue. This pyrolysis approach provided a fast heating rate (37.5°/min) and short process time (20 min) in transforming WPS into WPSAC, recording a product yield of 40 wt%. The WPSAC was detected with high BET surface area (≥ 1200 m2/g), low ash content (< 5 wt%), and high pore volume (≥ 0.54 cm3/g), thus recording high adsorption efficiency of 440 mg of dye/g. The desirable process features (fast heating rate, short process time) and the recovery of WPSAC suggest the exceptional promise of the single-step microwave pyrolysis approach to produce high-grade WPSAC from WPS.

Talbot-Lau x-ray deflectometry phase-retrieval methods for electron density diagnostics in high-energy density experiments.

PubMed

Valdivia, Maria Pia; Stutman, Dan; Stoeckl, Christian; Mileham, Chad; Begishev, Ildar A; Bromage, Jake; Regan, Sean P

2018-01-10

Talbot-Lau x-ray interferometry uses incoherent x-ray sources to measure refraction index changes in matter. These measurements can provide accurate electron density mapping through phase retrieval. An adaptation of the interferometer has been developed in order to meet the specific requirements of high-energy density experiments. This adaptation is known as a moiré deflectometer, which allows for single-shot capabilities in the form of interferometric fringe patterns. The moiré x-ray deflectometry technique requires a set of object and reference images in order to provide electron density maps, which can be costly in the high-energy density environment. In particular, synthetic reference phase images obtained ex situ through a phase-scan procedure, can provide a feasible solution. To test this procedure, an object phase map was retrieved from a single-shot moiré image obtained from a plasma-produced x-ray source. A reference phase map was then obtained from phase-stepping measurements using a continuous x-ray tube source in a small laboratory setting. The two phase maps were used to retrieve an electron density map. A comparison of the moiré and phase-stepping phase-retrieval methods was performed to evaluate single-exposure plasma electron density mapping for high-energy density and other transient plasma experiments. It was found that a combination of phase-retrieval methods can deliver accurate refraction angle mapping. Once x-ray backlighter quality is optimized, the ex situ method is expected to deliver electron density mapping with improved resolution. The steps necessary for improved diagnostic performance are discussed.

Comparison of single-step and two-step purified coagulants from Moringa oleifera seed for turbidity and DOC removal.

PubMed

Sánchez-Martín, J; Ghebremichael, K; Beltrán-Heredia, J

2010-08-01

The coagulant proteins from Moringa oleifera purified with single-step and two-step ion-exchange processes were used for the coagulation of surface water from Meuse river in The Netherlands. The performances of the two purified coagulants and the crude extract were assessed in terms of turbidity and DOC removal. The results indicated that the optimum dosage of the single-step purified coagulant was more than two times higher compared to the two-step purified coagulant in terms of turbidity removal. And the residual DOC in the two-step purified coagulant was lower than in single-step purified coagulant or crude extract. (c) 2010 Elsevier Ltd. All rights reserved.

Factors affecting GEBV accuracy with single-step Bayesian models.

PubMed

Zhou, Lei; Mrode, Raphael; Zhang, Shengli; Zhang, Qin; Li, Bugao; Liu, Jian-Feng

2018-01-01

A single-step approach to obtain genomic prediction was first proposed in 2009. Many studies have investigated the components of GEBV accuracy in genomic selection. However, it is still unclear how the population structure and the relationships between training and validation populations influence GEBV accuracy in terms of single-step analysis. Here, we explored the components of GEBV accuracy in single-step Bayesian analysis with a simulation study. Three scenarios with various numbers of QTL (5, 50, and 500) were simulated. Three models were implemented to analyze the simulated data: single-step genomic best linear unbiased prediction (GBLUP; SSGBLUP), single-step BayesA (SS-BayesA), and single-step BayesB (SS-BayesB). According to our results, GEBV accuracy was influenced by the relationships between the training and validation populations more significantly for ungenotyped animals than for genotyped animals. SS-BayesA/BayesB showed an obvious advantage over SSGBLUP with the scenarios of 5 and 50 QTL. SS-BayesB model obtained the lowest accuracy with the 500 QTL in the simulation. SS-BayesA model was the most efficient and robust considering all QTL scenarios. Generally, both the relationships between training and validation populations and LD between markers and QTL contributed to GEBV accuracy in the single-step analysis, and the advantages of single-step Bayesian models were more apparent when the trait is controlled by fewer QTL.

Single-shot diffusion measurement in laser-polarized Gas

NASA Technical Reports Server (NTRS)

Peled, S.; Tseng, C. H.; Sodickson, A. A.; Mair, R. W.; Walsworth, R. L.; Cory, D. G.

1999-01-01

A single-shot pulsed gradient stimulated echo sequence is introduced to address the challenges of diffusion measurements of laser polarized 3He and 129Xe gas. Laser polarization enhances the NMR sensitivity of these noble gases by >10(3), but creates an unstable, nonthermal polarization that is not readily renewable. A new method is presented which permits parallel acquisition of the several measurements required to determine a diffusive attenuation curve. The NMR characterization of a sample's diffusion behavior can be accomplished in a single measurement, using only a single polarization step. As a demonstration, the diffusion coefficient of a sample of laser-polarized 129Xe gas is measured via this method. Copyright 1999 Academic Press.

Nanohole optical tweezers in heterogeneous mixture analysis

NASA Astrophysics Data System (ADS)

Hacohen, Noa; Ip, Candice J. X.; Laxminarayana, Gurunatha K.; DeWolf, Timothy S.; Gordon, Reuven

2017-08-01

Nanohole optical trapping is a tool that has been shown to analyze proteins at the single molecule level using pure samples. The next step is to detect and study single molecules with dirty samples. We demonstrate that using our double nanohole optical tweezing configuration, single particles in an egg white solution can be classified when trapped. Different sized molecules provide different signal variations in their trapped state, allowing the proteins to be statistically characterized. Root mean squared variation and trap stiffness are methods used on trapped signals to distinguish between the different proteins. This method to isolate and determine single molecules in heterogeneous samples provides huge potential to become a reliable tool for use within biomedical and scientific communities.

An Improved Optical Tweezers Assay for Measuring the Force Generation of Single Kinesin Molecules

PubMed Central

Nicholas, Matthew P.; Rao, Lu; Gennerich, Arne

2014-01-01

Numerous microtubule-associated molecular motors, including several kinesins and cytoplasmic dynein, produce opposing forces that regulate spindle and chromosome positioning during mitosis. The motility and force generation of these motors are therefore critical to normal cell division, and dysfunction of these processes may contribute to human disease. Optical tweezers provide a powerful method for studying the nanometer motility and piconewton force generation of single motor proteins in vitro. Using kinesin-1 as a prototype, we present a set of step-by-step, optimized protocols for expressing a kinesin construct (K560-GFP) in Escherichia coli, purifying it, and studying its force generation in an optical tweezers microscope. We also provide detailed instructions on proper alignment and calibration of an optical trapping microscope. These methods provide a foundation for a variety of similar experiments. PMID:24633799

Simultaneous genotyping of single-nucleotide polymorphisms in alcoholism-related genes using duplex and triplex allele-specific PCR with two-step thermal cycles.

PubMed

Shirasu, Naoto; Kuroki, Masahide

2014-01-01

We developed a time- and cost-effective multiplex allele-specific polymerase chain reaction (AS-PCR) method based on the two-step PCR thermal cycles for genotyping single-nucleotide polymorphisms in three alcoholism-related genes: alcohol dehydrogenase 1B, aldehyde dehydrogenase 2 and μ-opioid receptor. Applying MightyAmp(®) DNA polymerase with optimized AS-primers and PCR conditions enabled us to achieve effective and selective amplification of the target alleles from alkaline lysates of a human hair root, and simultaneously to determine the genotypes within less than 1.5 h using minimal lab equipment.

Single-step generation of metal-plasma polymer multicore@shell nanoparticles from the gas phase.

PubMed

Solař, Pavel; Polonskyi, Oleksandr; Olbricht, Ansgar; Hinz, Alexander; Shelemin, Artem; Kylián, Ondřej; Choukourov, Andrei; Faupel, Franz; Biederman, Hynek

2017-08-17

Nanoparticles composed of multiple silver cores and a plasma polymer shell (multicore@shell) were prepared in a single step with a gas aggregation cluster source operating with Ar/hexamethyldisiloxane mixtures and optionally oxygen. The size distribution of the metal inclusions as well as the chemical composition and the thickness of the shells were found to be controlled by the composition of the working gas mixture. Shell matrices ranging from organosilicon plasma polymer to nearly stoichiometric SiO 2 were obtained. The method allows facile fabrication of multicore@shell nanoparticles with tailored functional properties, as demonstrated here with the optical response.

Comparison of 10 single and stepped methods to identify frail older persons in primary care: diagnostic and prognostic accuracy.

PubMed

Sutorius, Fleur L; Hoogendijk, Emiel O; Prins, Bernard A H; van Hout, Hein P J

2016-08-03

Many instruments have been developed to identify frail older adults in primary care. A direct comparison of the accuracy and prevalence of identification methods is rare and most studies ignore the stepped selection typically employed in routine care practice. Also it is unclear whether the various methods select persons with different characteristics. We aimed to estimate the accuracy of 10 single and stepped methods to identify frailty in older adults and to predict adverse health outcomes. In addition, the methods were compared on their prevalence of the identified frail persons and on the characteristics of persons identified. The Groningen Frailty Indicator (GFI), the PRISMA-7, polypharmacy, the clinical judgment of the general practitioner (GP), the self-rated health of the older adult, the Edmonton Frail Scale (EFS), the Identification Seniors At Risk Primary Care (ISAR PC), the Frailty Index (FI), the InterRAI screener and gait speed were compared to three measures: two reference standards (the clinical judgment of a multidisciplinary expert panel and Fried's frailty criteria) and 6-years mortality or long term care admission. Data were used from the Dutch Identification of Frail Elderly Study, consisting of 102 people aged 65 and over from a primary care practice in Amsterdam. Frail older adults were oversampled. The accuracy of each instrument and several stepped strategies was estimated by calculating the area under the ROC-curve. Prevalence rates of frailty ranged from 14.8 to 52.9 %. The accuracy for recommended cut off values ranged from poor (AUC = 0.556 ISAR-PC) to good (AUC = 0.865 gait speed). PRISMA-7 performed best over two reference standards, GP predicted adversities best. Stepped strategies resulted in lower prevalence rates and accuracy. Persons selected by the different instruments varied greatly in age, IADL dependency, receiving homecare and mood. We found huge differences between methods to identify frail persons in prevalence, accuracy and in characteristics of persons they select. A necessary next step is to find out which frail persons can benefit from intervention before case finding programs are implemented. Further evidence is needed to guide this emerging clinical field.

[Purification of arsenic-binding proteins in hamster plasma after oral administration of arsenite].

PubMed

Wang, Wenwen; Zhang, Min; Li, Chunhui; Qin, Yingjie; Hua, Naranmandura

2013-01-01

To purify the arsenic-binding proteins (As-BP) in hamster plasma after a single oral administration of arsenite (iAs(III)). Arsenite was given to hamsters in a single dose. Three types of HPLC columns, size exclusion, gel filtration and anion exchange columns, combined with an inductively coupled argon plasma mass spectrometer (ICP MS) were used to purify the As-BP in hamster plasma. SDS-PAGE was used to confirm the arsenic-binding proteins at each purification step. The three-step purification process successfully separated As-BP from other proteins (ie, arsenic unbound proteins) in hamster plasma. The molecular mass of purified As-BP in plasma was approximately 40-50 kD on SDS-PAGE. The three-step purification method is a simple and fast approach to purify the As-BP in plasma samples.

Effectively-truncated large-scale shell-model calculations and nuclei around 100Sn

NASA Astrophysics Data System (ADS)

Gargano, A.; Coraggio, L.; Itaco, N.

2017-09-01

This paper presents a short overview of a procedure we have recently introduced, dubbed the double-step truncation method, which is aimed to reduce the computational complexity of large-scale shell-model calculations. Within this procedure, one starts with a realistic shell-model Hamiltonian defined in a large model space, and then, by analyzing the effective single particle energies of this Hamiltonian as a function of the number of valence protons and/or neutrons, reduced model spaces are identified containing only the single-particle orbitals relevant to the description of the spectroscopic properties of a certain class of nuclei. As a final step, new effective shell-model Hamiltonians defined within the reduced model spaces are derived by way of a unitary transformation of the original large-scale Hamiltonian. A detailed account of this transformation is given and the merit of the double-step truncation method is illustrated by discussing few selected results for 96Mo, described as four protons and four neutrons outside 88Sr. Some new preliminary results for light odd-tin isotopes from A = 101 to 107 are also reported.

Whole-genome multiple displacement amplification from single cells.

PubMed

Spits, Claudia; Le Caignec, Cédric; De Rycke, Martine; Van Haute, Lindsey; Van Steirteghem, André; Liebaers, Inge; Sermon, Karen

2006-01-01

Multiple displacement amplification (MDA) is a recently described method of whole-genome amplification (WGA) that has proven efficient in the amplification of small amounts of DNA, including DNA from single cells. Compared with PCR-based WGA methods, MDA generates DNA with a higher molecular weight and shows better genome coverage. This protocol was developed for preimplantation genetic diagnosis, and details a method for performing single-cell MDA using the phi29 DNA polymerase. It can also be useful for the amplification of other minute quantities of DNA, such as from forensic material or microdissected tissue. The protocol includes the collection and lysis of single cells, and all materials and steps involved in the MDA reaction. The whole procedure takes 3 h and generates 1-2 microg of DNA from a single cell, which is suitable for multiple downstream applications, such as sequencing, short tandem repeat analysis or array comparative genomic hybridization.

A Simple Method to Simultaneously Detect and Identify Spikes from Raw Extracellular Recordings.

PubMed

Petrantonakis, Panagiotis C; Poirazi, Panayiota

2015-01-01

The ability to track when and which neurons fire in the vicinity of an electrode, in an efficient and reliable manner can revolutionize the neuroscience field. The current bottleneck lies in spike sorting algorithms; existing methods for detecting and discriminating the activity of multiple neurons rely on inefficient, multi-step processing of extracellular recordings. In this work, we show that a single-step processing of raw (unfiltered) extracellular signals is sufficient for both the detection and identification of active neurons, thus greatly simplifying and optimizing the spike sorting approach. The efficiency and reliability of our method is demonstrated in both real and simulated data.

Algorithm-enabled partial-angular-scan configurations for dual-energy CT.

PubMed

Chen, Buxin; Zhang, Zheng; Xia, Dan; Sidky, Emil Y; Pan, Xiaochuan

2018-05-01

We seek to investigate an optimization-based one-step method for image reconstruction that explicitly compensates for nonlinear spectral response (i.e., the beam-hardening effect) in dual-energy CT, to investigate the feasibility of the one-step method for enabling two dual-energy partial-angular-scan configurations, referred to as the short- and half-scan configurations, on standard CT scanners without involving additional hardware, and to investigate the potential of the short- and half-scan configurations in reducing imaging dose and scan time in a single-kVp-switch full-scan configuration in which two full rotations are made for collection of dual-energy data. We use the one-step method to reconstruct images directly from dual-energy data through solving a nonconvex optimization program that specifies the images to be reconstructed in dual-energy CT. Dual-energy full-scan data are generated from numerical phantoms and collected from physical phantoms with the standard single-kVp-switch full-scan configuration, whereas dual-energy short- and half-scan data are extracted from the corresponding full-scan data. Besides visual inspection and profile-plot comparison, the reconstructed images are analyzed also in quantitative studies based upon tasks of linear-attenuation-coefficient and material-concentration estimation and of material differentiation. Following the performance of a computer-simulation study to verify that the one-step method can reconstruct numerically accurately basis and monochromatic images of numerical phantoms, we reconstruct basis and monochromatic images by using the one-step method from real data of physical phantoms collected with the full-, short-, and half-scan configurations. Subjective inspection based upon visualization and profile-plot comparison reveals that monochromatic images, which are used often in practical applications, reconstructed from the full-, short-, and half-scan data are largely visually comparable except for some differences in texture details. Moreover, quantitative studies based upon tasks of linear-attenuation-coefficient and material-concentration estimation and of material differentiation indicate that the short- and half-scan configurations yield results in close agreement with the ground-truth information and that of the full-scan configuration. The one-step method considered can compensate effectively for the nonlinear spectral response in full- and partial-angular-scan dual-energy CT. It can be exploited for enabling partial-angular-scan configurations on standard CT scanner without involving additional hardware. Visual inspection and quantitative studies reveal that, with the one-step method, partial-angular-scan configurations considered can perform at a level comparable to that of the full-scan configuration, thus suggesting the potential of the two partial-angular-scan configurations in reducing imaging dose and scan time in the standard single-kVp-switch full-scan CT in which two full rotations are performed. The work also yields insights into the investigation and design of other nonstandard scan configurations of potential practical significance in dual-energy CT. © 2018 American Association of Physicists in Medicine.

Time-Extended Policies in Mult-Agent Reinforcement Learning

NASA Technical Reports Server (NTRS)

Tumer, Kagan; Agogino, Adrian K.

2004-01-01

Reinforcement learning methods perform well in many domains where a single agent needs to take a sequence of actions to perform a task. These methods use sequences of single-time-step rewards to create a policy that tries to maximize a time-extended utility, which is a (possibly discounted) sum of these rewards. In this paper we build on our previous work showing how these methods can be extended to a multi-agent environment where each agent creates its own policy that works towards maximizing a time-extended global utility over all agents actions. We show improved methods for creating time-extended utilities for the agents that are both "aligned" with the global utility and "learnable." We then show how to crate single-time-step rewards while avoiding the pi fall of having rewards aligned with the global reward leading to utilities not aligned with the global utility. Finally, we apply these reward functions to the multi-agent Gridworld problem. We explicitly quantify a utility's learnability and alignment, and show that reinforcement learning agents using the prescribed reward functions successfully tradeoff learnability and alignment. As a result they outperform both global (e.g., team games ) and local (e.g., "perfectly learnable" ) reinforcement learning solutions by as much as an order of magnitude.

A Minimally Invasive Method for Retrieving Single Adherent Cells of Different Types from Cultures

PubMed Central

Zeng, Jia; Mohammadreza, Aida; Gao, Weimin; Merza, Saeed; Smith, Dean; Kelbauskas, Laimonas; Meldrum, Deirdre R.

2014-01-01

The field of single-cell analysis has gained a significant momentum over the last decade. Separation and isolation of individual cells is an indispensable step in almost all currently available single-cell analysis technologies. However, stress levels introduced by such manipulations remain largely unstudied. We present a method for minimally invasive retrieval of selected individual adherent cells of different types from cell cultures. The method is based on a combination of mechanical (shear flow) force and biochemical (trypsin digestion) treatment. We quantified alterations in the transcription levels of stress response genes in individual cells exposed to varying levels of shear flow and trypsinization. We report optimal temperature, RNA preservation reagents, shear force and trypsinization conditions necessary to minimize changes in the stress-related gene expression levels. The method and experimental findings are broadly applicable and can be used by a broad research community working in the field of single cell analysis. PMID:24957932

A novel method to accurately locate and count large numbers of steps by photobleaching

PubMed Central

Tsekouras, Konstantinos; Custer, Thomas C.; Jashnsaz, Hossein; Walter, Nils G.; Pressé, Steve

2016-01-01

Photobleaching event counting is a single-molecule fluorescence technique that is increasingly being used to determine the stoichiometry of protein and RNA complexes composed of many subunits in vivo as well as in vitro. By tagging protein or RNA subunits with fluorophores, activating them, and subsequently observing as the fluorophores photobleach, one obtains information on the number of subunits in a complex. The noise properties in a photobleaching time trace depend on the number of active fluorescent subunits. Thus, as fluorophores stochastically photobleach, noise properties of the time trace change stochastically, and these varying noise properties have created a challenge in identifying photobleaching steps in a time trace. Although photobleaching steps are often detected by eye, this method only works for high individual fluorophore emission signal-to-noise ratios and small numbers of fluorophores. With filtering methods or currently available algorithms, it is possible to reliably identify photobleaching steps for up to 20–30 fluorophores and signal-to-noise ratios down to ∼1. Here we present a new Bayesian method of counting steps in photobleaching time traces that takes into account stochastic noise variation in addition to complications such as overlapping photobleaching events that may arise from fluorophore interactions, as well as on-off blinking. Our method is capable of detecting ≥50 photobleaching steps even for signal-to-noise ratios as low as 0.1, can find up to ≥500 steps for more favorable noise profiles, and is computationally inexpensive. PMID:27654946

Microbial Certification of the MER spacecraft

NASA Technical Reports Server (NTRS)

Schubert, W. W.; Arakelian, T.; Barengoltz, J. B.; Chough, N. G.; Chung, S. Y.; Law, J.; Kirschner, L.; Koukol, R. C.; Newlin, L. E.; Morales, F.

2003-01-01

Spacecraft such as the Mars Exploration Rovers (MER) must meet acceptable microbial population levels prior to launch. Sensitive parts and materials prevent any single sterilization method from being used as a final step on the assembled spacecraft.

QUICR-learning for Multi-Agent Coordination

NASA Technical Reports Server (NTRS)

Agogino, Adrian K.; Tumer, Kagan

2006-01-01

Coordinating multiple agents that need to perform a sequence of actions to maximize a system level reward requires solving two distinct credit assignment problems. First, credit must be assigned for an action taken at time step t that results in a reward at time step t > t. Second, credit must be assigned for the contribution of agent i to the overall system performance. The first credit assignment problem is typically addressed with temporal difference methods such as Q-learning. The second credit assignment problem is typically addressed by creating custom reward functions. To address both credit assignment problems simultaneously, we propose the "Q Updates with Immediate Counterfactual Rewards-learning" (QUICR-learning) designed to improve both the convergence properties and performance of Q-learning in large multi-agent problems. QUICR-learning is based on previous work on single-time-step counterfactual rewards described by the collectives framework. Results on a traffic congestion problem shows that QUICR-learning is significantly better than a Q-learner using collectives-based (single-time-step counterfactual) rewards. In addition QUICR-learning provides significant gains over conventional and local Q-learning. Additional results on a multi-agent grid-world problem show that the improvements due to QUICR-learning are not domain specific and can provide up to a ten fold increase in performance over existing methods.

Effect of double-layer application on bond quality of adhesive systems.

PubMed

Fujiwara, Satoshi; Takamizawa, Toshiki; Barkmeier, Wayne W; Tsujimoto, Akimasa; Imai, Arisa; Watanabe, Hidehiko; Erickson, Robert L; Latta, Mark A; Nakatsuka, Toshiyuki; Miyazaki, Masashi

2018-01-01

The aim of this study was to determine the effect of double-layer application of universal adhesives on the bond quality and compare to other adhesive systems. Two universal adhesives used were in this study: Scotchbond Universal (SU), [3M ESPE] and Prime & Bond elect (PE), [Dentsply Caulk]. The conventional single-step self-etch adhesives G-ӕnial Bond (GB), [GC Corporation.] and BeautiBond (BB), [Shofu Inc.], and a two-step self-etch adhesive, Optibond XTR (OX), [Kerr Corporation], were used as comparison adhesives. Shear bond strengths (SBS) and shear fatigue strengths (SFS) to human enamel and dentin were measured in single application mode and double application mode. For each test condition, 15 specimens were prepared for SBS testing and 30 specimens for SFS testing. Enamel and dentin SBS of the universal adhesives in the double application mode were significantly higher than those of the single application mode. In addition, the universal adhesives in the double application mode had significantly higher dentin SFS values than those of the single application mode. The two-step self-etch adhesive OX tended to have lower bond strengths in the double application mode, regardless of the test method or adherent substrate. The double application mode is effective in enhancing SBS and SFS of universal adhesives, but not conventional two-step self-etch adhesives. These results suggest that, although the double application mode may enhance the bonding quality of a universal adhesive, it may be counter-productive for two-step self-etch adhesives in clinical use. Copyright © 2017 Elsevier Ltd. All rights reserved.

In-depth analysis and characterization of a dual damascene process with respect to different CD

NASA Astrophysics Data System (ADS)

Krause, Gerd; Hofmann, Detlef; Habets, Boris; Buhl, Stefan; Gutsch, Manuela; Lopez-Gomez, Alberto; Kim, Wan-Soo; Thrun, Xaver

2018-03-01

In a 200 mm high volume environment, we studied data from a dual damascene process. Dual damascene is a combination of lithography, etch and CMP that is used to create copper lines and contacts in one single step. During these process steps, different metal CD are measured by different measurement methods. In this study, we analyze the key numbers of the different measurements after different process steps and develop simple models to predict the electrical behavior* . In addition, radial profiles have been analyzed of both inline measurement parameters and electrical parameters. A matching method was developed based on inline and electrical data. Finally, correlation analysis for radial signatures is presented that can be used to predict excursions in electrical signatures.

Method for forming single phase, single crystalline 2122 BCSCO superconductor thin films by liquid phase epitaxy

NASA Technical Reports Server (NTRS)

Pandey, Raghvendra K. (Inventor); Raina, Kanwal (Inventor); Solayappan, Narayanan (Inventor)

1994-01-01

A substantially single phase, single crystalline, highly epitaxial film of Bi.sub.2 CaSr.sub.2 Cu.sub.2 O.sub.8 superconductor which has a T.sub.c (zero resistance) of 83 K is provided on a lattice-matched substrate with no intergrowth. This film is produced by a Liquid Phase Epitaxy method which includes the steps of forming a dilute supercooled molten solution of a single phase superconducting mixture of oxides of Bi, Ca, Sr, and Cu having an atomic ratio of about 2:1:2:2 in a nonreactive flux such as KCl, introducing the substrate, e.g., NdGaO.sub.3, into the molten solution at 850.degree. C., cooling the solution from 850.degree. C. to 830.degree. C. to grow the film and rapidly cooling the substrate to room temperature to maintain the desired single phase, single crystalline film structure.

Massively parallel whole genome amplification for single-cell sequencing using droplet microfluidics.

PubMed

Hosokawa, Masahito; Nishikawa, Yohei; Kogawa, Masato; Takeyama, Haruko

2017-07-12

Massively parallel single-cell genome sequencing is required to further understand genetic diversities in complex biological systems. Whole genome amplification (WGA) is the first step for single-cell sequencing, but its throughput and accuracy are insufficient in conventional reaction platforms. Here, we introduce single droplet multiple displacement amplification (sd-MDA), a method that enables massively parallel amplification of single cell genomes while maintaining sequence accuracy and specificity. Tens of thousands of single cells are compartmentalized in millions of picoliter droplets and then subjected to lysis and WGA by passive droplet fusion in microfluidic channels. Because single cells are isolated in compartments, their genomes are amplified to saturation without contamination. This enables the high-throughput acquisition of contamination-free and cell specific sequence reads from single cells (21,000 single-cells/h), resulting in enhancement of the sequence data quality compared to conventional methods. This method allowed WGA of both single bacterial cells and human cancer cells. The obtained sequencing coverage rivals those of conventional techniques with superior sequence quality. In addition, we also demonstrate de novo assembly of uncultured soil bacteria and obtain draft genomes from single cell sequencing. This sd-MDA is promising for flexible and scalable use in single-cell sequencing.

Method to fabricate multi-level silicon-based microstructures via use of an etching delay layer

DOEpatents

Manginell, Ronald P.; Schubert, W. Kent; Shul, Randy J.

2005-08-16

New methods for fabrication of silicon microstructures have been developed. In these methods, an etching delay layer is deposited and patterned so as to provide differential control on the depth of features being etched into a substrate material. Structures having features with different depth can be formed thereby in a single etching step.

Cascading pressure reactor and method for solar-thermochemical reactions

DOEpatents

Ermanoski, Ivan

2017-11-14

Reactors and methods for solar thermochemical reactions are disclosed. The reactors and methods include a cascade of reduction chambers at successively lower pressures that leads to over an order of magnitude pressure decrease compared to a single-chambered design. The resulting efficiency gains are substantial, and represent an important step toward practical and efficient solar fuel production on a large scale.

Quantification and characterisation of fatty acid methyl esters in microalgae: Comparison of pretreatment and purification methods.

PubMed

Lage, Sandra; Gentili, Francesco G

2018-06-01

A systematic qualitative and quantitative analysis of fatty acid methyl esters (FAMEs) is crucial for microalgae species selection for biodiesel production. The aim of this study is to identify the best method to assess microalgae FAMEs composition and content. A single-step method, was tested with and without purification steps-that is, separation of lipid classes by thin-layer chromatography (TLC) or solid-phase extraction (SPE). The efficiency of a direct transesterification method was also evaluated. Additionally, the yield of the FAMEs and the profiles of the microalgae samples with different pretreatments (boiled in isopropanol, freezing, oven-dried and freeze-dried) were compared. The application of a purification step after lipid extraction proved to be essential for an accurate FAMEs characterisation. The purification methods, which included TLC and SPE, provided superior results compared to not purifying the samples. Freeze-dried microalgae produced the lowest FAMEs yield. However, FAMEs profiles were generally equivalent among the pretreatments. Copyright © 2018 Elsevier Ltd. All rights reserved.

Comparison of Methods to Trace Multiple Subskills: Is LR-DBN Best?

ERIC Educational Resources Information Center

Xu, Yanbo; Mostow, Jack

2012-01-01

A long-standing challenge for knowledge tracing is how to update estimates of multiple subskills that underlie a single observable step. We characterize approaches to this problem by how they model knowledge tracing, fit its parameters, predict performance, and update subskill estimates. Previous methods allocated blame or credit among subskills…

Rapid habitability assessment of Mars samples by pyrolysis-FTIR

NASA Astrophysics Data System (ADS)

Gordon, Peter R.; Sephton, Mark A.

2016-02-01

Pyrolysis Fourier transform infrared spectroscopy (pyrolysis FTIR) is a potential sample selection method for Mars Sample Return missions. FTIR spectroscopy can be performed on solid and liquid samples but also on gases following preliminary thermal extraction, pyrolysis or gasification steps. The detection of hydrocarbon and non-hydrocarbon gases can reveal information on sample mineralogy and past habitability of the environment in which the sample was created. The absorption of IR radiation at specific wavenumbers by organic functional groups can indicate the presence and type of any organic matter present. Here we assess the utility of pyrolysis-FTIR to release water, carbon dioxide, sulfur dioxide and organic matter from Mars relevant materials to enable a rapid habitability assessment of target rocks for sample return. For our assessment a range of minerals were analyzed by attenuated total reflectance FTIR. Subsequently, the mineral samples were subjected to single step pyrolysis and multi step pyrolysis and the products characterised by gas phase FTIR. Data from both single step and multi step pyrolysis-FTIR provide the ability to identify minerals that reflect habitable environments through their water and carbon dioxide responses. Multi step pyrolysis-FTIR can be used to gain more detailed information on the sources of the liberated water and carbon dioxide owing to the characteristic decomposition temperatures of different mineral phases. Habitation can be suggested when pyrolysis-FTIR indicates the presence of organic matter within the sample. Pyrolysis-FTIR, therefore, represents an effective method to assess whether Mars Sample Return target rocks represent habitable conditions and potential records of habitation and can play an important role in sample triage operations.

Nonlinear Analyte Concentration Gradients for One-Step Kinetic Analysis Employing Optical Microring Resonators

PubMed Central

Marty, Michael T.; Kuhnline Sloan, Courtney D.; Bailey, Ryan C.; Sligar, Stephen G.

2012-01-01

Conventional methods to probe the binding kinetics of macromolecules at biosensor surfaces employ a stepwise titration of analyte concentrations and measure the association and dissociation to the immobilized ligand at each concentration level. It has previously been shown that kinetic rates can be measured in a single step by monitoring binding as the analyte concentration increases over time in a linear gradient. We report here the application of nonlinear analyte concentration gradients for determining kinetic rates and equilibrium binding affinities in a single experiment. A versatile nonlinear gradient maker is presented, which is easily applied to microfluidic systems. Simulations validate that accurate kinetic rates can be extracted for a wide range of association and dissociation rates, gradient slopes and curvatures, and with models for mass transport. The nonlinear analyte gradient method is demonstrated with a silicon photonic microring resonator platform to measure prostate specific antigen-antibody binding kinetics. PMID:22686186

Nonlinear analyte concentration gradients for one-step kinetic analysis employing optical microring resonators.

PubMed

Marty, Michael T; Sloan, Courtney D Kuhnline; Bailey, Ryan C; Sligar, Stephen G

2012-07-03

Conventional methods to probe the binding kinetics of macromolecules at biosensor surfaces employ a stepwise titration of analyte concentrations and measure the association and dissociation to the immobilized ligand at each concentration level. It has previously been shown that kinetic rates can be measured in a single step by monitoring binding as the analyte concentration increases over time in a linear gradient. We report here the application of nonlinear analyte concentration gradients for determining kinetic rates and equilibrium binding affinities in a single experiment. A versatile nonlinear gradient maker is presented, which is easily applied to microfluidic systems. Simulations validate that accurate kinetic rates can be extracted for a wide range of association and dissociation rates, gradient slopes, and curvatures, and with models for mass transport. The nonlinear analyte gradient method is demonstrated with a silicon photonic microring resonator platform to measure prostate specific antigen-antibody binding kinetics.

Improving Signal-to-Noise Ratio in Scanning Transmission Electron Microscopy Energy-Dispersive X-Ray (STEM-EDX) Spectrum Images Using Single-Atomic-Column Cross-Correlation Averaging.

PubMed

Jeong, Jong Seok; Mkhoyan, K Andre

2016-06-01

Acquiring an atomic-resolution compositional map of crystalline specimens has become routine practice, thus opening possibilities for extracting subatomic information from such maps. A key challenge for achieving subatomic precision is the improvement of signal-to-noise ratio (SNR) of compositional maps. Here, we report a simple and reliable solution for achieving high-SNR energy-dispersive X-ray (EDX) spectroscopy spectrum images for individual atomic columns. The method is based on standard cross-correlation aided by averaging of single-column EDX maps with modifications in the reference image. It produces EDX maps with minimal specimen drift, beam drift, and scan distortions. Step-by-step procedures to determine a self-consistent reference map with a discussion on the reliability, stability, and limitations of the method are presented here.

Heterogeneity of Metazoan Cells and Beyond: To Integrative Analysis of Cellular Populations at Single-Cell Level.

PubMed

Barteneva, Natasha S; Vorobjev, Ivan A

2018-01-01

In this paper, we review some of the recent advances in cellular heterogeneity and single-cell analysis methods. In modern research of cellular heterogeneity, there are four major approaches: analysis of pooled samples, single-cell analysis, high-throughput single-cell analysis, and lately integrated analysis of cellular population at a single-cell level. Recently developed high-throughput single-cell genetic analysis methods such as RNA-Seq require purification step and destruction of an analyzed cell often are providing a snapshot of the investigated cell without spatiotemporal context. Correlative analysis of multiparameter morphological, functional, and molecular information is important for differentiation of more uniform groups in the spectrum of different cell types. Simplified distributions (histograms and 2D plots) can underrepresent biologically significant subpopulations. Future directions may include the development of nondestructive methods for dissecting molecular events in intact cells, simultaneous correlative cellular analysis of phenotypic and molecular features by hybrid technologies such as imaging flow cytometry, and further progress in supervised and non-supervised statistical analysis algorithms.

DNA combing on low-pressure oxygen plasma modified polysilsesquioxane substrates for single-molecule studies

PubMed Central

Sriram, K. K.; Chang, Chun-Ling; Rajesh Kumar, U.; Chou, Chia-Fu

2014-01-01

Molecular combing and flow-induced stretching are the most commonly used methods to immobilize and stretch DNA molecules. While both approaches require functionalization steps for the substrate surface and the molecules, conventionally the former does not take advantage of, as the latter, the versatility of microfluidics regarding robustness, buffer exchange capability, and molecule manipulation using external forces for single molecule studies. Here, we demonstrate a simple one-step combing process involving only low-pressure oxygen (O2) plasma modified polysilsesquioxane (PSQ) polymer layer to facilitate both room temperature microfluidic device bonding and immobilization of stretched single DNA molecules without molecular functionalization step. Atomic force microscopy and Kelvin probe force microscopy experiments revealed a significant increase in surface roughness and surface potential on low-pressure O2 plasma treated PSQ, in contrast to that with high-pressure O2 plasma treatment, which are proposed to be responsible for enabling effective DNA immobilization. We further demonstrate the use of our platform to observe DNA-RNA polymerase complexes and cancer drug cisplatin induced DNA condensation using wide-field fluorescence imaging. PMID:25332730

Single-step fabrication of electrodes with controlled nanostructured surface roughness using optically-induced electrodeposition

NASA Astrophysics Data System (ADS)

Liu, N.; Li, M.; Liu, L.; Yang, Y.; Mai, J.; Pu, H.; Sun, Y.; Li, W. J.

2018-02-01

The customized fabrication of microelectrodes from gold nanoparticles (AuNPs) has attracted much attention due to their numerous applications in chemistry and biomedical engineering, such as for surface-enhanced Raman spectroscopy (SERS) and as catalyst sites for electrochemistry. Herein, we present a novel optically-induced electrodeposition (OED) method for rapidly fabricating gold electrodes which are also surface-modified with nanoparticles in one single step. The electrodeposition mechanism, with respect to the applied AC voltage signal and the elapsed deposition time, on the resulting morphology and particle sizes was investigated. The results from SEM and AFM analysis demonstrated that 80-200 nm gold particles can be formed on the surface of the gold electrodes. Simultaneously, both the size of the nanoparticles and the roughness of the fabricated electrodes can be regulated by the deposition time. Compared to state-of-the-art methods for fabricating microelectrodes with AuNPs, such as nano-seed-mediated growth and conventional electrodeposition, this OED technique has several advantages including: (1) electrode fabrication and surface modification using nanoparticles are completed in a single step, eliminating the need for prefabricating micro electrodes; (2) the patterning of electrodes is defined using a digitally-customized, projected optical image rather than using fixed physical masks; and (3) both the fabrication and surface modification processes are rapid, and the entire fabrication process only requires less than 6 s.

A colorimetric probe based on desensitized ionene-stabilized gold nanoparticles for single-step test for sulfate ions.

PubMed

Arkhipova, Viktoriya V; Apyari, Vladimir V; Dmitrienko, Stanislava G

2015-03-15

Desensitized ionene-stabilized gold nanoparticles have been prepared and applied as a colorimetric probe for the single-step test for sulfate ions at the relatively high concentration level. The approach is based on aggregation of the nanoparticles leading to the change in absorption spectra and color of the solution. These nanoparticles are characterized by the decreased sensitivity due to both electrostatic and steric stabilization, which allows for simple, and rapid direct single-step determination of sulfate at the relatively high concentration level in real water samples without sample pretreatment or dilution. Influence of different factors (the time of interaction, pH, the concentrations of sulfate ions and the nanoparticles) on the aggregation and analytical performance of the procedure was investigated. The method allows for the determination of sulfate ions in the mass range of 0.2-0.4 mg with RSD of 5% from the sample volume of less than 2 mL. It has a sharp dependence of the colorimetric response on the concentration of sulfate, which makes it prospective for indicating deviations of the sulfate concentration regarding some declared value chosen within the above range. The time of the analysis is 2 min. The method was applied to the analysis of mineral water samples. Copyright © 2014 Elsevier B.V. All rights reserved.

Laser surface structuring of AZ31 Mg alloy for controlled wettability.

PubMed

Gökhan Demir, Ali; Furlan, Valentina; Lecis, Nora; Previtali, Barbara

2014-06-01

Structured surfaces exhibit functional properties that can enhance the performance of a bioimplant in terms of biocompatibility, adhesion, or corrosion behavior. In order to tailor the surface property, chemical and physical methods can be used in a sequence of many steps. On the other hand, laser surface processing can provide a single step solution to achieve the designated surface function with the use of simpler equipment and high repeatability. This work provides the details on the surface structuring of AZ31, a biocompatible and biodegradable Mg alloy, by a single-step laser surface structuring based on remelting. The surfaces are characterized in terms of topography, chemistry, and physical integrity, as well as the effective change in the surface wetting behavior is demonstrated. The results imply a great potential in local or complete surface structuring of medical implants for functionalization by the flexible positioning of the laser beam.

Image segmentation and dynamic lineage analysis in single-cell fluorescence microscopy.

PubMed

Wang, Quanli; Niemi, Jarad; Tan, Chee-Meng; You, Lingchong; West, Mike

2010-01-01

An increasingly common component of studies in synthetic and systems biology is analysis of dynamics of gene expression at the single-cell level, a context that is heavily dependent on the use of time-lapse movies. Extracting quantitative data on the single-cell temporal dynamics from such movies remains a major challenge. Here, we describe novel methods for automating key steps in the analysis of single-cell, fluorescent images-segmentation and lineage reconstruction-to recognize and track individual cells over time. The automated analysis iteratively combines a set of extended morphological methods for segmentation, and uses a neighborhood-based scoring method for frame-to-frame lineage linking. Our studies with bacteria, budding yeast and human cells, demonstrate the portability and usability of these methods, whether using phase, bright field or fluorescent images. These examples also demonstrate the utility of our integrated approach in facilitating analyses of engineered and natural cellular networks in diverse settings. The automated methods are implemented in freely available, open-source software.

PCR-mediated site-directed mutagenesis.

PubMed

Carey, Michael F; Peterson, Craig L; Smale, Stephen T

2013-08-01

Unlike traditional site-directed mutagenesis, this protocol requires only a single PCR step using full plasmid amplification to generate point mutants. The method can introduce small mutations into promoter sites and is even better suited for introducing single or double mutations into proteins. It is elegant in its simplicity and can be applied quite easily in any laboratory using standard protein expression vectors and commercially available reagents.

Linking pedestrian flow characteristics with stepping locomotion

NASA Astrophysics Data System (ADS)

Wang, Jiayue; Boltes, Maik; Seyfried, Armin; Zhang, Jun; Ziemer, Verena; Weng, Wenguo

2018-06-01

While properties of human traffic flow are described by speed, density and flow, the locomotion of pedestrian is based on steps. To relate characteristics of human locomotor system with properties of human traffic flow, this paper aims to connect gait characteristics like step length, step frequency, swaying amplitude and synchronization with speed and density and thus to build a ground for advanced pedestrian models. For this aim, observational and experimental study on the single-file movement of pedestrians at different densities is conducted. Methods to measure step length, step frequency, swaying amplitude and step synchronization are proposed by means of trajectories of the head. Mathematical models for the relations of step length or frequency and speed are evaluated. The problem how step length and step duration are influenced by factors like body height and density is investigated. It is shown that the effect of body height on step length and step duration changes with density. Furthermore, two different types of step in-phase synchronization between two successive pedestrians are observed and the influence of step synchronization on step length is examined.

Comparison of Single and Multi-Scale Method for Leaf and Wood Points Classification from Terrestrial Laser Scanning Data

NASA Astrophysics Data System (ADS)

Wei, Hongqiang; Zhou, Guiyun; Zhou, Junjie

2018-04-01

The classification of leaf and wood points is an essential preprocessing step for extracting inventory measurements and canopy characterization of trees from the terrestrial laser scanning (TLS) data. The geometry-based approach is one of the widely used classification method. In the geometry-based method, it is common practice to extract salient features at one single scale before the features are used for classification. It remains unclear how different scale(s) used affect the classification accuracy and efficiency. To assess the scale effect on the classification accuracy and efficiency, we extracted the single-scale and multi-scale salient features from the point clouds of two oak trees of different sizes and conducted the classification on leaf and wood. Our experimental results show that the balanced accuracy of the multi-scale method is higher than the average balanced accuracy of the single-scale method by about 10 % for both trees. The average speed-up ratio of single scale classifiers over multi-scale classifier for each tree is higher than 30.

Estimation of genomic breeding values for milk yield in UK dairy goats.

PubMed

Mucha, S; Mrode, R; MacLaren-Lee, I; Coffey, M; Conington, J

2015-11-01

The objective of this study was to estimate genomic breeding values for milk yield in crossbred dairy goats. The research was based on data provided by 2 commercial goat farms in the UK comprising 590,409 milk yield records on 14,453 dairy goats kidding between 1987 and 2013. The population was created by crossing 3 breeds: Alpine, Saanen, and Toggenburg. In each generation the best performing animals were selected for breeding, and as a result, a synthetic breed was created. The pedigree file contained 30,139 individuals, of which 2,799 were founders. The data set contained test-day records of milk yield, lactation number, farm, age at kidding, and year and season of kidding. Data on milk composition was unavailable. In total 1,960 animals were genotyped with the Illumina 50K caprine chip. Two methods for estimation of genomic breeding value were compared-BLUP at the single nucleotide polymorphism level (BLUP-SNP) and single-step BLUP. The highest accuracy of 0.61 was obtained with single-step BLUP, and the lowest (0.36) with BLUP-SNP. Linkage disequilibrium (r(2), the squared correlation of the alleles at 2 loci) at 50 kb (distance between 2 SNP) was 0.18. This is the first attempt to implement genomic selection in UK dairy goats. Results indicate that the single-step method provides the highest accuracy for populations with a small number of genotyped individuals, where the number of genotyped males is low and females are predominant in the reference population. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

A Newly Developed Nested PCR Assay for the Detection of Helicobacter pylori in the Oral Cavity.

PubMed

Ismail, Hawazen; Morgan, Claire; Griffiths, Paul; Williams, John; Jenkins, Gareth

2016-01-01

To develop a new nested polymerase chain reaction (PCR) assay for identifying Helicobacter pylori DNA from dental plaque. H. pylori is one of the most common chronic bacterial pathogens in humans. The accurate detection of this organism is essential for proper patient management and for the eradication of the bacteria following treatment. Forty-nine patients (24 males and 25 females; mean age: 51; range, 19 to 94 y) were investigated for the presence of H. pylori in dental plaque by single-step PCR and nested PCR and in the stomach by single-step PCR, nested PCR, and histologic examination. The newly developed nested PCR assay identified H. pylori DNA in gastric biopsies of 18 patients who were histologically classified as H. pylori-positive and 2 additional biopsies of patients who were H. pylori-negative by histologic examination (20/49; 40.8%). Dental plaque samples collected before and after endoscopy from the 49 patients revealed that single-step PCR did not detect H. pylori but nested PCR was able to detect H. pylori DNA in 40.8% (20/49) patients. Nested PCR gave a higher detection rate (40.8%, 20/49) than that of histology (36.7%, 18/49) and single-step PCR. When nested PCR results were compared with histology results there was no significant difference between the 2 methods. Our newly developed nested PCR assay is at least as sensitive as histology and may be useful for H. pylori detection in patients unfit for endoscopic examination.

[Methods of substances and organelles introduction in living cell for cell engineering technologies].

PubMed

Nikitin, V A

2007-01-01

We have presented the classification of more than 40 methods of genetic material, substances and organelles introduction into a living cell. Each of them has its characteristic advantages, disadvantages and limitations with respect to cell viability, transfer efficiency, general applicability, and technical requirements. It this article we have enlarged on the description of our developments of several new and improved approaches, methods and devices of the direct microinjection into a single cell and cell microsurgery with the help of glass micropipettes. The problem of low efficiency of mammalian cloning is discussed with emphasis on the necessity of expertizing of each step of single cell reconstruction to begin with microsurgical manipulations and necessity of the development of such methods of single cell resonstruction that could minimize the possible damage of the cell.

Algorithms for image recovery calculation in extended single-shot phase-shifting digital holography

NASA Astrophysics Data System (ADS)

Hasegawa, Shin-ya; Hirata, Ryo

2018-04-01

The single-shot phase-shifting method of image recovery using an inclined reference wave has the advantages of reducing the effects of vibration, being capable of operating in real time, and affording low-cost sensing. In this method, relatively low reference angles compared with that in the conventional method using phase shift between three or four pixels has been required. We propose an extended single-shot phase-shifting technique which uses the multiple-step phase-shifting algorithm and the corresponding multiple pixels which are the same as that of the period of an interference fringe. We have verified the theory underlying this recovery method by means of Fourier spectral analysis and its effectiveness by evaluating the visibility of the image using a high-resolution pattern. Finally, we have demonstrated high-contrast image recovery experimentally using a resolution chart. This method can be used in a variety of applications such as color holographic interferometry.

Methods of preparing and using single chain anti-tumor antibodies

DOEpatents

Cheung, Nai-Kong; Guo, Hong-Fen

2010-02-23

This invention provides a method for identifying cells expressing a target single chain antibody (scFv) directed against a target antigen from a collection of cells that includes cells that do not express the target scFv, comprising the step of combining the collection of cells with an anti-idiotype directed to an antibody specific for the target antigen and detecting interaction, if any, of the anti-idiotype with the cells, wherein the occurrence of an interaction identifies the cell as one which expresses the target scFv. This invention also provides a method for making a single chain antibody (scFv) directed against an antigen, wherein the selection of clones is made based upon interaction of those clones with an appropriate anti-idiotype, and heretofore inaccessible scFv so made. This invention provides the above methods or any combination thereof. Finally, this invention provides various uses of these methods.

Method for preparation of single chain antibodies

DOEpatents

Cheung, Nai-Kong V [New York, NY; Guo, Hong-fen [New York, NY

2012-04-03

This invention provides a method for identifying cells expressing a target single chain antibody (scFv) directed against a target antigen from a collection of cells that includes cells that do not express the target scFv, comprising the step of combining the collection of cells with an anti-idiotype directed to an antibody specific for the target antigen and detecting interaction, if any, of the anti-idiotype with the cells, wherein the occurrence of an interaction identifies the cell as one which expresses the target scFv. This invention also provides a method for making a single chain antibody (scFv) directed against an antigen, wherein the selection of clones is made based upon interaction of those clones with an appropriate anti-idiotype, and heretofore inaccessible scFv so made. This invention provides the above methods or any combination thereof. Finally, this invention provides various uses of these methods.

Method of forming catalyst layer by single step infiltration

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

Gerdes, Kirk; Lee, Shiwoo; Dowd, Regis

Provided herein is a method for electrocatalyst infiltration of a porous substrate, of particular use for preparation of a cathode for a solid oxide fuel cell. The method generally comprises preparing an electrocatalyst infiltrate solution comprising an electrocatalyst, surfactant, chelating agent, and a solvent; pretreating a porous mixed ionic-electric conductive substrate; and applying the electrocatalyst infiltration solution to the porous mixed ionic-electric conductive substrate.

TagDust2: a generic method to extract reads from sequencing data.

PubMed

Lassmann, Timo

2015-01-28

Arguably the most basic step in the analysis of next generation sequencing data (NGS) involves the extraction of mappable reads from the raw reads produced by sequencing instruments. The presence of barcodes, adaptors and artifacts subject to sequencing errors makes this step non-trivial. Here I present TagDust2, a generic approach utilizing a library of hidden Markov models (HMM) to accurately extract reads from a wide array of possible read architectures. TagDust2 extracts more reads of higher quality compared to other approaches. Processing of multiplexed single, paired end and libraries containing unique molecular identifiers is fully supported. Two additional post processing steps are included to exclude known contaminants and filter out low complexity sequences. Finally, TagDust2 can automatically detect the library type of sequenced data from a predefined selection. Taken together TagDust2 is a feature rich, flexible and adaptive solution to go from raw to mappable NGS reads in a single step. The ability to recognize and record the contents of raw reads will help to automate and demystify the initial, and often poorly documented, steps in NGS data analysis pipelines. TagDust2 is freely available at: http://tagdust.sourceforge.net .

One-step generation of complete gene knockout mice and monkeys by CRISPR/Cas9-mediated gene editing with multiple sgRNAs.

PubMed

Zuo, Erwei; Cai, Yi-Jun; Li, Kui; Wei, Yu; Wang, Bang-An; Sun, Yidi; Liu, Zhen; Liu, Jiwei; Hu, Xinde; Wei, Wei; Huo, Xiaona; Shi, Linyu; Tang, Cheng; Liang, Dan; Wang, Yan; Nie, Yan-Hong; Zhang, Chen-Chen; Yao, Xuan; Wang, Xing; Zhou, Changyang; Ying, Wenqin; Wang, Qifang; Chen, Ren-Chao; Shen, Qi; Xu, Guo-Liang; Li, Jinsong; Sun, Qiang; Xiong, Zhi-Qi; Yang, Hui

2017-07-01

The CRISPR/Cas9 system is an efficient gene-editing method, but the majority of gene-edited animals showed mosaicism, with editing occurring only in a portion of cells. Here we show that single gene or multiple genes can be completely knocked out in mouse and monkey embryos by zygotic injection of Cas9 mRNA and multiple adjacent single-guide RNAs (spaced 10-200 bp apart) that target only a single key exon of each gene. Phenotypic analysis of F0 mice following targeted deletion of eight genes on the Y chromosome individually demonstrated the robustness of this approach in generating knockout mice. Importantly, this approach delivers complete gene knockout at high efficiencies (100% on Arntl and 91% on Prrt2) in monkey embryos. Finally, we could generate a complete Prrt2 knockout monkey in a single step, demonstrating the usefulness of this approach in rapidly establishing gene-edited monkey models.

Single step sequential polydimethylsiloxane wet etching to fabricate a microfluidic channel with various cross-sectional geometries

NASA Astrophysics Data System (ADS)

Wang, C.-K.; Liao, W.-H.; Wu, H.-M.; Lo, Y.-H.; Lin, T.-R.; Tung, Y.-C.

2017-11-01

Polydimethylsiloxane (PDMS) has become a widely used material to construct microfluidic devices for various biomedical and chemical applications due to its desirable material properties and manufacturability. PDMS microfluidic devices are usually fabricated using soft lithography replica molding methods with master molds made of photolithogrpahy patterned photoresist layers on silicon wafers. The fabricated microfluidic channels often have rectangular cross-sectional geometries with single or multiple heights. In this paper, we develop a single step sequential PDMS wet etching process that can be used to fabricate microfluidic channels with various cross-sectional geometries from single-layer PDMS microfluidic channels. The cross-sections of the fabricated channel can be non-rectangular, and varied along the flow direction. Furthermore, the fabricated cross-sectional geometries can be numerically simulated beforehand. In the experiments, we fabricate microfluidic channels with various cross-sectional geometries using the developed technique. In addition, we fabricate a microfluidic mixer with alternative mirrored cross-sectional geometries along the flow direction to demonstrate the practical usage of the developed technique.

Detection of canine distemper virus (CDV) through one step RT-PCR combined with nested PCR.

PubMed

Kim, Y H; Cho, K W; Youn, H Y; Yoo, H S; Han, H R

2001-04-01

A one step reverse transcription PCR (RT-PCR) combined nested PCR was set up to increase efficiency in the diagnosis of canine distemper virus (CDV) infection after developement of nested PCR. Two PCR primer sets were designed based on the sequence of nucleocapsid gene of CDV Onderstepoort strain. One-step RT-PCR with the outer primer pair was revealed to detect 10(2) PFU/ml. The sensitivity was increased hundredfold using the one-step RT-PCR combined with the nested PCR. Specificity of the PCR was also confirmed using other related canine virus and peripheral blood mononuclear cells (PBMC) and body secretes of healthy dogs. Of the 51 blood samples from dogs clinically suspected of CD, 45 samples were revealed as positive by one-step RT-PCR combined with nested PCR. However, only 15 samples were identified as positive with a single one step RT-PCR. Therefore approximately 60% increase in the efficiency of the diagnosis was observed by the combined method. These results suggested that one step RT-PCR combined with nested PCR could be a sensitive, specific, and practical method for diagnosis of CDV infection.

A one-step strategy for ultra-fast and low-cost mass production of plastic membrane microfluidic chips.

PubMed

Hu, Chong; Lin, Sheng; Li, Wanbo; Sun, Han; Chen, Yangfan; Chan, Chiu-Wing; Leung, Chung-Hang; Ma, Dik-Lung; Wu, Hongkai; Ren, Kangning

2016-10-05

An ultra-fast, extremely cost-effective, and environmentally friendly method was developed for fabricating flexible microfluidic chips with plastic membranes. With this method, we could fabricate plastic microfluidic chips rapidly (within 12 seconds per piece) at an extremely low cost (less than $0.02 per piece). We used a heated perfluoropolymer perfluoroalkoxy (often called Teflon PFA) solid stamp to press a pile of two pieces of plastic membranes, low density polyethylene (LDPE) and polyethylene terephthalate (PET) coated with an ethylene-vinyl acetate copolymer (EVA). During the short period of contact with the heated PFA stamp, the pressed area of the membranes permanently bonded, while the LDPE membrane spontaneously rose up at the area not pressed, forming microchannels automatically. These two regions were clearly distinguishable even at the micrometer scale so we were able to fabricate microchannels with widths down to 50 microns. This method combines the two steps in the conventional strategy for microchannel fabrication, generating microchannels and sealing channels, into a single step. The production is a green process without using any solvent or generating any waste. Also, the chips showed good resistance against the absorption of Rhodamine 6G, oligonucleotides, and green fluorescent protein (GFP). We demonstrated some typical microfluidic manipulations with the flexible plastic membrane chips, including droplet formation, on-chip capillary electrophoresis, and peristaltic pumping for quantitative injection of samples and reagents. In addition, we demonstrated convenient on-chip detection of lead ions in water samples by a peristaltic-pumping design, as an example of the application of the plastic membrane chips in a resource-limited environment. Due to the high speed and low cost of the fabrication process, this single-step method will facilitate the mass production of microfluidic chips and commercialization of microfluidic technologies.

A numerical method for computing unsteady 2-D boundary layer flows

NASA Technical Reports Server (NTRS)

Krainer, Andreas

1988-01-01

A numerical method for computing unsteady two-dimensional boundary layers in incompressible laminar and turbulent flows is described and applied to a single airfoil changing its incidence angle in time. The solution procedure adopts a first order panel method with a simple wake model to solve for the inviscid part of the flow, and an implicit finite difference method for the viscous part of the flow. Both procedures integrate in time in a step-by-step fashion, in the course of which each step involves the solution of the elliptic Laplace equation and the solution of the parabolic boundary layer equations. The Reynolds shear stress term of the boundary layer equations is modeled by an algebraic eddy viscosity closure. The location of transition is predicted by an empirical data correlation originating from Michel. Since transition and turbulence modeling are key factors in the prediction of viscous flows, their accuracy will be of dominant influence to the overall results.

A study of the impact of freezing on the lyophilization of a concentrated formulation with a high fill depth.

PubMed

Liu, Jinsong; Viverette, Todd; Virgin, Marlin; Anderson, Mitch; Paresh, Dalal

2005-01-01

The objective of this study was to evaluate the impact of freezing on the lyophilization of a concentrated formulation with a high fill depth. A model system consisting of a 15-mL fill of 15% (w/w) sulfobutylether 7-beta-cyclodextrin (SBECD) solution in a 30-mL vial was selected for this study. Various freezing methods including single-step freezing, two-step freezing with a super-cooling holding, annealing, vacuum-induced freezing, changing ice habit using tert-butyl-alcohol (TBA), ice nucleation with silver iodide (AgI), as well as combinations of some of the methods, were used in the lyophilization of this model system. This work demonstrated that the freezing process had a significant impact on primary drying rate and product quality of a concentrated formulation with a high fill depth. Annealing, vacuum-induced freezing, and addition of either TBA or an ice nucleating agent (AgI) to the formulation accelerated the subsequent ice sublimation process. Two-step freezing or addition of TBA improved the product quality by eliminating vertical heterogeneity within the cake. The combination of two-step freezing in conjunction with an annealing step was shown to be a method of choice for freezing in the lyophilization of a product with a high fill depth. In addition to being an effective method of freezing, it is most applicable for scaling up. An alternative approach is to add a certain amount of TBA to the formulation, if the TBA-formulation interaction or regulatory concerns can be demonstrated as not being an issue. An evaluation of vial size performed in this study showed that although utilizing large-diameter vials to reduce the fill depth can greatly shorten the cycle time of a single batch, it will substantially decrease the product throughput in a large-scale freeze-dryer.

A state space based approach to localizing single molecules from multi-emitter images.

PubMed

Vahid, Milad R; Chao, Jerry; Ward, E Sally; Ober, Raimund J

2017-01-28

Single molecule super-resolution microscopy is a powerful tool that enables imaging at sub-diffraction-limit resolution. In this technique, subsets of stochastically photoactivated fluorophores are imaged over a sequence of frames and accurately localized, and the estimated locations are used to construct a high-resolution image of the cellular structures labeled by the fluorophores. Available localization methods typically first determine the regions of the image that contain emitting fluorophores through a process referred to as detection. Then, the locations of the fluorophores are estimated accurately in an estimation step. We propose a novel localization method which combines the detection and estimation steps. The method models the given image as the frequency response of a multi-order system obtained with a balanced state space realization algorithm based on the singular value decomposition of a Hankel matrix, and determines the locations of intensity peaks in the image as the pole locations of the resulting system. The locations of the most significant peaks correspond to the locations of single molecules in the original image. Although the accuracy of the location estimates is reasonably good, we demonstrate that, by using the estimates as the initial conditions for a maximum likelihood estimator, refined estimates can be obtained that have a standard deviation close to the Cramér-Rao lower bound-based limit of accuracy. We validate our method using both simulated and experimental multi-emitter images.

FIBER AND INTEGRATED OPTICS: Use of the offset method in an analysis of a non-Gaussian field distribution in single-mode fiber waveguides

NASA Astrophysics Data System (ADS)

Belov, A. V.; Kurkov, Andrei S.; Chikolini, A. V.

1990-08-01

An offset method is modified to allow an analysis of the distribution of fields in a single-mode fiber waveguide without recourse to the Gaussian approximation. A new approximation for the field is obtained for fiber waveguides with a step refractive index profile and a special analysis employing the Hankel transformation is applied to waveguides with a distributed refractive index. The field distributions determined by this method are compared with the corresponding distributions calculated from the refractive index of a preform from which the fibers are drawn. It is shown that these new approaches can be used to determine the dimensions of a mode spot defined in different ways and to forecast the dispersion characteristics of single-mode fiber waveguides.

Pretreatment methods to improve nerve immunostaining in corneas from long-term fixed embryonic quail eyes

NASA Technical Reports Server (NTRS)

Barrett, J. E.; Wells, D. C.; Conrad, G. W.

1999-01-01

Pretreatment methods were used to improve neurofilament immunostaining in corneas from embryonic day 16 Japanese quail corneas that had been stored in fixative solution for several months. A sequential combination of the following three pretreatments: brief microwave heating in saline, followed by extraction with sodium dodecyl sulfate (SDS) at 37 degrees C, followed by digestion with hyaluronidase at 37 degrees C, produced significantly increased antibody staining of corneal neurofilament proteins, compared with embryonic corneas subjected to no prior pretreatments or to single or two-step protocols. After applying the sequence of all three pretreatments, darkest nerve staining and increased numbers of fine branches were observed, together with lower background staining. Thus, the result of applying the three-step pretreatment sequence is better than that of applying any of its component single pretreatments or even combinations of any two of them. These findings therefore suggest that each of these three pretreatments causes a unique effect, beneficial to immunostaining of neurofilament proteins, and that their individual effects are independent and additive. In addition to embryonic corneas, the three-step procedure also may be useful for immunostaining of nerves in other very delicate, highly-hydrated tissues containing an abundance of extracellular matrix.

Demonstration of Single-Barium-Ion Sensitivity for Neutrinoless Double-Beta Decay Using Single-Molecule Fluorescence Imaging.

PubMed

McDonald, A D; Jones, B J P; Nygren, D R; Adams, C; Álvarez, V; Azevedo, C D R; Benlloch-Rodríguez, J M; Borges, F I G M; Botas, A; Cárcel, S; Carrión, J V; Cebrián, S; Conde, C A N; Díaz, J; Diesburg, M; Escada, J; Esteve, R; Felkai, R; Fernandes, L M P; Ferrario, P; Ferreira, A L; Freitas, E D C; Goldschmidt, A; Gómez-Cadenas, J J; González-Díaz, D; Gutiérrez, R M; Guenette, R; Hafidi, K; Hauptman, J; Henriques, C A O; Hernandez, A I; Hernando Morata, J A; Herrero, V; Johnston, S; Labarga, L; Laing, A; Lebrun, P; Liubarsky, I; López-March, N; Losada, M; Martín-Albo, J; Martínez-Lema, G; Martínez, A; Monrabal, F; Monteiro, C M B; Mora, F J; Moutinho, L M; Muñoz Vidal, J; Musti, M; Nebot-Guinot, M; Novella, P; Palmeiro, B; Para, A; Pérez, J; Querol, M; Repond, J; Renner, J; Riordan, S; Ripoll, L; Rodríguez, J; Rogers, L; Santos, F P; Dos Santos, J M F; Simón, A; Sofka, C; Sorel, M; Stiegler, T; Toledo, J F; Torrent, J; Tsamalaidze, Z; Veloso, J F C A; Webb, R; White, J T; Yahlali, N

2018-03-30

A new method to tag the barium daughter in the double-beta decay of ^{136}Xe is reported. Using the technique of single molecule fluorescent imaging (SMFI), individual barium dication (Ba^{++}) resolution at a transparent scanning surface is demonstrated. A single-step photobleach confirms the single ion interpretation. Individual ions are localized with superresolution (∼2  nm), and detected with a statistical significance of 12.9σ over backgrounds. This lays the foundation for a new and potentially background-free neutrinoless double-beta decay technology, based on SMFI coupled to high pressure xenon gas time projection chambers.

Demonstration of Single-Barium-Ion Sensitivity for Neutrinoless Double-Beta Decay Using Single-Molecule Fluorescence Imaging

NASA Astrophysics Data System (ADS)

McDonald, A. D.; Jones, B. J. P.; Nygren, D. R.; Adams, C.; Álvarez, V.; Azevedo, C. D. R.; Benlloch-Rodríguez, J. M.; Borges, F. I. G. M.; Botas, A.; Cárcel, S.; Carrión, J. V.; Cebrián, S.; Conde, C. A. N.; Díaz, J.; Diesburg, M.; Escada, J.; Esteve, R.; Felkai, R.; Fernandes, L. M. P.; Ferrario, P.; Ferreira, A. L.; Freitas, E. D. C.; Goldschmidt, A.; Gómez-Cadenas, J. J.; González-Díaz, D.; Gutiérrez, R. M.; Guenette, R.; Hafidi, K.; Hauptman, J.; Henriques, C. A. O.; Hernandez, A. I.; Hernando Morata, J. A.; Herrero, V.; Johnston, S.; Labarga, L.; Laing, A.; Lebrun, P.; Liubarsky, I.; López-March, N.; Losada, M.; Martín-Albo, J.; Martínez-Lema, G.; Martínez, A.; Monrabal, F.; Monteiro, C. M. B.; Mora, F. J.; Moutinho, L. M.; Muñoz Vidal, J.; Musti, M.; Nebot-Guinot, M.; Novella, P.; Palmeiro, B.; Para, A.; Pérez, J.; Querol, M.; Repond, J.; Renner, J.; Riordan, S.; Ripoll, L.; Rodríguez, J.; Rogers, L.; Santos, F. P.; dos Santos, J. M. F.; Simón, A.; Sofka, C.; Sorel, M.; Stiegler, T.; Toledo, J. F.; Torrent, J.; Tsamalaidze, Z.; Veloso, J. F. C. A.; Webb, R.; White, J. T.; Yahlali, N.; NEXT Collaboration

2018-03-01

A new method to tag the barium daughter in the double-beta decay of Xe 136 is reported. Using the technique of single molecule fluorescent imaging (SMFI), individual barium dication (Ba++ ) resolution at a transparent scanning surface is demonstrated. A single-step photobleach confirms the single ion interpretation. Individual ions are localized with superresolution (˜2 nm ), and detected with a statistical significance of 12.9 σ over backgrounds. This lays the foundation for a new and potentially background-free neutrinoless double-beta decay technology, based on SMFI coupled to high pressure xenon gas time projection chambers.

"Silicon millefeuille": From a silicon wafer to multiple thin crystalline films in a single step

NASA Astrophysics Data System (ADS)

Hernández, David; Trifonov, Trifon; Garín, Moisés; Alcubilla, Ramon

2013-04-01

During the last years, many techniques have been developed to obtain thin crystalline films from commercial silicon ingots. Large market applications are foreseen in the photovoltaic field, where important cost reductions are predicted, and also in advanced microelectronics technologies as three-dimensional integration, system on foil, or silicon interposers [Dross et al., Prog. Photovoltaics 20, 770-784 (2012); R. Brendel, Thin Film Crystalline Silicon Solar Cells (Wiley-VCH, Weinheim, Germany 2003); J. N. Burghartz, Ultra-Thin Chip Technology and Applications (Springer Science + Business Media, NY, USA, 2010)]. Existing methods produce "one at a time" silicon layers, once one thin film is obtained, the complete process is repeated to obtain the next layer. Here, we describe a technology that, from a single crystalline silicon wafer, produces a large number of crystalline films with controlled thickness in a single technological step.

Comprehensive Numerical Analysis of Finite Difference Time Domain Methods for Improving Optical Waveguide Sensor Accuracy

PubMed Central

Samak, M. Mosleh E. Abu; Bakar, A. Ashrif A.; Kashif, Muhammad; Zan, Mohd Saiful Dzulkifly

2016-01-01

This paper discusses numerical analysis methods for different geometrical features that have limited interval values for typically used sensor wavelengths. Compared with existing Finite Difference Time Domain (FDTD) methods, the alternating direction implicit (ADI)-FDTD method reduces the number of sub-steps by a factor of two to three, which represents a 33% time savings in each single run. The local one-dimensional (LOD)-FDTD method has similar numerical equation properties, which should be calculated as in the previous method. Generally, a small number of arithmetic processes, which result in a shorter simulation time, are desired. The alternating direction implicit technique can be considered a significant step forward for improving the efficiency of unconditionally stable FDTD schemes. This comparative study shows that the local one-dimensional method had minimum relative error ranges of less than 40% for analytical frequencies above 42.85 GHz, and the same accuracy was generated by both methods.

Single-molecule fluorescence reveals the unwinding stepping mechanism of replicative helicase.

PubMed

Syed, Salman; Pandey, Manjula; Patel, Smita S; Ha, Taekjip

2014-03-27

Bacteriophage T7 gp4 serves as a model protein for replicative helicases that couples deoxythymidine triphosphate (dTTP) hydrolysis to directional movement and DNA strand separation. We employed single-molecule fluorescence resonance energy transfer methods to resolve steps during DNA unwinding by T7 helicase. We confirm that the unwinding rate of T7 helicase decreases with increasing base pair stability. For duplexes containing >35% guanine-cytosine (GC) base pairs, we observed stochastic pauses every 2-3 bp during unwinding. The dwells on each pause were distributed nonexponentially, consistent with two or three rounds of dTTP hydrolysis before each unwinding step. Moreover, we observed backward movements of the enzyme on GC-rich DNAs at low dTTP concentrations. Our data suggest a coupling ratio of 1:1 between base pairs unwound and dTTP hydrolysis, and they further support the concept that nucleic acid motors can have a hierarchy of different-sized steps or can accumulate elastic energy before transitioning to a subsequent phase. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Single-Cell RT-PCR in Microfluidic Droplets with Integrated Chemical Lysis.

PubMed

Kim, Samuel C; Clark, Iain C; Shahi, Payam; Abate, Adam R

2018-01-16

Droplet microfluidics can identify and sort cells using digital reverse transcription polymerase chain reaction (RT-PCR) signals from individual cells. However, current methods require multiple microfabricated devices for enzymatic cell lysis and PCR reagent addition, making the process complex and prone to failure. Here, we describe a new approach that integrates all components into a single device. The method enables controlled exposure of isolated single cells to a high pH buffer, which lyses cells and inactivates reaction inhibitors but can be instantly neutralized with RT-PCR buffer. Using our chemical lysis approach, we distinguish individual cells' gene expression with data quality equivalent to more complex two-step workflows. Our system accepts cells and produces droplets ready for amplification, making single-cell droplet RT-PCR faster and more reliable.

Universal single level implicit algorithm for gasdynamics

NASA Technical Reports Server (NTRS)

Lombard, C. K.; Venkatapthy, E.

1984-01-01

A single level effectively explicit implicit algorithm for gasdynamics is presented. The method meets all the requirements for unconditionally stable global iteration over flows with mixed supersonic and supersonic zones including blunt body flow and boundary layer flows with strong interaction and streamwise separation. For hyperbolic (supersonic flow) regions the method is automatically equivalent to contemporary space marching methods. For elliptic (subsonic flow) regions, rapid convergence is facilitated by alternating direction solution sweeps which bring both sets of eigenvectors and the influence of both boundaries of a coordinate line equally into play. Point by point updating of the data with local iteration on the solution procedure at each spatial step as the sweeps progress not only renders the method single level in storage but, also, improves nonlinear accuracy to accelerate convergence by an order of magnitude over related two level linearized implicit methods. The method derives robust stability from the combination of an eigenvector split upwind difference method (CSCM) with diagonally dominant ADI(DDADI) approximate factorization and computed characteristic boundary approximations.

Proton irradiation of [18O]O2: production of [18F]F2 and [18F]F2 + [18F] OF2.

PubMed

Bishop, A; Satyamurthy, N; Bida, G; Hendry, G; Phelps, M; Barrio, J R

1996-04-01

The production of 18F electrophilic reagents via the 18O(p,n)18F reaction has been investigated in small-volume target bodies made of aluminum, copper, gold-plated copper and nickel, having straight or conical bore shapes. Three irradiation protocols-single-step, two-step and modified two-step-were used for the recovery of the 18F activity. The single-step irradiation protocol was tested in all the target bodies. Based on the single-step performance, aluminum targets were utilized extensively in the investigation of the two-step and modified two-step irradiation protocols. With an 11-MeV cyclotron and using the two-step irradiation protocol, > 1Ci [18F]F2 was recovered reproducibly from an aluminum target body. Probable radical mechanisms for the formation of OF2 and FONO2 (fluorine nitrate) in the single-step and modified two-step targets are proposed based on the amount of ozone generated and the nitrogen impurity present in the target gases, respectively.

Quantitative reconstruction of refractive index distribution and imaging of glucose concentration by using diffusing light.

PubMed

Liang, Xiaoping; Zhang, Qizhi; Jiang, Huabei

2006-11-10

We show that a two-step reconstruction method can be adapted to improve the quantitative accuracy of the refractive index reconstruction in phase-contrast diffuse optical tomography (PCDOT). We also describe the possibility of imaging tissue glucose concentration with PCDOT. In this two-step method, we first use our existing finite-element reconstruction algorithm to recover the position and shape of a target. We then use the position and size of the target as a priori information to reconstruct a single value of the refractive index within the target and background regions using a region reconstruction method. Due to the extremely low contrast available in the refractive index reconstruction, we incorporate a data normalization scheme into the two-step reconstruction to combat the associated low signal-to-noise ratio. Through a series of phantom experiments we find that this two-step reconstruction method can considerably improve the quantitative accuracy of the refractive index reconstruction. The results show that the relative error of the reconstructed refractive index is reduced from 20% to within 1.5%. We also demonstrate the possibility of PCDOT for recovering glucose concentration using these phantom experiments.

Lower limb muscle moments and power during recovery from forward loss of balance in male and female single and multiple steppers.

PubMed

Carty, Christopher P; Cronin, Neil J; Lichtwark, Glen A; Mills, Peter M; Barrett, Rod S

2012-12-01

Studying recovery responses to loss of balance may help to explain why older adults are susceptible to falls. The purpose of the present study was to assess whether male and female older adults, that use a single or multiple step recovery strategy, differ in the proportion of lower limb strength used and power produced during the stepping phase of balance recovery. Eighty-four community-dwelling older adults (47 men, 37 women) participated in the study. Isometric strength of the ankle, knee and hip joint flexors and extensors was assessed using a dynamometer. Loss of balance was induced by releasing participants from a static forward lean (4 trials at each of 3 forward lean angles). Participants were instructed to recover with a single step and were subsequently classified as using a single or multiple step recovery strategy for each trial. (1) Females were weaker than males and the proportion of females that were able to recover with a single step were lower than for males at each lean magnitude. (2) Multiple compared to single steppers used a significantly higher proportion of their hip extension strength and produced less knee and ankle joint peak power during stepping, at the intermediate lean angle. Strength deficits in female compared to male participants may explain why a lower proportion of female participants were able to recover with a single step. The inability to generate sufficient power in the stepping limb appears to be a limiting factor in single step recovery from forward loss of balance. Crown Copyright © 2012. Published by Elsevier Ltd. All rights reserved.

Single-step fabrication of thin-film linear variable bandpass filters based on metal-insulator-metal geometry.

PubMed

Williams, Calum; Rughoobur, Girish; Flewitt, Andrew J; Wilkinson, Timothy D

2016-11-10

A single-step fabrication method is presented for ultra-thin, linearly variable optical bandpass filters (LVBFs) based on a metal-insulator-metal arrangement using modified evaporation deposition techniques. This alternate process methodology offers reduced complexity and cost in comparison to conventional techniques for fabricating LVBFs. We are able to achieve linear variation of insulator thickness across a sample, by adjusting the geometrical parameters of a typical physical vapor deposition process. We demonstrate LVBFs with spectral selectivity from 400 to 850 nm based on Ag (25 nm) and MgF₂ (75-250 nm). Maximum spectral transmittance is measured at ∼70% with a Q-factor of ∼20.

Decision tree-based method for integrating gene expression, demographic, and clinical data to determine disease endotypes

PubMed Central

2013-01-01

Background Complex diseases are often difficult to diagnose, treat and study due to the multi-factorial nature of the underlying etiology. Large data sets are now widely available that can be used to define novel, mechanistically distinct disease subtypes (endotypes) in a completely data-driven manner. However, significant challenges exist with regard to how to segregate individuals into suitable subtypes of the disease and understand the distinct biological mechanisms of each when the goal is to maximize the discovery potential of these data sets. Results A multi-step decision tree-based method is described for defining endotypes based on gene expression, clinical covariates, and disease indicators using childhood asthma as a case study. We attempted to use alternative approaches such as the Student’s t-test, single data domain clustering and the Modk-prototypes algorithm, which incorporates multiple data domains into a single analysis and none performed as well as the novel multi-step decision tree method. This new method gave the best segregation of asthmatics and non-asthmatics, and it provides easy access to all genes and clinical covariates that distinguish the groups. Conclusions The multi-step decision tree method described here will lead to better understanding of complex disease in general by allowing purely data-driven disease endotypes to facilitate the discovery of new mechanisms underlying these diseases. This application should be considered a complement to ongoing efforts to better define and diagnose known endotypes. When coupled with existing methods developed to determine the genetics of gene expression, these methods provide a mechanism for linking genetics and exposomics data and thereby accounting for both major determinants of disease. PMID:24188919

Single step generation of protein arrays from DNA by cell-free expression and in situ immobilisation (PISA method).

PubMed

He, M; Taussig, M J

2001-08-01

We describe a format for production of protein arrays termed 'protein in situ array' (PISA). A PISA is rapidly generated in one step directly from PCR-generated DNA fragments by cell-free protein expression and in situ immobilisation at a surface. The template for expression is DNA encoding individual proteins or domains, which is produced by PCR using primers designed from information in DNA databases. Coupled transcription and translation is carried out on a surface to which the tagged protein adheres as soon as it is synthesised. Because proteins generated by cell-free synthesis are usually soluble and functional, this method can overcome problems of insolubility or degradation associated with bacterial expression of recombinant proteins. Moreover, the use of PCR-generated DNA enables rapid production of proteins or domains based on genome information alone and will be particularly useful where cloned material is not available. Here we show that human single-chain antibody fragments (three domain, V(H)/K form) and an enzyme (luciferase) can be functionally arrayed by the PISA method.

ROOM TEMPERATURE BULK AND TEMPLATE-FREE SYNTHESIS OF LEUCOEMARLDINE POLYANILINE NANOFIBERS

EPA Science Inventory

An extremely simple single-step method is described for the bulk synthesis of nanofibers of the electronic polymer polyaniline in fully reduced state (leucoemarldine form) without using any reducing agents, surfactants, and/or large amounts of insoluble templates. Chemical oxida...

Gallium arsenide single crystal solar cell structure and method of making

NASA Technical Reports Server (NTRS)

Stirn, Richard J. (Inventor)

1983-01-01

A production method and structure for a thin-film GaAs crystal for a solar cell on a single-crystal silicon substrate (10) comprising the steps of growing a single-crystal interlayer (12) of material having a closer match in lattice and thermal expansion with single-crystal GaAs than the single-crystal silicon of the substrate, and epitaxially growing a single-crystal film (14) on the interlayer. The material of the interlayer may be germanium or graded germanium-silicon alloy, with low germanium content at the silicon substrate interface, and high germanium content at the upper surface. The surface of the interface layer (12) is annealed for recrystallization by a pulsed beam of energy (laser or electron) prior to growing the interlayer. The solar cell structure may be grown as a single-crystal n.sup.+ /p shallow homojunction film or as a p/n or n/p junction film. A Ga(Al)AS heteroface film may be grown over the GaAs film.

Single layer multi-color luminescent display and method of making

NASA Technical Reports Server (NTRS)

Robertson, James B. (Inventor)

1992-01-01

The invention is a multi-color luminescent display comprising an insulator substrate and a single layer of host material, which may be a phosphor deposited thereon that hosts one or more different impurities, therein forming a pattern of selected and distinctly colored phosphors such as blue, green, and red phosphors in a single layer of host material. Transparent electrical conductor means may be provided for subjecting selected portions of the pattern of colored phosphors to an electric field, thereby forming a multi-color, single layer electroluminescent display. A method of forming a multi-color luminescent display includes the steps of depositing on an insulator substrate a single layer of host material, which itself may be a phosphor, with the properties to host varying quantities of different impurities and introducing one or more of said different impurities into selected areas of the said single layer of host material by thermal diffusion or ion implantation to form a pattern of phosphors of different colors in the said single layer of host material.

General Methods for Analysis of Sequential “n-step” Kinetic Mechanisms: Application to Single Turnover Kinetics of Helicase-Catalyzed DNA Unwinding

PubMed Central

Lucius, Aaron L.; Maluf, Nasib K.; Fischer, Christopher J.; Lohman, Timothy M.

2003-01-01

Helicase-catalyzed DNA unwinding is often studied using “all or none” assays that detect only the final product of fully unwound DNA. Even using these assays, quantitative analysis of DNA unwinding time courses for DNA duplexes of different lengths, L, using “n-step” sequential mechanisms, can reveal information about the number of intermediates in the unwinding reaction and the “kinetic step size”, m, defined as the average number of basepairs unwound between two successive rate limiting steps in the unwinding cycle. Simultaneous nonlinear least-squares analysis using “n-step” sequential mechanisms has previously been limited by an inability to float the number of “unwinding steps”, n, and m, in the fitting algorithm. Here we discuss the behavior of single turnover DNA unwinding time courses and describe novel methods for nonlinear least-squares analysis that overcome these problems. Analytic expressions for the time courses, fss(t), when obtainable, can be written using gamma and incomplete gamma functions. When analytic expressions are not obtainable, the numerical solution of the inverse Laplace transform can be used to obtain fss(t). Both methods allow n and m to be continuous fitting parameters. These approaches are generally applicable to enzymes that translocate along a lattice or require repetition of a series of steps before product formation. PMID:14507688

Photocleavable DNA Barcoding Antibodies for Multiplexed Protein Analysis in Single Cells.

PubMed

Ullal, Adeeti V; Weissleder, Ralph

2015-01-01

We describe a DNA-barcoded antibody sensing technique for single cell protein analysis in which the barcodes are photocleaved and digitally detected without amplification steps (Ullal et al., Sci Transl Med 6:219, 2014). After photocleaving the unique ~70 mer DNA barcodes we use a fluorescent hybridization technology for detection, similar to what is commonly done for nucleic acid readouts. This protocol offers a simple method for multiplexed protein detection using 100+ antibodies and can be performed on clinical samples as well as single cells.

Single-step electrodeposition of CIS thin films with the complexing agent triethanolamine

NASA Astrophysics Data System (ADS)

Chiu, Yu-Shuen; Hsieh, Mu-Tao; Chang, Chih-Min; Chen, Chun-Shuo; Whang, Thou-Jen

2014-04-01

Some difficulties have long been encountered by single-step electrodeposition such as the optimization of electrolyte composition, deposition potentials, deposition time, and pH values. The approach of introducing ternary components into single-step electrodeposition is rather challenging especially due to the different values of the equilibrium potential for each constituent. Complexing agents play an important role in single-step electrodeposition of CuInSe2 (CIS), since the equilibrium potential of every constituent can be brought closer to each other when complexing agents are employed. In this work, single-step electrodeposition of CIS was enhanced by adding triethanolamine (TEA) into deposition bath, the CIS thin films were improved consequently in the form of polycrystalline cauliflower structures through the examination of SEM images and XRD patterns. The optimum composition of the solution for single-step electrodeposition of CIS is found to be 5 mM CuCl2, 22 mM InCl3, and 22 mM SeO2 at pH 1.5 with 0.1 M TEA. The structures, compositions, and morphologies of as-deposited and of annealed films were investigated.

Design and fabrication of a chitosan hydrogel with gradient structures via a step-by-step cross-linking process.

PubMed

Xu, Yongxiang; Yuan, Shenpo; Han, Jianmin; Lin, Hong; Zhang, Xuehui

2017-11-15

The development of scaffolds to mimic the gradient structure of natural tissue is an important consideration for effective tissue engineering. In the present study, a physical cross-linking chitosan hydrogel with gradient structures was fabricated via a step-by-step cross-linking process using sodium tripolyphosphate and sodium hydroxide as sequential cross-linkers. Chitosan hydrogels with different structures (single, double, and triple layers) were prepared by modifying the gelling process. The properties of the hydrogels were further adjusted by varying the gelling conditions, such as gelling time, pH, and composition of the crosslinking solution. Slight cytotoxicity was showed in MTT assay for hydrogels with uncross-linking chitosan solution and non-cytotoxicity was showed for other hydrogels. The results suggest that step-by-step cross-linking represents a practicable method to fabricate scaffolds with gradient structures. Copyright © 2017. Published by Elsevier Ltd.

Drop-on-Demand Single Cell Isolation and Total RNA Analysis

PubMed Central

Moon, Sangjun; Kim, Yun-Gon; Dong, Lingsheng; Lombardi, Michael; Haeggstrom, Edward; Jensen, Roderick V.; Hsiao, Li-Li; Demirci, Utkan

2011-01-01

Technologies that rapidly isolate viable single cells from heterogeneous solutions have significantly contributed to the field of medical genomics. Challenges remain both to enable efficient extraction, isolation and patterning of single cells from heterogeneous solutions as well as to keep them alive during the process due to a limited degree of control over single cell manipulation. Here, we present a microdroplet based method to isolate and pattern single cells from heterogeneous cell suspensions (10% target cell mixture), preserve viability of the extracted cells (97.0±0.8%), and obtain genomic information from isolated cells compared to the non-patterned controls. The cell encapsulation process is both experimentally and theoretically analyzed. Using the isolated cells, we identified 11 stem cell markers among 1000 genes and compare to the controls. This automated platform enabling high-throughput cell manipulation for subsequent genomic analysis employs fewer handling steps compared to existing methods. PMID:21412416

visnormsc: A Graphical User Interface to Normalize Single-cell RNA Sequencing Data.

PubMed

Tang, Lijun; Zhou, Nan

2017-12-26

Single-cell RNA sequencing (RNA-seq) allows the analysis of gene expression with high resolution. The intrinsic defects of this promising technology imports technical noise into the single-cell RNA-seq data, increasing the difficulty of accurate downstream inference. Normalization is a crucial step in single-cell RNA-seq data pre-processing. SCnorm is an accurate and efficient method that can be used for this purpose. An R implementation of this method is currently available. On one hand, the R package possesses many excellent features from R. On the other hand, R programming ability is required, which prevents the biologists who lack the skills from learning to use it quickly. To make this method more user-friendly, we developed a graphical user interface, visnormsc, for normalization of single-cell RNA-seq data. It is implemented in Python and is freely available at https://github.com/solo7773/visnormsc . Although visnormsc is based on the existing method, it contributes to this field by offering a user-friendly alternative. The out-of-the-box and cross-platform features make visnormsc easy to learn and to use. It is expected to serve biologists by simplifying single-cell RNA-seq normalization.

Efficient Mutagenesis Independent of Ligation (EMILI).

PubMed

Füzik, Tibor; Ulbrich, Pavel; Ruml, Tomáš

2014-11-01

Site-directed mutagenesis is one of the most widely used techniques in life sciences. Here we describe an improved and simplified method for introducing mutations at desired sites. It consists of an inverse PCR using a plasmid template and two partially complementary primers. The synthesis step is followed by annealing of the PCR product's sticky ends, which are generated by exonuclease digestion. This method is fast, extremely efficient and cost-effective. It can be used to introduce large insertions and deletions, but also for multiple point mutations in a single step. To show the principle and to prove the efficiency of the method, we present a series of basic mutations (insertions, deletions, point mutations) on pUC19 plasmid DNA. Copyright © 2014 Elsevier B.V. All rights reserved.

A novel method to accurately locate and count large numbers of steps by photobleaching.

PubMed

Tsekouras, Konstantinos; Custer, Thomas C; Jashnsaz, Hossein; Walter, Nils G; Pressé, Steve

2016-11-07

Photobleaching event counting is a single-molecule fluorescence technique that is increasingly being used to determine the stoichiometry of protein and RNA complexes composed of many subunits in vivo as well as in vitro. By tagging protein or RNA subunits with fluorophores, activating them, and subsequently observing as the fluorophores photobleach, one obtains information on the number of subunits in a complex. The noise properties in a photobleaching time trace depend on the number of active fluorescent subunits. Thus, as fluorophores stochastically photobleach, noise properties of the time trace change stochastically, and these varying noise properties have created a challenge in identifying photobleaching steps in a time trace. Although photobleaching steps are often detected by eye, this method only works for high individual fluorophore emission signal-to-noise ratios and small numbers of fluorophores. With filtering methods or currently available algorithms, it is possible to reliably identify photobleaching steps for up to 20-30 fluorophores and signal-to-noise ratios down to ∼1. Here we present a new Bayesian method of counting steps in photobleaching time traces that takes into account stochastic noise variation in addition to complications such as overlapping photobleaching events that may arise from fluorophore interactions, as well as on-off blinking. Our method is capable of detecting ≥50 photobleaching steps even for signal-to-noise ratios as low as 0.1, can find up to ≥500 steps for more favorable noise profiles, and is computationally inexpensive. © 2016 Tsekouras et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Method of casting patterned dielectric structures

DOEpatents

Poco, John F.; Hrubesh, Lawrence W.

2001-01-01

A pattern of dielectric structures are formed directly on a substrate in a single step using sol-gel chemistry and molding procedures. The resulting dielectric structures are useful in vacuum applications for electronic devices. Porous, lightweight structures having a high aspect ratio that are suitable for use as spacers between the faceplate and baseplate of a field emission display can be manufactured using this method.

Analysis of health trait data from on-farm computer systems in the U.S. II: Comparison of genomic analyses including two-stage and single-step methods

USDA-ARS?s Scientific Manuscript database

The development of genomic selection methodology, with accompanying substantial gains in reliability for low-heritability traits, may dramatically improve the feasibility of genetic improvement of dairy cow health. Many methods for genomic analysis have now been developed, including the “Bayesian Al...

Single-step CE for miniaturized and easy-to-use system.

PubMed

Ono, Koichi; Kaneda, Shohei; Fujii, Teruo

2013-03-01

We developed a novel single-step capillary electrophoresis (SSCE) scheme for miniaturized and easy to use system by using a microchannel chip, which was made from the hydrophilic material polymethyl methacrylate (PMMA), equipped with a capillary stop valve. Taking the surface tension property of liquids into consideration, the capillary effect was used to introduce liquids and control capillary stop valves in a partial barrier structure in the wall of the microchannel. Through the combined action of stop valves and air vents, both sample plug formation for electrophoresis and sample injection into a separation channel were successfully performed in a single step. To optimize SSCE, different stop valve structures were evaluated using actual microchannel chips and the finite element method with the level set method. A partial barrier structure at the bottom of the channel functioned efficiently as a stop valve. The stability of stop valve was confirmed by a shock test, which was performed by dropping the microchannel chip to a floor. Sample plug deformation could be reduced by minimizing the size of the side partial barrier. By dissolving hydroxyl ethyl cellulose and using it as the sample solution, the EOF and adsorption of the sample into the PMMA microchannel were successfully reduced. Using this method, a 100-bp DNA ladder was concentrated; good separation was observed within 1 min. At a separation length of 5 mm, the signal was approximately 20-fold higher than a signal of original sample solution by field-amplified sample stacking effect. All operations, including liquid introduction and sample separation, can be completed within 2 min by using the SSCE scheme. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Isothermal circular-strand-displacement polymerization of DNA and microRNA in digital microfluidic devices.

PubMed

Giuffrida, Maria Chiara; Zanoli, Laura Maria; D'Agata, Roberta; Finotti, Alessia; Gambari, Roberto; Spoto, Giuseppe

2015-02-01

Nucleic-acid amplification is a crucial step in nucleic-acid-sequence-detection assays. The use of digital microfluidic devices to miniaturize amplification techniques reduces the required sample volume and the analysis time and offers new possibilities for process automation and integration in a single device. The recently introduced droplet polymerase-chain-reaction (PCR) amplification methods require repeated cycles of two or three temperature-dependent steps during the amplification of the nucleic-acid target sequence. In contrast, low-temperature isothermal-amplification methods have no need for thermal cycling, thus requiring simplified microfluidic-device features. Here, the combined use of digital microfluidics and molecular-beacon (MB)-assisted isothermal circular-strand-displacement polymerization (ICSDP) to detect microRNA-210 sequences is described. MicroRNA-210 has been described as the most consistently and predominantly upregulated hypoxia-inducible factor. The nmol L(-1)-pmol L(-1) detection capabilities of the method were first tested by targeting single-stranded DNA sequences from the genetically modified Roundup Ready soybean. The ability of the droplet-ICSDP method to discriminate between full-matched, single-mismatched, and unrelated sequences was also investigated. The detection of a range of nmol L(-1)-pmol L(-1) microRNA-210 solutions compartmentalized in nanoliter-sized droplets was performed, establishing the ability of the method to detect as little as 10(-18) mol of microRNA target sequences compartmentalized in 20 nL droplets. The suitability of the method for biological samples was tested by detecting microRNA-210 from transfected K562 cells.

One-step formation of w/o/w multiple emulsions stabilized by single amphiphilic block copolymers.

PubMed

Hong, Liangzhi; Sun, Guanqing; Cai, Jinge; Ngai, To

2012-02-07

Multiple emulsions are complex polydispersed systems in which both oil-in-water (O/W) and water-in-oil (W/O) emulsion exists simultaneously. They are often prepared accroding to a two-step process and commonly stabilized using a combination of hydrophilic and hydrophobic surfactants. Recently, some reports have shown that multiple emulsions can also be produced through one-step method with simultaneous occurrence of catastrophic and transitional phase inversions. However, these reported multiple emulsions need surfactant blends and are usually described as transitory or temporary systems. Herein, we report a one-step phase inversion process to produce water-in-oil-in-water (W/O/W) multiple emulsions stabilized solely by a synthetic diblock copolymer. Unlike the use of small molecule surfactant combinations, block copolymer stabilized multiple emulsions are remarkably stable and show the ability to separately encapsulate both polar and nonpolar cargos. The importance of the conformation of the copolymer surfactant at the interfaces with regards to the stability of the multiple emulsions using the one-step method is discussed.

Laser pyrolysis fabrication of ferromagnetic gamma'-Fe4N and FeC nanoparticles

NASA Technical Reports Server (NTRS)

Grimes, C. A.; Qian, D.; Dickey, E. C.; Allen, J. L.; Eklund, P. C.

2000-01-01

Using the laser pyrolysis method, single phase gamma'-Fe4N nanoparticles were prepared by a two step method involving preparation of nanoscale iron oxide and a subsequent gas-solid nitridation reaction. Single phase Fe3C and Fe7C3 could be prepared by laser pyrolysis from Fe(CO)5 and 3C2H4 directly. Characterization techniques such as XRD, TEM and vibrating sample magnetometer were used to measure phase structure, particle size and magnetic properties of these nanoscale nitride and carbide particles. c2000 American Journal of Physics.

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

PubMed

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

2014-07-14

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

Method of making self-aligned lightly-doped-drain structure for MOS transistors

DOEpatents

Weiner, Kurt H.; Carey, Paul G.

2001-01-01

A process for fabricating lightly-doped-drains (LDD) for short-channel metal oxide semiconductor (MOS) transistors. The process utilizes a pulsed laser process to incorporate the dopants, thus eliminating the prior oxide deposition and etching steps. During the process, the silicon in the source/drain region is melted by the laser energy. Impurities from the gas phase diffuse into the molten silicon to appropriately dope the source/drain regions. By controlling the energy of the laser, a lightly-doped-drain can be formed in one processing step. This is accomplished by first using a single high energy laser pulse to melt the silicon to a significant depth and thus the amount of dopants incorporated into the silicon is small. Furthermore, the dopants incorporated during this step diffuse to the edge of the MOS transistor gate structure. Next, many low energy laser pulses are used to heavily dope the source/drain silicon only in a very shallow region. Because of two-dimensional heat transfer at the MOS transistor gate edge, the low energy pulses are inset from the region initially doped by the high energy pulse. By computer control of the laser energy, the single high energy laser pulse and the subsequent low energy laser pulses are carried out in a single operational step to produce a self-aligned lightly-doped-drain-structure.

From cookbooks to single sentences: The evolution of my labs

NASA Astrophysics Data System (ADS)

Morrison, Andrew

2014-11-01

Like many physics teachers, I love to have my students spend time working in the laboratory. There is often no better way to test an idea about how the physical world works than to actually set up an experiment and see if the idea can be ruled out or not. This process is an authentic representation of the scientific method, which can take a winding and unpredictable path rather than a clean step-by-step recipe that students want to believe science follows.

The SCUBA-2 Data Reduction Cookbook

NASA Astrophysics Data System (ADS)

Thomas, Holly S.; Currie, Malcolm J.

This cookbook provides a short introduction to Starlink facilities, especially SMURF, the Sub-Millimetre User Reduction Facility, for reducing, displaying, and calibrating SCUBA-2 data. It describes some of the data artefacts present in SCUBA-2 time-series and methods to mitigate them. In particular, this cookbook illustrates the various steps required to reduce the data; and gives an overview of the Dynamic Iterative Map-Maker, which carries out all of these steps using a single command controlled by a configuration file. Specialised configuration files are presented.

The SCUBA-2 SRO data reduction cookbook

NASA Astrophysics Data System (ADS)

Chapin, Edward; Dempsey, Jessica; Jenness, Tim; Scott, Douglas; Thomas, Holly; Tilanus, Remo P. J.

This cookbook provides a short introduction to starlink\\ facilities, especially smurf, the Sub-Millimetre User Reduction Facility, for reducing and displaying SCUBA-2 SRO data. We describe some of the data artefacts present in SCUBA-2 time series and methods we employ to mitigate them. In particular, we illustrate the various steps required to reduce the data, and the Dynamic Iterative Map-Maker, which carries out all of these steps using a single command. For information on SCUBA-2 data reduction since SRO, please SC/21.

Comparative evaluation of border molding using two different techniques in maxillary edentulous arches: A clinical study

PubMed Central

Qanungo, Anchal; Aras, Meena Ajay; Chitre, Vidya; Coutinho, Ivy; Rajagopal, Praveen; Mysore, Ashwin

2016-01-01

Purpose: The aim of this in vivo study was to compare the single-step border molding technique using injectable heavy viscosity addition silicone with sectional border molding technique using low fusing impression compound by evaluating the retention of heat cure trial denture bases. Materials and Methods: Ten completely edentulous patients in need of prostheses were included in this study. Two border molding techniques, single-step (Group 1) and sectional (Group 2), were compared for retention. Both border molding techniques were performed in each patient. In both techniques, definitive wash impression was made with light viscosity addition silicone. The final results were analyzed using paired t-test to determine whether significant differences existed between the groups. Results: The t-value (3.031) infers that there was a significant difference between Group 1 and Group 2 (P = 0.014). The retention obtained in Group 2 (mean = 9.05 kgf) was significantly higher than that of Group 1 (mean = 8.26 kgf). Conclusion: Sectional border molding technique proved to be more retentive as compared to single-step border molding although clinically the retention appeared comparable. PMID:27746597

A new method for water quality assessment: by harmony degree equation.

PubMed

Zuo, Qiting; Han, Chunhui; Liu, Jing; Ma, Junxia

2018-02-22

Water quality assessment is an important basic work in the development, utilization, management, and protection of water resources, and also a prerequisite for water safety. In this paper, the harmony degree equation (HDE) was introduced into the research of water quality assessment, and a new method for water quality assessment was proposed according to the HDE: by harmony degree equation (WQA-HDE). First of all, the calculation steps and ideas of this method were described in detail, and then, this method with some other important methods of water quality assessment (single factor assessment method, mean-type comprehensive index assessment method, and multi-level gray correlation assessment method) were used to assess the water quality of the Shaying River (the largest tributary of the Huaihe in China). For this purpose, 2 years (2013-2014) dataset of nine water quality variables covering seven monitoring sites, and approximately 189 observations were used to compare and analyze the characteristics and advantages of the new method. The results showed that the calculation steps of WQA-HDE are similar to the comprehensive assessment method, and WQA-HDE is more operational comparing with the results of other water quality assessment methods. In addition, this new method shows good flexibility by setting the judgment criteria value HD 0 of water quality; when HD 0  = 0.8, the results are closer to reality, and more realistic and reliable. Particularly, when HD 0  = 1, the results of WQA-HDE are consistent with the single factor assessment method, both methods are subject to the most stringent "one vote veto" judgment condition. So, WQA-HDE is a composite method that combines the single factor assessment and comprehensive assessment. This research not only broadens the research field of theoretical method system of harmony theory but also promotes the unity of water quality assessment method and can be used for reference in other comprehensive assessment.

Pelvic Inflammatory Disease

MedlinePlus

... No single step can protect you from every single type of STI. Can women who have sex with women get PID? Yes. ... No single step can protect you from every single type of STI. Can women who have sex with women get PID? Yes. ...

Detection and isolation of rare cells by 2-step enrichment high-speed flow cytometry/cell sorting and single cell LEAP laser ablation

NASA Astrophysics Data System (ADS)

Zordan, M. D.; Leary, James F.

2011-02-01

The clonal isolation of rare cells, especially cancer and stem cells, in a population is important to the development of improved medical treatment. We have demonstrated that the Laser-Enabled Analysis and Processing (LEAP, Cyntellect Inc., San Diego, CA) instrument can be used to efficiently produce single cell clones by photoablative dilution. Additionally, we have also shown that cells present at low frequencies can be cloned by photoablative dilution after they are pre-enriched by flow cytometry based cell sorting. Circulating tumor cells were modeled by spiking isolated peripheral blood cells with cells from the lung carcinoma cell line A549. Flow cytometry based cell sorting was used to perform an enrichment sort of A549 cells directly into a 384 well plate. Photoablative dilution was performed with the LEAPTM instrument to remove any contaminating cells, and clonally isolate 1 side population cell per well. We were able to isolate and grow single clones of side population cells using this method at greater than 90% efficiency. We have developed a 2 step method that is able to perform the clonal isolation of rare cells based on a medically relevant functional phenotype.

Macro-fingerprint analysis-through-separation of licorice based on FT-IR and 2DCOS-IR

NASA Astrophysics Data System (ADS)

Wang, Yang; Wang, Ping; Xu, Changhua; Yang, Yan; Li, Jin; Chen, Tao; Li, Zheng; Cui, Weili; Zhou, Qun; Sun, Suqin; Li, Huifen

2014-07-01

In this paper, a step-by-step analysis-through-separation method under the navigation of multi-step IR macro-fingerprint (FT-IR integrated with second derivative IR (SD-IR) and 2DCOS-IR) was developed for comprehensively characterizing the hierarchical chemical fingerprints of licorice from entirety to single active components. Subsequently, the chemical profile variation rules of three parts (flavonoids, saponins and saccharides) in the separation process were holistically revealed and the number of matching peaks and correlation coefficients with standards of pure compounds was increasing along the extracting directions. The findings were supported by UPLC results and a verification experiment of aqueous separation process. It has been demonstrated that the developed multi-step IR macro-fingerprint analysis-through-separation approach could be a rapid, effective and integrated method not only for objectively providing comprehensive chemical characterization of licorice and all its separated parts, but also for rapidly revealing the global enrichment trend of the active components in licorice separation process.

An initial study on the estimation of time-varying volumetric treatment images and 3D tumor localization from single MV cine EPID images

PubMed Central

Mishra, Pankaj; Li, Ruijiang; Mak, Raymond H.; Rottmann, Joerg; Bryant, Jonathan H.; Williams, Christopher L.; Berbeco, Ross I.; Lewis, John H.

2014-01-01

Purpose: In this work the authors develop and investigate the feasibility of a method to estimate time-varying volumetric images from individual MV cine electronic portal image device (EPID) images. Methods: The authors adopt a two-step approach to time-varying volumetric image estimation from a single cine EPID image. In the first step, a patient-specific motion model is constructed from 4DCT. In the second step, parameters in the motion model are tuned according to the information in the EPID image. The patient-specific motion model is based on a compact representation of lung motion represented in displacement vector fields (DVFs). DVFs are calculated through deformable image registration (DIR) of a reference 4DCT phase image (typically peak-exhale) to a set of 4DCT images corresponding to different phases of a breathing cycle. The salient characteristics in the DVFs are captured in a compact representation through principal component analysis (PCA). PCA decouples the spatial and temporal components of the DVFs. Spatial information is represented in eigenvectors and the temporal information is represented by eigen-coefficients. To generate a new volumetric image, the eigen-coefficients are updated via cost function optimization based on digitally reconstructed radiographs and projection images. The updated eigen-coefficients are then multiplied with the eigenvectors to obtain updated DVFs that, in turn, give the volumetric image corresponding to the cine EPID image. Results: The algorithm was tested on (1) Eight digital eXtended CArdiac-Torso phantom datasets based on different irregular patient breathing patterns and (2) patient cine EPID images acquired during SBRT treatments. The root-mean-squared tumor localization error is (0.73 ± 0.63 mm) for the XCAT data and (0.90 ± 0.65 mm) for the patient data. Conclusions: The authors introduced a novel method of estimating volumetric time-varying images from single cine EPID images and a PCA-based lung motion model. This is the first method to estimate volumetric time-varying images from single MV cine EPID images, and has the potential to provide volumetric information with no additional imaging dose to the patient. PMID:25086523

An initial study on the estimation of time-varying volumetric treatment images and 3D tumor localization from single MV cine EPID images

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

Mishra, Pankaj, E-mail: pankaj.mishra@varian.com; Mak, Raymond H.; Rottmann, Joerg

2014-08-15

Purpose: In this work the authors develop and investigate the feasibility of a method to estimate time-varying volumetric images from individual MV cine electronic portal image device (EPID) images. Methods: The authors adopt a two-step approach to time-varying volumetric image estimation from a single cine EPID image. In the first step, a patient-specific motion model is constructed from 4DCT. In the second step, parameters in the motion model are tuned according to the information in the EPID image. The patient-specific motion model is based on a compact representation of lung motion represented in displacement vector fields (DVFs). DVFs are calculatedmore » through deformable image registration (DIR) of a reference 4DCT phase image (typically peak-exhale) to a set of 4DCT images corresponding to different phases of a breathing cycle. The salient characteristics in the DVFs are captured in a compact representation through principal component analysis (PCA). PCA decouples the spatial and temporal components of the DVFs. Spatial information is represented in eigenvectors and the temporal information is represented by eigen-coefficients. To generate a new volumetric image, the eigen-coefficients are updated via cost function optimization based on digitally reconstructed radiographs and projection images. The updated eigen-coefficients are then multiplied with the eigenvectors to obtain updated DVFs that, in turn, give the volumetric image corresponding to the cine EPID image. Results: The algorithm was tested on (1) Eight digital eXtended CArdiac-Torso phantom datasets based on different irregular patient breathing patterns and (2) patient cine EPID images acquired during SBRT treatments. The root-mean-squared tumor localization error is (0.73 ± 0.63 mm) for the XCAT data and (0.90 ± 0.65 mm) for the patient data. Conclusions: The authors introduced a novel method of estimating volumetric time-varying images from single cine EPID images and a PCA-based lung motion model. This is the first method to estimate volumetric time-varying images from single MV cine EPID images, and has the potential to provide volumetric information with no additional imaging dose to the patient.« less

Protein complex purification from Thermoplasma acidophilum using a phage display library.

PubMed

Hubert, Agnes; Mitani, Yasuo; Tamura, Tomohiro; Boicu, Marius; Nagy, István

2014-03-01

We developed a novel protein complex isolation method using a single-chain variable fragment (scFv) based phage display library in a two-step purification procedure. We adapted the antibody-based phage display technology which has been developed for single target proteins to a protein mixture containing about 300 proteins, mostly subunits of Thermoplasma acidophilum complexes. T. acidophilum protein specific phages were selected and corresponding scFvs were expressed in Escherichia coli. E. coli cell lysate containing the expressed His-tagged scFv specific against one antigen protein and T. acidophilum crude cell lysate containing intact target protein complexes were mixed, incubated and subjected to protein purification using affinity and size exclusion chromatography steps. This method was confirmed to isolate intact particles of thermosome and proteasome suitable for electron microscopy analysis and provides a novel protein complex isolation strategy applicable to organisms where no genetic tools are available. Copyright © 2013 Elsevier B.V. All rights reserved.

A successful backward step correlates with hip flexion moment of supporting limb in elderly people.

PubMed

Takeuchi, Yahiko

2018-01-01

The objective of this study was to determine the positional relationship between the center of mass (COM) and the center of pressure (COP) at the time of step landing, and to examine their relationship with the joint moments exerted by the supporting limb, with regard to factors of the successful backward step response. The study population comprised 8 community-dwelling elderly people that were observed to take successive multi steps after the landing of a backward stepping. Using a motion capture system and force plate, we measured the COM, COP and COM-COP deviation distance on landing during backward stepping. In addition, we measured the moment of the supporting limb joint during backward stepping. The multi-step data were compared with data from instances when only one step was taken (single-step). Variables that differed significantly between the single- and multi-step data were used as objective variables and the joint moments of the supporting limb were used as explanatory variables in single regression analyses. The COM-COP deviation in the anteroposterior was significantly larger in the single-step. A regression analysis with COM-COP deviation as the objective variable obtained a significant regression equation in the hip flexion moment (R2 = 0.74). The hip flexion moment of supporting limb was shown to be a significant explanatory variable in both the PS and SS phases for the relationship with COM-COP distance. This study found that to create an appropriate backward step response after an external disturbance (i.e. the ability to stop after 1 step), posterior braking of the COM by a hip flexion moment are important during the single-limbed standing phase.

Single-shot digital holography by use of the fractional Talbot effect.

PubMed

Martínez-León, Lluís; Araiza-E, María; Javidi, Bahram; Andrés, Pedro; Climent, Vicent; Lancis, Jesús; Tajahuerce, Enrique

2009-07-20

We present a method for recording in-line single-shot digital holograms based on the fractional Talbot effect. In our system, an image sensor records the interference between the light field scattered by the object and a properly codified parallel reference beam. A simple binary two-dimensional periodic grating is used to codify the reference beam generating a periodic three-step phase distribution over the sensor plane by fractional Talbot effect. This provides a method to perform single-shot phase-shifting interferometry at frame rates only limited by the sensor capabilities. Our technique is well adapted for dynamic wavefront sensing applications. Images of the object are digitally reconstructed from the digital hologram. Both computer simulations and experimental results are presented.

New encoded single-indicator sequences based on physico-chemical parameters for efficient exon identification.

PubMed

Meher, J K; Meher, P K; Dash, G N; Raval, M K

2012-01-01

The first step in gene identification problem based on genomic signal processing is to convert character strings into numerical sequences. These numerical sequences are then analysed spectrally or using digital filtering techniques for the period-3 peaks, which are present in exons (coding areas) and absent in introns (non-coding areas). In this paper, we have shown that single-indicator sequences can be generated by encoding schemes based on physico-chemical properties. Two new methods are proposed for generating single-indicator sequences based on hydration energy and dipole moments. The proposed methods produce high peak at exon locations and effectively suppress false exons (intron regions having greater peak than exon regions) resulting in high discriminating factor, sensitivity and specificity.

Helicase Stepping Investigated with One-Nucleotide Resolution Fluorescence Resonance Energy Transfer

NASA Astrophysics Data System (ADS)

Lin, Wenxia; Ma, Jianbing; Nong, Daguan; Xu, Chunhua; Zhang, Bo; Li, Jinghua; Jia, Qi; Dou, Shuoxing; Ye, Fangfu; Xi, Xuguang; Lu, Ying; Li, Ming

2017-09-01

Single-molecule Förster resonance energy transfer is widely applied to study helicases by detecting distance changes between a pair of dyes anchored to overhangs of a forked DNA. However, it has been lacking single-base pair (1-bp) resolution required for revealing stepping kinetics of helicases. We designed a nanotensioner in which a short DNA is bent to exert force on the overhangs, just as in optical or magnetic tweezers. The strategy improved the resolution of Förster resonance energy transfer to 0.5 bp, high enough to uncover differences in DNA unwinding by yeast Pif1 and E. coli RecQ whose unwinding behaviors cannot be differentiated by currently practiced methods. We found that Pif1 exhibits 1-bp-stepping kinetics, while RecQ breaks 1 bp at a time but sequesters the nascent nucleotides and releases them randomly. The high-resolution data allowed us to propose a three-parameter model to quantitatively interpret the apparently different unwinding behaviors of the two helicases which belong to two superfamilies.

Gold Nanorod-based Photo-PCR System for One-Step, Rapid Detection of Bacteria

PubMed Central

Kim, Jinjoo; Kim, Hansol; Park, Ji Ho; Jon, Sangyong

2017-01-01

The polymerase chain reaction (PCR) has been an essential tool for diagnosis of infectious diseases, but conventional PCR still has some limitations with respect to applications to point-of-care (POC) diagnostic systems that require rapid detection and miniaturization. Here we report a light-based PCR method, termed as photo-PCR, which enables rapid detection of bacteria in a single step. In the photo-PCR system, poly(enthylene glycol)-modified gold nanorods (PEG-GNRs), used as a heat generator, are added into the PCR mixture, which is subsequently periodically irradiated with a 808-nm laser to create thermal cycling. Photo-PCR was able to significantly reduce overall thermal cycling time by integrating bacterial cell lysis and DNA amplification into a single step. Furthermore, when combined with KAPA2G fast polymerase and cooling system, the entire process of bacterial genomic DNA extraction and amplification was further shortened, highlighting the potential of photo-PCR for use in a portable, POC diagnostic system. PMID:29071186

Demonstration of Single-Barium-Ion Sensitivity for Neutrinoless Double-Beta Decay Using Single-Molecule Fluorescence Imaging

DOE PAGES

McDonald, A. D.; Jones, B. J. P.; Nygren, D. R.; ...

2018-03-26

A new method to tag the barium daughter in the double beta decay ofmore » $$^{136}$$Xe is reported. Using the technique of single molecule fluorescent imaging (SMFI), individual barium dication (Ba$$^{++}$$) resolution at a transparent scanning surface has been demonstrated. A single-step photo-bleach confirms the single ion interpretation. Individual ions are localized with super-resolution ($$\\sim$$2~nm), and detected with a statistical significance of 12.9~$$\\sigma$$ over backgrounds. This lays the foundation for a new and potentially background-free neutrinoless double beta decay technology, based on SMFI coupled to high pressure xenon gas time projection chambers.« less

Vectorial strain gauge method using single flexible orthogonal polydimethylsiloxane gratings

NASA Astrophysics Data System (ADS)

Guo, Hao; Tang, Jun; Qian, Kun; Tsoukalas, Dimitris; Zhao, Miaomiao; Yang, Jiangtao; Zhang, Binzhen; Chou, Xiujian; Liu, Jun; Xue, Chenyang; Zhang, Wendong

2016-03-01

A vectorial strain gauge method using a single sensing element is reported based on the double-sided polydimethylsiloxane (PDMS) Fraunhofer diffraction gratings structures. Using O2 plasma treatment steps, orthogonal wrinkled gratings were fabricated on both sides of a pre-strained PDMS film. Diffracted laser spots from this structure have been used to experimentally demonstrate, that any applied strain can be quantitatively characterized in both the x and y directions with an error of less than 0.6% and with a gauge factor of approximately 10. This simple and low cost technology which is completely different from the traditional vectorial strain gauge method, can be applied to surface vectorial strain measurement and multi-axis integrated mechanical sensors.

Fibers comprised of epitaxially grown single-wall carbon nanotubes, and a method for added catalyst and continuous growth at the tip

DOEpatents

Kittrell, W. Carter; Wang, Yuhuang; Kim, Myung Jong; Hauge, Robert H.; Smalley, Richard E.; Marek leg, Irene Morin

2010-06-01

The present invention is directed to fibers of epitaxially grown single-wall carbon nanotubes (SWNTs) and methods of making same. Such methods generally comprise the steps of: (a) providing a spun SWNT fiber; (b) cutting the fiber substantially perpendicular to the fiber axis to yield a cut fiber; (c) etching the cut fiber at its end with a plasma to yield an etched cut fiber; (d) depositing metal catalyst on the etched cut fiber end to form a continuous SWNT fiber precursor; and (e) introducing feedstock gases under SWNT growth conditions to grow the continuous SWNT fiber precursor into a continuous SWNT fiber.

GOTHIC: Gravitational oct-tree code accelerated by hierarchical time step controlling

NASA Astrophysics Data System (ADS)

Miki, Yohei; Umemura, Masayuki

2017-04-01

The tree method is a widely implemented algorithm for collisionless N-body simulations in astrophysics well suited for GPU(s). Adopting hierarchical time stepping can accelerate N-body simulations; however, it is infrequently implemented and its potential remains untested in GPU implementations. We have developed a Gravitational Oct-Tree code accelerated by HIerarchical time step Controlling named GOTHIC, which adopts both the tree method and the hierarchical time step. The code adopts some adaptive optimizations by monitoring the execution time of each function on-the-fly and minimizes the time-to-solution by balancing the measured time of multiple functions. Results of performance measurements with realistic particle distribution performed on NVIDIA Tesla M2090, K20X, and GeForce GTX TITAN X, which are representative GPUs of the Fermi, Kepler, and Maxwell generation of GPUs, show that the hierarchical time step achieves a speedup by a factor of around 3-5 times compared to the shared time step. The measured elapsed time per step of GOTHIC is 0.30 s or 0.44 s on GTX TITAN X when the particle distribution represents the Andromeda galaxy or the NFW sphere, respectively, with 224 = 16,777,216 particles. The averaged performance of the code corresponds to 10-30% of the theoretical single precision peak performance of the GPU.

Broad application and optimization of a single wash-step for integrated endotoxin depletion during protein purification.

PubMed

Koziel, David; Michaelis, Uwe; Kruse, Tobias

2018-08-01

Endotoxins contaminate proteins that are produced in E. coli. High levels of endotoxins can influence cellular assays and cause severe adverse effects when administered to humans. Thus, endotoxin removal is important in protein purification for academic research and in GMP manufacturing of biopharmaceuticals. Several methods exist to remove endotoxin, but often require additional downstream-processing steps, decrease protein yield and are costly. These disadvantages can be avoided by using an integrated endotoxin depletion (iED) wash-step that utilizes Triton X-114 (TX114). In this paper, we show that the iED wash-step is broadly applicable in most commonly used chromatographies: it reduces endotoxin by a factor of 10 3 to 10 6 during NiNTA-, MBP-, SAC-, GST-, Protein A and CEX-chromatography but not during AEX or HIC-chromatography. We characterized the iED wash-step using Design of Experiments (DoE) and identified optimal experimental conditions for application scenarios that are relevant to academic research or industrial GMP manufacturing. A single iED wash-step with 0.75% (v/v) TX114 added to the feed and wash buffer can reduce endotoxin levels to below 2 EU/ml or deplete most endotoxin while keeping the manufacturing costs as low as possible. The comprehensive characterization enables academia and industry to widely adopt the iED wash-step for a routine, efficient and cost-effective depletion of endotoxin during protein purification at any scale. Copyright © 2018. Published by Elsevier B.V.

A High-yield Two-step Transfer Printing Method for Large-scale Fabrication of Organic Single-crystal Devices on Arbitrary Substrates

PubMed Central

Deng, Wei; Zhang, Xiujuan; Pan, Huanhuan; Shang, Qixun; Wang, Jincheng; Zhang, Xiaohong; Zhang, Xiwei; Jie, Jiansheng

2014-01-01

Single-crystal organic nanostructures show promising applications in flexible and stretchable electronics, while their applications are impeded by the large incompatibility with the well-developed photolithography techniques. Here we report a novel two-step transfer printing (TTP) method for the construction of organic nanowires (NWs) based devices onto arbitrary substrates. Copper phthalocyanine (CuPc) NWs are first transfer-printed from the growth substrate to the desired receiver substrate by contact-printing (CP) method, and then electrode arrays are transfer-printed onto the resulting receiver substrate by etching-assisted transfer printing (ETP) method. By utilizing a thin copper (Cu) layer as sacrificial layer, microelectrodes fabricated on it via photolithography could be readily transferred to diverse conventional or non-conventional substrates that are not easily accessible before with a high transfer yield of near 100%. The ETP method also exhibits an extremely high flexibility; various electrodes such as Au, Ti, and Al etc. can be transferred, and almost all types of organic devices, such as resistors, Schottky diodes, and field-effect transistors (FETs), can be constructed on planar or complex curvilinear substrates. Significantly, these devices can function properly and exhibit closed or even superior performance than the device counterparts fabricated by conventional approach. PMID:24942458

Step-scan T cell-based differential Fourier transform infrared photoacoustic spectroscopy (DFTIR-PAS) for detection of ambient air contaminants

NASA Astrophysics Data System (ADS)

Liu, Lixian; Mandelis, Andreas; Huan, Huiting; Melnikov, Alexander

2016-10-01

A step-scan differential Fourier transform infrared photoacoustic spectroscopy (DFTIR-PAS) using a commercial FTIR spectrometer was developed theoretically and experimentally for air contaminant monitoring. The configuration comprises two identical, small-size and low-resonance-frequency T cells satisfying the conflicting requirements of low chopping frequency and limited space in the sample compartment. Carbon dioxide (CO2) IR absorption spectra were used to demonstrate the capability of the DFTIR-PAS method to detect ambient pollutants. A linear amplitude response to CO2 concentrations from 100 to 10,000 ppmv was observed, leading to a theoretical detection limit of 2 ppmv. The differential mode was able to suppress the coherent noise, thereby imparting the DFTIR-PAS method with a better signal-to-noise ratio and lower theoretical detection limit than the single mode. The results indicate that it is possible to use step-scan DFTIR-PAS with T cells as a quantitative method for high sensitivity analysis of ambient contaminants.

Stepwise detection of recombination breakpoints in sequence alignments.

PubMed

Graham, Jinko; McNeney, Brad; Seillier-Moiseiwitsch, Françoise

2005-03-01

We propose a stepwise approach to identify recombination breakpoints in a sequence alignment. The approach can be applied to any recombination detection method that uses a permutation test and provides estimates of breakpoints. We illustrate the approach by analyses of a simulated dataset and alignments of real data from HIV-1 and human chromosome 7. The presented simulation results compare the statistical properties of one-step and two-step procedures. More breakpoints are found with a two-step procedure than with a single application of a given method, particularly for higher recombination rates. At higher recombination rates, the additional breakpoints were located at the cost of only a slight increase in the number of falsely declared breakpoints. However, a large proportion of breakpoints still go undetected. A makefile and C source code for phylogenetic profiling and the maximum chi2 method, tested with the gcc compiler on Linux and WindowsXP, are available at http://stat-db.stat.sfu.ca/stepwise/ jgraham@stat.sfu.ca.

Unexpected Reaction Pathway for butyrylcholinesterase-catalyzed inactivation of “hunger hormone” ghrelin

NASA Astrophysics Data System (ADS)

Yao, Jianzhuang; Yuan, Yaxia; Zheng, Fang; Zhan, Chang-Guo

2016-02-01

Extensive computational modeling and simulations have been carried out, in the present study, to uncover the fundamental reaction pathway for butyrylcholinesterase (BChE)-catalyzed hydrolysis of ghrelin, demonstrating that the acylation process of BChE-catalyzed hydrolysis of ghrelin follows an unprecedented single-step reaction pathway and the single-step acylation process is rate-determining. The free energy barrier (18.8 kcal/mol) calculated for the rate-determining step is reasonably close to the experimentally-derived free energy barrier (~19.4 kcal/mol), suggesting that the obtained mechanistic insights are reasonable. The single-step reaction pathway for the acylation is remarkably different from the well-known two-step acylation reaction pathway for numerous ester hydrolysis reactions catalyzed by a serine esterase. This is the first time demonstrating that a single-step reaction pathway is possible for an ester hydrolysis reaction catalyzed by a serine esterase and, therefore, one no longer can simply assume that the acylation process must follow the well-known two-step reaction pathway.

Contribution of lower limb eccentric work and different step responses to balance recovery among older adults.

PubMed

Nagano, Hanatsu; Levinger, Pazit; Downie, Calum; Hayes, Alan; Begg, Rezaul

2015-09-01

Falls during walking reflect susceptibility to balance loss and the individual's capacity to recover stability. Balance can be recovered using either one step or multiple steps but both responses are impaired with ageing. To investigate older adults' (n=15, 72.5±4.8 yrs) recovery step control a tether-release procedure was devised to induce unanticipated forward balance loss. Three-dimensional position-time data combined with foot-ground reaction forces were used to measure balance recovery. Dependent variables were; margin of stability (MoS) and available response time (ART) for spatial and temporal balance measures in the transverse and sagittal planes; lower limb joint angles and joint negative/positive work; and spatio-temporal gait parameters. Relative to multi-step responses, single-step recovery was more effective in maintaining balance, indicated by greater MoS and longer ART. MoS in the sagittal plane measure and ART in the transverse plane distinguished single step responses from multiple steps. When MoS and ART were negative (<0), balance was not secured and additional steps would be required to establish the new base of support for balance recovery. Single-step responses demonstrated greater step length and velocity and when the recovery foot landed, greater centre of mass downward velocity. Single-step strategies also showed greater ankle dorsiflexion, increased knee maximum flexion and more negative work at the ankle and knee. Collectively these findings suggest that single-step responses are more effective in forward balance recovery by directing falling momentum downward to be absorbed as lower limb eccentric work. Copyright © 2015 Elsevier B.V. All rights reserved.

Single-crystalline nanogap electrodes: enhancing the nanowire-breakdown process with a gaseous environment.

PubMed

Suga, Hiroshi; Sumiya, Touru; Furuta, Shigeo; Ueki, Ryuichi; Miyazawa, Yosuke; Nishijima, Takuya; Fujita, Jun-ichi; Tsukagoshi, Kazuhito; Shimizu, Tetsuo; Naitoh, Yasuhisa

2012-10-24

A method for fabricating single-crystalline nanogaps on Si substrates was developed. Polycrystalline Pt nanowires on Si substrates were broken down by current flow under various gaseous environments. The crystal structure of the nanogap electrode was evaluated using scanning electron microscopy and transmission electron microscopy. Nanogap electrodes sandwiched between Pt-large-crystal-grains were obtained by the breakdown of the wire in an O(2) or H(2) atmosphere. These nanogap electrodes show intense spots in the electron diffraction pattern. The diffraction pattern corresponds to Pt (111), indicating that single-crystal grains are grown by the electrical wire breakdown process in an O(2) or H(2) atmosphere. The Pt wires that have (111)-texture and coherent boundaries can be considered ideal as interconnectors for single molecular electronics. The simple method for fabrication of a single-crystalline nanogap is one of the first steps toward standard nanogap electrodes for single molecular instruments and opens the door to future research on physical phenomena in nanospaces.

Single-step controlled-NOT logic from any exchange interaction

NASA Astrophysics Data System (ADS)

Galiautdinov, Andrei

2007-11-01

A self-contained approach to studying the unitary evolution of coupled qubits is introduced, capable of addressing a variety of physical systems described by exchange Hamiltonians containing Rabi terms. The method automatically determines both the Weyl chamber steering trajectory and the accompanying local rotations. Particular attention is paid to the case of anisotropic exchange with tracking controls, which is solved analytically. It is shown that, if computational subspace is well isolated, any exchange interaction can always generate high fidelity, single-step controlled-NOT (CNOT) logic, provided that both qubits can be individually manipulated. The results are then applied to superconducting qubit architectures, for which several CNOT gate implementations are identified. The paper concludes with consideration of two CNOT gate designs having high efficiency and operating with no significant leakage to higher-lying noncomputational states.

Separation of Be and Al for AMS using single-step column chromatography

NASA Astrophysics Data System (ADS)

Binnie, Steven A.; Dunai, Tibor J.; Voronina, Elena; Goral, Tomasz; Heinze, Stefan; Dewald, Alfred

2015-10-01

With the aim of simplifying AMS target preparation procedures for TCN measurements we tested a new extraction chromatography approach which couples an anion exchange resin (WBEC) to a chelating resin (Beryllium resin) to separate Be and Al from dissolved quartz samples. Results show that WBEC-Beryllium resin stacks can be used to provide high purity Be and Al separations using a combination of hydrochloric/oxalic and nitric acid elutions. 10Be and 26Al concentrations from quartz samples prepared using more standard procedures are compared with results from replicate samples prepared using the coupled WBEC-Beryllium resin approach and show good agreement. The new column procedure is performed in a single step, reducing sample preparation times relative to more traditional methods of TCN target production.

Comparison of the phenolic composition of fruit juices by single step gradient HPLC analysis of multiple components versus multiple chromatographic runs optimised for individual families.

PubMed

Bremner, P D; Blacklock, C J; Paganga, G; Mullen, W; Rice-Evans, C A; Crozier, A

2000-06-01

After minimal sample preparation, two different HPLC methodologies, one based on a single gradient reversed-phase HPLC step, the other on multiple HPLC runs each optimised for specific components, were used to investigate the composition of flavonoids and phenolic acids in apple and tomato juices. The principal components in apple juice were identified as chlorogenic acid, phloridzin, caffeic acid and p-coumaric acid. Tomato juice was found to contain chlorogenic acid, caffeic acid, p-coumaric acid, naringenin and rutin. The quantitative estimates of the levels of these compounds, obtained with the two HPLC procedures, were very similar, demonstrating that either method can be used to analyse accurately the phenolic components of apple and tomato juices. Chlorogenic acid in tomato juice was the only component not fully resolved in the single run study and the multiple run analysis prior to enzyme treatment. The single run system of analysis is recommended for the initial investigation of plant phenolics and the multiple run approach for analyses where chromatographic resolution requires improvement.

Method for fabricating silicon cells

DOEpatents

Ruby, Douglas S.; Basore, Paul A.; Schubert, W. Kent

1998-08-11

A process for making high-efficiency solar cells. This is accomplished by forming a diffusion junction and a passivating oxide layer in a single high-temperature process step. The invention includes the class of solar cells made using this process, including high-efficiency solar cells made using Czochralski-grown silicon.

Bioaugmentation with Vaults: Novel In Situ Remediation Strategy for Transformation of Perfluoroalkyl Compounds

DTIC Science & Technology

2016-01-01

degradation of poly- and perfluoroalkyl compounds (PFCs), and potentially other water contaminants, without the need for repeated bioaugmentation with...active cultures or stimulation with nutrients. We designed a single-step method for encapsulating lignin peroxidases (LiP), manganese peroxidases (MnP

Comparison of genomic-enhanced EPD systems using an external phenotypic database

USDA-ARS?s Scientific Manuscript database

The American Angus Association (AAA) is currently evaluating two methods to incorporate genomic information into their genetic evaluation program: 1) multi-trait incorporation of an externally produced molecular breeding value as an indicator trait (MT) and 2) single-step evaluation with an unweight...

Iterative combination of national phenotype, genotype, pedigree, and foreign information

USDA-ARS?s Scientific Manuscript database

Single step methods can combine all sources of information into accurate rankings for animals with and without genotypes. Equations that require inverting the genomic relationship matrix G work well with limited numbers of animals, but equivalent models without inversion are needed as numbers increa...

Method for conversion of carbohydrate polymers to value-added chemical products

DOEpatents

Zhang, Zongchao C [Norwood, NJ; Brown, Heather M [Kennewick, WA; Su, Yu [Richland, WA

2012-02-07

Methods are described for conversion of carbohydrate polymers in ionic liquids, including cellulose, that yield value-added chemicals including, e.g., glucose and 5-hydroxylmethylfurfural (HMF) at temperatures below 120.degree. C. Catalyst compositions that include various mixed metal halides are described that are selective for specified products with yields, e.g., of up to about 56% in a single step process.

Interference lithography for optical devices and coatings

NASA Astrophysics Data System (ADS)

Juhl, Abigail Therese

Interference lithography can create large-area, defect-free nanostructures with unique optical properties. In this thesis, interference lithography will be utilized to create photonic crystals for functional devices or coatings. For instance, typical lithographic processing techniques were used to create 1, 2 and 3 dimensional photonic crystals in SU8 photoresist. These structures were in-filled with birefringent liquid crystal to make active devices, and the orientation of the liquid crystal directors within the SU8 matrix was studied. Most of this thesis will be focused on utilizing polymerization induced phase separation as a single-step method for fabrication by interference lithography. For example, layered polymer/nanoparticle composites have been created through the one-step two-beam interference lithographic exposure of a dispersion of 25 and 50 nm silica particles within a photopolymerizable mixture at a wavelength of 532 nm. In the areas of constructive interference, the monomer begins to polymerize via a free-radical process and concurrently the nanoparticles move into the regions of destructive interference. The holographic exposure of the particles within the monomer resin offers a single-step method to anisotropically structure the nanoconstituents within a composite. A one-step holographic exposure was also used to fabricate self-healing coatings that use water from the environment to catalyze polymerization. Polymerization induced phase separation was used to sequester an isocyanate monomer within an acrylate matrix. Due to the periodic modulation of the index of refraction between the monomer and polymer, the coating can reflect a desired wavelength, allowing for tunable coloration. When the coating is scratched, polymerization of the liquid isocyanate is catalyzed by moisture in air; if the indices of the two polymers are matched, the coatings turn transparent after healing. Interference lithography offers a method of creating multifunctional self-healing coatings that readout when damage has occurred.

Detection of Listeria spp. using ACTERO listeria enrichment media.

PubMed

Claveau, David; Olishevskyy, Sergiy; Giuffre, Michael; Martinez, Gabriela

2014-01-01

ACTERO Listeria Enrichment Media (ACTERO Listeria) is a selective medium developed for a single-step recovery and enrichment of Listeria spp. from environmental samples. Robustness testing of the ACTERO Listeria medium demonstrated good performance when minor changes were introduced to the incubation temperature and time. All 54 Listeria strains tested, representing the most frequently isolated Listeria species from food (L. monocytogenes, L. ivanovii, L. seeligeri, L. welshimeri, and L. grayi), were successfully enriched in ACTERO Listeria. None of the 30 nontarget strains tested in the exclusivity study was recovered after incubation in ACTERO Listeria. Recovery of Listeria was consistent across three independently produced lots of the ACTERO Listeria, and the prepared medium was stable for 45 days when stored at 4 degrees C in the dark. Matrix studies performed with environmental sponge samples from plastic and stainless steel surfaces demonstrated similar recovery of Listeria spp. in a single-step enrichment using ACTERO Listeria from plastic, and significantly better recovery from stainless steel surfaces when compared to the U.S. Department of Agriculture-Food Safety and Inspection Service reference method. The results of this study prove that ACTERO Listeria Enrichment Media can be effectively used in replacement of the two-step enrichment suggested by the reference method without affecting the recovery of Listeria spp. from environmental samples.

Comment on 'Shang S. 2012. Calculating actual crop evapotranspiration under soil water stress conditions with appropriate numerical methods and time step. Hydrological Processes 26: 3338-3343. DOI: 10.1002/hyp.8405'

NASA Technical Reports Server (NTRS)

Yatheendradas, Soni; Narapusetty, Balachandrudu; Peters-Lidard, Christa; Funk, Christopher; Verdin, James

2014-01-01

A previous study analyzed errors in the numerical calculation of actual crop evapotranspiration (ET(sub a)) under soil water stress. Assuming no irrigation or precipitation, it constructed equations for ET(sub a) over limited soil-water ranges in a root zone drying out due to evapotranspiration. It then used a single crop-soil composite to provide recommendations about the appropriate usage of numerical methods under different values of the time step and the maximum crop evapotranspiration (ET(sub c)). This comment reformulates those ET(sub a) equations for applicability over the full range of soil water values, revealing a dependence of the relative error in numerical ET(sub a) on the initial soil water that was not seen in the previous study. It is shown that the recommendations based on a single crop-soil composite can be invalid for other crop-soil composites. Finally, a consideration of the numerical error in the time-cumulative value of ET(sub a) is discussed besides the existing consideration of that error over individual time steps as done in the previous study. This cumulative ET(sub a) is more relevant to the final crop yield.

Simplified Large-Scale Refolding, Purification, and Characterization of Recombinant Human Granulocyte-Colony Stimulating Factor in Escherichia coli

PubMed Central

Kim, Chang Kyu; Lee, Chi Ho; Lee, Seung-Bae; Oh, Jae-Wook

2013-01-01

Granulocyte-colony stimulating factor (G-CSF) is a pleiotropic cytokine that stimulates the development of committed hematopoietic progenitor cells and enhances the functional activity of mature cells. Here, we report a simplified method for fed-batch culture as well as the purification of recombinant human (rh) G-CSF. The new system for rhG-CSF purification was performed using not only temperature shift strategy without isopropyl-l-thio-β-d-galactoside (IPTG) induction but also the purification method by a single step of prep-HPLC after the pH precipitation of the refolded samples. Through these processes, the final cell density and overall yield of homogenous rhG-CSF were obtained 42.8 g as dry cell weights, 1.75 g as purified active proteins, from 1 L culture broth, respectively. The purity of rhG-CSF was finally 99% since the isoforms of rhG-CSF could be separated through the prep-HPLC step. The result of biological activity indicated that purified rhG-CSF has a similar profile to the World Health Organization (WHO) 2nd International Standard for G-CSF. Taken together, our results demonstrate that the simple purification through a single step of prep-HPLC may be valuable for the industrial-scale production of biologically active proteins. PMID:24224041

Computer-Aided Design of RNA Origami Structures.

PubMed

Sparvath, Steffen L; Geary, Cody W; Andersen, Ebbe S

2017-01-01

RNA nanostructures can be used as scaffolds to organize, combine, and control molecular functionalities, with great potential for applications in nanomedicine and synthetic biology. The single-stranded RNA origami method allows RNA nanostructures to be folded as they are transcribed by the RNA polymerase. RNA origami structures provide a stable framework that can be decorated with functional RNA elements such as riboswitches, ribozymes, interaction sites, and aptamers for binding small molecules or protein targets. The rich library of RNA structural and functional elements combined with the possibility to attach proteins through aptamer-based binding creates virtually limitless possibilities for constructing advanced RNA-based nanodevices.In this chapter we provide a detailed protocol for the single-stranded RNA origami design method using a simple 2-helix tall structure as an example. The first step involves 3D modeling of a double-crossover between two RNA double helices, followed by decoration with tertiary motifs. The second step deals with the construction of a 2D blueprint describing the secondary structure and sequence constraints that serves as the input for computer programs. In the third step, computer programs are used to design RNA sequences that are compatible with the structure, and the resulting outputs are evaluated and converted into DNA sequences to order.

[Current strategy in PCI for CTO].

PubMed

Asakura, Yasushi

2011-02-01

Recently, CTO PCI has come into wide use all over the world and it has been standardized. The 1st step is an antegrade approach using single wire. The 2nd strategy would be parallel wire technique. And the next would be a retrograde approach. In this method, retrograde wiring with Corsair is done at first. If it is successful, externalization is established using 300 cm wire, and this system is able to provide strong back-up support. If it fails, reverse CART technique is the next step. IVUS guided wiring is a last resort. The 2nd wire is manipulated with IVUS guidance. Now, initial success rate is more than 90% with these methods.

One-step production of multiple emulsions: microfluidic, polymer-stabilized and particle-stabilized approaches.

PubMed

Clegg, Paul S; Tavacoli, Joe W; Wilde, Pete J

2016-01-28

Multiple emulsions have great potential for application in food science as a means to reduce fat content or for controlled encapsulation and release of actives. However, neither production nor stability is straightforward. Typically, multiple emulsions are prepared via two emulsification steps and a variety of approaches have been deployed to give long-term stability. It is well known that multiple emulsions can be prepared in a single step by harnessing emulsion inversion, although the resulting emulsions are usually short lived. Recently, several contrasting methods have been demonstrated which give rise to stable multiple emulsions via one-step production processes. Here we review the current state of microfluidic, polymer-stabilized and particle-stabilized approaches; these rely on phase separation, the role of electrolyte and the trapping of solvent with particles respectively.

A one-step method to fabricate PLLA scaffolds with deposition of bioactive hydroxyapatite and collagen using ice-based microporogens

PubMed Central

Li, Jiashen; Chen, Yun; Mak, Arthur F.T.; Tuan, Rocky S.; Li, Lin; Li, Yi

2010-01-01

Porous poly(L-lactic acid) (PLLA) scaffolds with bioactive coatings were prepared by a novel one-step method. In this process, ice-based microporogens containing bioactive molecules, such as hydroxyapatite (HA) and collagen, served as both porogens to form the porous structure and vehicles to transfer the bioactive molecules to the inside of PLLA scaffolds in a single step. Based on scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDX), X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR) analysis, the bioactive components were found to be transferred successfully from the porogens to PLLA scaffolds evenly. Osteoblast cells were used to evaluate the cellular behaviors of the composite scaffolds. After 8 days culturing, MTT assay and alkaline phosphatase (ALP) activity results suggested that HA/collagen could improve the interactions between osteoblast cells and the polymeric scaffold. PMID:20004261

A framework for simultaneous aerodynamic design optimization in the presence of chaos

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

Günther, Stefanie, E-mail: stefanie.guenther@scicomp.uni-kl.de; Gauger, Nicolas R.; Wang, Qiqi

Integrating existing solvers for unsteady partial differential equations into a simultaneous optimization method is challenging due to the forward-in-time information propagation of classical time-stepping methods. This paper applies the simultaneous single-step one-shot optimization method to a reformulated unsteady constraint that allows for both forward- and backward-in-time information propagation. Especially in the presence of chaotic and turbulent flow, solving the initial value problem simultaneously with the optimization problem often scales poorly with the time domain length. The new formulation relaxes the initial condition and instead solves a least squares problem for the discrete partial differential equations. This enables efficient one-shot optimizationmore » that is independent of the time domain length, even in the presence of chaos.« less

A robust approach for a filter-based monocular simultaneous localization and mapping (SLAM) system.

PubMed

Munguía, Rodrigo; Castillo-Toledo, Bernardino; Grau, Antoni

2013-07-03

Simultaneous localization and mapping (SLAM) is an important problem to solve in robotics theory in order to build truly autonomous mobile robots. This work presents a novel method for implementing a SLAM system based on a single camera sensor. The SLAM with a single camera, or monocular SLAM, is probably one of the most complex SLAM variants. In this case, a single camera, which is freely moving through its environment, represents the sole sensor input to the system. The sensors have a large impact on the algorithm used for SLAM. Cameras are used more frequently, because they provide a lot of information and are well adapted for embedded systems: they are light, cheap and power-saving. Nevertheless, and unlike range sensors, which provide range and angular information, a camera is a projective sensor providing only angular measurements of image features. Therefore, depth information (range) cannot be obtained in a single step. In this case, special techniques for feature system-initialization are needed in order to enable the use of angular sensors (as cameras) in SLAM systems. The main contribution of this work is to present a novel and robust scheme for incorporating and measuring visual features in filtering-based monocular SLAM systems. The proposed method is based in a two-step technique, which is intended to exploit all the information available in angular measurements. Unlike previous schemes, the values of parameters used by the initialization technique are derived directly from the sensor characteristics, thus simplifying the tuning of the system. The experimental results show that the proposed method surpasses the performance of previous schemes.

A simple and rapid method for high-resolution visualization of single-ion tracks

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

Omichi, Masaaki; Center for Collaborative Research, Anan National College of Technology, Anan, Tokushima 774-0017; Choi, Wookjin

2014-11-15

Prompt determination of spatial points of single-ion tracks plays a key role in high-energy particle induced-cancer therapy and gene/plant mutations. In this study, a simple method for the high-resolution visualization of single-ion tracks without etching was developed through the use of polyacrylic acid (PAA)-N, N’-methylene bisacrylamide (MBAAm) blend films. One of the steps of the proposed method includes exposure of the irradiated films to water vapor for several minutes. Water vapor was found to promote the cross-linking reaction of PAA and MBAAm to form a bulky cross-linked structure; the ion-track scars were detectable at a nanometer scale by atomic forcemore » microscopy. This study demonstrated that each scar is easily distinguishable, and the amount of generated radicals of the ion tracks can be estimated by measuring the height of the scars, even in highly dense ion tracks. This method is suitable for the visualization of the penumbra region in a single-ion track with a high spatial resolution of 50 nm, which is sufficiently small to confirm that a single ion hits a cell nucleus with a size ranging between 5 and 20 μm.« less

A short review of variants calling for single-cell-sequencing data with applications.

PubMed

Wei, Zhuohui; Shu, Chang; Zhang, Changsheng; Huang, Jingying; Cai, Hongmin

2017-11-01

The field of single-cell sequencing is fleetly expanding, and many techniques have been developed in the past decade. With this technology, biologists can study not only the heterogeneity between two adjacent cells in the same tissue or organ, but also the evolutionary relationships and degenerative processes in a single cell. Calling variants is the main purpose in analyzing single cell sequencing (SCS) data. Currently, some popular methods used for bulk-cell-sequencing data analysis are tailored directly to be applied in dealing with SCS data. However, SCS requires an extra step of genome amplification to accumulate enough quantity for satisfying sequencing needs. The amplification yields large biases and thus raises challenge for using the bulk-cell-sequencing methods. In order to provide guidance for the development of specialized analyzed methods as well as using currently developed tools for SNS, this paper aims to bridge the gap. In this paper, we firstly introduced two popular genome amplification methods and compared their capabilities. Then we introduced a few popular models for calling single-nucleotide polymorphisms and copy-number variations. Finally, break-through applications of SNS were summarized to demonstrate its potential in researching cell evolution. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evaluation of the occlusal contact of crowns fabricated with the bite impression method.

PubMed

Makino, Sachi; Okada, Daizo; Shin, Chiharu; Ogura, Reiko; Ikeda, Masaomi; Miura, Hiroyuki

2013-09-30

In prosthodontic treatment, reconstruction of a proper occlusal contact relationship is very important as well as reconstruction of a proper interproximal relationship and marginal fitness. Unfortunately, occlusal relationships are sometimes lost in the process of occlusal adjustment of crowns. The purpose of this study was to compare the occlusal contacts of single crown fabricated by two different types of impression techniques. Nine subjects, whose molars required treatment with crown restoration, were enrolled in this study. Full cast crowns were fabricated using two types of impression techniques: the conventional impression method (CIM) and the bite impression method (BIM). The occlusal contacts of crowns were precisely evaluated at the following stages: after occlusal adjustment on the articulator (Step 0), before occlusal adjustment in the mouth (Step 1), after occlusal adjustment at the intercuspal position (Step 2), and after occlusal adjustment during lateral and protrusive excursions (Step 3). The number of occlusal contacts of the crowns on the functional cusps fabricated with BIM was significantly greater than that with CIM after occlusal adjustment. For this reason, the crowns fabricated with BIM might have a more functionally desirable occlusal surface compared to the crowns fabricated with CIM.

Documentation of spreadsheets for the analysis of aquifer-test and slug-test data

USGS Publications Warehouse

Halford, Keith J.; Kuniansky, Eve L.

2002-01-01

Several spreadsheets have been developed for the analysis of aquifer-test and slug-test data. Each spreadsheet incorporates analytical solution(s) of the partial differential equation for ground-water flow to a well for a specific type of condition or aquifer. The derivations of the analytical solutions were previously published. Thus, this report abbreviates the theoretical discussion, but includes practical information about each method and the important assumptions for the applications of each method. These spreadsheets were written in Microsoft Excel 9.0 (use of trade names does not constitute endorsement by the USGS). Storage properties should not be estimated with many of the spreadsheets because most are for analyzing single-well tests. Estimation of storage properties from single-well tests is generally discouraged because single-well tests are affected by wellbore storage and by well construction. These non-ideal effects frequently cause estimates of storage to be erroneous by orders of magnitude. Additionally, single-well tests are not sensitive to aquifer-storage properties. Single-well tests include all slug tests (Bouwer and Rice Method, Cooper, Bredehoeft, Papadopulos Method, and van der Kamp Method), the Cooper-Jacob straight-line Method, Theis recovery-data analysis, Jacob-Lohman method for flowing wells in a confined aquifer, and the step-drawdown test. Multi-well test spreadsheets included in this report are; Hantush-Jacob Leaky Aquifer Method and Distance-Drawdown Methods. The distance-drawdown method is an equilibrium or steady-state method, thus storage cannot be estimated.

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

McDonald, A. D.; Jones, B. J. P.; Nygren, D. R.

A new method to tag the barium daughter in the double beta decay ofmore » $$^{136}$$Xe is reported. Using the technique of single molecule fluorescent imaging (SMFI), individual barium dication (Ba$$^{++}$$) resolution at a transparent scanning surface has been demonstrated. A single-step photo-bleach confirms the single ion interpretation. Individual ions are localized with super-resolution ($$\\sim$$2~nm), and detected with a statistical significance of 12.9~$$\\sigma$$ over backgrounds. This lays the foundation for a new and potentially background-free neutrinoless double beta decay technology, based on SMFI coupled to high pressure xenon gas time projection chambers.« less

Highly Multiplexed, Single Cell Transcriptomic Analysis of T-Cells by Microfluidic PCR.

PubMed

Dominguez, Maria; Roederer, Mario; Chattopadhyay, Pratip K

2017-01-01

Recently, technologies have been developed to measure expression of 96 (or more) mRNA transcripts at once from a single cell. Here we describe methods and important considerations for use of Fluidigm's BioMark platform for multiplexed single cell gene expression. We describe how to qualify primer/probes, select genes to examine in 96-parameter panels, perform the reverse transcription/cDNA synthesis step, and operate the instrument. In addition, we describe data analysis considerations. This technology has enormous value for characterizing the heterogeneity of T-cells, thereby providing a useful tool for immune monitoring.

Phase reconstruction using compressive two-step parallel phase-shifting digital holography

NASA Astrophysics Data System (ADS)

Ramachandran, Prakash; Alex, Zachariah C.; Nelleri, Anith

2018-04-01

The linear relationship between the sample complex object wave and its approximated complex Fresnel field obtained using single shot parallel phase-shifting digital holograms (PPSDH) is used in compressive sensing framework and an accurate phase reconstruction is demonstrated. It is shown that the accuracy of phase reconstruction of this method is better than that of compressive sensing adapted single exposure inline holography (SEOL) method. It is derived that the measurement model of PPSDH method retains both the real and imaginary parts of the Fresnel field but with an approximation noise and the measurement model of SEOL retains only the real part exactly equal to the real part of the complex Fresnel field and its imaginary part is completely not available. Numerical simulation is performed for CS adapted PPSDH and CS adapted SEOL and it is demonstrated that the phase reconstruction is accurate for CS adapted PPSDH and can be used for single shot digital holographic reconstruction.

A Novel Method of Fabricating a Well-Faceted Large-Crystal Diamond Through MPCVD

NASA Astrophysics Data System (ADS)

Man, Weidong; Weng, Jun; Wu, Yuqiong; Chen, Peng; Yu, Xuechao; Wang, Jianhua

2009-12-01

A novel method was developed to deposit a large crystal diamond with good facets up to 1000 μm on a tungsten substrate using a microwave plasma enhanced chemical vapor deposition (MPCVD). This method consists of two steps, namely single-crystal nucleation and growth. Prior to the fabrication of the well-faceted, large crystal diamond, an investigation was made into the nucleation and growth of the diamond which were affected by the O2 concentration and substrate temperature. Deposited diamond crystals were characterized by scanning electron microscopy and micro-Raman spectroscopy. The results showed that the conditions of single-crystal nucleation were appropriate when the ratio of H2/CH4/O2 was about 200/7.0/2.0, while the substrate temperature Ts of 1000°C to 1050°C was the appropriate range for single-crystal diamond growth. Under the optimum parameters, a well-faceted large crystal diamond was obtained.

Single Day Construction of Multigene Circuits with 3G Assembly.

PubMed

Halleran, Andrew D; Swaminathan, Anandh; Murray, Richard M

2018-05-18

The ability to rapidly design, build, and test prototypes is of key importance to every engineering discipline. DNA assembly often serves as a rate limiting step of the prototyping cycle for synthetic biology. Recently developed DNA assembly methods such as isothermal assembly and type IIS restriction enzyme systems take different approaches to accelerate DNA construction. We introduce a hybrid method, Golden Gate-Gibson (3G), that takes advantage of modular part libraries introduced by type IIS restriction enzyme systems and isothermal assembly's ability to build large DNA constructs in single pot reactions. Our method is highly efficient and rapid, facilitating construction of entire multigene circuits in a single day. Additionally, 3G allows generation of variant libraries enabling efficient screening of different possible circuit constructions. We characterize the efficiency and accuracy of 3G assembly for various construct sizes, and demonstrate 3G by characterizing variants of an inducible cell-lysis circuit.

Realisation of all 16 Boolean logic functions in a single magnetoresistance memory cell

NASA Astrophysics Data System (ADS)

Gao, Shuang; Yang, Guang; Cui, Bin; Wang, Shouguo; Zeng, Fei; Song, Cheng; Pan, Feng

2016-06-01

Stateful logic circuits based on next-generation nonvolatile memories, such as magnetoresistance random access memory (MRAM), promise to break the long-standing von Neumann bottleneck in state-of-the-art data processing devices. For the successful commercialisation of stateful logic circuits, a critical step is realizing the best use of a single memory cell to perform logic functions. In this work, we propose a method for implementing all 16 Boolean logic functions in a single MRAM cell, namely a magnetoresistance (MR) unit. Based on our experimental results, we conclude that this method is applicable to any MR unit with a double-hump-like hysteresis loop, especially pseudo-spin-valve magnetic tunnel junctions with a high MR ratio. Moreover, after simply reversing the correspondence between voltage signals and output logic values, this method could also be applicable to any MR unit with a double-pit-like hysteresis loop. These results may provide a helpful solution for the final commercialisation of MRAM-based stateful logic circuits in the near future.Stateful logic circuits based on next-generation nonvolatile memories, such as magnetoresistance random access memory (MRAM), promise to break the long-standing von Neumann bottleneck in state-of-the-art data processing devices. For the successful commercialisation of stateful logic circuits, a critical step is realizing the best use of a single memory cell to perform logic functions. In this work, we propose a method for implementing all 16 Boolean logic functions in a single MRAM cell, namely a magnetoresistance (MR) unit. Based on our experimental results, we conclude that this method is applicable to any MR unit with a double-hump-like hysteresis loop, especially pseudo-spin-valve magnetic tunnel junctions with a high MR ratio. Moreover, after simply reversing the correspondence between voltage signals and output logic values, this method could also be applicable to any MR unit with a double-pit-like hysteresis loop. These results may provide a helpful solution for the final commercialisation of MRAM-based stateful logic circuits in the near future. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr03169b

Method for fabricating silicon cells

DOEpatents

Ruby, D.S.; Basore, P.A.; Schubert, W.K.

1998-08-11

A process is described for making high-efficiency solar cells. This is accomplished by forming a diffusion junction and a passivating oxide layer in a single high-temperature process step. The invention includes the class of solar cells made using this process, including high-efficiency solar cells made using Czochralski-grown silicon. 9 figs.

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

Damian, Luminita, E-mail: luminitadamian@microcal.eu.com; Universite de Toulouse, UPS, IPBS, F-31077 Toulouse; IUB, School of Engineering and Science, D-28727 Bremen

Is single-strand DNA translatable? Since the 60s, the question still remains whether or not DNA could be directly translated into protein. Some discrepancies in the results were reported about functional translation of single-strand DNA but all results converged on a similar behavior of RNA and ssDNA in the initiation step. Isothermal Titration Calorimetry method was used to determine thermodynamic constants of interaction between single-strand DNA and S30 extract of Escherichia coli. Our results showed that the binding was not affected by the nature of the template tested and the dissociation constants were in the same range when ssDNA (K{sub d}more » = 3.62 {+-} 2.1 x 10{sup -8} M) or the RNA corresponding sequence (K{sub d} = 2.7 {+-} 0.82 x 10{sup -8} M) bearing SD/ATG sequences were used. The binding specificity was confirmed by antibiotic interferences which block the initiation complex formation. These results suggest that the limiting step in translation of ssDNA is the elongation process.« less

Single-step ambient-air synthesis of graphene from renewable precursors as electrochemical genosensor.

PubMed

Seo, Dong Han; Pineda, Shafique; Fang, Jinghua; Gozukara, Yesim; Yick, Samuel; Bendavid, Avi; Lam, Simon Kwai Hung; Murdock, Adrian T; Murphy, Anthony B; Han, Zhao Jun; Ostrikov, Kostya Ken

2017-01-30

Thermal chemical vapour deposition techniques for graphene fabrication, while promising, are thus far limited by resource-consuming and energy-intensive principles. In particular, purified gases and extensive vacuum processing are necessary for creating a highly controlled environment, isolated from ambient air, to enable the growth of graphene films. Here we exploit the ambient-air environment to enable the growth of graphene films, without the need for compressed gases. A renewable natural precursor, soybean oil, is transformed into continuous graphene films, composed of single-to-few layers, in a single step. The enabling parameters for controlled synthesis and tailored properties of the graphene film are discussed, and a mechanism for the ambient-air growth is proposed. Furthermore, the functionality of the graphene is demonstrated through direct utilization as an electrode to realize an effective electrochemical genosensor. Our method is applicable to other types of renewable precursors and may open a new avenue for low-cost synthesis of graphene films.

Single-step ambient-air synthesis of graphene from renewable precursors as electrochemical genosensor

NASA Astrophysics Data System (ADS)

Seo, Dong Han; Pineda, Shafique; Fang, Jinghua; Gozukara, Yesim; Yick, Samuel; Bendavid, Avi; Lam, Simon Kwai Hung; Murdock, Adrian T.; Murphy, Anthony B.; Han, Zhao Jun; Ostrikov, Kostya (Ken)

2017-01-01

Thermal chemical vapour deposition techniques for graphene fabrication, while promising, are thus far limited by resource-consuming and energy-intensive principles. In particular, purified gases and extensive vacuum processing are necessary for creating a highly controlled environment, isolated from ambient air, to enable the growth of graphene films. Here we exploit the ambient-air environment to enable the growth of graphene films, without the need for compressed gases. A renewable natural precursor, soybean oil, is transformed into continuous graphene films, composed of single-to-few layers, in a single step. The enabling parameters for controlled synthesis and tailored properties of the graphene film are discussed, and a mechanism for the ambient-air growth is proposed. Furthermore, the functionality of the graphene is demonstrated through direct utilization as an electrode to realize an effective electrochemical genosensor. Our method is applicable to other types of renewable precursors and may open a new avenue for low-cost synthesis of graphene films.

General linear methods and friends: Toward efficient solutions of multiphysics problems

NASA Astrophysics Data System (ADS)

Sandu, Adrian

2017-07-01

Time dependent multiphysics partial differential equations are of great practical importance as they model diverse phenomena that appear in mechanical and chemical engineering, aeronautics, astrophysics, meteorology and oceanography, financial modeling, environmental sciences, etc. There is no single best time discretization for the complex multiphysics systems of practical interest. We discuss "multimethod" approaches that combine different time steps and discretizations using the rigourous frameworks provided by Partitioned General Linear Methods and Generalize-structure Additive Runge Kutta Methods..

Single step modified ink staining for Tzanck test: quick detection of herpetic giant cells in Tzanck smear.

PubMed

Mizutani, Hitoshi; Akeda, Tomoko; Yamanaka, Kei-Ichi; Isoda, Kenichi; Gabazza, Esteban C

2012-02-01

Tzanck test has been recently re-evaluated as a method for the diagnosis of herpes virus infection. Giemsa staining for the Tzanck test is time-consuming and laborious. There is a need to develop simple and quick staining methods for bedside diagnosis of this disease. We report a single step and quick method for staining herpes giant cells in Tzanck smears using routinely available inks and physiological saline. A keratinocyte cell line (HaCaT) was cultured on a slide glass and stained with various commercially available blue, blue-black and black inks serially diluted with physiological saline. Clinical smear samples from herpes lesions were also stained with these solutions without specific pretreatment. The nuclei of HaCaT were clearly stained showing high contrast with the cytoplasm using 5% Parker-Quink blue-black ink saline solution. Concentration of ink solution higher or lower than 5% resulted in less contrast. Blue or black inks or other manufacturers' inks can also be used, but staining of the cultured keratinocytes was less clear. Smear of clinical samples from herpes lesions were also stained with 5% ink solution. The nuclei of the multinucleated giant cells were clearly stained, and the sample could be immediately used for microscopic examination. One step staining of Tzanck smear using this diluted ink solution is an inexpensive and a convenient bedside diagnostic tool for the dermatologist. © 2011 Japanese Dermatological Association.

Identification of microRNA-mRNA modules using microarray data.

PubMed

Jayaswal, Vivek; Lutherborrow, Mark; Ma, David D F; Yang, Yee H

2011-03-06

MicroRNAs (miRNAs) are post-transcriptional regulators of mRNA expression and are involved in numerous cellular processes. Consequently, miRNAs are an important component of gene regulatory networks and an improved understanding of miRNAs will further our knowledge of these networks. There is a many-to-many relationship between miRNAs and mRNAs because a single miRNA targets multiple mRNAs and a single mRNA is targeted by multiple miRNAs. However, most of the current methods for the identification of regulatory miRNAs and their target mRNAs ignore this biological observation and focus on miRNA-mRNA pairs. We propose a two-step method for the identification of many-to-many relationships between miRNAs and mRNAs. In the first step, we obtain miRNA and mRNA clusters using a combination of miRNA-target mRNA prediction algorithms and microarray expression data. In the second step, we determine the associations between miRNA clusters and mRNA clusters based on changes in miRNA and mRNA expression profiles. We consider the miRNA-mRNA clusters with statistically significant associations to be potentially regulatory and, therefore, of biological interest. Our method reduces the interactions between several hundred miRNAs and several thousand mRNAs to a few miRNA-mRNA groups, thereby facilitating a more meaningful biological analysis and a more targeted experimental validation.

A simple, fast, and inexpensive CTAB-PVP-silica based method for genomic DNA isolation from single, small insect larvae and pupae.

PubMed

Huanca-Mamani, W; Rivera-Cabello, D; Maita-Maita, J

2015-07-17

In this study, we report a modified CTAB-PVP method combined with silicon dioxide (silica) treatment for the extraction of high quality genomic DNA from a single larva or pupa. This method efficiently obtains DNA from small specimens, which is difficult and challenging because of the small amount of starting tissue. Maceration with liquid nitrogen, phenol treatment, and the ethanol precipitation step are eliminated using this methodology. The A260/A280 absorbance ratios of the isolated DNA were approximately 1.8, suggesting that the DNA is pure and can be used for further molecular analysis. The quality of the isolated DNA permits molecular applications and represents a fast, cheap, and effective alternative method for laboratories with low budgets.

Laser-assisted fabrication of single-layer flexible touch sensor

PubMed Central

Son, Seokwoo; Park, Jong Eun; Lee, Joohyung; Yang, Minyang; Kang, Bongchul

2016-01-01

Single-layer flexible touch sensor that is designed for the indium-tin-oxide (ITO)-free, bendable, durable, multi-sensible, and single layer transparent touch sensor was developed via a low-cost and one-step laser-induced fabrication technology. To this end, an entirely novel approach involving material, device structure, and even fabrication method was adopted. Conventional metal oxides based multilayer touch structure was substituted by the single layer structure composed of integrated silver wire networks of sensors and bezel interconnections. This structure is concurrently fabricated on a glass substitutive plastic film via the laser-induced fabrication method using the low-cost organometallic/nanoparticle hybrid complex. In addition, this study addresses practical solutions to heterochromia and interference problem with a color display unit. As a result, a practical touch sensor is successfully demonstrated through resolving the heterochromia and interference problems with color display unit. This study could provide the breakthrough for early realization of wearable device. PMID:27703204

Two-step relaxation mode analysis with multiple evolution times applied to all-atom molecular dynamics protein simulation.

PubMed

Karasawa, N; Mitsutake, A; Takano, H

2017-12-01

Proteins implement their functionalities when folded into specific three-dimensional structures, and their functions are related to the protein structures and dynamics. Previously, we applied a relaxation mode analysis (RMA) method to protein systems; this method approximately estimates the slow relaxation modes and times via simulation and enables investigation of the dynamic properties underlying the protein structural fluctuations. Recently, two-step RMA with multiple evolution times has been proposed and applied to a slightly complex homopolymer system, i.e., a single [n]polycatenane. This method can be applied to more complex heteropolymer systems, i.e., protein systems, to estimate the relaxation modes and times more accurately. In two-step RMA, we first perform RMA and obtain rough estimates of the relaxation modes and times. Then, we apply RMA with multiple evolution times to a small number of the slowest relaxation modes obtained in the previous calculation. Herein, we apply this method to the results of principal component analysis (PCA). First, PCA is applied to a 2-μs molecular dynamics simulation of hen egg-white lysozyme in aqueous solution. Then, the two-step RMA method with multiple evolution times is applied to the obtained principal components. The slow relaxation modes and corresponding relaxation times for the principal components are much improved by the second RMA.

Two-step relaxation mode analysis with multiple evolution times applied to all-atom molecular dynamics protein simulation

NASA Astrophysics Data System (ADS)

Karasawa, N.; Mitsutake, A.; Takano, H.

2017-12-01

Proteins implement their functionalities when folded into specific three-dimensional structures, and their functions are related to the protein structures and dynamics. Previously, we applied a relaxation mode analysis (RMA) method to protein systems; this method approximately estimates the slow relaxation modes and times via simulation and enables investigation of the dynamic properties underlying the protein structural fluctuations. Recently, two-step RMA with multiple evolution times has been proposed and applied to a slightly complex homopolymer system, i.e., a single [n ] polycatenane. This method can be applied to more complex heteropolymer systems, i.e., protein systems, to estimate the relaxation modes and times more accurately. In two-step RMA, we first perform RMA and obtain rough estimates of the relaxation modes and times. Then, we apply RMA with multiple evolution times to a small number of the slowest relaxation modes obtained in the previous calculation. Herein, we apply this method to the results of principal component analysis (PCA). First, PCA is applied to a 2-μ s molecular dynamics simulation of hen egg-white lysozyme in aqueous solution. Then, the two-step RMA method with multiple evolution times is applied to the obtained principal components. The slow relaxation modes and corresponding relaxation times for the principal components are much improved by the second RMA.

Enhanced Single-Step Bioproduction of the Simvastatin Precursor Monacolin J in an Industrial Strain of Aspergillus terreus by Employing the Evolved Lovastatin Hydrolase.

PubMed

Liang, Bo; Huang, Xuenian; Teng, Yun; Liang, Yajing; Yang, Yong; Zheng, Linghui; Lu, Xuefeng

2018-06-01

Biosynthesis of simvastatin, the active pharmaceutical ingredient of cholesterol-lowering drug Zocor, has drawn increasing global attention in recent years. Although single-step in vivo production of monacolin J, the intermediate biosynthetic precursor of simvastatin, has been realized by utilizing lovastatin hydrolase (PcEST) in our previous study, about 5% of residual lovastatin is still a problem for industrial production and quality control. In order to improve conversion efficiency and reduce lovastatin residues, modification of PcEST is carried out through directed evolution and a novel two-step high-throughput screening method. The mutant Q140L shows 18-fold improved whole-cell activity as compared to the wild-type, and one fold enhanced catalytic efficiency and 3 °C increased T 50 10 over the wild-type are observed by characterizing the purified protein. Finally, the engineered A. terreus strain overexpressing Q140L mutant exhibited the increased conversion efficiency and the reduced lovastatin residues by comparing with A. terreus strain overexpressing the wild-type PcEST, where almost 100% of the produced lovastatin is hydrolyzed to monacolin J. Therefore, this improved microbial cell factory can realize single-step bioproduction of monacolin J in a more efficient way, providing an attractive and eco-friendly substitute over the existing chemical synthetic routes of monacolin J and promoting complete bioproduction of simvastatin at industrial scale. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Determining heterogeneous slip activity on multiple slip systems from single crystal orientation pole figures

DOE PAGES

Pagan, Darren C.; Miller, Matthew P.

2016-09-01

A new experimental method to determine heterogeneity of shear strains associated with crystallographic slip in the bulk of ductile, crystalline materials is outlined. The method quantifies the time resolved evolution of misorientation within plastically deforming crystals using single crystal orientation pole figures (SCPFs) measured in-situ with X-ray diffraction. A multiplicative decomposition of the crystal kinematics is used to interpret the distributions of lattice plane orientation observed on the SCPFs in terms of heterogeneous slip activity (shear strains) on multiple slip systems. Here, to show the method’s utility, the evolution of heterogeneous slip is quantified in a silicon single crystal plasticallymore » deformed at high temperature at multiple load steps, with slip activity in sub-volumes of the crystal analyzed simultaneously.« less

Step-to-step spatiotemporal variables and ground reaction forces of intra-individual fastest sprinting in a single session.

PubMed

Nagahara, Ryu; Mizutani, Mirai; Matsuo, Akifumi; Kanehisa, Hiroaki; Fukunaga, Tetsuo

2018-06-01

We aimed to investigate the step-to-step spatiotemporal variables and ground reaction forces during the acceleration phase for characterising intra-individual fastest sprinting within a single session. Step-to-step spatiotemporal variables and ground reaction forces produced by 15 male athletes were measured over a 50-m distance during repeated (three to five) 60-m sprints using a long force platform system. Differences in measured variables between the fastest and slowest trials were examined at each step until the 22nd step using a magnitude-based inferences approach. There were possibly-most likely higher running speed and step frequency (2nd to 22nd steps) and shorter support time (all steps) in the fastest trial than in the slowest trial. Moreover, for the fastest trial there were likely-very likely greater mean propulsive force during the initial four steps and possibly-very likely larger mean net anterior-posterior force until the 17th step. The current results demonstrate that better sprinting performance within a single session is probably achieved by 1) a high step frequency (except the initial step) with short support time at all steps, 2) exerting a greater mean propulsive force during initial acceleration, and 3) producing a greater mean net anterior-posterior force during initial and middle acceleration.

Foot-mounted inertial measurement unit for activity classification.

PubMed

Ghobadi, Mostafa; Esfahani, Ehsan T

2014-01-01

This paper proposes a classification technique for daily base activity recognition for human monitoring during physical therapy in home. The proposed method estimates the foot motion using single inertial measurement unit, then segments the motion into steps classify them by template-matching as walking, stairs up or stairs down steps. The results show a high accuracy of activity recognition. Unlike previous works which are limited to activity recognition, the proposed approach is more qualitative by providing similarity index of any activity to its desired template which can be used to assess subjects improvement.

A MISO-ARX-Based Method for Single-Trial Evoked Potential Extraction.

PubMed

Yu, Nannan; Wu, Lingling; Zou, Dexuan; Chen, Ying; Lu, Hanbing

2017-01-01

In this paper, we propose a novel method for solving the single-trial evoked potential (EP) estimation problem. In this method, the single-trial EP is considered as a complex containing many components, which may originate from different functional brain sites; these components can be distinguished according to their respective latencies and amplitudes and are extracted simultaneously by multiple-input single-output autoregressive modeling with exogenous input (MISO-ARX). The extraction process is performed in three stages: first, we use a reference EP as a template and decompose it into a set of components, which serve as subtemplates for the remaining steps. Then, a dictionary is constructed with these subtemplates, and EPs are preliminarily extracted by sparse coding in order to roughly estimate the latency of each component. Finally, the single-trial measurement is parametrically modeled by MISO-ARX while characterizing spontaneous electroencephalographic activity as an autoregression model driven by white noise and with each component of the EP modeled by autoregressive-moving-average filtering of the subtemplates. Once optimized, all components of the EP can be extracted. Compared with ARX, our method has greater tracking capabilities of specific components of the EP complex as each component is modeled individually in MISO-ARX. We provide exhaustive experimental results to show the effectiveness and feasibility of our method.

Optimization of Empirical Force Fields by Parameter Space Mapping: A Single-Step Perturbation Approach.

PubMed

Stroet, Martin; Koziara, Katarzyna B; Malde, Alpeshkumar K; Mark, Alan E

2017-12-12

A general method for parametrizing atomic interaction functions is presented. The method is based on an analysis of surfaces corresponding to the difference between calculated and target data as a function of alternative combinations of parameters (parameter space mapping). The consideration of surfaces in parameter space as opposed to local values or gradients leads to a better understanding of the relationships between the parameters being optimized and a given set of target data. This in turn enables for a range of target data from multiple molecules to be combined in a robust manner and for the optimal region of parameter space to be trivially identified. The effectiveness of the approach is illustrated by using the method to refine the chlorine 6-12 Lennard-Jones parameters against experimental solvation free enthalpies in water and hexane as well as the density and heat of vaporization of the liquid at atmospheric pressure for a set of 10 aromatic-chloro compounds simultaneously. Single-step perturbation is used to efficiently calculate solvation free enthalpies for a wide range of parameter combinations. The capacity of this approach to parametrize accurate and transferrable force fields is discussed.

Single-step inline hydroxyapatite enrichment facilitates identification and quantitation of phosphopeptides from mass-limited proteomes with MudPIT

PubMed Central

Fonslow, Bryan R.; Niessen, Sherry M.; Singh, Meha; Wong, Catherine C.; Xu, Tao; Carvalho, Paulo C.; Choi, Jeong; Park, Sung Kyu; Yates, John R.

2012-01-01

Herein we report the characterization and optimization of single-step inline enrichment of phosphopeptides directly from small amounts of whole cell and tissue lysates (100 – 500 μg) using a hydroxyapatite (HAP) microcolumn and Multidimensional Protein Identification Technology (MudPIT). In comparison to a triplicate HILIC-IMAC phosphopeptide enrichment study, ~80% of the phosphopeptides identified using HAP-MudPIT were unique. Similarly, analysis of the consensus phosphorylation motifs between the two enrichment methods illustrates the complementarity of calcium-and iron-based enrichment methods and the higher sensitivity and selectivity of HAP-MudPIT for acidic motifs. We demonstrate how the identification of more multiply phosphorylated peptides from HAP-MudPIT can be used to quantify phosphorylation cooperativity. Through optimization of HAP-MudPIT on a whole cell lysate we routinely achieved identification and quantification of ca. 1000 phosphopeptides from a ~1 hr enrichment and 12 hr MudPIT analysis on small quantities of material. Finally, we applied this optimized method to identify phosphorylation sites from a mass-limited mouse brain region, the amygdala (200 – 500 μg), identifying up to 4000 phosphopeptides per run. PMID:22509746

A highly relevant and efficient single step method for simultaneous depletion and isolation of human regulatory T cells in a clinical setting.

PubMed

Brezar, Vedran; Ruffin, Nicolas; Lévy, Yves; Seddiki, Nabila

2014-09-01

Regulatory T cells (Tregs) are pivotal in preventing autoimmunity. They play a major but still ambiguous role in cancer and viral infections. Functional studies of human Tregs are often hampered by numerous technical difficulties arising from imperfections in isolating and depleting protocols, together with the usual low cell number available from clinical samples. We standardized a simple procedure (Single Step Method, SSM), based on magnetic beads technology, in which both depletion and isolation of human Tregs with high purities are simultaneously achieved. SSM is suitable when using low cell numbers either fresh or frozen from both patients and healthy individuals. It allows simultaneous Tregs isolation and depletion that can be used for further functional work to monitor suppressive function of isolated Tregs (in vitro suppression assay) and also effector IFN-γ responses of Tregs-depleted cell fraction (OX40 assay). To our knowledge, there is no accurate standardized method for Tregs isolation and depletion in a clinical context. SSM could thus be used and easily standardized across different laboratories. Copyright © 2014 Elsevier B.V. All rights reserved.

Combined gradient projection/single component artificial force induced reaction (GP/SC-AFIR) method for an efficient search of minimum energy conical intersection (MECI) geometries

NASA Astrophysics Data System (ADS)

Harabuchi, Yu; Taketsugu, Tetsuya; Maeda, Satoshi

2017-04-01

We report a new approach to search for structures of minimum energy conical intersection (MECIs) automatically. Gradient projection (GP) method and single component artificial force induced reaction (SC-AFIR) method were combined in the present approach. As case studies, MECIs of benzene and naphthalene between their ground and first excited singlet electronic states (S0/S1-MECIs) were explored. All S0/S1-MECIs reported previously were obtained automatically. Furthermore, the number of force calculations was reduced compared to the one required in the previous search. Improved convergence in a step in which various geometrical displacements are induced by SC-AFIR would contribute to the cost reduction.

Structural and spectroscopic study of mechanically synthesized SnO2 nanostructures

NASA Astrophysics Data System (ADS)

Vij, Ankush; Kumar, Ravi

2016-05-01

We report the single step synthesis of SnO2 nanostructures using high energy mechanical attrition method. X-ray diffraction (XRD) pattern reveals the single phase rutile structure with appreciable broadening of diffraction peaks, which is a signature of nanostructure formation. The average crystallite size of SnO2 nanostructures has been calculated to be ~15 nm. The micro-Raman study reveals the shifting of A1g Raman mode towards lower wave number, which is correlated with the nanostructure formation.

The Effects of Multiple-Step and Single-Step Directions on Fourth and Fifth Grade Students' Grammar Assessment Performance

ERIC Educational Resources Information Center

Mazerik, Matthew B.

2006-01-01

The mean scores of English Language Learners (ELL) and English Only (EO) students in 4th and 5th grade (N = 110), across the teacher-administered Grammar Skills Test, were examined for differences in participants' scores on assessments containing single-step directions and assessments containing multiple-step directions. The results indicated no…

Solid state synthesis of poly(dichlorophosphazene)

DOEpatents

Allen, Christopher W.; Hneihen, Azzam S.; Peterson, Eric S.

2001-01-01

A method for making poly(dichlorophosphazene) using solid state reactants is disclosed and described. The present invention improves upon previous methods by removing the need for chlorinated hydrocarbon solvents, eliminating complicated equipment and simplifying the overall process by providing a "single pot" two step reaction sequence. This may be accomplished by the condensation reaction of raw materials in the melt phase of the reactants and in the absence of an environmentally damaging solvent.

Accuracy of Multiple Pour Cast from Various Elastomer Impression Methods

PubMed Central

Saad Toman, Majed; Ali Al-Shahrani, Abdullah; Ali Al-Qarni, Abdullah

2016-01-01

The accurate duplicate cast obtained from a single impression reduces the profession clinical time, patient inconvenience, and extra material cost. The stainless steel working cast model assembly consisting of two abutments and one pontic area was fabricated. Two sets of six each custom aluminum trays were fabricated, with five mm spacer and two mm spacer. The impression methods evaluated during the study were additional silicone putty reline (two steps), heavy-light body (one step), monophase (one step), and polyether (one step). Type IV gypsum casts were poured at the interval of one hour, 12 hours, 24 hours, and 48 hours. The resultant cast was measured with traveling microscope for the comparative dimensional accuracy. The data obtained were subjected to Analysis of Variance test at significance level <0.05. The die obtained from two-step putty reline impression techniques had the percentage of variation for the height −0.36 to −0.97%, while diameter was increased by 0.40–0.90%. The values for one-step heavy-light body impression dies, additional silicone monophase impressions, and polyether were −0.73 to −1.21%, −1.34%, and −1.46% for the height and 0.50–0.80%, 1.20%, and −1.30% for the width, respectively. PMID:28096815

Evaluation of accuracy in implant site preparation performed in single- or multi-step drilling procedures.

PubMed

Marheineke, Nadine; Scherer, Uta; Rücker, Martin; von See, Constantin; Rahlf, Björn; Gellrich, Nils-Claudius; Stoetzer, Marcus

2018-06-01

Dental implant failure and insufficient osseointegration are proven results of mechanical and thermal damage during the surgery process. We herein performed a comparative study of a less invasive single-step drilling preparation protocol and a conventional multiple drilling sequence. Accuracy of drilling holes was precisely analyzed and the influence of different levels of expertise of the handlers and additional use of drill template guidance was evaluated. Six experimental groups, deployed in an osseous study model, were representing template-guided and freehanded drilling actions in a stepwise drilling procedure in comparison to a single-drill protocol. Each experimental condition was studied by the drilling actions of respectively three persons without surgical knowledge as well as three highly experienced oral surgeons. Drilling actions were performed and diameters were recorded with a precision measuring instrument. Less experienced operators were able to significantly increase the drilling accuracy using a guiding template, especially when multi-step preparations are performed. Improved accuracy without template guidance was observed when experienced operators were executing single-step versus multi-step technique. Single-step drilling protocols have shown to produce more accurate results than multi-step procedures. The outcome of any protocol can be further improved by use of guiding templates. Operator experience can be a contributing factor. Single-step preparations are less invasive and are promoting osseointegration. Even highly experienced surgeons are achieving higher levels of accuracy by combining this technique with template guidance. Hereby template guidance enables a reduction of hands-on time and side effects during surgery and lead to a more predictable clinical diameter.

Texas two-step: a framework for optimal multi-input single-output deconvolution.

PubMed

Neelamani, Ramesh; Deffenbaugh, Max; Baraniuk, Richard G

2007-11-01

Multi-input single-output deconvolution (MISO-D) aims to extract a deblurred estimate of a target signal from several blurred and noisy observations. This paper develops a new two step framework--Texas Two-Step--to solve MISO-D problems with known blurs. Texas Two-Step first reduces the MISO-D problem to a related single-input single-output deconvolution (SISO-D) problem by invoking the concept of sufficient statistics (SSs) and then solves the simpler SISO-D problem using an appropriate technique. The two-step framework enables new MISO-D techniques (both optimal and suboptimal) based on the rich suite of existing SISO-D techniques. In fact, the properties of SSs imply that a MISO-D algorithm is mean-squared-error optimal if and only if it can be rearranged to conform to the Texas Two-Step framework. Using this insight, we construct new wavelet- and curvelet-based MISO-D algorithms with asymptotically optimal performance. Simulated and real data experiments verify that the framework is indeed effective.

Anomalous high capacitance in a coaxial single nanowire capacitor.

PubMed

Liu, Zheng; Zhan, Yongjie; Shi, Gang; Moldovan, Simona; Gharbi, Mohamed; Song, Li; Ma, Lulu; Gao, Wei; Huang, Jiaqi; Vajtai, Robert; Banhart, Florian; Sharma, Pradeep; Lou, Jun; Ajayan, Pulickel M

2012-06-06

Building entire multiple-component devices on single nanowires is a promising strategy for miniaturizing electronic applications. Here we demonstrate a single nanowire capacitor with a coaxial asymmetric Cu-Cu(2)O-C structure, fabricated using a two-step chemical reaction and vapour deposition method. The capacitance measured from a single nanowire device corresponds to ~140 μF cm(-2), exceeding previous reported values for metal-insulator-metal micro-capacitors and is more than one order of magnitude higher than what is predicted by classical electrostatics. Quantum mechanical calculations indicate that this unusually high capacitance may be attributed to a negative quantum capacitance of the dielectric-metal interface, enhanced significantly at the nanoscale.

Single-step electrochemical functionalization of double-walled carbon nanotube (DWCNT) membranes and the demonstration of ionic rectification

PubMed Central

2013-01-01

Carbon nanotube (CNT) membranes allow the mimicking of natural ion channels for applications in drug delivery and chemical separation. Double-walled carbon nanotube membranes were simply functionalized with dye in a single step instead of the previous two-step functionalization. Non-faradic electrochemical impedance spectra indicated that the functionalized gatekeeper by single-step modification can be actuated to mimic the protein channel under bias. This functional chemistry was proven by a highly efficient ion rectification, wherein the highest experimental rectification factor of ferricyanide was up to 14.4. One-step functionalization by electrooxidation of amine provides a simple and promising functionalization chemistry for the application of CNT membranes. PMID:23758999

Single-Nanoparticle Photoelectrochemistry at a Nanoparticulate TiO2 -Filmed Ultramicroelectrode.

PubMed

Peng, Yue-Yi; Ma, Hui; Ma, Wei; Long, Yi-Tao; Tian, He

2018-03-26

An ultrasensitive photoelectrochemical method for achieving real-time detection of single nanoparticle collision events is presented. Using a micrometer-thick nanoparticulate TiO 2 -filmed Au ultra-microelectrode (TiO 2 @Au UME), a sub-millisecond photocurrent transient was observed for an individual N719-tagged TiO 2 (N719@TiO 2 ) nanoparticle and is due to the instantaneous collision process. Owing to a trap-limited electron diffusion process as the rate-limiting step, a random three-dimensional diffusion model was developed to simulate electron transport dynamics in TiO 2 film. The combination of theoretical simulation and high-resolution photocurrent measurement allow electron-transfer information of a single N719@TiO 2 nanoparticle to be quantified at single-molecule accuracy and the electron diffusivity and the electron-collection efficiency of TiO 2 @Au UME to be estimated. This method provides a test for studies of photoinduced electron transfer at the single-nanoparticle level. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Rapid detection of avian influenza virus a and subtype H5N1 by single step multiplex reverse transcription-polymerase chain reaction.

PubMed

Wei, Hui-Ling; Bai, Gui-Rong; Mweene, Aaron S; Zhou, Ying-Chun; Cong, Yan-Long; Pu, Juan; Wang, Shuai; Kida, Hiroshi; Liu, Jin-Hua

2006-06-01

Outbreaks of H5N1 highly pathogenic avian influenza (HPAI) virus caused great economic losses to the poultry industry and resulted in human deaths in Thailand and Viet Nam in 2004. Rapid typing and subtyping of H5N1 viruses, especially from clinical specimens, are desirable for taking prompt control measures to prevent the spread of the disease. Here, we developed a set of oligonucleotide primers able to detect, type and subtype H5 and N1 influenza viruses in a single step multiplex reverse transcription-polymerase chain reaction (RT-PCR). RNA was extracted from allantoic fluid or from specimens with guanidinium isothiocyanate reagent. Reverse transcription and PCR were carried out with a mixture of primers specific for influenza viruses of type A, subtype H5 and N1 in a single reaction system under identical conditions. The amplified DNA fragments were analyzed by agarose gel electrophoresis. All the H5N1 viruses tested in the study and the experimental specimens presented three specific bands by the method established here. The results presented here suggest that the method described below is rapid and specific and, therefore, could be valuable in the rapid detection of H5N1 influenza viruses in clinics.

Stability analysis of Eulerian-Lagrangian methods for the one-dimensional shallow-water equations

USGS Publications Warehouse

Casulli, V.; Cheng, R.T.

1990-01-01

In this paper stability and error analyses are discussed for some finite difference methods when applied to the one-dimensional shallow-water equations. Two finite difference formulations, which are based on a combined Eulerian-Lagrangian approach, are discussed. In the first part of this paper the results of numerical analyses for an explicit Eulerian-Lagrangian method (ELM) have shown that the method is unconditionally stable. This method, which is a generalized fixed grid method of characteristics, covers the Courant-Isaacson-Rees method as a special case. Some artificial viscosity is introduced by this scheme. However, because the method is unconditionally stable, the artificial viscosity can be brought under control either by reducing the spatial increment or by increasing the size of time step. The second part of the paper discusses a class of semi-implicit finite difference methods for the one-dimensional shallow-water equations. This method, when the Eulerian-Lagrangian approach is used for the convective terms, is also unconditionally stable and highly accurate for small space increments or large time steps. The semi-implicit methods seem to be more computationally efficient than the explicit ELM; at each time step a single tridiagonal system of linear equations is solved. The combined explicit and implicit ELM is best used in formulating a solution strategy for solving a network of interconnected channels. The explicit ELM is used at channel junctions for each time step. The semi-implicit method is then applied to the interior points in each channel segment. Following this solution strategy, the channel network problem can be reduced to a set of independent one-dimensional open-channel flow problems. Numerical results support properties given by the stability and error analyses. ?? 1990.

[First attempts of detecting fetal cells in the maternal circulation].

PubMed

Nagy, Gyula Richárd; Bán, Zoltán; Sipos, Ferenc; Fent, János; Oroszné Nagy, Judit; Beke, Artúr; Furész, József; Papp, Zoltán

2004-10-31

In prenatal diagnosis there is great interest for noninvasive diagnostic methods. Authors report their first results in detecting fetal cells in the maternal circulation during pregnancy. The aim of the study was to detect fetal gender from maternal peripheral blood samples during pregnancy. Authors have analysed fetal nucleated red blood cells. In 12 cases after a double density Percoll gradient separation they labelled the surface antigens of the cells with anti-glycophorin-A and anti-CD45 fluorescent antibodies, did an intracellular staining of the epsilon haemoglobin chain, and analysed the cells with flow cytometry. The CD45 negative/glycophorin-A positive/epsilon-haemoglobin chain positive cells were considered as fetal cells. Having the results, in another 13 cases magnetic activated cell sorting with CD71 antibody were used as an enrichment step. Authors made an intracellular staining of the epsilon haemoglobin chain, the positive cells were isolated by micromanipulation, and analysed by single cell fluorescent polymerase chain reaction. Primers for the amelogenin gene were used to detect fetal gender. Only the Percoll enrichment step itself is not enough for using the samples for diagnostic molecular-biologic examinations, a following enrichment step is needed. For this the authors used magnetic activated cell sorting with CD71 antibody. With the help of this enrichment step, after the intracellular staining of the epsilon haemoglobin chain the direct micromanipulator isolation of the epsilon haemoglobin chain positive cells could be done. After analysing single cells by fluorescent polymerase chain reaction, in 8 out of the 11 comparable cases the results were similar to those, what was found during the genetic amniocentesis. In 2 cases from this 8, genetic amniocentesis proved Klinefelter syndrome, which they could also confirm with the examination of fetal cells in the maternal circulation. The results of the study suggest that the method described above can be useful in prenatal genetic diagnosis, and improving it could be useful to detect other genetic abnormalities (chromosomal abnormalities, single gene disorders) as well.

One-step fabrication of 3D silver paste electrodes into microfluidic devices for enhanced droplet-based cell sorting

NASA Astrophysics Data System (ADS)

Rao, Lang; Cai, Bo; Yu, Xiao-Lei; Guo, Shi-Shang; Liu, Wei; Zhao, Xing-Zhong

2015-05-01

3D microelectrodes are one-step fabricated into a microfluidic droplet separator by filling conductive silver paste into PDMS microchambers. The advantages of 3D silver paste electrodes in promoting droplet sorting accuracy are systematically demonstrated by theoretical calculation, numerical simulation and experimental validation. The employment of 3D electrodes also helps to decrease the droplet sorting voltage, guaranteeing that cells encapsulated in droplets undergo chip-based sorting processes are at better metabolic status for further potential cellular assays. At last, target droplet containing single cell are selectively sorted out from others by an appropriate electric pulse. This method provides a simple and inexpensive alternative to fabricate 3D electrodes, and it is expected our 3D electrode-integrated microfluidic droplet separator platform can be widely used in single cell operation and analysis.

Advanced Neuropsychological Diagnostics Infrastructure (ANDI): A Normative Database Created from Control Datasets

PubMed Central

de Vent, Nathalie R.; Agelink van Rentergem, Joost A.; Schmand, Ben A.; Murre, Jaap M. J.; Huizenga, Hilde M.

2016-01-01

In the Advanced Neuropsychological Diagnostics Infrastructure (ANDI), datasets of several research groups are combined into a single database, containing scores on neuropsychological tests from healthy participants. For most popular neuropsychological tests the quantity, and range of these data surpasses that of traditional normative data, thereby enabling more accurate neuropsychological assessment. Because of the unique structure of the database, it facilitates normative comparison methods that were not feasible before, in particular those in which entire profiles of scores are evaluated. In this article, we describe the steps that were necessary to combine the separate datasets into a single database. These steps involve matching variables from multiple datasets, removing outlying values, determining the influence of demographic variables, and finding appropriate transformations to normality. Also, a brief description of the current contents of the ANDI database is given. PMID:27812340

Advanced Neuropsychological Diagnostics Infrastructure (ANDI): A Normative Database Created from Control Datasets.

PubMed

de Vent, Nathalie R; Agelink van Rentergem, Joost A; Schmand, Ben A; Murre, Jaap M J; Huizenga, Hilde M

2016-01-01

In the Advanced Neuropsychological Diagnostics Infrastructure (ANDI), datasets of several research groups are combined into a single database, containing scores on neuropsychological tests from healthy participants. For most popular neuropsychological tests the quantity, and range of these data surpasses that of traditional normative data, thereby enabling more accurate neuropsychological assessment. Because of the unique structure of the database, it facilitates normative comparison methods that were not feasible before, in particular those in which entire profiles of scores are evaluated. In this article, we describe the steps that were necessary to combine the separate datasets into a single database. These steps involve matching variables from multiple datasets, removing outlying values, determining the influence of demographic variables, and finding appropriate transformations to normality. Also, a brief description of the current contents of the ANDI database is given.

Nickel ferrite aerogels with monodisperse nanoscale building blocks--the importance of processing temperature and atmosphere.

PubMed

Pettigrew, Katherine A; Long, Jeffrey W; Carpenter, Everett E; Baker, Colin C; Lytle, Justin C; Chervin, Christopher N; Logan, Michael S; Stroud, Rhonda M; Rolison, Debra R

2008-04-01

Using two-step (air/argon) thermal processing, sol-gel-derived nickel-iron oxide aerogels are transformed into monodisperse, networked nanocrystalline magnetic oxides of NiFe(2)O(4) with particle diameters that can be ripened with increasing temperature under argon to 4.6, 6.4, and 8.8 nm. Processing in air alone yields poorly crystalline materials; heating in argon alone leads to single phase, but diversiform, polydisperse NiFe(2)O(4), which hampers interpretation of the magnetic properties of the nanoarchitectures. The two-step method yields an improved model system to study magnetic effects as a function of size on the nanoscale while maintaining the particles within the size regime of single domain magnets, as networked building blocks, not agglomerates, and without stabilizing ligands capping the surface.

Fabrication of Long Period Gratings by Periodically Removing the Coating of Cladding-Etched Single Mode Optical Fiber Towards Optical Fiber Sensor Development.

PubMed

Ascorbe, Joaquin; Corres, Jesus M; Del Villar, Ignacio; Matias, Ignacio R

2018-06-07

Here, we present a novel method to fabricate long period gratings using standard single mode optical fibers (SMF). These optical devices were fabricated in a three-step process, which consisted of etching the SMF, then coating it with a thin-film and, the final step, which involved removing sections of the coating periodically by laser ablation. Tin dioxide was chosen as the material for this study and it was sputtered using a pulsed DC sputtering system. Theoretical simulations were performed in order to select the appropriate parameters for the experiments. The responses of two different devices to different external refractive indices was studied, and the maximum sensitivity obtained was 6430 nm/RIU for external refractive indices ranging from 1.37 to 1.39.

Development of a rapid and sensitive one-step reverse transcription-nested polymerase chain reaction in a single tube using the droplet-polymerase chain reaction machine.

PubMed

Yamaguchi, Akemi; Matsuda, Kazuyuki; Sueki, Akane; Taira, Chiaki; Uehara, Masayuki; Saito, Yasunori; Honda, Takayuki

2015-08-25

Reverse transcription (RT)-nested polymerase chain reaction (PCR) is a time-consuming procedure because it has several handling steps and is associated with the risk of cross-contamination during each step. Therefore, a rapid and sensitive one-step RT-nested PCR was developed that could be performed in a single tube using a droplet-PCR machine. The K562 BCR-ABL mRNA-positive cell line as well as bone marrow aspirates from 5 patients with chronic myelogenous leukemia (CML) and 5 controls without CML were used. We evaluated one-step RT-nested PCR using the droplet-PCR machine. One-step RT-nested PCR performed in a single tube using the droplet-PCR machine enabled the detection of BCR-ABL mRNA within 40min, which was 10(3)-fold superior to conventional RT nested PCR using three steps in separate tubes. The sensitivity of the one-step RT-nested PCR was 0.001%, with sample reactivity comparable to that of the conventional assay. One-step RT-nested PCR was developed using the droplet-PCR machine, which enabled all reactions to be performed in a single tube accurately and rapidly and with high sensitivity. This one-step RT-nested PCR may be applicable to a wide spectrum of genetic tests in clinical laboratories. Copyright © 2015 Elsevier B.V. All rights reserved.

A General Method for Solving Systems of Non-Linear Equations

NASA Technical Reports Server (NTRS)

Nachtsheim, Philip R.; Deiss, Ron (Technical Monitor)

1995-01-01

The method of steepest descent is modified so that accelerated convergence is achieved near a root. It is assumed that the function of interest can be approximated near a root by a quadratic form. An eigenvector of the quadratic form is found by evaluating the function and its gradient at an arbitrary point and another suitably selected point. The terminal point of the eigenvector is chosen to lie on the line segment joining the two points. The terminal point found lies on an axis of the quadratic form. The selection of a suitable step size at this point leads directly to the root in the direction of steepest descent in a single step. Newton's root finding method not infrequently diverges if the starting point is far from the root. However, the current method in these regions merely reverts to the method of steepest descent with an adaptive step size. The current method's performance should match that of the Levenberg-Marquardt root finding method since they both share the ability to converge from a starting point far from the root and both exhibit quadratic convergence near a root. The Levenberg-Marquardt method requires storage for coefficients of linear equations. The current method which does not require the solution of linear equations requires more time for additional function and gradient evaluations. The classic trade off of time for space separates the two methods.

Bayesian Analysis of Evolutionary Divergence with Genomic Data under Diverse Demographic Models.

PubMed

Chung, Yujin; Hey, Jody

2017-06-01

We present a new Bayesian method for estimating demographic and phylogenetic history using population genomic data. Several key innovations are introduced that allow the study of diverse models within an Isolation-with-Migration framework. The new method implements a 2-step analysis, with an initial Markov chain Monte Carlo (MCMC) phase that samples simple coalescent trees, followed by the calculation of the joint posterior density for the parameters of a demographic model. In step 1, the MCMC sampling phase, the method uses a reduced state space, consisting of coalescent trees without migration paths, and a simple importance sampling distribution without the demography of interest. Once obtained, a single sample of trees can be used in step 2 to calculate the joint posterior density for model parameters under multiple diverse demographic models, without having to repeat MCMC runs. Because migration paths are not included in the state space of the MCMC phase, but rather are handled by analytic integration in step 2 of the analysis, the method is scalable to a large number of loci with excellent MCMC mixing properties. With an implementation of the new method in the computer program MIST, we demonstrate the method's accuracy, scalability, and other advantages using simulated data and DNA sequences of two common chimpanzee subspecies: Pan troglodytes (P. t.) troglodytes and P. t. verus. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Comparison of two stand-alone CADe systems at multiple operating points

NASA Astrophysics Data System (ADS)

Sahiner, Berkman; Chen, Weijie; Pezeshk, Aria; Petrick, Nicholas

2015-03-01

Computer-aided detection (CADe) systems are typically designed to work at a given operating point: The device displays a mark if and only if the level of suspiciousness of a region of interest is above a fixed threshold. To compare the standalone performances of two systems, one approach is to select the parameters of the systems to yield a target false-positive rate that defines the operating point, and to compare the sensitivities at that operating point. Increasingly, CADe developers offer multiple operating points, which necessitates the comparison of two CADe systems involving multiple comparisons. To control the Type I error, multiple-comparison correction is needed for keeping the family-wise error rate (FWER) less than a given alpha-level. The sensitivities of a single modality at different operating points are correlated. In addition, the sensitivities of the two modalities at the same or different operating points are also likely to be correlated. It has been shown in the literature that when test statistics are correlated, well-known methods for controlling the FWER are conservative. In this study, we compared the FWER and power of three methods, namely the Bonferroni, step-up, and adjusted step-up methods in comparing the sensitivities of two CADe systems at multiple operating points, where the adjusted step-up method uses the estimated correlations. Our results indicate that the adjusted step-up method has a substantial advantage over other the two methods both in terms of the FWER and power.

UV-transmitting step-index fluorophosphate glass fiber fabricated by the crucible technique

NASA Astrophysics Data System (ADS)

Galleani, Gustavo; Ledemi, Yannick; de Lima Filho, Elton Soares; Morency, Steeve; Delaizir, Gaëlle; Chenu, Sébastien; Duclere, Jean René; Messaddeq, Younes

2017-02-01

In this study, we report on the fabrication process of highly pure step-index fluorophosphate glass optical fibers by a modified crucible technique. High-purity fluorophosphate glasses based on 10 mol% of barium metaphosphate and 90 mol% of metal fluorides (AlF3sbnd CaF2sbnd MgF2sbnd SrF2) have been studied in order to produce step-index optical fibers transmitting in the deep-ultraviolet (DUV) region. The characteristic temperatures, viscosity around softening temperature and optical transmission in the UV-visible region of the prepared bulk glasses were characterized in a first step. The selected glass compositions were then used to prepare core-cladding optical preforms by using a modified built-in casting technique. While uncontrolled crystallization of the fiber was observed during the preform stretching by using the conventional method, we successfully obtained crystal-free fiber by using a modified crucible technique. In this alternative approach, the produced core-cladding preforms were inserted into a home-designed fused silica crucible assembly and heated at 643 °C to allow glass flowing throughout the crucible, preventing the formation of crystals. Single index fluorophosphate glass fibers were fabricated following the same process as well. The optical attenuation at 244 nm and in the interval 350-1750 nm was measured on both single index and step-index optical fibers. Their potential for using in DUV applications is discussed.

Characteristics of camel-gate structures with active doping channel profiles

NASA Astrophysics Data System (ADS)

Tsai, Jung-Hui; Lour, Wen-Shiung; Laih, Lih-Wen; Liu, Rong-Chau; Liu, Wen-Chau

1996-03-01

In this paper, we demonstrate the influence of channel doping profile on the performances of camel-gate field effect transistors (CAMFETs). For comparison, single and tri-step doping channel structures with identical doping thickness products are employed, while other parameters are kept unchanged. The results of a theoretical analysis show that the single doping channel FET with lightly doping active layer has higher barrier height and drain-source saturation current. However, the transconductance is decreased. For a tri-step doping channel structure, it is found that the output drain-source saturation current and the barrier height are enhanced. Furthermore, the relatively voltage independent performances are improved. Two CAMFETs with single and tri-step doping channel structures have been fabricated and discussed. The devices exhibit nearly voltage independent transconductances of 144 mS mm -1 and 222 mS mm -1 for single and tri-step doping channel CAMFETs, respectively. The operation gate voltage may extend to ± 1.5 V for a tri-step doping channel CAMFET. In addition, the drain current densities of > 750 and 405 mA mm -1 are obtained for the tri-step and single doping CAMFETs. These experimental results are inconsistent with theoretical analysis.

CFD and Thermo Mechanical Analysis on Effect of Curved vs Step Surface in IC Engine Cylinder Head

NASA Astrophysics Data System (ADS)

Balaji, S.; Ganesh, N.; Kumarasamy, A.

2017-05-01

Current research in IC engines mainly focus on various methods to achieve higher efficiency and high specific power. As a single design parameter, combustion chamber peak spring pressure has increased more than before. Apart from the structural aspects of withstanding these loads, designer faces challenges of resolving thermal aspects of cylinder head. Methods to enhance the heat transfer without compromising load withstanding capability are being constantly explored. Conventional cylinder heads have got sat inner surface. In this paper we have suggested a modification in inner surface to enhance the heat transfer capability. To increase the heat transfer rate, inner same deck surface is configured as a curved and stepped surface instead of sat. We have reported the effectiveness of extend of curvature in the inner same deck surface in a different technical paper. Here, we are making a direct comparison between stepped and curved surface only. From this analysis it has been observed that curved surface reduces the ame deck temperature considerably without compromising the structural strength factors compared to step and sat surface.

A GPU-accelerated semi-implicit fractional-step method for numerical solutions of incompressible Navier-Stokes equations

NASA Astrophysics Data System (ADS)

Ha, Sanghyun; Park, Junshin; You, Donghyun

2018-01-01

Utility of the computational power of Graphics Processing Units (GPUs) is elaborated for solutions of incompressible Navier-Stokes equations which are integrated using a semi-implicit fractional-step method. The Alternating Direction Implicit (ADI) and the Fourier-transform-based direct solution methods used in the semi-implicit fractional-step method take advantage of multiple tridiagonal matrices whose inversion is known as the major bottleneck for acceleration on a typical multi-core machine. A novel implementation of the semi-implicit fractional-step method designed for GPU acceleration of the incompressible Navier-Stokes equations is presented. Aspects of the programing model of Compute Unified Device Architecture (CUDA), which are critical to the bandwidth-bound nature of the present method are discussed in detail. A data layout for efficient use of CUDA libraries is proposed for acceleration of tridiagonal matrix inversion and fast Fourier transform. OpenMP is employed for concurrent collection of turbulence statistics on a CPU while the Navier-Stokes equations are computed on a GPU. Performance of the present method using CUDA is assessed by comparing the speed of solving three tridiagonal matrices using ADI with the speed of solving one heptadiagonal matrix using a conjugate gradient method. An overall speedup of 20 times is achieved using a Tesla K40 GPU in comparison with a single-core Xeon E5-2660 v3 CPU in simulations of turbulent boundary-layer flow over a flat plate conducted on over 134 million grids. Enhanced performance of 48 times speedup is reached for the same problem using a Tesla P100 GPU.

Development and Single-Laboratory Validation of a Liquid Chromatography Tandem Mass Spectrometry Method for Quantitation of Tetrodotoxin in Mussels and Oysters.

PubMed

Turner, Andrew D; Boundy, Michael J; Rapkova, Monika Dhanji

2017-09-01

In recent years, evidence has grown for the presence of tetrodotoxin (TTX) in bivalve mollusks, leading to the potential for consumers of contaminated products to be affected by Tetrodotoxin Shellfish Poisoning (TSP). A single-laboratory validation was conducted for the hydrophilic interaction LC (HILIC) tandem MS (MS/MS) analysis of TTX in common mussels and Pacific oysters-the bivalve species that have been found to contain TTXs in the United Kingdom in recent years. The method consists of a single-step dispersive extraction in 1% acetic acid, followed by a carbon SPE cleanup step before dilution and instrumental analysis. The full method was developed as a rapid tool for the quantitation of TTX, as well as for the associated analogs 4-epi-TTX; 5,6,11-trideoxy TTX; 11-nor TTX-6-ol; 5-deoxy TTX; and 4,9-anhydro TTX. The method can also be run as the acquisition of TTX together with paralytic shellfish toxins. Results demonstrated acceptable method performance characteristics for specificity, linearity, recovery, ruggedness, repeatability, matrix variability, and within-laboratory reproducibility for the analysis of TTX. The LOD and LOQ were fit-for-purpose in comparison to the current action limit for TTX enforced in The Netherlands. In addition, aspects of method performance (LOD, LOQ, and within-laboratory reproducibility) were found to be satisfactory for three other TTX analogs (11-nor TTX-6-ol, 5-deoxy TTX, and 4,9-anhydro TTX). The method was found to be practical and suitable for use in regulatory testing, providing rapid turnaround of sample analysis. Plans currently underway on a full collaborative study to validate a HILIC-MS/MS method for paralytic shellfish poisoning toxins will be extended to include TTX in order to generate international acceptance, ultimately for use as an alternative official control testing method should regulatory controls be adopted.

Methods for Integrated Air Sampling and DNA Analysis for Detection of Airborne Fungal Spores

PubMed Central

Williams, Roger H.; Ward, Elaine; McCartney, H. Alastair

2001-01-01

Integrated air sampling and PCR-based methods for detecting airborne fungal spores, using Penicillium roqueforti as a model fungus, are described. P. roqueforti spores were collected directly into Eppendorf tubes using a miniature cyclone-type air sampler. They were then suspended in 0.1% Nonidet P-40, and counted using microscopy. Serial dilutions of the spores were made. Three methods were used to produce DNA for PCR tests: adding untreated spores to PCRs, disrupting spores (fracturing of spore walls to release the contents) using Ballotini beads, and disrupting spores followed by DNA purification. Three P. roqueforti-specific assays were tested: single-step PCR, nested PCR, and PCR followed by Southern blotting and probing. Disrupting the spores was found to be essential for achieving maximum sensitivity of the assay. Adding untreated spores to the PCR did allow the detection of P. roqueforti, but this was never achieved when fewer than 1,000 spores were added to the PCR. By disrupting the spores, with or without subsequent DNA purification, it was possible to detect DNA from a single spore. When known quantities of P. roqueforti spores were added to air samples consisting of high concentrations of unidentified fungal spores, pollen, and dust, detection sensitivity was reduced. P. roqueforti DNA could not be detected using untreated or disrupted spore suspensions added to the PCRs. However, using purified DNA, it was possible to detect 10 P. roqueforti spores in a background of 4,500 other spores. For all DNA extraction methods, nested PCR was more sensitive than single-step PCR or PCR followed by Southern blotting. PMID:11375150

Exploring transduction mechanisms of protein transduction domains (PTDs) in living cells utilizing single-quantum dot tracking (SQT) technology.

PubMed

Suzuki, Yasuhiro

2012-01-01

Specific protein domains known as protein transduction domains (PTDs) can permeate cell membranes and deliver proteins or bioactive materials into living cells. Various approaches have been applied for improving their transduction efficacy. It is, therefore, crucial to clarify the entry mechanisms and to identify the rate-limiting steps. Because of technical limitations for imaging PTD behavior on cells with conventional fluorescent-dyes, how PTDs enter the cells has been a topic of much debate. Utilizing quantum dots (QDs), we recently tracked the behavior of PTD that was derived from HIV-1 Tat (TatP) in living cells at the single-molecule level with 7-nm special precision. In this review article, we initially summarize the controversy on TatP entry mechanisms; thereafter, we will focus on our recent findings on single-TatP-QD tracking (SQT), to identify the major sequential steps of intracellular delivery in living cells and to discuss how SQT can easily provide direct information on TatP entry mechanisms. As a primer for SQT study, we also discuss the latest findings on single particle tracking of various molecules on the plasma membrane. Finally, we discuss the problems of QDs and the challenges for the future in utilizing currently available QD probes for SQT. In conclusion, direct identification of the rate-limiting steps of PTD entry with SQT should dramatically improve the methods for enhancing transduction efficiency.

Functionalization of Probe Tips and Supports for Single-Molecule Recognition Force Microscopy

NASA Astrophysics Data System (ADS)

Ebner, Andreas; Wildling, Linda; Zhu, Rong; Rankl, Christian; Haselgrübler, Thomas; Hinterdorfer, Peter; Gruber, Hermann J.

The measuring tip of a force microscope can be converted into a monomolecular sensor if one or few "ligand" molecules are attached to the apex of the tip while maintaining ligand function. Functionalized tips are used to study fine details of receptor-ligand interaction by force spectroscopy or to map cognate "receptor" molecules on the sample surface. The receptor (or target) molecules can be present on the surface of a biological specimen; alternatively, soluble target molecules must be immobilized on ultraflat supports. This review describes the methods of tip functionalization, as well as target molecule immobilization. Silicon nitride tips, silicon chips, and mica have usually been functionalized in three steps: (1) aminofunctionalization, (2) crosslinker attachment, and (3) ligand/receptor coupling, whereby numerous crosslinkers are available to couple widely different ligand molecules. Gold-covered tips and/or supports have usually been coated with a self-assembled monolayer, on top of which the ligand/receptor molecule has been coupled either directly or via a crosslinker molecule. Apart from these general strategies, many simplified methods have been used for tip and/or support functionalization, even single-step methods such as adsorption or chemisorption being very efficient under suitable circumstances. All methods are described with the same explicitness and critical parameters are discussed. In conclusion, this review should help to find suitable methods for specific problems of tip and support functionalization.

Preparation of next-generation sequencing libraries using Nextera™ technology: simultaneous DNA fragmentation and adaptor tagging by in vitro transposition.

PubMed

Caruccio, Nicholas

2011-01-01

DNA library preparation is a common entry point and bottleneck for next-generation sequencing. Current methods generally consist of distinct steps that often involve significant sample loss and hands-on time: DNA fragmentation, end-polishing, and adaptor-ligation. In vitro transposition with Nextera™ Transposomes simultaneously fragments and covalently tags the target DNA, thereby combining these three distinct steps into a single reaction. Platform-specific sequencing adaptors can be added, and the sample can be enriched and bar-coded using limited-cycle PCR to prepare di-tagged DNA fragment libraries. Nextera technology offers a streamlined, efficient, and high-throughput method for generating bar-coded libraries compatible with multiple next-generation sequencing platforms.

Super-resolution imaging applied to moving object tracking

NASA Astrophysics Data System (ADS)

Swalaganata, Galandaru; Ratna Sulistyaningrum, Dwi; Setiyono, Budi

2017-10-01

Moving object tracking in a video is a method used to detect and analyze changes that occur in an object that being observed. Visual quality and the precision of the tracked target are highly wished in modern tracking system. The fact that the tracked object does not always seem clear causes the tracking result less precise. The reasons are low quality video, system noise, small object, and other factors. In order to improve the precision of the tracked object especially for small object, we propose a two step solution that integrates a super-resolution technique into tracking approach. First step is super-resolution imaging applied into frame sequences. This step was done by cropping the frame in several frame or all of frame. Second step is tracking the result of super-resolution images. Super-resolution image is a technique to obtain high-resolution images from low-resolution images. In this research single frame super-resolution technique is proposed for tracking approach. Single frame super-resolution was a kind of super-resolution that it has the advantage of fast computation time. The method used for tracking is Camshift. The advantages of Camshift was simple calculation based on HSV color that use its histogram for some condition and color of the object varies. The computational complexity and large memory requirements required for the implementation of super-resolution and tracking were reduced and the precision of the tracked target was good. Experiment showed that integrate a super-resolution imaging into tracking technique can track the object precisely with various background, shape changes of the object, and in a good light conditions.

A comparison of two methods of eluting insect DNA from Flinders Technology Associates Cards

USDA-ARS?s Scientific Manuscript database

Flinders Technology Associates (FTA) technology lyses cells and stabilizes DNA for room-temperature storage in a single step but it has been infrequently used with arthropods. One possible reason is the paucity of quick and inexpensive protocols to subsequently elute the DNA from the card matrix. Th...

Determination of pyrophosphate and sulfate using polyhexamethylene guanidine hydrochloride-stabilized silver nanoparticles.

PubMed

Terenteva, E A; Apyari, V V; Dmitrienko, S G; Garshev, A V; Volkov, P A; Zolotov, Yu A

2018-04-01

Positively charged polyhexamethylene guanidine hydrochloride-stabilized silver nanoparticles (PHMG-AgNPs) were prepared and applied as a colorimetric probe for single-step determination of pyrophosphate and sulfate. The approach is based on the nanoparticles aggregation leading to change in their absorption spectra and color of the solution. Due to both electrostatic and steric stabilization these nanoparticles show decreased sensitivity relatively to many common anions, which allows for simple and rapid direct single-step determination of pyrophosphate and sulfate. Effects of different factors (time of interaction, pH, concentrations of anions and the nanoparticles) on aggregation of PHMG-AgNPs and analytical performance of the procedure were investigated. The method allows for the determination of pyrophosphate and sulfate in the range of 0.16-2μgmL -1 and 20-80μgmL -1 with RSD of 2-5%, respectively. The analysis can be performed using either spectrophotometry or naked-eye detection. Practical application of the method was shown by the example of pyrophosphate determination in baking powder sample. Copyright © 2017 Elsevier B.V. All rights reserved.

Dye sensitized solar cells using catalytically active CuO-ZnO nanocomposite synthesized by single step method

NASA Astrophysics Data System (ADS)

Abraham, Nelsa; Rufus, Alex; Unni, C.; Philip, Daizy

2018-07-01

In the present paper we report a low cost, single step preparation method for the synthesis of CuO-ZnO nanocomposite through simple co-precipitation technique using oxalic acid. To have a better idea about the deviations brought about by the inclusion of CuO in ZnO lattice, pure ZnO nanoparticles synthesized from 0.1 M solutions were also investigated. X-ray diffraction studies showed that the composite contains only hexagonal wurtzite ZnO and monoclinic CuO structures. The magnetic studies of CuO-ZnO heterostructures were also conducted in order to elucidate the source of the ferromagnetism observed at room temperature. The catalytic efficiency of the as prepared nanocomposite was estimated by the degradation of methylene blue and eosin yellowish which also shows its suitability as a promising candidate in waste water treatment. The effect of chenodeoxycholic acid as a co-adsorbent in the performance of dye sensitized solar cells fabricated using the synthesized ZnO and the nanocomposite was also studied and significant improvement in photovoltaic performance has been obtained for nanocomposite based solar cell.

Single photon emission from plasma treated 2D hexagonal boron nitride.

PubMed

Xu, Zai-Quan; Elbadawi, Christopher; Tran, Toan Trong; Kianinia, Mehran; Li, Xiuling; Liu, Daobin; Hoffman, Timothy B; Nguyen, Minh; Kim, Sejeong; Edgar, James H; Wu, Xiaojun; Song, Li; Ali, Sajid; Ford, Mike; Toth, Milos; Aharonovich, Igor

2018-05-03

Artificial atomic systems in solids are becoming increasingly important building blocks in quantum information processing and scalable quantum nanophotonic networks. Amongst numerous candidates, 2D hexagonal boron nitride has recently emerged as a promising platform hosting single photon emitters. Here, we report a number of robust plasma and thermal annealing methods for fabrication of emitters in tape-exfoliated hexagonal boron nitride (hBN) crystals. A two-step process comprising Ar plasma etching and subsequent annealing in Ar is highly robust, and yields an eight-fold increase in the concentration of emitters in hBN. The initial plasma-etching step generates emitters that suffer from blinking and bleaching, whereas the two-step process yields emitters that are photostable at room temperature with emission wavelengths greater than ∼700 nm. Density functional theory modeling suggests that the emitters might be associated with defect complexes that contain oxygen. This is further confirmed by generating the emitters via annealing hBN in air. Our findings advance the present understanding of the structure of quantum emitters in hBN and enhance the nanofabrication toolkit needed to realize integrated quantum nanophotonic circuits.

Diffraction Techniques in Structural Biology

PubMed Central

Egli, Martin

2010-01-01

A detailed understanding of chemical and biological function and the mechanisms underlying the activities ultimately requires atomic-resolution structural data. Diffraction-based techniques such as single-crystal X-ray crystallography, electron microscopy and neutron diffraction are well established and have paved the road to the stunning successes of modern-day structural biology. The major advances achieved in the last 20 years in all aspects of structural research, including sample preparation, crystallization, the construction of synchrotron and spallation sources, phasing approaches and high-speed computing and visualization, now provide specialists and non-specialists alike with a steady flow of molecular images of unprecedented detail. The present chapter combines a general overview of diffraction methods with a step-by-step description of the process of a single-crystal X-ray structure determination experiment, from chemical synthesis or expression to phasing and refinement, analysis and quality control. For novices it may serve as a stepping-stone to more in-depth treatises of the individual topics. Readers relying on structural information for interpreting functional data may find it a useful consumer guide. PMID:20517991

PLE in the analysis of plant compounds. Part II: One-cycle PLE in determining total amount of analyte in plant material.

PubMed

Dawidowicz, Andrzej L; Wianowska, Dorota

2005-04-29

Pressurised liquid extraction (PLE) is recognised as one of the most effective sample preparation methods. Despite the enhanced extraction power of PLE, the full recovery of an analyte from plant material may require multiple extractions of the same sample. The presented investigations show the possibility of estimating the true concentration value of an analyte in plant material employing one-cycle PLE in which plant samples of different weight are used. The performed experiments show a linear dependence between the reciprocal value of the analyte amount (E*), extracted in single-step PLE from a plant matrix, and the ratio of plant material mass to extrahent volume (m(p)/V(s)). Hence, time-consuming multi-step PLE can be replaced by a few single-step PLEs performed at different (m(p)/V(s)) ratios. The concentrations of rutin in Sambucus nigra L. and caffeine in tea and coffee estimated by means of the tested procedure are almost the same as their concentrations estimated by multiple PLE.

Increased knee valgus alignment and moment during single-leg landing after overhead stroke as a potential risk factor of anterior cruciate ligament injury in badminton.

PubMed

Kimura, Yuka; Ishibashi, Yasuyuki; Tsuda, Eiichi; Yamamoto, Yuji; Hayashi, Yoshimitsu; Sato, Shuichi

2012-03-01

In badminton, knees opposite to the racket-hand side received anterior cruciate ligament (ACL) injuries during single-leg landing after overhead stroke. Most of them occurred in the backhand-side of the rear court. Comparing lower limb biomechanics during single-leg landing after overhead stroke between the forehand-side and backhand-side court may help explain the different injury rates depending on court position. The knee kinematics and kinetics during single-leg landing after overhead stroke following back-stepping were different between the forehand-side and backhand-side court. Controlled laboratory study. Hip, knee and ankle joint kinematic and knee kinetic data were collected for 17 right-handed female college badminton players using a 3-dimensional motion analysis system. Subjects performed single-left-legged landing after an overhead stroke following left and right back-stepping. The kinematic and kinetic data of the left lower extremities during landing were measured and compared between left and right back-steps. Hip flexion and abduction and knee valgus at the initial contact, hip and knee flexion and knee valgus at the maximum knee flexion and the maximum knee valgus moment were significantly larger for the left back-step than the right back-step (p<0.05). Significant differences in joint kinematics and kinetics of the lower extremity during single-leg landing after overhead stroke were observed between different back-step directions. Increased knee valgus angle and moment following back-stepping to the backhand-side might be related to the higher incidence of ACL injury during single-leg landing after overhead stroke.

Temperature- and field-dependent characterization of a conductor on round core cable

NASA Astrophysics Data System (ADS)

Barth, C.; van der Laan, D. C.; Bagrets, N.; Bayer, C. M.; Weiss, K.-P.; Lange, C.

2015-06-01

The conductor on round core (CORC) cable is one of the major high temperature superconductor cable concepts combining scalability, flexibility, mechanical strength, ease of fabrication and high current density; making it a possible candidate as conductor for large, high field magnets. To simulate the boundary conditions of such magnets as well as the temperature dependence of CORC cables a 1.16 m long sample consisting of 15, 4 mm wide SuperPower REBCO tapes was characterized using the ‘FBI’ (force—field—current) superconductor test facility of the Institute for Technical Physics of the Karlsruhe Institute of Technology. In a five step investigation, the CORC cable’s performance was determined at different transverse mechanical loads, magnetic background fields and temperatures as well as its response to swift current changes. In the first step, the sample’s 77 K, self-field current was measured in a liquid nitrogen bath. In the second step, the temperature dependence was measured at self-field condition and compared with extrapolated single tape data. In the third step, the magnetic background field was repeatedly cycled while measuring the current carrying capabilities to determine the impact of transverse Lorentz forces on the CORC cable sample’s performance. In the fourth step, the sample’s current carrying capabilities were measured at different background fields (2-12 T) and surface temperatures (4.2-51.5 K). Through finite element method simulations, the surface temperatures are converted into average sample temperatures and the gained field- and temperature dependence is compared with extrapolated single tape data. In the fifth step, the response of the CORC cable sample to rapid current changes (8.3 kA s-1) was observed with a fast data acquisition system. During these tests, the sample performance remains constant, no degradation is observed. The sample’s measured current carrying capabilities correlate to those of single tapes assuming field- and temperature dependence as published by the manufacturer.

Method for implantation of high dopant concentrations in wide band gap materials

DOEpatents

Usov, Igor [Los Alamos, NM; Arendt, Paul N [Los Alamos, NM

2009-09-15

A method that combines alternate low/medium ion dose implantation with rapid thermal annealing at relatively low temperatures. At least one dopant is implanted in one of a single crystal and an epitaxial film of the wide band gap compound by a plurality of implantation cycles. The number of implantation cycles is sufficient to implant a predetermined concentration of the dopant in one of the single crystal and the epitaxial film. Each of the implantation cycles includes the steps of: implanting a portion of the predetermined concentration of the one dopant in one of the single crystal and the epitaxial film; annealing one of the single crystal and the epitaxial film and implanted portion at a predetermined temperature for a predetermined time to repair damage to one of the single crystal and the epitaxial film caused by implantation and activates the implanted dopant; and cooling the annealed single crystal and implanted portion to a temperature of less than about 100.degree. C. This combination produces high concentrations of dopants, while minimizing the defect concentration.

Method for measuring thermal properties using a long-wavelength infrared thermal image

DOEpatents

Walker, Charles L [Albuquerque, NM; Costin, Laurence S [Albuquerque, NM; Smith, Jody L [Albuquerque, NM; Moya, Mary M [Albuquerque, NM; Mercier, Jeffrey A [Albuquerque, NM

2007-01-30

A method for estimating the thermal properties of surface materials using long-wavelength thermal imagery by exploiting the differential heating histories of ground points in the vicinity of shadows. The use of differential heating histories of different ground points of the same surface material allows the use of a single image acquisition step to provide the necessary variation in measured parameters for calculation of the thermal properties of surface materials.

Volume measurements of individual muscles in human quadriceps femoris using atlas-based segmentation approaches.

PubMed

Le Troter, Arnaud; Fouré, Alexandre; Guye, Maxime; Confort-Gouny, Sylviane; Mattei, Jean-Pierre; Gondin, Julien; Salort-Campana, Emmanuelle; Bendahan, David

2016-04-01

Atlas-based segmentation is a powerful method for automatic structural segmentation of several sub-structures in many organs. However, such an approach has been very scarcely used in the context of muscle segmentation, and so far no study has assessed such a method for the automatic delineation of individual muscles of the quadriceps femoris (QF). In the present study, we have evaluated a fully automated multi-atlas method and a semi-automated single-atlas method for the segmentation and volume quantification of the four muscles of the QF and for the QF as a whole. The study was conducted in 32 young healthy males, using high-resolution magnetic resonance images (MRI) of the thigh. The multi-atlas-based segmentation method was conducted in 25 subjects. Different non-linear registration approaches based on free-form deformable (FFD) and symmetric diffeomorphic normalization algorithms (SyN) were assessed. Optimal parameters of two fusion methods, i.e., STAPLE and STEPS, were determined on the basis of the highest Dice similarity index (DSI) considering manual segmentation (MSeg) as the ground truth. Validation and reproducibility of this pipeline were determined using another MRI dataset recorded in seven healthy male subjects on the basis of additional metrics such as the muscle volume similarity values, intraclass coefficient, and coefficient of variation. Both non-linear registration methods (FFD and SyN) were also evaluated as part of a single-atlas strategy in order to assess longitudinal muscle volume measurements. The multi- and the single-atlas approaches were compared for the segmentation and the volume quantification of the four muscles of the QF and for the QF as a whole. Considering each muscle of the QF, the DSI of the multi-atlas-based approach was high 0.87 ± 0.11 and the best results were obtained with the combination of two deformation fields resulting from the SyN registration method and the STEPS fusion algorithm. The optimal variables for FFD and SyN registration methods were four templates and a kernel standard deviation ranging between 5 and 8. The segmentation process using a single-atlas-based method was more robust with DSI values higher than 0.9. From the vantage of muscle volume measurements, the multi-atlas-based strategy provided acceptable results regarding the QF muscle as a whole but highly variable results regarding individual muscle. On the contrary, the performance of the single-atlas-based pipeline for individual muscles was highly comparable to the MSeg, thereby indicating that this method would be adequate for longitudinal tracking of muscle volume changes in healthy subjects. In the present study, we demonstrated that both multi-atlas and single-atlas approaches were relevant for the segmentation of individual muscles of the QF in healthy subjects. Considering muscle volume measurements, the single-atlas method provided promising perspectives regarding longitudinal quantification of individual muscle volumes.

Direct digestion of proteins in living cells into peptides for proteomic analysis.

PubMed

Chen, Qi; Yan, Guoquan; Gao, Mingxia; Zhang, Xiangmin

2015-01-01

To analyze the proteome of an extremely low number of cells or even a single cell, we established a new method of digesting whole cells into mass-spectrometry-identifiable peptides in a single step within 2 h. Our sampling method greatly simplified the processes of cell lysis, protein extraction, protein purification, and overnight digestion, without compromising efficiency. We used our method to digest hundred-scale cells. As far as we know, there is no report of proteome analysis starting directly with as few as 100 cells. We identified an average of 109 proteins from 100 cells, and with three replicates, the number of proteins rose to 204. Good reproducibility was achieved, showing stability and reliability of the method. Gene Ontology analysis revealed that proteins in different cellular compartments were well represented.

Tools for probing local circuits: high-density silicon probes combined with optogenetics

PubMed Central

Buzsáki, György; Stark, Eran; Berényi, Antal; Khodagholy, Dion; Kipke, Daryl R.; Yoon, Euisik; Wise, Kensall

2015-01-01

To understand how function arises from the interactions between neurons, it is necessary to use methods that allow the monitoring of brain activity at the single-neuron, single-spike level and the targeted manipulation of the diverse neuron types selectively in a closed-loop manner. Large-scale recordings of neuronal spiking combined with optogenetic perturbation of identified individual neurons has emerged as a suitable method for such tasks in behaving animals. To fully exploit the potential power of these methods, multiple steps of technical innovation are needed. We highlight the current state-of-the-art in electrophysiological recording methods, combined with optogenetics, and discuss directions for progress. In addition, we point to areas where rapid development is in progress and discuss topics where near-term improvements are possible and needed. PMID:25856489

A Robust Approach for a Filter-Based Monocular Simultaneous Localization and Mapping (SLAM) System

PubMed Central

Munguía, Rodrigo; Castillo-Toledo, Bernardino; Grau, Antoni

2013-01-01

Simultaneous localization and mapping (SLAM) is an important problem to solve in robotics theory in order to build truly autonomous mobile robots. This work presents a novel method for implementing a SLAM system based on a single camera sensor. The SLAM with a single camera, or monocular SLAM, is probably one of the most complex SLAM variants. In this case, a single camera, which is freely moving through its environment, represents the sole sensor input to the system. The sensors have a large impact on the algorithm used for SLAM. Cameras are used more frequently, because they provide a lot of information and are well adapted for embedded systems: they are light, cheap and power-saving. Nevertheless, and unlike range sensors, which provide range and angular information, a camera is a projective sensor providing only angular measurements of image features. Therefore, depth information (range) cannot be obtained in a single step. In this case, special techniques for feature system-initialization are needed in order to enable the use of angular sensors (as cameras) in SLAM systems. The main contribution of this work is to present a novel and robust scheme for incorporating and measuring visual features in filtering-based monocular SLAM systems. The proposed method is based in a two-step technique, which is intended to exploit all the information available in angular measurements. Unlike previous schemes, the values of parameters used by the initialization technique are derived directly from the sensor characteristics, thus simplifying the tuning of the system. The experimental results show that the proposed method surpasses the performance of previous schemes. PMID:23823972

Matching Aerial Images to 3D Building Models Using Context-Based Geometric Hashing

PubMed Central

Jung, Jaewook; Sohn, Gunho; Bang, Kiin; Wichmann, Andreas; Armenakis, Costas; Kada, Martin

2016-01-01

A city is a dynamic entity, which environment is continuously changing over time. Accordingly, its virtual city models also need to be regularly updated to support accurate model-based decisions for various applications, including urban planning, emergency response and autonomous navigation. A concept of continuous city modeling is to progressively reconstruct city models by accommodating their changes recognized in spatio-temporal domain, while preserving unchanged structures. A first critical step for continuous city modeling is to coherently register remotely sensed data taken at different epochs with existing building models. This paper presents a new model-to-image registration method using a context-based geometric hashing (CGH) method to align a single image with existing 3D building models. This model-to-image registration process consists of three steps: (1) feature extraction; (2) similarity measure; and matching, and (3) estimating exterior orientation parameters (EOPs) of a single image. For feature extraction, we propose two types of matching cues: edged corner features representing the saliency of building corner points with associated edges, and contextual relations among the edged corner features within an individual roof. A set of matched corners are found with given proximity measure through geometric hashing, and optimal matches are then finally determined by maximizing the matching cost encoding contextual similarity between matching candidates. Final matched corners are used for adjusting EOPs of the single airborne image by the least square method based on collinearity equations. The result shows that acceptable accuracy of EOPs of a single image can be achievable using the proposed registration approach as an alternative to a labor-intensive manual registration process. PMID:27338410

Step-reduced synthesis of starch-silver nanoparticles.

PubMed

Raghavendra, Gownolla Malegowd; Jung, Jeyoung; Kim, Dowan; Seo, Jongchul

2016-05-01

In the present process, silver nanoparticles were directly synthesized in a single step by microwave irradiation of a mixture of starch, silver nitrate, and deionized water. This is different from the commonly adopted procedure for starch-silver nanoparticle synthesis in which silver nanoparticles are synthesized by preparing a starch solution as a reaction medium first. Thus, the additional step associated with the preparation of the starch solution was eliminated. In addition, no additional reducing agent was utilized. The adopted method was facile and straight forward, affording spherical silver nanoparticles with diameter below 10nm that exhibited good antibacterial activity. Further, influence of starch on the size of the silver nanoparticles was noticed. Copyright © 2016 Elsevier B.V. All rights reserved.

Influence of frequency on shear fatigue strength of resin composite to enamel bonds using self-etch adhesives.

PubMed

Takamizawa, Toshiki; Scheidel, Donal D; Barkmeier, Wayne W; Erickson, Robert L; Tsujimoto, Akimasa; Latta, Mark A; Miyazaki, Masashi

2016-09-01

The purpose of this study was to determine the influence of different frequency rates on of bond durability of self-etch adhesives to enamel using shear fatigue strength (SFS) testing. A two-step self-etch adhesive (OX, OptiBond XTR), and two single step self-etch adhesives (GB, G-ӕnial Bond and SU, Scotchbond Universal) were used in this study. The shear fatigue strength (SFS) to enamel was obtained. A staircase method was used to determine the SFS values with 50,000 cycles or until failure occurred. Fatigue testing was performed at frequencies of 5Hz, 10Hz, and 20Hz. For each test condition, 30 specimens were prepared for the SFS testing. Regardless of the bond strength test method, OX showed significantly higher SFS values than the two single-step self-etch adhesives. For each of the three individual self-etch adhesives, there was no significant difference in SFS depending on the frequency rate, although 20Hz results tended to be higher. Regardless of the self-etch adhesive system, frequencies of 5Hz, 10Hz, and 20Hz produced similar results in fatigue strength of resin composite bonded to enamel using 50,000 cycles or until bond failure. Accelerated fatigue testing provides valuable information regarding the long term durability of resin composite to enamel bonding using self-etch adhesive system. Copyright © 2016 Elsevier Ltd. All rights reserved.

Detection of walking periods and number of steps in older adults and patients with Parkinson's disease: accuracy of a pedometer and an accelerometry-based method.

PubMed

Dijkstra, Baukje; Zijlstra, Wiebren; Scherder, Erik; Kamsma, Yvo

2008-07-01

The aim of this study was to examine if walking periods and number of steps can accurately be detected by a single small body-fixed device in older adults and patients with Parkinson's disease (PD). Results of an accelerometry-based method (DynaPort MicroMod) and a pedometer (Yamax Digi-Walker SW-200) worn on each hip were evaluated against video observation. Twenty older adults and 32 PD patients walked straight-line trajectories at different speeds, of different lengths and while doing secondary tasks in an indoor hallway. Accuracy of the instruments was expressed as absolute percentage error (older adults versus PD patients). Based on the video observation, a total of 236.8 min of gait duration and 24,713 steps were assessed. The DynaPort method predominantly overestimated gait duration (10.7 versus 11.1%) and underestimated the number of steps (7.4 versus 6.9%). Accuracy decreased significantly as walking distance decreased. Number of steps were also mainly underestimated by the pedometers, the left Yamax (6.8 versus 11.1%) being more accurate than the right Yamax (11.1 versus 16.3%). Step counting of both pedometers was significantly less accurate for short trajectories (3 or 5 m) and as walking pace decreased. It is concluded that the Yamax pedometer can be reliably used for this study population when walking at sufficiently high gait speeds (>1.0 m/s). The accelerometry-based method is less speed-dependent and proved to be more appropriate in the PD patients for walking trajectories of 5 m or more.

Multiple node remote messaging

DOEpatents

Blumrich, Matthias A.; Chen, Dong; Gara, Alan G.; Giampapa, Mark E.; Heidelberger, Philip; Ohmacht, Martin; Salapura, Valentina; Steinmacher-Burow, Burkhard; Vranas, Pavlos

2010-08-31

A method for passing remote messages in a parallel computer system formed as a network of interconnected compute nodes includes that a first compute node (A) sends a single remote message to a remote second compute node (B) in order to control the remote second compute node (B) to send at least one remote message. The method includes various steps including controlling a DMA engine at first compute node (A) to prepare the single remote message to include a first message descriptor and at least one remote message descriptor for controlling the remote second compute node (B) to send at least one remote message, including putting the first message descriptor into an injection FIFO at the first compute node (A) and sending the single remote message and the at least one remote message descriptor to the second compute node (B).

Antibody-ribosome-mRNA (ARM) complexes as efficient selection particles for in vitro display and evolution of antibody combining sites.

PubMed Central

He, M; Taussig, M J

1997-01-01

We describe a rapid, eukaryotic, in vitro method for selection and evolution of antibody combining sites using antibody-ribosome-mRNA (ARM) complexes as selection particles. ARMs carrying single-chain (VH/K) binding fragments specific for progesterone were selected using antigen-coupled magnetic beads; selection simultaneously captured the genetic information as mRNA, making it possible to generate and amplify cDNA by single-step RT-PCR on the ribosome-bound mRNA for further manipulation. Using mutant libraries, antigen-binding ARMs were enriched by a factor of 10(4)-10(5)-fold in a single cycle, with further enrichment in repeated cycles. While demonstrated here for antibodies, the method has the potential to be applied equally for selection of receptors or peptides from libraries. PMID:9396828

Antibody-ribosome-mRNA (ARM) complexes as efficient selection particles for in vitro display and evolution of antibody combining sites.

PubMed

He, M; Taussig, M J

1997-12-15

We describe a rapid, eukaryotic, in vitro method for selection and evolution of antibody combining sites using antibody-ribosome-mRNA (ARM) complexes as selection particles. ARMs carrying single-chain (VH/K) binding fragments specific for progesterone were selected using antigen-coupled magnetic beads; selection simultaneously captured the genetic information as mRNA, making it possible to generate and amplify cDNA by single-step RT-PCR on the ribosome-bound mRNA for further manipulation. Using mutant libraries, antigen-binding ARMs were enriched by a factor of 10(4)-10(5)-fold in a single cycle, with further enrichment in repeated cycles. While demonstrated here for antibodies, the method has the potential to be applied equally for selection of receptors or peptides from libraries.

Profiling DNA methylome landscapes of mammalian cells with single-cell reduced-representation bisulfite sequencing.

PubMed

Guo, Hongshan; Zhu, Ping; Guo, Fan; Li, Xianlong; Wu, Xinglong; Fan, Xiaoying; Wen, Lu; Tang, Fuchou

2015-05-01

The heterogeneity of DNA methylation within a population of cells necessitates DNA methylome profiling at single-cell resolution. Recently, we developed a single-cell reduced-representation bisulfite sequencing (scRRBS) technique in which we modified the original RRBS method by integrating all the experimental steps before PCR amplification into a single-tube reaction. These modifications enable scRRBS to provide digitized methylation information on ∼1 million CpG sites within an individual diploid mouse or human cell at single-base resolution. Compared with the single-cell bisulfite sequencing (scBS) technique, scRRBS covers fewer CpG sites, but it provides better coverage for CpG islands (CGIs), which are likely to be the most informative elements for DNA methylation. The entire procedure takes ∼3 weeks, and it requires strong molecular biology skills.

A biomechanical analysis of common lunge tasks in badminton.

PubMed

Kuntze, Gregor; Mansfield, Neil; Sellers, William

2010-01-01

The lunge is regularly used in badminton and is recognized for the high physical demands it places on the lower limbs. Despite its common occurrence, little information is available on the biomechanics of lunging in the singles game. A video-based pilot study confirmed the relatively high frequency of lunging, approximately 15% of all movements, in competitive singles games. The biomechanics and performance characteristics of three badminton-specific lunge tasks (kick, step-in, and hop lunge) were investigated in the laboratory with nine experienced male badminton players. Ground reaction forces and kinematic data were collected and lower limb joint kinetics calculated using an inverse dynamics approach. The step-in lunge was characterized by significantly lower mean horizontal reaction force at drive-off and lower mean peak hip joint power than the kick lunge. The hop lunge resulted in significantly larger mean reaction forces during loading and drive-off phases, as well as significantly larger mean peak ankle joint moments and knee and ankle joint powers than the kick or step-in lunges. These findings indicate that, within the setting of this investigation, the step-in lunge may be beneficial for reducing the muscular demands of lunge recovery and that the hop lunge allows for higher positive power output, thereby presenting an efficient lunging method.

Use of aluminum phosphate as the dehydration catalyst in single step dimethyl ether process

DOEpatents

Peng, Xiang-Dong; Parris, Gene E.; Toseland, Bernard A.; Battavio, Paula J.

1998-01-01

The present invention pertains to a process for the coproduction of methanol and dimethyl ether (DME) directly from a synthesis gas in a single step (hereafter, the "single step DME process"). In this process, the synthesis gas comprising hydrogen and carbon oxides is contacted with a dual catalyst system comprising a physical mixture of a methanol synthesis catalyst and a methanol dehydration catalyst. The present invention is an improvement to this process for providing an active and stable catalyst system. The improvement comprises the use of an aluminum phosphate based catalyst as the methanol dehydration catalyst. Due to its moderate acidity, such a catalyst avoids the coke formation and catalyst interaction problems associated with the conventional dual catalyst systems taught for the single step DME process.

Single-reactor process for producing liquid-phase organic compounds from biomass

DOEpatents

Dumesic, James A.; Simonetti, Dante A.; Kunkes, Edward L.

2015-12-08

Disclosed is a method for preparing liquid fuel and chemical intermediates from biomass-derived oxygenated hydrocarbons. The method includes the steps of reacting in a single reactor an aqueous solution of a biomass-derived, water-soluble oxygenated hydrocarbon reactant, in the presence of a catalyst comprising a metal selected from the group consisting of Cr, Mn, Fe, Co, Ni, Cu, Mo, Tc, Ru, Rh, Pd, Ag, W, Re, Os, Ir, Pt, and Au, at a temperature, and a pressure, and for a time sufficient to yield a self-separating, three-phase product stream comprising a vapor phase, an organic phase containing linear and/or cyclic mono-oxygenated hydrocarbons, and an aqueous phase.

Single-reactor process for producing liquid-phase organic compounds from biomass

DOEpatents

Dumesic, James A [Verona, WI; Simonetti, Dante A [Middleton, WI; Kunkes, Edward L [Madison, WI

2011-12-13

Disclosed is a method for preparing liquid fuel and chemical intermediates from biomass-derived oxygenated hydrocarbons. The method includes the steps of reacting in a single reactor an aqueous solution of a biomass-derived, water-soluble oxygenated hydrocarbon reactant, in the presence of a catalyst comprising a metal selected from the group consisting of Cr, Mn, Fe, Co, Ni, Cu, Mo, Tc, Ru, Rh, Pd, Ag, W, Re, Os, Ir, Pt, and Au, at a temperature, and a pressure, and for a time sufficient to yield a self-separating, three-phase product stream comprising a vapor phase, an organic phase containing linear and/or cyclic mono-oxygenated hydrocarbons, and an aqueous phase.

Voluntary stepping behavior under single- and dual-task conditions in chronic stroke survivors: A comparison between the involved and uninvolved legs.

PubMed

Melzer, Itshak; Goldring, Melissa; Melzer, Yehudit; Green, Elad; Tzedek, Irit

2010-12-01

If balance is lost, quick step execution can prevent falls. Research has shown that speed of voluntary stepping was able to predict future falls in old adults. The aim of the study was to investigate voluntary stepping behavior, as well as to compare timing and leg push-off force-time relation parameters of involved and uninvolved legs in stroke survivors during single- and dual-task conditions. We also aimed to compare timing and leg push-off force-time relation parameters between stroke survivors and healthy individuals in both task conditions. Ten stroke survivors performed a voluntary step execution test with their involved and uninvolved legs under two conditions: while focusing only on the stepping task and while a separate attention-demanding task was performed simultaneously. Temporal parameters related to the step time were measured including the duration of the step initiation phase, the preparatory phase, the swing phase, and the total step time. In addition, force-time parameters representing the push-off power during stepping were calculated from ground reaction data and compared with 10 healthy controls. The involved legs of stroke survivors had a significantly slower stepping time than uninvolved legs due to increased swing phase duration during both single- and dual-task conditions. For dual compared to single task, the stepping time increased significantly due to a significant increase in the duration of step initiation. In general, the force time parameters were significantly different in both legs of stroke survivors as compared to healthy controls, with no significant effect of dual compared with single-task conditions in both groups. The inability of stroke survivors to swing the involved leg quickly may be the most significant factor contributing to the large number of falls to the paretic side. The results suggest that stroke survivors were unable to rapidly produce muscle force in fast actions. This may be the mechanism of delayed execution of a fast step when balance is lost, thus increasing the likelihood of falls in stroke survivors. Copyright © 2010 Elsevier Ltd. All rights reserved.

Multiple-3D-object secure information system based on phase shifting method and single interference.

PubMed

Li, Wei-Na; Shi, Chen-Xiao; Piao, Mei-Lan; Kim, Nam

2016-05-20

We propose a multiple-3D-object secure information system for encrypting multiple three-dimensional (3D) objects based on the three-step phase shifting method. During the decryption procedure, five phase functions (PFs) are decreased to three PFs, in comparison with our previous method, which implies that one cross beam splitter is utilized to implement the single decryption interference. Moreover, the advantages of the proposed scheme also include: each 3D object can be decrypted discretionarily without decrypting a series of other objects earlier; the quality of the decrypted slice image of each object is high according to the correlation coefficient values, none of which is lower than 0.95; no iterative algorithm is involved. The feasibility of the proposed scheme is demonstrated by computer simulation results.

Targeted sorting of single virus-infected cells of the coccolithophore Emiliania huxleyi.

PubMed

Martínez Martínez, Joaquín; Poulton, Nicole J; Stepanauskas, Ramunas; Sieracki, Michael E; Wilson, William H

2011-01-01

Discriminating infected from healthy cells is the first step to understanding the mechanisms and ecological implications of viral infection. We have developed a method for detecting, sorting, and performing molecular analysis of individual, infected cells of the important microalga Emiliania huxleyi, based on known physiological responses to viral infection. Of three fluorescent dyes tested, FM 1-43 (for detecting membrane blebbing) gave the most unequivocal and earliest separation of cells. Furthermore, we were able to amplify the genomes of single infected cells using Multiple Displacement Amplification. This novel method to reliably discriminate infected from healthy cells in cultures will allow researchers to answer numerous questions regarding the mechanisms and implications of viral infection of E. huxleyi. The method may be transferable to other virus-host systems.

Development of a One-Step Duplex RT-PCR Method for the Simultaneous Detection of VP3/VP1 and VP1/P2B Regions of the Hepatitis A Virus.

PubMed

Kim, Mi-Ju; Lee, Shin-Young; Kim, Hyun-Joong; Lee, Jeong Su; Joo, In Sun; Kwak, Hyo Sun; Kim, Hae-Yeong

2016-08-28

The simultaneous detection and accurate identification of hepatitis A virus (HAV) is critical in food safety and epidemiological studies to prevent the spread of HAV outbreaks. Towards this goal, a one-step duplex reverse-transcription (RT)-PCR method was developed targeting the VP1/P2B and VP3/VP1 regions of the HAV genome for the qualitative detection of HAV. An HAV RT-qPCR standard curve was produced for the quantification of HAV RNA. The detection limit of the duplex RT-PCR method was 2.8 × 10(1) copies of HAV. The PCR products enabled HAV genotyping analysis through DNA sequencing, which can be applied for epidemiological investigations. The ability of this duplex RT-PCR method to detect HAV was evaluated with HAV-spiked samples of fresh lettuce, frozen strawberries, and oysters. The limit of detection of the one-step duplex RT-PCR for each food model was 9.4 × 10(2) copies/20 g fresh lettuce, 9.7 × 10(3) copies/20 g frozen strawberries, and 4.1 × 10(3) copies/1.5 g oysters. Use of a one-step duplex RT-PCR method has advantages such as shorter time, decreased cost, and decreased labor owing to the single amplification reaction instead of four amplifications necessary for nested RT-PCR.

Electrode Reactions Coupled with Chemical Reactions of Oxygen, Water and Acetaldehyde in an Ionic Liquid: New Approaches for Sensing Volatile Organic Compounds.

PubMed

Chi, Xiaowei; Tang, Yongan; Zeng, Xiangqun

2016-10-20

Water and oxygen are ubiquitous present in ambient conditions. This work studies the unique oxygen, trace water and a volatile organic compound (VOC) acetaldehyde redox chemistry in a hydrophobic and aprotic ionic liquid (IL), 1-butyl-1-methylpyrrolidinium bis(trifluoromethanesulfonyl)imide ([Bmpy] [NTf 2 ]) by cyclic voltammetry and potential step methods. One electron oxygen reduction leads to superoxide radical formation in the IL. Trace water in the IL acts as a protic species that reacts with the superoxide radical. Acetaldehyde is a stronger protic species than water for reacting with the superoxide radical. The presence of trace water in the IL was also demonstrated to facilitate the electro-oxidation of acetaldehyde, with similar mechanism to that in the aqueous solutions. A multiple-step coupling reaction mechanism between water, superoxide radical and acetaldehyde has been described. The unique characteristics of redox chemistry of acetaldehyde in [Bmpy][NTf 2 ] in the presence of oxygen and trace water can be controlled by electrochemical potentials. By controlling the electrode potential windows, several methods including cyclic voltammetry, potential step methods (single-potential, double-potential and triple-potential step methods) were established for the quantification of acetaldehyde. Instead of treating water and oxygen as frustrating interferents to ILs, we found that oxygen and trace water chemistry in [Bmpy][NTf 2 ] can be utilized to develop innovative electrochemical methods for electroanalysis of acetaldehyde.

Multiple Imputation of Completely Missing Repeated Measures Data within Person from a Complex Sample: Application to Accelerometer Data in the National Health and Nutrition Examination Survey

PubMed Central

Liu, Benmei; Yu, Mandi; Graubard, Barry I; Troiano, Richard P; Schenker, Nathaniel

2016-01-01

The Physical Activity Monitor (PAM) component was introduced into the 2003-2004 National Health and Nutrition Examination Survey (NHANES) to collect objective information on physical activity including both movement intensity counts and ambulatory steps. Due to an error in the accelerometer device initialization process, the steps data were missing for all participants in several primary sampling units (PSUs), typically a single county or group of contiguous counties, who had intensity count data from their accelerometers. To avoid potential bias and loss in efficiency in estimation and inference involving the steps data, we considered methods to accurately impute the missing values for steps collected in the 2003-2004 NHANES. The objective was to come up with an efficient imputation method which minimized model-based assumptions. We adopted a multiple imputation approach based on Additive Regression, Bootstrapping and Predictive mean matching (ARBP) methods. This method fits alternative conditional expectation (ace) models, which use an automated procedure to estimate optimal transformations for both the predictor and response variables. This paper describes the approaches used in this imputation and evaluates the methods by comparing the distributions of the original and the imputed data. A simulation study using the observed data is also conducted as part of the model diagnostics. Finally some real data analyses are performed to compare the before and after imputation results. PMID:27488606

Electrode Reactions Coupled with Chemical Reactions of Oxygen, Water and Acetaldehyde in an Ionic Liquid: New Approaches for Sensing Volatile Organic Compounds

PubMed Central

Chi, Xiaowei; Tang, Yongan; Zeng, Xiangqun

2017-01-01

Water and oxygen are ubiquitous present in ambient conditions. This work studies the unique oxygen, trace water and a volatile organic compound (VOC) acetaldehyde redox chemistry in a hydrophobic and aprotic ionic liquid (IL), 1-butyl-1-methylpyrrolidinium bis(trifluoromethanesulfonyl)imide ([Bmpy] [NTf2]) by cyclic voltammetry and potential step methods. One electron oxygen reduction leads to superoxide radical formation in the IL. Trace water in the IL acts as a protic species that reacts with the superoxide radical. Acetaldehyde is a stronger protic species than water for reacting with the superoxide radical. The presence of trace water in the IL was also demonstrated to facilitate the electro-oxidation of acetaldehyde, with similar mechanism to that in the aqueous solutions. A multiple-step coupling reaction mechanism between water, superoxide radical and acetaldehyde has been described. The unique characteristics of redox chemistry of acetaldehyde in [Bmpy][NTf2] in the presence of oxygen and trace water can be controlled by electrochemical potentials. By controlling the electrode potential windows, several methods including cyclic voltammetry, potential step methods (single-potential, double-potential and triple-potential step methods) were established for the quantification of acetaldehyde. Instead of treating water and oxygen as frustrating interferents to ILs, we found that oxygen and trace water chemistry in [Bmpy][NTf2] can be utilized to develop innovative electrochemical methods for electroanalysis of acetaldehyde. PMID:29142331

Adaptive [theta]-methods for pricing American options

NASA Astrophysics Data System (ADS)

Khaliq, Abdul Q. M.; Voss, David A.; Kazmi, Kamran

2008-12-01

We develop adaptive [theta]-methods for solving the Black-Scholes PDE for American options. By adding a small, continuous term, the Black-Scholes PDE becomes an advection-diffusion-reaction equation on a fixed spatial domain. Standard implementation of [theta]-methods would require a Newton-type iterative procedure at each time step thereby increasing the computational complexity of the methods. Our linearly implicit approach avoids such complications. We establish a general framework under which [theta]-methods satisfy a discrete version of the positivity constraint characteristic of American options, and numerically demonstrate the sensitivity of the constraint. The positivity results are established for the single-asset and independent two-asset models. In addition, we have incorporated and analyzed an adaptive time-step control strategy to increase the computational efficiency. Numerical experiments are presented for one- and two-asset American options, using adaptive exponential splitting for two-asset problems. The approach is compared with an iterative solution of the two-asset problem in terms of computational efficiency.

Effective size selection of MoS2 nanosheets by a novel liquid cascade centrifugation: Influences of the flakes dimensions on electrochemical and photoelectrochemical applications.

PubMed

Kajbafvala, Marzieh; Farbod, Mansoor

2018-05-14

Although liquid phase exfoliation is a powerful method to produce MoS 2 nanosheets in large scale, but its effectiveness is limited by the diversity of produced nanosheets sizes. Here a novel approach for separation of MoS 2 flakes having various lateral sizes and thicknesses based on the cascaded centrifugation has been introduced. This method involves a pre-separation step which is performed through low-speed centrifugation to avoid the deposition of large area single and few-layers by the heavier particles. The bulk MoS 2 powders were dispersed in an aqueous solution of sodium cholate (SC) and sonicated for 12 h. The main separation step was performed using different speed centrifugation intervals of 10-11, 8-10, 6-8, 4-6, 2-4 and 0.5-2 krpm by which nanosheets containing 2, 4, 7, 8, 14, 18 and 29 layers were obtained respectively. The samples were characterized using XRD, FESEM, AFM, TEM, DLS and also UV-vis, Raman and PL spectroscopy measurements. Dynamic light scattering (DLS) measurements have confirmed the existence of a larger number of single or few-layers MoS 2 nanosheets compared to when the pre-separation step was not used. Finally, Photocurrent and cyclic voltammetry of different samples were measured and found that the flakes with bigger surface area had larger CV loop area. Our results provide a method for the preparation of a MoS 2 monolayer enriched suspension which can be used for different applications. Copyright © 2018 Elsevier Inc. All rights reserved.

Self-digitization microfluidic chip for absolute quantification of mRNA in single cells.

PubMed

Thompson, Alison M; Gansen, Alexander; Paguirigan, Amy L; Kreutz, Jason E; Radich, Jerald P; Chiu, Daniel T

2014-12-16

Quantification of mRNA in single cells provides direct insight into how intercellular heterogeneity plays a role in disease progression and outcomes. Quantitative polymerase chain reaction (qPCR), the current gold standard for evaluating gene expression, is insufficient for providing absolute measurement of single-cell mRNA transcript abundance. Challenges include difficulties in handling small sample volumes and the high variability in measurements. Microfluidic digital PCR provides far better sensitivity for minute quantities of genetic material, but the typical format of this assay does not allow for counting of the absolute number of mRNA transcripts samples taken from single cells. Furthermore, a large fraction of the sample is often lost during sample handling in microfluidic digital PCR. Here, we report the absolute quantification of single-cell mRNA transcripts by digital, one-step reverse transcription PCR in a simple microfluidic array device called the self-digitization (SD) chip. By performing the reverse transcription step in digitized volumes, we find that the assay exhibits a linear signal across a wide range of total RNA concentrations and agrees well with standard curve qPCR. The SD chip is found to digitize a high percentage (86.7%) of the sample for single-cell experiments. Moreover, quantification of transferrin receptor mRNA in single cells agrees well with single-molecule fluorescence in situ hybridization experiments. The SD platform for absolute quantification of single-cell mRNA can be optimized for other genes and may be useful as an independent control method for the validation of mRNA quantification techniques.

SU-G-BRB-05: Automation of the Photon Dosimetric Quality Assurance Program of a Linear Accelerator

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

Lebron, S; Lu, B; Yan, G

Purpose: To develop an automated method to calculate a linear accelerator (LINAC) photon radiation field size, flatness, symmetry, output and beam quality in a single delivery for flattened (FF) and flattening-filter-free (FFF) beams using an ionization chamber array. Methods: The proposed method consists of three control points that deliver 30×30, 10×10 and 5×5cm{sup 2} fields (FF or FFF) in a step-and-shoot sequence where the number of monitor units is weighted for each field size. The IC Profiler (Sun Nuclear Inc.) with 5mm detector spacing was used for this study. The corrected counts (CCs) were calculated and the locations of themore » maxima and minima values of the first-order gradient determined data of each sub field. Then, all CCs for each field size are summed in order to obtain the final profiles. For each profile, the radiation field size, symmetry, flatness, output factor and beam quality were calculated. For field size calculation, a parameterized gradient method was used. For method validation, profiles were collected in the detector array both, individually and as part of the step-and-shoot plan, with 9.9cm buildup for FF and FFF beams at 90cm source-to-surface distance. The same data were collected with the device (plus buildup) placed on a movable platform to achieve a 1mm resolution. Results: The differences between the dosimetric quantities calculated from both deliveries, individually and step-and-shoot, were within 0.31±0.20% and 0.04±0.02mm. The differences between the calculated field sizes with 5mm and 1mm resolution were ±0.1mm. Conclusion: The proposed single delivery method proved to be simple and efficient in automating the photon dosimetric monthly and annual quality assurance.« less

Effects of dual task on turning ability in stroke survivors and older adults.

PubMed

Hollands, K L; Agnihotri, D; Tyson, S F

2014-09-01

Turning is an integral component of independent mobility in which stroke survivors frequently fall. This study sought to measure the effects of competing cognitive demands on the stepping patterns of stroke survivors, compared to healthy age-match adults, during turning as a putative mechanism for falls. Walking and turning (90°) was assessed under single (walking and turning alone) and dual task (subtracting serial 3s while walking and turning) conditions using an electronic, pressure-sensitive walkway. Dependent measures were time to turn, variability in time to turn, step length, step width and single support time during three steps of the turn. Turning ability in single and dual task conditions was compared between stroke survivors (n=17, mean ± SD: 59 ± 113 months post-stroke, 64 ± 10 years of age) and age-matched healthy counterparts (n=15). Both groups took longer, were more variable, tended to widen the second step and, crucially, increased single support time on the inside leg of the turn while turning and distracted. Increased single support time during turning may represent biomechanical mechanism, within stepping patterns of turning under distraction, for increased risk of falls for both stroke survivors and older adults. Crown Copyright © 2014. Published by Elsevier B.V. All rights reserved.

Method for producing redox shuttles

DOEpatents

Pupek, Krzysztof Z.; Dzwiniel, Trevor L.; Krumdick, Gregory K.

2015-03-03

A single step method for producing a redox shuttle having the formula 2,5-di-tert-butyl-1,4-phenylene tetraethyl bis(phosphate) is provided, the method comprising phosphorylating tert butyl hydroquinone with a phosphate-containing reagent. Also provided is method for producing 2,5-di-tert-butyl-1,4-phenylene tetraethyl bis(phosphate), the method comprising solubilizing tert-butyl hydroquinone and tetrabutylammonium bromide with methyltetrahydrofuran to create a mixture; heating the mixture while adding base to the mixture in an amount to turn the mixture orange; and adding diethyl chlorophosphate to the orange mixture in an amount to phosphorylate the hydroquinone.

Optofluidic Cell Selection from Complex Microbial Communities for Single-Genome Analysis

PubMed Central

Landry, Zachary C.; Giovanonni, Stephen J.; Quake, Stephen R.; Blainey, Paul C.

2013-01-01

Genetic analysis of single cells is emerging as a powerful approach for studies of heterogeneous cell populations. Indeed, the notion of homogeneous cell populations is receding as approaches to resolve genetic and phenotypic variation between single cells are applied throughout the life sciences. A key step in single-cell genomic analysis today is the physical isolation of individual cells from heterogeneous populations, particularly microbial populations, which often exhibit high diversity. Here, we detail the construction and use of instrumentation for optical trapping inside microfluidic devices to select individual cells for analysis by methods including nucleic acid sequencing. This approach has unique advantages for analyses of rare community members, cells with irregular morphologies, small quantity samples, and studies that employ advanced optical microscopy. PMID:24060116

Flexible nano- and microliter injections on a single liquid chromatography-mass spectrometry system: Minimizing sample preparation and maximizing linear dynamic range.

PubMed

Lubin, Arnaud; Sheng, Sheng; Cabooter, Deirdre; Augustijns, Patrick; Cuyckens, Filip

2017-11-17

Lack of knowledge on the expected concentration range or insufficient linear dynamic range of the analytical method applied are common challenges for the analytical scientist. Samples that are above the upper limit of quantification are typically diluted and reanalyzed. The analysis of undiluted highly concentrated samples can cause contamination of the system, while the dilution step is time consuming and as the case for any sample preparation step, also potentially leads to precipitation, adsorption or degradation of the analytes. Copyright © 2017 Elsevier B.V. All rights reserved.

Zone clearance in an infinite TASEP with a step initial condition

NASA Astrophysics Data System (ADS)

Cividini, Julien; Appert-Rolland, Cécile

2017-06-01

The TASEP is a paradigmatic model of out-of-equilibrium statistical physics, for which many quantities have been computed, either exactly or by approximate methods. In this work we study two new kinds of observables that have some relevance in biological or traffic models. They represent the probability for a given clearance zone of the lattice to be empty (for the first time) at a given time, starting from a step density profile. Exact expressions are obtained for single-time quantities, while more involved history-dependent observables are studied by Monte Carlo simulation, and partially predicted by a phenomenological approach.

Cell separation and electrofusion in space

NASA Technical Reports Server (NTRS)

Morrison, D. R.; Hofmann, G. A.

1990-01-01

In microgravity, free-fluid electrophoretic methods for separating living cells and proteins are improved significantly by the absence of gravity-driven phenomena. Cell fusion, culture, and other bioprocessing steps are being investigated to understand the limits of earth-based processing. A multistep space bioprocess is described that includes electrophoretic separation of human target cells, single-cell manipulations using receptor-specific antibodies, electrofusion to produce immortal hybridomas, gentle suspension culture, and monoclonal antibody recovery using continuous-flow electrophoresis or recirculating isoelectric focusing. Improvements in several key steps already have been demonstrated by space experiments, and others will be studied on Space Station Freedom.

Ultrasensitive protein detection in blood serum using gold nanoparticle probes by single molecule spectroscopy

NASA Astrophysics Data System (ADS)

Chen, Jiji; Wang, Chungang; Irudayaraj, Joseph

2009-07-01

A one-step rapid and ultrasensitive immunoassay capable of detecting proteins in blood serum is developed using gold nanoprobes and fluorescence correlation spectroscopy (FCS). In this approach we take advantage of the inherent photoluminescence property of gold nanoparticles (GNPs) to develop a fluorophore-free assay to observe binding entities by monitoring the diffusion of bound versus unbound molecules in a limited confocal volume. 40-nm GNPs conjugated separately with rabbit anti-IgG (Fc) and goat anti-IgG (Fab) when incubated in blood serum containing IgG forms a sandwich structure constituting dimers and oligomers that can be differentiated by to detect IgG in blood serum at a limit of detection (LOD) of 5 pg/ml. The novelty of integrating GNPs with FCS to develop a sensitive blood immunoassay brings single molecule methods one step closer to the clinic.

Estimation of the transmissivity of thin leaky-confined aquifers from single-well pumping tests

NASA Astrophysics Data System (ADS)

Worthington, Paul F.

1981-01-01

Data from the quasi-equilibrium phases of a step-drawdown test are used to evaluate the coefficient of non-linear head losses subject to the assumption of a constant effective well radius. After applying a well-loss correction to the observed drawdowns of the first step, an approximation method is used to estimate a pseudo-transmissivity of the aquifer from a single value of time-variant drawdown. The pseudo-transmissivities computed for each of a sequence of values of time pass through a minimum when there is least manifestation of casing-storage and leakage effects, phenomena to which pumping-test data of this kind are particularly susceptible. This minimum pseudo-transmissivity, adjusted for partial penetration effects where appropriate, constitutes the best possible estimate of aquifer transmissivity. The ease of application of the overall procedure is illustrated by a practical example.

Single-Step Reagentless Laser Scribing Fabrication of Electrochemical Paper-Based Analytical Devices.

PubMed

de Araujo, William R; Frasson, Carolina M R; Ameku, Wilson A; Silva, José R; Angnes, Lúcio; Paixão, Thiago R L C

2017-11-20

A single-step laser scribing process is used to pattern nanostructured electrodes on paper-based devices. The facile and low-cost technique eliminates the need for chemical reagents or controlled conditions. This process involves the use of a CO 2 laser to pyrolyze the surface of the paperboard, producing a conductive porous non-graphitizing carbon material composed of graphene sheets and composites with aluminosilicate nanoparticles. The new electrode material was extensively characterized, and it exhibits high conductivity and an enhanced active/geometric area ratio; it is thus well-suited for electrochemical purposes. As a proof-of-concept, the devices were successfully employed for different analytical applications in the clinical, pharmaceutical, food, and forensic fields. The scalable and green fabrication method associated with the features of the new material is highly promising for the development of portable electrochemical devices. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mechanism-Based Condition Screening for Sustainable Catalysis in Single-Electron Steps by Cyclic Voltammetry.

PubMed

Liedtke, Theresa; Spannring, Peter; Riccardi, Ludovico; Gansäuer, Andreas

2018-04-23

A cyclic-voltammetry-based screening method for Cp 2 TiX-catalyzed reactions is introduced. Our mechanism-based approach enables the study of the influence of various additives on the electrochemically generated active catalyst Cp 2 TiX, which is in equilibrium with catalytically inactive [Cp 2 TiX 2 ] - . Thioureas and ureas are most efficient in the generation of Cp 2 TiX in THF. Knowing the precise position of the equilibrium between Cp 2 TiX and [Cp 2 TiX 2 ] - allowed us to identify reaction conditions for the bulk electrolysis of Cp 2 TiX 2 complexes and for Cp 2 TiX-catayzed radical arylations without having to carry out the reactions. Our time- and resource-efficient approach is of general interest for the design of catalytic reactions that proceed in single-electron steps. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evaluating quality of patient care communication in integrated care settings: a mixed method approach.

PubMed

Gulmans, J; Vollenbroek-Hutten, M M R; Van Gemert-Pijnen, J E W C; Van Harten, W H

2007-10-01

Owing to the involvement of multiple professionals from various institutions, integrated care settings are prone to suboptimal patient care communication. To assure continuity, communication gaps should be identified for targeted improvement initiatives. However, available assessment methods are often one-sided evaluations not appropriate for integrated care settings. We developed an evaluation approach that takes into account the multiple communication links and evaluation perspectives inherent to these settings. In this study, we describe this approach, using the integrated care setting of Cerebral Palsy as illustration. The approach follows a three-step mixed design in which the results of each step are used to mark out the subsequent step's focus. The first step patient questionnaire aims to identify quality gaps experienced by patients, comparing their expectancies and experiences with respect to patient-professional and inter-professional communication. Resulting gaps form the input of in-depth interviews with a subset of patients to evaluate underlying factors of ineffective communication. Resulting factors form the input of the final step's focus group meetings with professionals to corroborate and complete the findings. By combining methods, the presented approach aims to minimize limitations inherent to the application of single methods. The comprehensiveness of the approach enables its applicability in various integrated care settings. Its sequential design allows for in-depth evaluation of relevant quality gaps. Further research is needed to evaluate the approach's feasibility in practice. In our subsequent study, we present the results of the approach in the integrated care setting of children with Cerebral Palsy in three Dutch care regions.

Sealed-bladdered chemical processing method and apparatus

DOEpatents

Harless, D. Phillip

1999-01-01

A method and apparatus which enables a complete multi-stepped chemical treatment process to occur within a single, sealed-bladdered vessel 31. The entire chemical process occurs without interruption of the sealed-bladdered vessel 31 such as opening the sealed-bladdered vessel 31 between various steps of the process. The sealed-bladdered vessel 31 is loaded with a batch to be dissolved, treated, decanted, rinsed and/or dried. A pressure filtration step may also occur. The self-contained chemical processing apparatus 32 contains a sealed-bladder 32, a fluid pump 34, a reservoir 20, a compressed gas inlet, a vacuum pump 24, and a cold trap 23 as well as the associated piping 33, numerous valves 21,22,25,26,29,30,35,36 and other controls associated with such an apparatus. The claimed invention allows for dissolution and/or chemical treatment without the operator of the self-contained chemical processing apparatus 38 coming into contact with any of the process materials.

Template-DTW based on inertial signals: Preliminary results for step characterization.

PubMed

Mantilla, Juan; Oudre, Laurent; Barrois, Remi; Vienne, Alienor; Ricard, Damien

2017-07-01

In this paper, we present a method for the creation of a library of inertial signals based on Dynamic Time Warping (DTW) for step characterization, with preliminary results in control subjects and patients with neurological diseases. Subjects performed a protocol including a 10 m straight walking, then turn back and walking for additional 10 m. The library is constructed with inertial signals (acceleration and angular velocities recorded in three directions) aligned with the DTW. Templates in the library are obtained for a specific cohort and for the different walking phases of the protocol. They are compared to the signal of a single subject by calculating a Pearson correlation coefficient. The method has been tested on a database of 864 exercises, obtained from 71 healthy controls, 24 patients with Parkinson disease and 48 patients with Radiation Induced Leukoencephalopathy (RIL). Pearson correlation classification reports a precision of about 85% for step detection. For exercise characterization the sensitivity is about 57%, 56% and 82% for Parkinson, RIL and control subjects respectively.

Development of a 3-step straight-through purification strategy combining membrane adsorbers and resins.

PubMed

Hughson, Michael D; Cruz, Thayana A; Carvalho, Rimenys J; Castilho, Leda R

2017-07-01

The pressures to efficiently produce complex biopharmaceuticals at reduced costs are driving the development of novel techniques, such as in downstream processing with straight-through processing (STP). This method involves directly and sequentially purifying a particular target with minimal holding steps. This work developed and compared six different 3-step STP strategies, combining membrane adsorbers, monoliths, and resins, to purify a large, complex, and labile glycoprotein from Chinese hamster ovary cell culture supernatant. The best performing pathway was cation exchange chromatography to hydrophobic interaction chromatography to affinity chromatography with an overall product recovery of up to 88% across the process and significant clearance of DNA and protein impurities. This work establishes a platform and considerations for the development of STP of biopharmaceutical products and highlights its suitability for integration with single-use technologies and continuous production methods. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:931-940, 2017. © 2017 American Institute of Chemical Engineers.

Source Detection with Bayesian Inference on ROSAT All-Sky Survey Data Sample

NASA Astrophysics Data System (ADS)

Guglielmetti, F.; Voges, W.; Fischer, R.; Boese, G.; Dose, V.

2004-07-01

We employ Bayesian inference for the joint estimation of sources and background on ROSAT All-Sky Survey (RASS) data. The probabilistic method allows for detection improvement of faint extended celestial sources compared to the Standard Analysis Software System (SASS). Background maps were estimated in a single step together with the detection of sources without pixel censoring. Consistent uncertainties of background and sources are provided. The source probability is evaluated for single pixels as well as for pixel domains to enhance source detection of weak and extended sources.

Structural and spectroscopic study of mechanically synthesized SnO{sub 2} nanostructures

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

Vij, Ankush, E-mail: vij-anx@yahoo.com; Kumar, Ravi; Presently at Beant College of Engineering and Technology, Gurdaspur-143521

2016-05-23

We report the single step synthesis of SnO{sub 2} nanostructures using high energy mechanical attrition method. X-ray diffraction (XRD) pattern reveals the single phase rutile structure with appreciable broadening of diffraction peaks, which is a signature of nanostructure formation. The average crystallite size of SnO{sub 2} nanostructures has been calculated to be ~15 nm. The micro-Raman study reveals the shifting of A{sub 1g} Raman mode towards lower wave number, which is correlated with the nanostructure formation.

Auxotonic to isometric contraction transitioning in a beating heart causes myosin step-size to down shift

PubMed Central

Sun, Xiaojing; Wang, Yihua; Ajtai, Katalin

2017-01-01

Myosin motors in cardiac ventriculum convert ATP free energy to the work of moving blood volume under pressure. The actin bound motor cyclically rotates its lever-arm/light-chain complex linking motor generated torque to the myosin filament backbone and translating actin against resisting force. Previous research showed that the unloaded in vitro motor is described with high precision by single molecule mechanical characteristics including unitary step-sizes of approximately 3, 5, and 8 nm and their relative step-frequencies of approximately 13, 50, and 37%. The 3 and 8 nm unitary step-sizes are dependent on myosin essential light chain (ELC) N-terminus actin binding. Step-size and step-frequency quantitation specifies in vitro motor function including duty-ratio, power, and strain sensitivity metrics. In vivo, motors integrated into the muscle sarcomere form the more complex and hierarchically functioning muscle machine. The goal of the research reported here is to measure single myosin step-size and step-frequency in vivo to assess how tissue integration impacts motor function. A photoactivatable GFP tags the ventriculum myosin lever-arm/light-chain complex in the beating heart of a live zebrafish embryo. Detected single GFP emission reports time-resolved myosin lever-arm orientation interpreted as step-size and step-frequency providing single myosin mechanical characteristics over the active cycle. Following step-frequency of cardiac ventriculum myosin transitioning from low to high force in relaxed to auxotonic to isometric contraction phases indicates that the imposition of resisting force during contraction causes the motor to down-shift to the 3 nm step-size accounting for >80% of all the steps in the near-isometric phase. At peak force, the ATP initiated actomyosin dissociation is the predominant strain inhibited transition in the native myosin contraction cycle. The proposed model for motor down-shifting and strain sensing involves ELC N-terminus actin binding. Overall, the approach is a unique bottom-up single molecule mechanical characterization of a hierarchically functional native muscle myosin. PMID:28423017

Comparison of Stepped Care Delivery Against a Single, Empirically Validated Cognitive-Behavioral Therapy Program for Youth With Anxiety: A Randomized Clinical Trial.

PubMed

Rapee, Ronald M; Lyneham, Heidi J; Wuthrich, Viviana; Chatterton, Mary Lou; Hudson, Jennifer L; Kangas, Maria; Mihalopoulos, Cathrine

2017-10-01

Stepped care is embraced as an ideal model of service delivery but is minimally evaluated. The aim of this study was to evaluate the efficacy of cognitive-behavioral therapy (CBT) for child anxiety delivered via a stepped-care framework compared against a single, empirically validated program. A total of 281 youth with anxiety disorders (6-17 years of age) were randomly allocated to receive either empirically validated treatment or stepped care involving the following: (1) low intensity; (2) standard CBT; and (3) individually tailored treatment. Therapist qualifications increased at each step. Interventions did not differ significantly on any outcome measures. Total therapist time per child was significantly shorter to deliver stepped care (774 minutes) compared with best practice (897 minutes). Within stepped care, the first 2 steps returned the strongest treatment gains. Stepped care and a single empirically validated program for youth with anxiety produced similar efficacy, but stepped care required slightly less therapist time. Restricting stepped care to only steps 1 and 2 would have led to considerable time saving with modest loss in efficacy. Clinical trial registration information-A Randomised Controlled Trial of Standard Care Versus Stepped Care for Children and Adolescents With Anxiety Disorders; http://anzctr.org.au/; ACTRN12612000351819. Copyright © 2017 American Academy of Child and Adolescent Psychiatry. Published by Elsevier Inc. All rights reserved.

Precision-engineering the Pseudomonas aeruginosa genome with two-step allelic exchange

PubMed Central

Hmelo, Laura R.; Borlee, Bradley R.; Almblad, Henrik; Love, Michelle E.; Randall, Trevor E.; Tseng, Boo Shan; Lin, Chuyang; Irie, Yasuhiko; Storek, Kelly M.; Yang, Jaeun Jane; Siehnel, Richard J.; Howell, P. Lynne; Singh, Pradeep K.; Tolker-Nielsen, Tim; Parsek, Matthew R.; Schweizer, Herbert P.; Harrison, Joe J.

2016-01-01

Allelic exchange is an efficient method of bacterial genome engineering. This protocol describes the use of this technique to make gene knockouts and knockins, as well as single nucleotide insertions, deletions and substitutions in Pseudomonas aeruginosa. Unlike other approaches to allelic exchange, this protocol does not require heterologous recombinases to insert or excise selective markers from the target chromosome. Rather, positive and negative selection are enabled solely by suicide vector-encoded functions and host cell proteins. Here, mutant alleles, which are flanked by regions of homology to the recipient chromosome, are synthesized in vitro and then cloned into allelic exchange vectors using standard procedures. These suicide vectors are then introduced into recipient cells by conjugation. Homologous recombination then results in antibiotic resistant single-crossover mutants in which the plasmid has integrated site-specifically into the chromosome. Subsequently, unmarked double-crossover mutants are isolated directly using sucrose-mediated counter-selection. This two-step process yields seamless mutations that are precise to a single base pair of DNA. The entire procedure requires ~2 weeks. PMID:26492139

Step Forward. Single Parent/Homemaker Annual Report for the Fiscal Year 1990-1991.

ERIC Educational Resources Information Center

Kentucky Tech Region 5, Elizabethtown.

The Step Forward Single Parent/Homemaker Program in Elizabethtown, Kentucky, was developed to provide information on career opportunities and assist the target individuals in career assessment, career counseling, and goal setting in order to develop self-esteem and time management skills. During the second year of the Step Forward program in…

Strategic Steps to Successful Service-Learning in TESOL: From Critical to Practical

ERIC Educational Resources Information Center

Perren, James

2013-01-01

The purpose of this article is to share pedagogical materials and activities which can help TESOL practitioners prepare service-learning activities inside and outside the classroom. This study utilizes action research tools to improve academic service-learning in TESOL as a holistic approach to problem solving rather than a single method for…

A stabilized Runge–Kutta–Legendre method for explicit super-time-stepping of parabolic and mixed equations

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

Meyer, Chad D.; Balsara, Dinshaw S.; Aslam, Tariq D.

2014-01-15

Parabolic partial differential equations appear in several physical problems, including problems that have a dominant hyperbolic part coupled to a sub-dominant parabolic component. Explicit methods for their solution are easy to implement but have very restrictive time step constraints. Implicit solution methods can be unconditionally stable but have the disadvantage of being computationally costly or difficult to implement. Super-time-stepping methods for treating parabolic terms in mixed type partial differential equations occupy an intermediate position. In such methods each superstep takes “s” explicit Runge–Kutta-like time-steps to advance the parabolic terms by a time-step that is s{sup 2} times larger than amore » single explicit time-step. The expanded stability is usually obtained by mapping the short recursion relation of the explicit Runge–Kutta scheme to the recursion relation of some well-known, stable polynomial. Prior work has built temporally first- and second-order accurate super-time-stepping methods around the recursion relation associated with Chebyshev polynomials. Since their stability is based on the boundedness of the Chebyshev polynomials, these methods have been called RKC1 and RKC2. In this work we build temporally first- and second-order accurate super-time-stepping methods around the recursion relation associated with Legendre polynomials. We call these methods RKL1 and RKL2. The RKL1 method is first-order accurate in time; the RKL2 method is second-order accurate in time. We verify that the newly-designed RKL1 and RKL2 schemes have a very desirable monotonicity preserving property for one-dimensional problems – a solution that is monotone at the beginning of a time step retains that property at the end of that time step. It is shown that RKL1 and RKL2 methods are stable for all values of the diffusion coefficient up to the maximum value. We call this a convex monotonicity preserving property and show by examples that it is very useful in parabolic problems with variable diffusion coefficients. This includes variable coefficient parabolic equations that might give rise to skew symmetric terms. The RKC1 and RKC2 schemes do not share this convex monotonicity preserving property. One-dimensional and two-dimensional von Neumann stability analyses of RKC1, RKC2, RKL1 and RKL2 are also presented, showing that the latter two have some advantages. The paper includes several details to facilitate implementation. A detailed accuracy analysis is presented to show that the methods reach their design accuracies. A stringent set of test problems is also presented. To demonstrate the robustness and versatility of our methods, we show their successful operation on problems involving linear and non-linear heat conduction and viscosity, resistive magnetohydrodynamics, ambipolar diffusion dominated magnetohydrodynamics, level set methods and flux limited radiation diffusion. In a prior paper (Meyer, Balsara and Aslam 2012 [36]) we have also presented an extensive test-suite showing that the RKL2 method works robustly in the presence of shocks in an anisotropically conducting, magnetized plasma.« less

A stabilized Runge-Kutta-Legendre method for explicit super-time-stepping of parabolic and mixed equations

NASA Astrophysics Data System (ADS)

Meyer, Chad D.; Balsara, Dinshaw S.; Aslam, Tariq D.

2014-01-01

Parabolic partial differential equations appear in several physical problems, including problems that have a dominant hyperbolic part coupled to a sub-dominant parabolic component. Explicit methods for their solution are easy to implement but have very restrictive time step constraints. Implicit solution methods can be unconditionally stable but have the disadvantage of being computationally costly or difficult to implement. Super-time-stepping methods for treating parabolic terms in mixed type partial differential equations occupy an intermediate position. In such methods each superstep takes “s” explicit Runge-Kutta-like time-steps to advance the parabolic terms by a time-step that is s2 times larger than a single explicit time-step. The expanded stability is usually obtained by mapping the short recursion relation of the explicit Runge-Kutta scheme to the recursion relation of some well-known, stable polynomial. Prior work has built temporally first- and second-order accurate super-time-stepping methods around the recursion relation associated with Chebyshev polynomials. Since their stability is based on the boundedness of the Chebyshev polynomials, these methods have been called RKC1 and RKC2. In this work we build temporally first- and second-order accurate super-time-stepping methods around the recursion relation associated with Legendre polynomials. We call these methods RKL1 and RKL2. The RKL1 method is first-order accurate in time; the RKL2 method is second-order accurate in time. We verify that the newly-designed RKL1 and RKL2 schemes have a very desirable monotonicity preserving property for one-dimensional problems - a solution that is monotone at the beginning of a time step retains that property at the end of that time step. It is shown that RKL1 and RKL2 methods are stable for all values of the diffusion coefficient up to the maximum value. We call this a convex monotonicity preserving property and show by examples that it is very useful in parabolic problems with variable diffusion coefficients. This includes variable coefficient parabolic equations that might give rise to skew symmetric terms. The RKC1 and RKC2 schemes do not share this convex monotonicity preserving property. One-dimensional and two-dimensional von Neumann stability analyses of RKC1, RKC2, RKL1 and RKL2 are also presented, showing that the latter two have some advantages. The paper includes several details to facilitate implementation. A detailed accuracy analysis is presented to show that the methods reach their design accuracies. A stringent set of test problems is also presented. To demonstrate the robustness and versatility of our methods, we show their successful operation on problems involving linear and non-linear heat conduction and viscosity, resistive magnetohydrodynamics, ambipolar diffusion dominated magnetohydrodynamics, level set methods and flux limited radiation diffusion. In a prior paper (Meyer, Balsara and Aslam 2012 [36]) we have also presented an extensive test-suite showing that the RKL2 method works robustly in the presence of shocks in an anisotropically conducting, magnetized plasma.

Realisation of all 16 Boolean logic functions in a single magnetoresistance memory cell.

PubMed

Gao, Shuang; Yang, Guang; Cui, Bin; Wang, Shouguo; Zeng, Fei; Song, Cheng; Pan, Feng

2016-07-07

Stateful logic circuits based on next-generation nonvolatile memories, such as magnetoresistance random access memory (MRAM), promise to break the long-standing von Neumann bottleneck in state-of-the-art data processing devices. For the successful commercialisation of stateful logic circuits, a critical step is realizing the best use of a single memory cell to perform logic functions. In this work, we propose a method for implementing all 16 Boolean logic functions in a single MRAM cell, namely a magnetoresistance (MR) unit. Based on our experimental results, we conclude that this method is applicable to any MR unit with a double-hump-like hysteresis loop, especially pseudo-spin-valve magnetic tunnel junctions with a high MR ratio. Moreover, after simply reversing the correspondence between voltage signals and output logic values, this method could also be applicable to any MR unit with a double-pit-like hysteresis loop. These results may provide a helpful solution for the final commercialisation of MRAM-based stateful logic circuits in the near future.

DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways

PubMed Central

Shao, Zengyi; Zhao, Hua; Zhao, Huimin

2009-01-01

The assembly of large recombinant DNA encoding a whole biochemical pathway or genome represents a significant challenge. Here, we report a new method, DNA assembler, which allows the assembly of an entire biochemical pathway in a single step via in vivo homologous recombination in Saccharomyces cerevisiae. We show that DNA assembler can rapidly assemble a functional d-xylose utilization pathway (∼9 kb DNA consisting of three genes), a functional zeaxanthin biosynthesis pathway (∼11 kb DNA consisting of five genes) and a functional combined d-xylose utilization and zeaxanthin biosynthesis pathway (∼19 kb consisting of eight genes) with high efficiencies (70–100%) either on a plasmid or on a yeast chromosome. As this new method only requires simple DNA preparation and one-step yeast transformation, it represents a powerful tool in the construction of biochemical pathways for synthetic biology, metabolic engineering and functional genomics studies. PMID:19074487

Counter-propagation network with variable degree variable step size LMS for single switch typing recognition.

PubMed

Yang, Cheng-Huei; Luo, Ching-Hsing; Yang, Cheng-Hong; Chuang, Li-Yeh

2004-01-01

Morse code is now being harnessed for use in rehabilitation applications of augmentative-alternative communication and assistive technology, including mobility, environmental control and adapted worksite access. In this paper, Morse code is selected as a communication adaptive device for disabled persons who suffer from muscle atrophy, cerebral palsy or other severe handicaps. A stable typing rate is strictly required for Morse code to be effective as a communication tool. This restriction is a major hindrance. Therefore, a switch adaptive automatic recognition method with a high recognition rate is needed. The proposed system combines counter-propagation networks with a variable degree variable step size LMS algorithm. It is divided into five stages: space recognition, tone recognition, learning process, adaptive processing, and character recognition. Statistical analyses demonstrated that the proposed method elicited a better recognition rate in comparison to alternative methods in the literature.

Multigrid methods for numerical simulation of laminar diffusion flames

NASA Technical Reports Server (NTRS)

Liu, C.; Liu, Z.; Mccormick, S.

1993-01-01

This paper documents the result of a computational study of multigrid methods for numerical simulation of 2D diffusion flames. The focus is on a simplified combustion model, which is assumed to be a single step, infinitely fast and irreversible chemical reaction with five species (C3H8, O2, N2, CO2 and H2O). A fully-implicit second-order hybrid scheme is developed on a staggered grid, which is stretched in the streamwise coordinate direction. A full approximation multigrid scheme (FAS) based on line distributive relaxation is developed as a fast solver for the algebraic equations arising at each time step. Convergence of the process for the simplified model problem is more than two-orders of magnitude faster than other iterative methods, and the computational results show good grid convergence, with second-order accuracy, as well as qualitatively agreement with the results of other researchers.

Methods for Isolation, Purification, and Propagation of Bacteriophages of Campylobacter jejuni.

PubMed

Gencay, Yilmaz Emre; Birk, Tina; Sørensen, Martine Camilla Holst; Brøndsted, Lone

2017-01-01

Here, we describe the methods for isolation, purification, and propagation of Campylobacter jejuni bacteriophages from samples expected to contain high number of phages such as chicken feces. The overall steps are (1) liberation of phages from the sample material; (2) observation of plaque-forming units on C. jejuni lawns using a spot assay; (3) isolation of single plaques; (4) consecutive purification procedures; and (5) propagation of purified phages from a plate lysate to prepare master stocks.

Purification of swine haptoglobin by affinity chromatography.

PubMed Central

Eurell, T E; Hall, W F; Bane, D P

1990-01-01

A globin-agarose affinity chromatography technique was used to purify swine haptoglobin. This technique provides a highly specific, single-step purification method without the contamination of extraneous serum proteins reported by previous studies. Complex formation between the haptoglobin isolate and swine hemoglobin confirmed that biological activity was maintained during the purification process. Immunoelectrophoretic and Ouchterlony immunodiffusion methods revealed that the swine haptoglobin isolate cross-reacted with polyvalent antisera against human haptoglobin. Images Fig. 2. Fig. 3. PMID:2123414

High-throughput purification of recombinant proteins using self-cleaving intein tags.

PubMed

Coolbaugh, M J; Shakalli Tang, M J; Wood, D W

2017-01-01

High throughput methods for recombinant protein production using E. coli typically involve the use of affinity tags for simple purification of the protein of interest. One drawback of these techniques is the occasional need for tag removal before study, which can be hard to predict. In this work, we demonstrate two high throughput purification methods for untagged protein targets based on simple and cost-effective self-cleaving intein tags. Two model proteins, E. coli beta-galactosidase (βGal) and superfolder green fluorescent protein (sfGFP), were purified using self-cleaving versions of the conventional chitin-binding domain (CBD) affinity tag and the nonchromatographic elastin-like-polypeptide (ELP) precipitation tag in a 96-well filter plate format. Initial tests with shake flask cultures confirmed that the intein purification scheme could be scaled down, with >90% pure product generated in a single step using both methods. The scheme was then validated in a high throughput expression platform using 24-well plate cultures followed by purification in 96-well plates. For both tags and with both target proteins, the purified product was consistently obtained in a single-step, with low well-to-well and plate-to-plate variability. This simple method thus allows the reproducible production of highly pure untagged recombinant proteins in a convenient microtiter plate format. Copyright © 2016 Elsevier Inc. All rights reserved.

Relation between the microstructure and the electromagnetic properties of BaTiO3/Ni0.5Zn0.5Fe2O4 ceramic composite

NASA Astrophysics Data System (ADS)

Xiao, Bin; Tang, Yu; Ma, Guodong; Ma, Ning; Du, Piyi

2015-06-01

The microstructure-property relation in ferroelectric/ferromagnetic composite is investigated in detail, exemplified by typical sol-gel-derived 0.3BTO/0.7NZFO ceramic composite. The effect of microstructural factors including intergrain connectivity, grain size and interfaces on the dielectric and magnetic properties of the composite prepared by conventional ceramic method and three-step sintering method is discussed both experimentally and theoretically. It reveals that the dielectric behavior of the composite is controlled by a hybrid dielectric process that combines the contribution of Debye-like dipoles and Maxwell-Wagner (M-W or interfacial) polarization. Enhanced dielectric, magnetic and conductive behaviors appear in the composite with better intergrain connectivity and larger grain size derived by sol-gel route and three-step sintering method. The effective permittivity contributed by Debye-like dipoles exhibits a value of ~130,000 in three-step sintered composite, which is almost the same as that in conventionally sintered one, but that contributed by M-W response is much smaller in the former. Compared with conventionally prepared samples, the relaxation time ( τ) is 3.476 × 10-6 s, about one order of magnitude smaller, and the dc electrical conductivity is 3.890 × 10-3 S/m, one order of magnitude higher in three-step sintered composite. The minimum dielectric loss reveals almost the same (~0.2) for all samples, but shows distinguishable difference in low-frequency region. Meanwhile, an initial permeability of 84, twice as large as that of conventionally prepared composite and 56 % the value of single-phased NZFO ferrite (~150), and a saturation magnetization of 63.5 emu/g, 32 % higher than that of conventional one and approximately 84 % the value of single-phased NZFO ferrite (~76 emu/g), appear simultaneously in three-step sintered composite with larger grain size and better intergrain connectivity. It is clear that the discovery is helpful for establishing a more explicit view on the physics of multi-functional composite materials, while the composite with optimized microstructure is beneficial to be used as a high-performance material.

Single step, pH induced gold nanoparticle chain formation in lecithin/water system.

PubMed

Sharma, Damyanti

2013-07-01

Gold nanoparticle (AuNP) chains have been formed by a single step method in a lecithin/water system where lecithin itself plays the role of a reductant and a template for AuNP chain formation. Two preparative strategies were explored: (1) evaporating lecithin solution with aqueous gold chloride (HAuCl4) at different pHs and (2) dispersing lecithin vesicles in aqueous HAuCl4 solutions of various pHs in the range of 2.5-11.3. In method 1, at initial pH 2.5, 20-50 nm AuNPs are found attached to lecithin vesicles. When pH is raised to 5.5 there are no vesicles present and 20 nm monodisperse particles are found aggregating. Chain formation of fine nanoparticles (3-5 nm) is observed from neutral to basic pH, between 6.5-10.3 The chains formed are hundreds of nanometers to micrometer long and are usually 2-3 nanoparticles wide. On further increasing pH to 11.3, particles form disk-like or raft-like structures. When method (ii) was used a little chain formation was observed. Most of the nanoparticles formed were found either sitting together as raft like structures or scattered on lecithin structures. Copyright © 2013 Elsevier B.V. All rights reserved.

Single-step preparation and deagglomeration of itraconazole microflakes by supercritical antisolvent method for dissolution enhancement.

PubMed

Sathigari, Sateesh Kumar; Ober, Courtney A; Sanganwar, Ganesh P; Gupta, Ram B; Babu, R Jayachandra

2011-07-01

Itraconazole (ITZ) microflakes were produced by supercritical antisolvent (SAS) method and simultaneously mixed with pharmaceutical excipients in a single step to prevent drug agglomeration. Simultaneous ITZ particle formation and mixing with fast-flo lactose (FFL) was performed in a high-pressure stirred vessel at 116 bar and 40 °C by the SAS-drug excipient mixing (SAS-DEM) method. The effects of stabilizers, such as sodium dodecyl sulfate and poloxamer 407 (PLX), on particle formation and drug dissolution were studied. Drug-excipient formulations were characterized for surface morphology, crystallinity, drug-excipient interactions, drug content uniformity, and drug dissolution rate. Mixture of drug microflakes and FFL formed by the SAS-DEM process shows that the process was successful in overcoming drug-drug agglomeration. PLX produced crystalline drug flakes in loose agglomerates with superior dissolution and flow properties even at higher drug loadings. Characterization studies confirmed the crystallinity of the drug and absence of chemical interactions during the SAS process. The dissolution of ITZ was substantially higher due to SAS and SAS-DEM processes; this improvement can be attributed to the microflake particle structures, effective deagglomeration, and wetting of the drug flakes with the excipients. Copyright © 2011 Wiley-Liss, Inc. and the American Pharmacists Association

Changes in step-width during dual-task walking predicts falls.

PubMed

Nordin, E; Moe-Nilssen, R; Ramnemark, A; Lundin-Olsson, L

2010-05-01

The aim was to evaluate whether gait pattern changes between single- and dual-task conditions were associated with risk of falling in older people. Dual-task cost (DTC) of 230 community living, physically independent people, 75 years or older, was determined with an electronic walkway. Participants were followed up each month for 1 year to record falls. Mean and variability measures of gait characteristics for 5 dual-task conditions were compared to single-task walking for each participant. Almost half (48%) of the participants fell at least once during follow-up. Risk of falling increased in individuals where DTC for performing a subtraction task demonstrated change in mean step-width compared to single-task walking. Risk of falling decreased in individuals where DTC for carrying a cup and saucer demonstrated change compared to single-task walking in mean step-width, mean step-time, and step-length variability. Degree of change in gait characteristics related to a change in risk of falling differed between measures. Prognostic guidance for fall risk was found for the above DTCs in mean step-width with a negative likelihood ratio of 0.5 and a positive likelihood ratio of 2.3, respectively. Findings suggest that changes in step-width, step-time, and step-length with dual tasking may be related to future risk of falling. Depending on the nature of the second task, DTC may indicate either an increased risk of falling, or a protective strategy to avoid falling. Copyright 2010. Published by Elsevier B.V.

Permeability of Dental Adhesives – A SEM Assessment

PubMed Central

Malacarne-Zanon, Juliana; de Andrade e Silva, Safira M.; Wang, Linda; de Goes, Mario F.; Martins, Adriano Luis; Narvaes-Romani, Eliene O.; Anido-Anido, Andrea; Carrilho, Marcela R. O.

2010-01-01

Objectives: To morphologically evaluate the permeability of different commercial dental adhesives using scanning electron microscopy. Methods: Seven adhesive systems were evaluated: one three-step system (Scotchbond Multi-Purpose - MP); one two-step self-etching primer system (Clearfil SE Bond – SE); three two-step etch-and-rinse systems (Single Bond 2 – SB; Excite – EX; One-Step – OS); and two single-step self-etching adhesives (Adper Prompt – AP; One-Up Bond F – OU). The mixture of primer and bond agents of the Clearfil SE Bond system (SE-PB) was also tested. The adhesives were poured into a brass mold (5.8 mm x 0.8 mm) and light-cured for 80 s at 650 mW/cm2. After a 24 h desiccation process, the specimens were immersed in a 50% ammoniac silver nitrate solution for tracer permeation. Afterwards, they were sectioned in ultra-fine slices, carbon-coated, and analyzed under backscattered electrons in a scanning electron microscopy. Results: MP and SE showed slight and superficial tracer permeation. In EX, SB, and OS, permeation extended beyond the inner superficies of the specimens. SE-PB did not mix well, and most of the tracer was precipitated into the primer agent. In AP and OU, “water-trees” were observed all over the specimens. Conclusions: Different materials showed distinct permeability in aqueous solution. The extent of tracer permeation varied according to the composition of each material and it was more evident in the more hydrophilic and solvated ones. PMID:20922163

On the performance of voltage stepping for the simulation of adaptive, nonlinear integrate-and-fire neuronal networks.

PubMed

Kaabi, Mohamed Ghaith; Tonnelier, Arnaud; Martinez, Dominique

2011-05-01

In traditional event-driven strategies, spike timings are analytically given or calculated with arbitrary precision (up to machine precision). Exact computation is possible only for simplified neuron models, mainly the leaky integrate-and-fire model. In a recent paper, Zheng, Tonnelier, and Martinez (2009) introduced an approximate event-driven strategy, named voltage stepping, that allows the generic simulation of nonlinear spiking neurons. Promising results were achieved in the simulation of single quadratic integrate-and-fire neurons. Here, we assess the performance of voltage stepping in network simulations by considering more complex neurons (quadratic integrate-and-fire neurons with adaptation) coupled with multiple synapses. To handle the discrete nature of synaptic interactions, we recast voltage stepping in a general framework, the discrete event system specification. The efficiency of the method is assessed through simulations and comparisons with a modified time-stepping scheme of the Runge-Kutta type. We demonstrated numerically that the original order of voltage stepping is preserved when simulating connected spiking neurons, independent of the network activity and connectivity.

Step-by-step magic state encoding for efficient fault-tolerant quantum computation

PubMed Central

Goto, Hayato

2014-01-01

Quantum error correction allows one to make quantum computers fault-tolerant against unavoidable errors due to decoherence and imperfect physical gate operations. However, the fault-tolerant quantum computation requires impractically large computational resources for useful applications. This is a current major obstacle to the realization of a quantum computer. In particular, magic state distillation, which is a standard approach to universality, consumes the most resources in fault-tolerant quantum computation. For the resource problem, here we propose step-by-step magic state encoding for concatenated quantum codes, where magic states are encoded step by step from the physical level to the logical one. To manage errors during the encoding, we carefully use error detection. Since the sizes of intermediate codes are small, it is expected that the resource overheads will become lower than previous approaches based on the distillation at the logical level. Our simulation results suggest that the resource requirements for a logical magic state will become comparable to those for a single logical controlled-NOT gate. Thus, the present method opens a new possibility for efficient fault-tolerant quantum computation. PMID:25511387

Step-by-step magic state encoding for efficient fault-tolerant quantum computation.

PubMed

Goto, Hayato

2014-12-16

Quantum error correction allows one to make quantum computers fault-tolerant against unavoidable errors due to decoherence and imperfect physical gate operations. However, the fault-tolerant quantum computation requires impractically large computational resources for useful applications. This is a current major obstacle to the realization of a quantum computer. In particular, magic state distillation, which is a standard approach to universality, consumes the most resources in fault-tolerant quantum computation. For the resource problem, here we propose step-by-step magic state encoding for concatenated quantum codes, where magic states are encoded step by step from the physical level to the logical one. To manage errors during the encoding, we carefully use error detection. Since the sizes of intermediate codes are small, it is expected that the resource overheads will become lower than previous approaches based on the distillation at the logical level. Our simulation results suggest that the resource requirements for a logical magic state will become comparable to those for a single logical controlled-NOT gate. Thus, the present method opens a new possibility for efficient fault-tolerant quantum computation.

Steps to achieve quantitative measurements of microRNA using two step droplet digital PCR.

PubMed

Stein, Erica V; Duewer, David L; Farkas, Natalia; Romsos, Erica L; Wang, Lili; Cole, Kenneth D

2017-01-01

Droplet digital PCR (ddPCR) is being advocated as a reference method to measure rare genomic targets. It has consistently been proven to be more sensitive and direct at discerning copy numbers of DNA than other quantitative methods. However, one of the largest obstacles to measuring microRNA (miRNA) using ddPCR is that reverse transcription efficiency depends upon the target, meaning small RNA nucleotide composition directly effects primer specificity in a manner that prevents traditional quantitation optimization strategies. Additionally, the use of reagents that are optimized for miRNA measurements using quantitative real-time PCR (qRT-PCR) appear to either cause false positive or false negative detection of certain targets when used with traditional ddPCR quantification methods. False readings are often related to using inadequate enzymes, primers and probes. Given that two-step miRNA quantification using ddPCR relies solely on reverse transcription and uses proprietary reagents previously optimized only for qRT-PCR, these barriers are substantial. Therefore, here we outline essential controls, optimization techniques, and an efficacy model to improve the quality of ddPCR miRNA measurements. We have applied two-step principles used for miRNA qRT-PCR measurements and leveraged the use of synthetic miRNA targets to evaluate ddPCR following cDNA synthesis with four different commercial kits. We have identified inefficiencies and limitations as well as proposed ways to circumvent identified obstacles. Lastly, we show that we can apply these criteria to a model system to confidently quantify miRNA copy number. Our measurement technique is a novel way to quantify specific miRNA copy number in a single sample, without using standard curves for individual experiments. Our methodology can be used for validation and control measurements, as well as a diagnostic technique that allows scientists, technicians, clinicians, and regulators to base miRNA measures on a single unit of measurement rather than a ratio of values.

Steps to achieve quantitative measurements of microRNA using two step droplet digital PCR

PubMed Central

Duewer, David L.; Farkas, Natalia; Romsos, Erica L.; Wang, Lili; Cole, Kenneth D.

2017-01-01

Droplet digital PCR (ddPCR) is being advocated as a reference method to measure rare genomic targets. It has consistently been proven to be more sensitive and direct at discerning copy numbers of DNA than other quantitative methods. However, one of the largest obstacles to measuring microRNA (miRNA) using ddPCR is that reverse transcription efficiency depends upon the target, meaning small RNA nucleotide composition directly effects primer specificity in a manner that prevents traditional quantitation optimization strategies. Additionally, the use of reagents that are optimized for miRNA measurements using quantitative real-time PCR (qRT-PCR) appear to either cause false positive or false negative detection of certain targets when used with traditional ddPCR quantification methods. False readings are often related to using inadequate enzymes, primers and probes. Given that two-step miRNA quantification using ddPCR relies solely on reverse transcription and uses proprietary reagents previously optimized only for qRT-PCR, these barriers are substantial. Therefore, here we outline essential controls, optimization techniques, and an efficacy model to improve the quality of ddPCR miRNA measurements. We have applied two-step principles used for miRNA qRT-PCR measurements and leveraged the use of synthetic miRNA targets to evaluate ddPCR following cDNA synthesis with four different commercial kits. We have identified inefficiencies and limitations as well as proposed ways to circumvent identified obstacles. Lastly, we show that we can apply these criteria to a model system to confidently quantify miRNA copy number. Our measurement technique is a novel way to quantify specific miRNA copy number in a single sample, without using standard curves for individual experiments. Our methodology can be used for validation and control measurements, as well as a diagnostic technique that allows scientists, technicians, clinicians, and regulators to base miRNA measures on a single unit of measurement rather than a ratio of values. PMID:29145448

Three-step HPLC-ESI-MS/MS procedure for screening and identifying non-target flavonoid derivatives

NASA Astrophysics Data System (ADS)

Rak, Gábor; Fodor, Péter; Abrankó, László

2010-02-01

A three-step HPLC-ESI-MS/MS procedure is designed for screening and identification of non-target flavonoid derivatives of selected flavonoid aglycones. In this method the five commonly appearing aglycones (apigenin, luteolin, myricetin, naringenin and quercetin) were selected. The method consists of three individual mass spectrometric experiments of which the first two were implemented within a single chromatographic acquisition. The third step was carried out during a replicate chromatographic run using the same RP-HPLC conditions. The first step, a multiple reaction monitoring (MRM) scan of the aglycones was performed to define the number of derivatives relating to the selected aglycones. For this purpose the characteristic aglycone parts of the unknowns were used as specific tags of the molecules, which were generated as in-source fragments. Secondly, a full scan MS experiment is performed to identify the masses of the potential derivatives of the selected aglycones. Finally, the third step had the capability to confirm the supposed derivatives. The developed method was applied to a commercially available black currant juice to demonstrate its capability to detect and identify various flavonoid glycosides without any preliminary information about their presence in the sample. As a result 13 compounds were detected and identified in total. Namely, 3 different myricetin glycosides and the myricetin aglycone 2 luteolin glycosides plus the aglycone and 3 quercetin glycosides plus the aglycone could be identified from the tested black currant sample. In the case of apigenin and naringenin only the aglycones could be detected.

A simple solution to systematic errors in density determination by X-ray reflectivity: The XRR-density evaluation (XRR-DE) method

NASA Astrophysics Data System (ADS)

Bergese, P.; Bontempi, E.; Depero, L. E.

2006-10-01

X-ray reflectivity (XRR) is a non-destructive, accurate and fast technique for evaluating film density. Indeed, sample-goniometer alignment is a critical experimental factor and the overriding error source in XRR density determination. With commercial single-wavelength X-ray reflectometers, alignment is difficult to control and strongly depends on the operator. In the present work, the contribution of misalignment on density evaluation error is discussed, and a novel procedure (named XRR-density evaluation or XRR-DE method) to minimize the problem will be presented. The method allows to overcome the alignment step through the extrapolation of the correct density value from appropriate non-specular XRR data sets. This procedure is operator independent and suitable for commercial single-wavelength X-ray reflectometers. To test the XRR-DE method, single crystals of TiO 2 and SrTiO 3 were used. In both cases the determined densities differed from the nominal ones less than 5.5%. Thus, the XRR-DE method can be successfully applied to evaluate the density of thin films for which only optical reflectivity is today used. The advantage is that this method can be considered thickness independent.

Single molecule thermodynamics in biological motors.

PubMed

Taniguchi, Yuichi; Karagiannis, Peter; Nishiyama, Masayoshi; Ishii, Yoshiharu; Yanagida, Toshio

2007-04-01

Biological molecular machines use thermal activation energy to carry out various functions. The process of thermal activation has the stochastic nature of output events that can be described according to the laws of thermodynamics. Recently developed single molecule detection techniques have allowed each distinct enzymatic event of single biological machines to be characterized providing clues to the underlying thermodynamics. In this study, the thermodynamic properties in the stepping movement of a biological molecular motor have been examined. A single molecule detection technique was used to measure the stepping movements at various loads and temperatures and a range of thermodynamic parameters associated with the production of each forward and backward step including free energy, enthalpy, entropy and characteristic distance were obtained. The results show that an asymmetry in entropy is a primary factor that controls the direction in which the motor will step. The investigation on single molecule thermodynamics has the potential to reveal dynamic properties underlying the mechanisms of how biological molecular machines work.

Sequence-specific sepsis-related DNA capture and fluorescent labeling in monoliths prepared by single-step photopolymerization in microfluidic devices.

PubMed

Knob, Radim; Hanson, Robert L; Tateoka, Olivia B; Wood, Ryan L; Guerrero-Arguero, Israel; Robison, Richard A; Pitt, William G; Woolley, Adam T

2018-05-21

Fast determination of antibiotic resistance is crucial in selecting appropriate treatment for sepsis patients, but current methods based on culture are time consuming. We are developing a microfluidic platform with a monolithic column modified with oligonucleotides designed for sequence-specific capture of target DNA related to the Klebsiella pneumoniae carbapenemase (KPC) gene. We developed a novel single-step monolith fabrication method with an acrydite-modified capture oligonucleotide in the polymerization mixture, enabling fast monolith preparation in a microfluidic channel using UV photopolymerization. These prepared columns had a threefold higher capacity compared to monoliths prepared in a multistep process involving Schiff-base DNA attachment. Conditions for denaturing, capture and fluorescence labeling using hybridization probes were optimized with synthetic 90-mer oligonucleotides. These procedures were applied for extraction of a PCR amplicon from the KPC antibiotic resistance gene in bacterial lysate obtained from a blood sample spiked with E. coli. The results showed similar eluted peak areas for KPC amplicon extracted from either hybridization buffer or bacterial lysate. Selective extraction of the KPC DNA was verified by real time PCR on eluted fractions. These results show great promise for application in an integrated microfluidic diagnostic system that combines upstream blood sample preparation and downstream single-molecule counting detection. Copyright © 2018 Elsevier B.V. All rights reserved.

Single-Run Single-Mask Inductively-Coupled-Plasma Reactive-Ion-Etching Process for Fabricating Suspended High-Aspect-Ratio Microstructures

NASA Astrophysics Data System (ADS)

Yang, Yao-Joe; Kuo, Wen-Cheng; Fan, Kuang-Chao

2006-01-01

In this work, we present a single-run single-mask (SRM) process for fabricating suspended high-aspect-ratio structures on standard silicon wafers using an inductively coupled plasma-reactive ion etching (ICP-RIE) etcher. This process eliminates extra fabrication steps which are required for structure release after trench etching. Released microstructures with 120 μm thickness are obtained by this process. The corresponding maximum aspect ratio of the trench is 28. The SRM process is an extended version of the standard process proposed by BOSCH GmbH (BOSCH process). The first step of the SRM process is a standard BOSCH process for trench etching, then a polymer layer is deposited on trench sidewalls as a protective layer for the subsequent structure-releasing step. The structure is released by dry isotropic etching after the polymer layer on the trench floor is removed. All the steps can be integrated into a single-run ICP process. Also, only one mask is required. Therefore, the process complexity and fabrication cost can be effectively reduced. Discussions on each SRM step and considerations for avoiding undesired etching of the silicon structures during the release process are also presented.

Unimolecular Reaction Pathways of a γ-Ketohydroperoxide from Combined Application of Automated Reaction Discovery Methods

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

Grambow, Colin A.; Jamal, Adeel; Li, Yi -Pei

Ketohydroperoxides are important in liquid-phase autoxidation and in gas-phase partial oxidation and pre-ignition chemistry, but because of their low concentration, instability, and various analytical chemistry limitations, it has been challenging to experimentally determine their reactivity, and only a few pathways are known. In the present work, 75 elementary-step unimolecular reactions of the simplest γ-ketohydroperoxide, 3-hydroperoxypropanal, were discovered by a combination of density functional theory with several automated transition-state search algorithms: the Berny algorithm coupled with the freezing string method, single- and double-ended growing string methods, the heuristic KinBot algorithm, and the single-component artificial force induced reaction method (SC-AFIR). The presentmore » joint approach significantly outperforms previous manual and automated transition-state searches – 68 of the reactions of γ-ketohydroperoxide discovered here were previously unknown and completely unexpected. All of the methods found the lowest-energy transition state, which corresponds to the first step of the Korcek mechanism, but each algorithm except for SC-AFIR detected several reactions not found by any of the other methods. We show that the low-barrier chemical reactions involve promising new chemistry that may be relevant in atmospheric and combustion systems. Our study highlights the complexity of chemical space exploration and the advantage of combined application of several approaches. Altogether, the present work demonstrates both the power and the weaknesses of existing fully automated approaches for reaction discovery which suggest possible directions for further method development and assessment in order to enable reliable discovery of all important reactions of any specified reactant(s).« less

Unimolecular Reaction Pathways of a γ-Ketohydroperoxide from Combined Application of Automated Reaction Discovery Methods

DOE PAGES

Grambow, Colin A.; Jamal, Adeel; Li, Yi -Pei; ...

2017-12-22

Ketohydroperoxides are important in liquid-phase autoxidation and in gas-phase partial oxidation and pre-ignition chemistry, but because of their low concentration, instability, and various analytical chemistry limitations, it has been challenging to experimentally determine their reactivity, and only a few pathways are known. In the present work, 75 elementary-step unimolecular reactions of the simplest γ-ketohydroperoxide, 3-hydroperoxypropanal, were discovered by a combination of density functional theory with several automated transition-state search algorithms: the Berny algorithm coupled with the freezing string method, single- and double-ended growing string methods, the heuristic KinBot algorithm, and the single-component artificial force induced reaction method (SC-AFIR). The presentmore » joint approach significantly outperforms previous manual and automated transition-state searches – 68 of the reactions of γ-ketohydroperoxide discovered here were previously unknown and completely unexpected. All of the methods found the lowest-energy transition state, which corresponds to the first step of the Korcek mechanism, but each algorithm except for SC-AFIR detected several reactions not found by any of the other methods. We show that the low-barrier chemical reactions involve promising new chemistry that may be relevant in atmospheric and combustion systems. Our study highlights the complexity of chemical space exploration and the advantage of combined application of several approaches. Altogether, the present work demonstrates both the power and the weaknesses of existing fully automated approaches for reaction discovery which suggest possible directions for further method development and assessment in order to enable reliable discovery of all important reactions of any specified reactant(s).« less

Printing 2-dimentional droplet array for single-cell reverse transcription quantitative PCR assay with a microfluidic robot.

PubMed

Zhu, Ying; Zhang, Yun-Xia; Liu, Wen-Wen; Ma, Yan; Fang, Qun; Yao, Bo

2015-04-01

This paper describes a nanoliter droplet array-based single-cell reverse transcription quantitative PCR (RT-qPCR) assay method for quantifying gene expression in individual cells. By sequentially printing nanoliter-scale droplets on microchip using a microfluidic robot, all liquid-handling operations including cell encapsulation, lysis, reverse transcription, and quantitative PCR with real-time fluorescence detection, can be automatically achieved. The inhibition effect of cell suspension buffer on RT-PCR assay was comprehensively studied to achieve high-sensitivity gene quantification. The present system was applied in the quantitative measurement of expression level of mir-122 in single Huh-7 cells. A wide distribution of mir-122 expression in single cells from 3061 copies/cell to 79998 copies/cell was observed, showing a high level of cell heterogeneity. With the advantages of full-automation in liquid-handling, simple system structure, and flexibility in achieving multi-step operations, the present method provides a novel liquid-handling mode for single cell gene expression analysis, and has significant potentials in transcriptional identification and rare cell analysis.

Printing 2-Dimentional Droplet Array for Single-Cell Reverse Transcription Quantitative PCR Assay with a Microfluidic Robot

PubMed Central

Zhu, Ying; Zhang, Yun-Xia; Liu, Wen-Wen; Ma, Yan; Fang, Qun; Yao, Bo

2015-01-01

This paper describes a nanoliter droplet array-based single-cell reverse transcription quantitative PCR (RT-qPCR) assay method for quantifying gene expression in individual cells. By sequentially printing nanoliter-scale droplets on microchip using a microfluidic robot, all liquid-handling operations including cell encapsulation, lysis, reverse transcription, and quantitative PCR with real-time fluorescence detection, can be automatically achieved. The inhibition effect of cell suspension buffer on RT-PCR assay was comprehensively studied to achieve high-sensitivity gene quantification. The present system was applied in the quantitative measurement of expression level of mir-122 in single Huh-7 cells. A wide distribution of mir-122 expression in single cells from 3061 copies/cell to 79998 copies/cell was observed, showing a high level of cell heterogeneity. With the advantages of full-automation in liquid-handling, simple system structure, and flexibility in achieving multi-step operations, the present method provides a novel liquid-handling mode for single cell gene expression analysis, and has significant potentials in transcriptional identification and rare cell analysis. PMID:25828383

GWAS with longitudinal phenotypes: performance of approximate procedures

PubMed Central

Sikorska, Karolina; Montazeri, Nahid Mostafavi; Uitterlinden, André; Rivadeneira, Fernando; Eilers, Paul HC; Lesaffre, Emmanuel

2015-01-01

Analysis of genome-wide association studies with longitudinal data using standard procedures, such as linear mixed model (LMM) fitting, leads to discouragingly long computation times. There is a need to speed up the computations significantly. In our previous work (Sikorska et al: Fast linear mixed model computations for genome-wide association studies with longitudinal data. Stat Med 2012; 32.1: 165–180), we proposed the conditional two-step (CTS) approach as a fast method providing an approximation to the P-value for the longitudinal single-nucleotide polymorphism (SNP) effect. In the first step a reduced conditional LMM is fit, omitting all the SNP terms. In the second step, the estimated random slopes are regressed on SNPs. The CTS has been applied to the bone mineral density data from the Rotterdam Study and proved to work very well even in unbalanced situations. In another article (Sikorska et al: GWAS on your notebook: fast semi-parallel linear and logistic regression for genome-wide association studies. BMC Bioinformatics 2013; 14: 166), we suggested semi-parallel computations, greatly speeding up fitting many linear regressions. Combining CTS with fast linear regression reduces the computation time from several weeks to a few minutes on a single computer. Here, we explore further the properties of the CTS both analytically and by simulations. We investigate the performance of our proposal in comparison with a related but different approach, the two-step procedure. It is analytically shown that for the balanced case, under mild assumptions, the P-value provided by the CTS is the same as from the LMM. For unbalanced data and in realistic situations, simulations show that the CTS method does not inflate the type I error rate and implies only a minimal loss of power. PMID:25712081

Epitaxial layers of 2122 BCSCO superconductor thin films having single crystalline structure

NASA Technical Reports Server (NTRS)

Pandey, Raghvendra K. (Inventor); Raina, Kanwal K. (Inventor); Solayappan, Narayanan (Inventor)

1995-01-01

A substantially single phase, single crystalline, highly epitaxial film of Bi.sub.2 CaSr.sub.2 Cu.sub.2 O.sub.8 superconductor which has a T.sub.c (zero resistance) of 83K is provided on a lattice-matched substrate with no intergrowth. This film is produced by a Liquid Phase Epitaxy method which includes the steps of forming a dilute supercooled molten solution of a single phase superconducting mixture of oxides of Bi, Ca, Sr, and Cu having an atomic ratio of about 2:1:2:2 in a nonreactive flux such as KCl, introducing the substrate, e.g., NdGaO.sub.3, into the molten solution at 850.degree. C., cooling the solution from 850.degree. C. to 830.degree. C. to grow the film and rapidly cooling the substrate to room temperature to maintain the desired single phase, single crystalline film structure.

Droplet Microfluidics for Compartmentalized Cell Lysis and Extension of DNA from Single-Cells

NASA Astrophysics Data System (ADS)

Zimny, Philip; Juncker, David; Reisner, Walter

Current single cell DNA analysis methods suffer from (i) bias introduced by the need for molecular amplification and (ii) limited ability to sequence repetitive elements, resulting in (iii) an inability to obtain information regarding long range genomic features. Recent efforts to circumvent these limitations rely on techniques for sensing single molecules of DNA extracted from single-cells. Here we demonstrate a droplet microfluidic approach for encapsulation and biochemical processing of single-cells inside alginate microparticles. In our approach, single-cells are first packaged inside the alginate microparticles followed by cell lysis, DNA purification, and labeling steps performed off-chip inside this microparticle system. The alginate microparticles are then introduced inside a micro/nanofluidic system where the alginate is broken down via a chelating buffer, releasing long DNA molecules which are then extended inside nanofluidic channels for analysis via standard mapping protocols.

Hierarchical tone mapping for high dynamic range image visualization

NASA Astrophysics Data System (ADS)

Qiu, Guoping; Duan, Jiang

2005-07-01

In this paper, we present a computationally efficient, practically easy to use tone mapping techniques for the visualization of high dynamic range (HDR) images in low dynamic range (LDR) reproduction devices. The new method, termed hierarchical nonlinear linear (HNL) tone-mapping operator maps the pixels in two hierarchical steps. The first step allocates appropriate numbers of LDR display levels to different HDR intensity intervals according to the pixel densities of the intervals. The second step linearly maps the HDR intensity intervals to theirs allocated LDR display levels. In the developed HNL scheme, the assignment of LDR display levels to HDR intensity intervals is controlled by a very simple and flexible formula with a single adjustable parameter. We also show that our new operators can be used for the effective enhancement of ordinary images.

Method of monolithic module assembly

DOEpatents

Gee, James M.; Garrett, Stephen E.; Morgan, William P.; Worobey, Walter

1999-01-01

Methods for "monolithic module assembly" which translate many of the advantages of monolithic module construction of thin-film PV modules to wafered c-Si PV modules. Methods employ using back-contact solar cells positioned atop electrically conductive circuit elements affixed to a planar support so that a circuit capable of generating electric power is created. The modules are encapsulated using encapsulant materials such as EVA which are commonly used in photovoltaic module manufacture. The methods of the invention allow multiple cells to be electrically connected in a single encapsulation step rather than by sequential soldering which characterizes the currently used commercial practices.

Serum protein measurement using a tapered fluorescent fibre-optic evanescent wave-based biosensor

NASA Astrophysics Data System (ADS)

Preejith, P. V.; Lim, C. S.; Chia, T. F.

2006-12-01

A novel method to measure the total serum protein concentration is described in this paper. The method is based on the principles of fibre-optic evanescent wave spectroscopy. The biosensor applies a fluorescent dye-immobilized porous glass coating on a multi-mode optical fibre. The evanescent wave's intensity at the fibre-optic core-cladding interface is used to monitor the protein-induced changes in the sensor element. The sensor offers a rapid, single-step method for quantifying protein concentrations without destroying the sample. This unique sensing method presents a sensitive and accurate platform for the quantification of protein.

Effect of time step size and turbulence model on the open water hydrodynamic performance prediction of contra-rotating propellers

NASA Astrophysics Data System (ADS)

Wang, Zhan-zhi; Xiong, Ying

2013-04-01

A growing interest has been devoted to the contra-rotating propellers (CRPs) due to their high propulsive efficiency, torque balance, low fuel consumption, low cavitations, low noise performance and low hull vibration. Compared with the single-screw system, it is more difficult for the open water performance prediction because forward and aft propellers interact with each other and generate a more complicated flow field around the CRPs system. The current work focuses on the open water performance prediction of contra-rotating propellers by RANS and sliding mesh method considering the effect of computational time step size and turbulence model. The validation study has been performed on two sets of contra-rotating propellers developed by David W Taylor Naval Ship R & D center. Compared with the experimental data, it shows that RANS with sliding mesh method and SST k-ω turbulence model has a good precision in the open water performance prediction of contra-rotating propellers, and small time step size can improve the level of accuracy for CRPs with the same blade number of forward and aft propellers, while a relatively large time step size is a better choice for CRPs with different blade numbers.

Design and Processing of a Novel Chaos-Based Stepped Frequency Synthesized Wideband Radar Signal.

PubMed

Zeng, Tao; Chang, Shaoqiang; Fan, Huayu; Liu, Quanhua

2018-03-26

The linear stepped frequency and linear frequency shift keying (FSK) signal has been widely used in radar systems. However, such linear modulation signals suffer from the range-Doppler coupling that degrades radar multi-target resolution. Moreover, the fixed frequency-hopping or frequency-coded sequence can be easily predicted by the interception receiver in the electronic countermeasures (ECM) environments, which limits radar anti-jamming performance. In addition, the single FSK modulation reduces the radar low probability of intercept (LPI) performance, for it cannot achieve a large time-bandwidth product. To solve such problems, we propose a novel chaos-based stepped frequency (CSF) synthesized wideband signal in this paper. The signal introduces chaotic frequency hopping between the coherent stepped frequency pulses, and adopts a chaotic frequency shift keying (CFSK) and phase shift keying (PSK) composited coded modulation in a subpulse, called CSF-CFSK/PSK. Correspondingly, the processing method for the signal has been proposed. According to our theoretical analyses and the simulations, the proposed signal and processing method achieve better multi-target resolution and LPI performance. Furthermore, flexible modulation is able to increase the robustness against identification of the interception receiver and improve the anti-jamming performance of the radar.

Treating electron transport in MCNP{sup trademark}

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

Hughes, H.G.

1996-12-31

The transport of electrons and other charged particles is fundamentally different from that of neutrons and photons. A neutron, in aluminum slowing down from 0.5 MeV to 0.0625 MeV will have about 30 collisions; a photon will have fewer than ten. An electron with the same energy loss will undergo 10{sup 5} individual interactions. This great increase in computational complexity makes a single- collision Monte Carlo approach to electron transport unfeasible for many situations of practical interest. Considerable theoretical work has been done to develop a variety of analytic and semi-analytic multiple-scattering theories for the transport of charged particles. Themore » theories used in the algorithms in MCNP are the Goudsmit-Saunderson theory for angular deflections, the Landau an theory of energy-loss fluctuations, and the Blunck-Leisegang enhancements of the Landau theory. In order to follow an electron through a significant energy loss, it is necessary to break the electron`s path into many steps. These steps are chosen to be long enough to encompass many collisions (so that multiple-scattering theories are valid) but short enough that the mean energy loss in any one step is small (for the approximations in the multiple-scattering theories). The energy loss and angular deflection of the electron during each step can then be sampled from probability distributions based on the appropriate multiple- scattering theories. This subsumption of the effects of many individual collisions into single steps that are sampled probabilistically constitutes the ``condensed history`` Monte Carlo method. This method is exemplified in the ETRAN series of electron/photon transport codes. The ETRAN codes are also the basis for the Integrated TIGER Series, a system of general-purpose, application-oriented electron/photon transport codes. The electron physics in MCNP is similar to that of the Integrated TIGER Series.« less

A GPU-accelerated semi-implicit fractional step method for numerical solutions of incompressible Navier-Stokes equations

NASA Astrophysics Data System (ADS)

Ha, Sanghyun; Park, Junshin; You, Donghyun

2017-11-01

Utility of the computational power of modern Graphics Processing Units (GPUs) is elaborated for solutions of incompressible Navier-Stokes equations which are integrated using a semi-implicit fractional-step method. Due to its serial and bandwidth-bound nature, the present choice of numerical methods is considered to be a good candidate for evaluating the potential of GPUs for solving Navier-Stokes equations using non-explicit time integration. An efficient algorithm is presented for GPU acceleration of the Alternating Direction Implicit (ADI) and the Fourier-transform-based direct solution method used in the semi-implicit fractional-step method. OpenMP is employed for concurrent collection of turbulence statistics on a CPU while Navier-Stokes equations are computed on a GPU. Extension to multiple NVIDIA GPUs is implemented using NVLink supported by the Pascal architecture. Performance of the present method is experimented on multiple Tesla P100 GPUs compared with a single-core Xeon E5-2650 v4 CPU in simulations of boundary-layer flow over a flat plate. Supported by the National Research Foundation of Korea (NRF) Grant funded by the Korea government (Ministry of Science, ICT and Future Planning NRF-2016R1E1A2A01939553, NRF-2014R1A2A1A11049599, and Ministry of Trade, Industry and Energy 201611101000230).

Finite element solution of nonlinear eddy current problems with periodic excitation and its industrial applications☆

PubMed Central

Bíró, Oszkár; Koczka, Gergely; Preis, Kurt

2014-01-01

An efficient finite element method to take account of the nonlinearity of the magnetic materials when analyzing three-dimensional eddy current problems is presented in this paper. The problem is formulated in terms of vector and scalar potentials approximated by edge and node based finite element basis functions. The application of Galerkin techniques leads to a large, nonlinear system of ordinary differential equations in the time domain. The excitations are assumed to be time-periodic and the steady-state periodic solution is of interest only. This is represented either in the frequency domain as a finite Fourier series or in the time domain as a set of discrete time values within one period for each finite element degree of freedom. The former approach is the (continuous) harmonic balance method and, in the latter one, discrete Fourier transformation will be shown to lead to a discrete harmonic balance method. Due to the nonlinearity, all harmonics, both continuous and discrete, are coupled to each other. The harmonics would be decoupled if the problem were linear, therefore, a special nonlinear iteration technique, the fixed-point method is used to linearize the equations by selecting a time-independent permeability distribution, the so-called fixed-point permeability in each nonlinear iteration step. This leads to uncoupled harmonics within these steps. As industrial applications, analyses of large power transformers are presented. The first example is the computation of the electromagnetic field of a single-phase transformer in the time domain with the results compared to those obtained by traditional time-stepping techniques. In the second application, an advanced model of the same transformer is analyzed in the frequency domain by the harmonic balance method with the effect of the presence of higher harmonics on the losses investigated. Finally a third example tackles the case of direct current (DC) bias in the coils of a single-phase transformer. PMID:24829517

Correction of the data generated by mass spectrometry analyses of biological tissues: application to food authentication.

PubMed

Engel, Erwan; Ratel, Jérémy

2007-06-22

The objective of the work was to assess the relevance for the authentication of food of a novel chemometric method developed to correct mass spectrometry (MS) data from instrumental drifts, namely, the comprehensive combinatory standard correction (CCSC). Applied to gas chromatography (GC)-MS data, the method consists in analyzing a liquid sample with a mixture of n internal standards and in using the best combination of standards to correct the MS signal provided by each compound. The paper focuses on the authentication of the type of feeding in farm animals based on the composition in volatile constituents of their adipose tissues. The first step of the work enabled on one hand to ensure the feasibility of the conversion of the adipose tissue sample into a liquid phase required for the use of the CCSC method and on the other hand, to determine the key parameters of the extraction of the volatile fraction from this liquid phase by dynamic headspace. The second step showed the relevance of the CCSC pre-processing of the MS fingerprints generated by dynamic headspace-MS analysis of lamb tissues, for the discrimination of animals fed exclusively with pasture (n=8) or concentrate (n=8). When compared with filtering of raw data, internal normalization and correction by a single standard, the CCSC method increased by 17.1-, 3.3- and 1.3-fold, respectively, the number of mass fragments which discriminated the type of feeding. The final step confirmed the advantage of the CCSC pre-processing of dynamic headspace-gas chromatography-MS data for revealing molecular tracers of the type of feeding those number (n=72) was greater when compared to the number of tracers obtained with raw data (n=42), internal normalization (n=63) and correction by a single standard (n=57). The relevance of the information gained by using the CCSC method is discussed.

Finite element solution of nonlinear eddy current problems with periodic excitation and its industrial applications.

PubMed

Bíró, Oszkár; Koczka, Gergely; Preis, Kurt

2014-05-01

An efficient finite element method to take account of the nonlinearity of the magnetic materials when analyzing three-dimensional eddy current problems is presented in this paper. The problem is formulated in terms of vector and scalar potentials approximated by edge and node based finite element basis functions. The application of Galerkin techniques leads to a large, nonlinear system of ordinary differential equations in the time domain. The excitations are assumed to be time-periodic and the steady-state periodic solution is of interest only. This is represented either in the frequency domain as a finite Fourier series or in the time domain as a set of discrete time values within one period for each finite element degree of freedom. The former approach is the (continuous) harmonic balance method and, in the latter one, discrete Fourier transformation will be shown to lead to a discrete harmonic balance method. Due to the nonlinearity, all harmonics, both continuous and discrete, are coupled to each other. The harmonics would be decoupled if the problem were linear, therefore, a special nonlinear iteration technique, the fixed-point method is used to linearize the equations by selecting a time-independent permeability distribution, the so-called fixed-point permeability in each nonlinear iteration step. This leads to uncoupled harmonics within these steps. As industrial applications, analyses of large power transformers are presented. The first example is the computation of the electromagnetic field of a single-phase transformer in the time domain with the results compared to those obtained by traditional time-stepping techniques. In the second application, an advanced model of the same transformer is analyzed in the frequency domain by the harmonic balance method with the effect of the presence of higher harmonics on the losses investigated. Finally a third example tackles the case of direct current (DC) bias in the coils of a single-phase transformer.

Single Molecule Stepping and Structural Dynamics of Myosin X

PubMed Central

Sun, Yujie; Sato, Osamu; Ruhnow, Felix; Arsenault, Mark E.; Ikebe, Mitsuo; Goldman, Yale E.

2010-01-01

Myosin X is an unconventional myosin with puzzling motility properties. We studied the motility of dimerized myosin X using single molecule fluorescence techniques – polTIRF, FIONA, and Parallax to measure rotation angles and 3-dimensional position of the molecule during its walk. It was found that Myosin X steps processively in a hand-over-hand manner following a left-handed helical path along both single actin filaments and bundles. Its step size and velocity are smaller on actin bundles than individual filaments, suggesting myosin X often steps onto neighboring filaments in a bundle. The data suggest that a previously postulated single α-helical domain mechanically extends the 3-IQ motif lever arm and either the neck-tail hinge or the tail is flexible. These structural features, in conjunction with the membrane and microtubule binding domains, enable myosin X to perform multiple functions on varied actin structures in cells. PMID:20364131

Fast numerical methods for simulating large-scale integrate-and-fire neuronal networks.

PubMed

Rangan, Aaditya V; Cai, David

2007-02-01

We discuss numerical methods for simulating large-scale, integrate-and-fire (I&F) neuronal networks. Important elements in our numerical methods are (i) a neurophysiologically inspired integrating factor which casts the solution as a numerically tractable integral equation, and allows us to obtain stable and accurate individual neuronal trajectories (i.e., voltage and conductance time-courses) even when the I&F neuronal equations are stiff, such as in strongly fluctuating, high-conductance states; (ii) an iterated process of spike-spike corrections within groups of strongly coupled neurons to account for spike-spike interactions within a single large numerical time-step; and (iii) a clustering procedure of firing events in the network to take advantage of localized architectures, such as spatial scales of strong local interactions, which are often present in large-scale computational models-for example, those of the primary visual cortex. (We note that the spike-spike corrections in our methods are more involved than the correction of single neuron spike-time via a polynomial interpolation as in the modified Runge-Kutta methods commonly used in simulations of I&F neuronal networks.) Our methods can evolve networks with relatively strong local interactions in an asymptotically optimal way such that each neuron fires approximately once in [Formula: see text] operations, where N is the number of neurons in the system. We note that quantifications used in computational modeling are often statistical, since measurements in a real experiment to characterize physiological systems are typically statistical, such as firing rate, interspike interval distributions, and spike-triggered voltage distributions. We emphasize that it takes much less computational effort to resolve statistical properties of certain I&F neuronal networks than to fully resolve trajectories of each and every neuron within the system. For networks operating in realistic dynamical regimes, such as strongly fluctuating, high-conductance states, our methods are designed to achieve statistical accuracy when very large time-steps are used. Moreover, our methods can also achieve trajectory-wise accuracy when small time-steps are used.

The association between the maximum step length test and the walking efficiency in children with cerebral palsy.

PubMed

Kimoto, Minoru; Okada, Kyoji; Sakamoto, Hitoshi; Kondou, Takanori

2017-05-01

[Purpose] To improve walking efficiency could be useful for reducing fatigue and extending possible period of walking in children with cerebral palsy (CP). For this purpose, current study compared conventional parameters of gross motor performance, step length, and cadence in the evaluation of walking efficiency in children with CP. [Subjects and Methods] Thirty-one children with CP (21 boys, 10 girls; mean age, 12.3 ± 2.7 years) participated. Parameters of gross motor performance, including the maximum step length (MSL), maximum side step length, step number, lateral step up number, and single leg standing time, were measured in both dominant and non-dominant sides. Spatio-temporal parameters of walking, including speed, step length, and cadence, were calculated. Total heart beat index (THBI), a parameter of walking efficiency, was also calculated from heartbeats and walking distance in 10 minutes of walking. To analyze the relationships between these parameters and the THBI, the coefficients of determination were calculated using stepwise analysis. [Results] The MSL of the dominant side best accounted for the THBI (R 2 =0.759). [Conclusion] The MSL of the dominant side was the best explanatory parameter for walking efficiency in children with CP.

Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data

PubMed Central

Tang, Cuong Q; Humphreys, Aelys M; Fontaneto, Diego; Barraclough, Timothy G; Paradis, Emmanuel

2014-01-01

Coalescent-based species delimitation methods combine population genetic and phylogenetic theory to provide an objective means for delineating evolutionarily significant units of diversity. The generalised mixed Yule coalescent (GMYC) and the Poisson tree process (PTP) are methods that use ultrametric (GMYC or PTP) or non-ultrametric (PTP) gene trees as input, intended for use mostly with single-locus data such as DNA barcodes. Here, we assess how robust the GMYC and PTP are to different phylogenetic reconstruction and branch smoothing methods. We reconstruct over 400 ultrametric trees using up to 30 different combinations of phylogenetic and smoothing methods and perform over 2000 separate species delimitation analyses across 16 empirical data sets. We then assess how variable diversity estimates are, in terms of richness and identity, with respect to species delimitation, phylogenetic and smoothing methods. The PTP method generally generates diversity estimates that are more robust to different phylogenetic methods. The GMYC is more sensitive, but provides consistent estimates for BEAST trees. The lower consistency of GMYC estimates is likely a result of differences among gene trees introduced by the smoothing step. Unresolved nodes (real anomalies or methodological artefacts) affect both GMYC and PTP estimates, but have a greater effect on GMYC estimates. Branch smoothing is a difficult step and perhaps an underappreciated source of bias that may be widespread among studies of diversity and diversification. Nevertheless, careful choice of phylogenetic method does produce equivalent PTP and GMYC diversity estimates. We recommend simultaneous use of the PTP model with any model-based gene tree (e.g. RAxML) and GMYC approaches with BEAST trees for obtaining species hypotheses. PMID:25821577

A system and methodology for high-content visual screening of individual intact living cells in suspension

NASA Astrophysics Data System (ADS)

Renaud, Olivier; Heintzmann, Rainer; Sáez-Cirión, Asier; Schnelle, Thomas; Mueller, Torsten; Shorte, Spencer

2007-02-01

Three dimensional imaging provides high-content information from living intact biology, and can serve as a visual screening cue. In the case of single cell imaging the current state of the art uses so-called "axial through-stacking". However, three-dimensional axial through-stacking requires that the object (i.e. a living cell) be adherently stabilized on an optically transparent surface, usually glass; evidently precluding use of cells in suspension. Aiming to overcome this limitation we present here the utility of dielectric field trapping of single cells in three-dimensional electrode cages. Our approach allows gentle and precise spatial orientation and vectored rotation of living, non-adherent cells in fluid suspension. Using various modes of widefield, and confocal microscope imaging we show how so-called "microrotation" can provide a unique and powerful method for multiple point-of-view (three-dimensional) interrogation of intact living biological micro-objects (e.g. single-cells, cell aggregates, and embryos). Further, we show how visual screening by micro-rotation imaging can be combined with micro-fluidic sorting, allowing selection of rare phenotype targets from small populations of cells in suspension, and subsequent one-step single cell cloning (with high-viability). Our methodology combining high-content 3D visual screening with one-step single cell cloning, will impact diverse paradigms, for example cytological and cytogenetic analysis on haematopoietic stem cells, blood cells including lymphocytes, and cancer cells.

A simplified approach to construct infectious cDNA clones of a tobamovirus in a binary vector.

PubMed

Junqueira, Bruna Rayane Teodoro; Nicolini, Cícero; Lucinda, Natalia; Orílio, Anelise Franco; Nagata, Tatsuya

2014-03-01

Infectious cDNA clones of RNA viruses are important tools to study molecular processes such as replication and host-virus interactions. However, the cloning steps necessary for construction of cDNAs of viral RNA genomes in binary vectors are generally laborious. In this study, a simplified method of producing an agro-infectious Pepper mild mottle virus (PMMoV) clone is described in detail. Initially, the complete genome of PMMoV was amplified by a single-step RT-PCR, cloned, and subcloned into a small plasmid vector under the T7 RNA polymerase promoter to confirm the infectivity of the cDNA clone through transcript inoculation. The complete genome was then transferred to a binary vector using a single-step, overlap-extension PCR. The selected clones were agro-infiltrated to Nicotiana benthamiana plants and showed to be infectious, causing typical PMMoV symptoms. No differences in host responses were observed when the wild-type PMMoV isolate, the T7 RNA polymerase-derived transcripts and the agroinfiltration-derived viruses were inoculated to N. benthamiana, Capsicum chinense PI 159236 and Capsicum annuum plants. Copyright © 2013 Elsevier B.V. All rights reserved.

Daily rainfall forecasting for one year in a single run using Singular Spectrum Analysis

NASA Astrophysics Data System (ADS)

Unnikrishnan, Poornima; Jothiprakash, V.

2018-06-01

Effective modelling and prediction of smaller time step rainfall is reported to be very difficult owing to its highly erratic nature. Accurate forecast of daily rainfall for longer duration (multi time step) may be exceptionally helpful in the efficient planning and management of water resources systems. Identification of inherent patterns in a rainfall time series is also important for an effective water resources planning and management system. In the present study, Singular Spectrum Analysis (SSA) is utilized to forecast the daily rainfall time series pertaining to Koyna watershed in Maharashtra, India, for 365 days after extracting various components of the rainfall time series such as trend, periodic component, noise and cyclic component. In order to forecast the time series for longer time step (365 days-one window length), the signal and noise components of the time series are forecasted separately and then added together. The results of the study show that the method of SSA could extract the various components of the time series effectively and could also forecast the daily rainfall time series for longer duration such as one year in a single run with reasonable accuracy.

Cu-Ni-Fe anodes having improved microstructure

DOEpatents

Bergsma, S. Craig; Brown, Craig W.

2004-04-20

A method of producing aluminum in a low temperature electrolytic cell containing alumina dissolved in an electrolyte. The method comprises the steps of providing a molten electrolyte having alumina dissolved therein in an electrolytic cell containing the electrolyte. A non-consumable anode and cathode is disposed in the electrolyte, the anode comprised of Cu--Ni--Fe alloys having single metallurgical phase. Electric current is passed from the anode, through the electrolyte to the cathode thereby depositing aluminum on the cathode, and molten aluminum is collected from the cathode.

Robust high-performance nanoliter-volume single-cell multiple displacement amplification on planar substrates.

PubMed

Leung, Kaston; Klaus, Anders; Lin, Bill K; Laks, Emma; Biele, Justina; Lai, Daniel; Bashashati, Ali; Huang, Yi-Fei; Aniba, Radhouane; Moksa, Michelle; Steif, Adi; Mes-Masson, Anne-Marie; Hirst, Martin; Shah, Sohrab P; Aparicio, Samuel; Hansen, Carl L

2016-07-26

The genomes of large numbers of single cells must be sequenced to further understanding of the biological significance of genomic heterogeneity in complex systems. Whole genome amplification (WGA) of single cells is generally the first step in such studies, but is prone to nonuniformity that can compromise genomic measurement accuracy. Despite recent advances, robust performance in high-throughput single-cell WGA remains elusive. Here, we introduce droplet multiple displacement amplification (MDA), a method that uses commercially available liquid dispensing to perform high-throughput single-cell MDA in nanoliter volumes. The performance of droplet MDA is characterized using a large dataset of 129 normal diploid cells, and is shown to exceed previously reported single-cell WGA methods in amplification uniformity, genome coverage, and/or robustness. We achieve up to 80% coverage of a single-cell genome at 5× sequencing depth, and demonstrate excellent single-nucleotide variant (SNV) detection using targeted sequencing of droplet MDA product to achieve a median allelic dropout of 15%, and using whole genome sequencing to achieve false and true positive rates of 9.66 × 10(-6) and 68.8%, respectively, in a G1-phase cell. We further show that droplet MDA allows for the detection of copy number variants (CNVs) as small as 30 kb in single cells of an ovarian cancer cell line and as small as 9 Mb in two high-grade serous ovarian cancer samples using only 0.02× depth. Droplet MDA provides an accessible and scalable method for performing robust and accurate CNV and SNV measurements on large numbers of single cells.

Virtual substitution scan via single-step free energy perturbation.

PubMed

Chiang, Ying-Chih; Wang, Yi

2016-02-05

With the rapid expansion of our computing power, molecular dynamics (MD) simulations ranging from hundreds of nanoseconds to microseconds or even milliseconds have become increasingly common. The majority of these long trajectories are obtained from plain (vanilla) MD simulations, where no enhanced sampling or free energy calculation method is employed. To promote the 'recycling' of these trajectories, we developed the Virtual Substitution Scan (VSS) toolkit as a plugin of the open-source visualization and analysis software VMD. Based on the single-step free energy perturbation (sFEP) method, VSS enables the user to post-process a vanilla MD trajectory for a fast free energy scan of substituting aryl hydrogens by small functional groups. Dihedrals of the functional groups are sampled explicitly in VSS, which improves the performance of the calculation and is found particularly important for certain groups. As a proof-of-concept demonstration, we employ VSS to compute the solvation free energy change upon substituting the hydrogen of a benzene molecule by 12 small functional groups frequently considered in lead optimization. Additionally, VSS is used to compute the relative binding free energy of four selected ligands of the T4 lysozyme. Overall, the computational cost of VSS is only a fraction of the corresponding multi-step FEP (mFEP) calculation, while its results agree reasonably well with those of mFEP, indicating that VSS offers a promising tool for rapid free energy scan of small functional group substitutions. This article is protected by copyright. All rights reserved. © 2016 Wiley Periodicals, Inc.

Ligation with Nucleic Acid Sequence–Based Amplification

PubMed Central

Ong, Carmichael; Tai, Warren; Sarma, Aartik; Opal, Steven M.; Artenstein, Andrew W.; Tripathi, Anubhav

2012-01-01

This work presents a novel method for detecting nucleic acid targets using a ligation step along with an isothermal, exponential amplification step. We use an engineered ssDNA with two variable regions on the ends, allowing us to design the probe for optimal reaction kinetics and primer binding. This two-part probe is ligated by T4 DNA Ligase only when both parts bind adjacently to the target. The assay demonstrates that the expected 72-nt RNA product appears only when the synthetic target, T4 ligase, and both probe fragments are present during the ligation step. An extraneous 38-nt RNA product also appears due to linear amplification of unligated probe (P3), but its presence does not cause a false-positive result. In addition, 40 mmol/L KCl in the final amplification mix was found to be optimal. It was also found that increasing P5 in excess of P3 helped with ligation and reduced the extraneous 38-nt RNA product. The assay was also tested with a single nucleotide polymorphism target, changing one base at the ligation site. The assay was able to yield a negative signal despite only a single-base change. Finally, using P3 and P5 with longer binding sites results in increased overall sensitivity of the reaction, showing that increasing ligation efficiency can improve the assay overall. We believe that this method can be used effectively for a number of diagnostic assays. PMID:22449695

Repetitive readout of a single electronic spin via quantum logic with nuclear spin ancillae.

PubMed

Jiang, L; Hodges, J S; Maze, J R; Maurer, P; Taylor, J M; Cory, D G; Hemmer, P R; Walsworth, R L; Yacoby, A; Zibrov, A S; Lukin, M D

2009-10-09

Robust measurement of single quantum bits plays a key role in the realization of quantum computation and communication as well as in quantum metrology and sensing. We have implemented a method for the improved readout of single electronic spin qubits in solid-state systems. The method makes use of quantum logic operations on a system consisting of a single electronic spin and several proximal nuclear spin ancillae in order to repetitively readout the state of the electronic spin. Using coherent manipulation of a single nitrogen vacancy center in room-temperature diamond, full quantum control of an electronic-nuclear system consisting of up to three spins was achieved. We took advantage of a single nuclear-spin memory in order to obtain a 10-fold enhancement in the signal amplitude of the electronic spin readout. We also present a two-level, concatenated procedure to improve the readout by use of a pair of nuclear spin ancillae, an important step toward the realization of robust quantum information processors using electronic- and nuclear-spin qubits. Our technique can be used to improve the sensitivity and speed of spin-based nanoscale diamond magnetometers.

Microwave Plasma Based Single-Step Method for Generation of Carbon Nanostructures

DTIC Science & Technology

2013-07-01

Técnico, Technical University of Lisbon, Portugal 2 Mechanical and Aerospace Engeneering , Naval Postgraduate School, Monterey, CA 93943, U.S.A...Plasma environments constitute powerful tools in materials science due to their operation as thermal and chemical reactors. A microwave, atmospheric...applications include electronic devices, transparent conductive films, mechanical devices, chemical sensors, spintronic devices. Moreover, it shows enormous

One-step synthesis of mesoporous pentasil zeolite with single-unit-cell lamellar structural features

DOEpatents

Tsapstsis, Michael; Zhang, Xueyi

2015-11-17

A method for making a pentasil zeolite material includes forming an aqueous solution that includes a structure directing agent and a silica precursor; and heating the solution at a sufficient temperature and for sufficient time to form a pentasil zeolite material from the silica precursor, wherein the structure directing agent includes a quaternary phosphonium ion.

One-pot synthesis of highly luminescent InP/ZnS nanocrystals without precursor injection.

PubMed

Li, Liang; Reiss, Peter

2008-09-03

InP/ZnS core/shell nanocrystals are prepared using a single-step heating-up method relying on the difference in reactivity of the applied InP and ZnS precursors. The obtained particles exhibit size-dependent emission in the range of 480-590 nm, a fluorescence quantum yield of 50-70%, and high photostability.

Empowering Students to Design and Evaluate Synthesis Procedures: A Sonogashira Coupling Project for Advanced Teaching Lab

ERIC Educational Resources Information Center

Ong, Jun-Yang; Chan, Shang-Ce; Hoang, Truong-Giang

2018-01-01

A Sonogashira experiment was transformed into a problem-based learning platform for third-year undergraduate students. Given a target that could be synthesized in a single step, students worked in groups to investigate which method was the best for large-scale production. Through this practical scenario, students learn to conduct a literature…

A Hierarchical Feature and Sample Selection Framework and Its Application for Alzheimer’s Disease Diagnosis

NASA Astrophysics Data System (ADS)

An, Le; Adeli, Ehsan; Liu, Mingxia; Zhang, Jun; Lee, Seong-Whan; Shen, Dinggang

2017-03-01

Classification is one of the most important tasks in machine learning. Due to feature redundancy or outliers in samples, using all available data for training a classifier may be suboptimal. For example, the Alzheimer’s disease (AD) is correlated with certain brain regions or single nucleotide polymorphisms (SNPs), and identification of relevant features is critical for computer-aided diagnosis. Many existing methods first select features from structural magnetic resonance imaging (MRI) or SNPs and then use those features to build the classifier. However, with the presence of many redundant features, the most discriminative features are difficult to be identified in a single step. Thus, we formulate a hierarchical feature and sample selection framework to gradually select informative features and discard ambiguous samples in multiple steps for improved classifier learning. To positively guide the data manifold preservation process, we utilize both labeled and unlabeled data during training, making our method semi-supervised. For validation, we conduct experiments on AD diagnosis by selecting mutually informative features from both MRI and SNP, and using the most discriminative samples for training. The superior classification results demonstrate the effectiveness of our approach, as compared with the rivals.

Differences in Lower Extremity and Trunk Kinematics between Single Leg Squat and Step Down Tasks

PubMed Central

Lewis, Cara L.; Foch, Eric; Luko, Marc M.; Loverro, Kari L.; Khuu, Anne

2015-01-01

The single leg squat and single leg step down are two commonly used functional tasks to assess movement patterns. It is unknown how kinematics compare between these tasks. The purpose of this study was to identify kinematic differences in the lower extremity, pelvis and trunk between the single leg squat and the step down. Fourteen healthy individuals participated in this research and performed the functional tasks while kinematic data were collected for the trunk, pelvis, and lower extremities using a motion capture system. For the single leg squat task, the participant was instructed to squat as low as possible. For the step down task, the participant was instructed to stand on top of a box, slowly lower him/herself until the non-stance heel touched the ground, and return to standing. This was done from two different heights (16cm and 24cm). The kinematics were evaluated at peak knee flexion as well as at 60° of knee flexion. Pearson correlation coefficients (r) between the angles at those two time points were also calculated to better understand the relationship between each task. The tasks resulted in kinematics differences at the knee, hip, pelvis, and trunk at both time points. The single leg squat was performed with less hip adduction (p ≤ 0.003), but more hip external rotation and knee abduction (p ≤ 0.030), than the step down tasks at 60° of knee flexion. These differences were maintained at peak knee flexion except hip external rotation was only significant in the 24cm step down task (p ≤ 0.029). While there were multiple differences between the two step heights at peak knee flexion, the only difference at 60° of knee flexion was in trunk flexion (p < 0.001). Angles at the knee and hip had a moderate to excellent correlation (r = 0.51–0.98), but less consistently so at the pelvis and trunk (r = 0.21–0.96). The differences in movement patterns between the single leg squat and the step down should be considered when selecting a single leg task for evaluation or treatment. The high correlation of knee and hip angles between the three tasks indicates that similar information about knee and hip kinematics was gained from each of these tasks, while pelvis and trunk angles were less well predicted. PMID:25955321

A Successful Synthesis of the CoCrFeNiAl0.3 Single-Crystal, High-Entropy Alloy by Bridgman Solidification

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

Ma, S. G.; Zhang, S. F.; Gao, M. C.

2013-08-22

For the first time, a face-centered-cubic, single-crystal CoCrFeNiAl{sub 0.3} (designated as Al0.3), high-entropy alloy (HEA) was successfully synthesized by the Bridgman solidification (BS) method, at an extremely low withdrawal velocity through a constant temperature gradient, for which it underwent two BS steps. Specially, at the first BS step, the alloy sample underwent several morphological transitions accompanying the crystal growth from the melt. This microstructure evolves from as-cast dendrites, to equiaxed grains, and then to columnar crystals, and last to the single crystal. In particular, at the equiaxed-grain region, some visible annealing twins were observed, which indicates a low stacking faultmore » energy of the Al0.3 alloy. Although a body-centered- cubic CoCrFeNiAl (Al1) HEA was also prepared under the same conditions, only a single columnar-crystal structure with instinctively preferential crystallographic orientations was obtained by the same procedure. A similar morphological transition from dendrites to equiaxed grains occurred at the equiaxed-grain region in Al1 alloy, but the annealing twins were not observed probably because a higher Al addition leads to a higher stacking fault energy for this alloy.« less

Rapid and Sensitive Isothermal Detection of Nucleic-acid Sequence by Multiple Cross Displacement Amplification.

PubMed

Wang, Yi; Wang, Yan; Ma, Ai-Jing; Li, Dong-Xun; Luo, Li-Juan; Liu, Dong-Xin; Jin, Dong; Liu, Kai; Ye, Chang-Yun

2015-07-08

We have devised a novel amplification strategy based on isothermal strand-displacement polymerization reaction, which was termed multiple cross displacement amplification (MCDA). The approach employed a set of ten specially designed primers spanning ten distinct regions of target sequence and was preceded at a constant temperature (61-65 °C). At the assay temperature, the double-stranded DNAs were at dynamic reaction environment of primer-template hybrid, thus the high concentration of primers annealed to the template strands without a denaturing step to initiate the synthesis. For the subsequent isothermal amplification step, a series of primer binding and extension events yielded several single-stranded DNAs and single-stranded single stem-loop DNA structures. Then, these DNA products enabled the strand-displacement reaction to enter into the exponential amplification. Three mainstream methods, including colorimetric indicators, agarose gel electrophoresis and real-time turbidity, were selected for monitoring the MCDA reaction. Moreover, the practical application of the MCDA assay was successfully evaluated by detecting the target pathogen nucleic acid in pork samples, which offered advantages on quick results, modest equipment requirements, easiness in operation, and high specificity and sensitivity. Here we expounded the basic MCDA mechanism and also provided details on an alternative (Single-MCDA assay, S-MCDA) to MCDA technique.

On-Chip Magnetic Platform for Single-Particle Manipulation with Integrated Electrical Feedback.

PubMed

Monticelli, Marco; Torti, Andrea; Cantoni, Matteo; Petti, Daniela; Albisetti, Edoardo; Manzin, Alessandra; Guerriero, Erica; Sordan, Roman; Gervasoni, Giacomo; Carminati, Marco; Ferrari, Giorgio; Sampietro, Marco; Bertacco, Riccardo

2016-02-17

Methods for the manipulation of single magnetic particles have become very interesting, in particular for in vitro biological studies. Most of these studies require an external microscope to provide the operator with feedback for controlling the particle motion, thus preventing the use of magnetic particles in high-throughput experiments. In this paper, a simple and compact system with integrated electrical feedback is presented, implementing in the very same device both the manipulation and detection of the transit of single particles. The proposed platform is based on zig-zag shaped magnetic nanostructures, where transverse magnetic domain walls are pinned at the corners and attract magnetic particles in suspension. By applying suitable external magnetic fields, the domain walls move to the nearest corner, thus causing the step by step displacement of the particles along the nanostructure. The very same structure is also employed for detecting the bead transit. Indeed, the presence of the magnetic particle in suspension over the domain wall affects the depinning field required for its displacement. This characteristic field can be monitored through anisotropic magnetoresistance measurements, thus implementing an integrated electrical feedback of the bead transit. In particular, the individual manipulation and detection of single 1-μm sized beads is demonstrated. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A single-step aerosol process for in-situ surface modification of nanoparticles: Preparation of stable aqueous nanoparticle suspensions.

PubMed

Sapra, Mahak; Pawar, Amol Ashok; Venkataraman, Chandra

2016-02-15

Surface modification of nanoparticles during aerosol or gas-phase synthesis, followed by direct transfer into liquid media can be used to produce stable water-dispersed nanoparticle suspensions. This work investigates a single-step, aerosol process for in-situ surface-modification of nanoparticles. Previous studies have used a two-step sublimation-condensation mechanism following droplet drying, for surface modification, while the present process uses a liquid precursor containing two solutes, a matrix lipid and a surface modifying agent. A precursor solution in chloroform, of stearic acid lipid, with 4 %w/w of surface-active, physiological molecules [1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dipalmitoyl-sn-glycero-3-phospho-(1'-rac-glycerol)-sodium salt (DPPG) or 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy (polyethylene glycol) 2000]-ammonium salt (DPPE-PEG)] was processed in an aerosol reactor at a low gas temperatures. The surface modified nanoparticles were characterized for morphology, surface composition and suspension properties. Spherical, surface-modified lipid nanoparticles with median mobility diameters in the range of 105-150nm and unimodal size distributions were obtained. Fourier transform infra-red spectroscopy (FTIR) measurements confirmed the presence of surface-active molecules on external surfaces of modified lipid nanoparticles. Surface modified nanoparticles exhibited improved suspension stability, compared to that of pure lipid nanoparticles for a period of 30days. Lowest aggregation was observed in DPPE-PEG modified nanoparticles from combined electrostatic and steric effects. The study provides a single-step aerosol method for in-situ surface modification of nanoparticles, using minimal amounts of surface active agents, to make stable, aqueous nanoparticle suspensions. Copyright © 2015 Elsevier Inc. All rights reserved.

Mirror gait retraining for the treatment of patellofemoral pain in female runners

PubMed Central

Willy, Richard W.; Scholz, John P.; Davis, Irene S.

2012-01-01

Background Abnormal hip mechanics are often implicated in female runners with patellofemoral pain. We sought to evaluate a simple gait retraining technique, using a full-length mirror, in female runners with patellofemoral pain and abnormal hip mechanics. Transfer of the new motor skill to the untrained tasks of single leg squat and step descent was also evaluated. Methods Ten female runners with patellofemoral pain completed 8 sessions of mirror and verbal feedback on their lower extremity alignment during treadmill running. During the last 4 sessions, mirror and verbal feedback were progressively removed. Hip mechanics were assessed during running gait, a single leg squat and a step descent, both pre- and post-retraining. Subjects returned to their normal running routines and analyses were repeated at 1-month and 3-month post-retraining. Data were analyzed via repeated measures analysis of variance. Findings Subjects reduced peaks of hip adduction, contralateral pelvic drop, and hip abduction moment during running (P<0.05, effect size=0.69–2.91). Skill transfer to single leg squatting and step descent was noted (P<0.05, effect size=0.91–1.35). At 1 and 3 months post retraining, most mechanics were maintained in the absence of continued feedback. Subjects reported improvements in pain and function (P<0.05, effect size=3.81–7.61) and maintained through 3 months post retraining. Interpretation Mirror gait retraining was effective in improving mechanics and measures of pain and function. Skill transfer to the untrained tasks of squatting and step descent indicated that a higher level of motor learning had occurred. Extended follow-up is needed to determine the long term efficacy of this treatment. PMID:22917625

What experimental experience affects dogs' comprehension of human communicative actions?

PubMed

Hauser, Marc D; Comins, Jordan A; Pytka, Lisa M; Cahill, Donal P; Velez-Calderon, Sofia

2011-01-01

Studies of dogs report that individuals reliably respond to the goal-directed communicative actions (e.g., pointing) of human experimenters. All of these studies use some version of a multi-trial approach, thereby allowing for the possibility of rapid learning within an experimental session. The experiments reported here ask whether dogs can respond correctly to a communicative action based on only a single presentation, thereby eliminating the possibility of learning within the experimental context. We tested 173 dogs. For each dog reaching our test criteria, we used a single presentation of six different goal-directed actions within a session, asking whether they correctly follow to a target goal (container with concealed food) a (1) distal hand point, (2) step toward one container, (3) hand point to one container followed by step toward the other, (4) step toward one container and point to the other, (5) distal foot point with the experimenter's hands free, and (6) distal foot point with the experimenter's hands occupied. Given only a single presentation, dogs selected the correct container when the experimenter hand pointed, foot pointed with hands occupied, or stepped closer to the target container, but failed on the other actions, despite using the same method. The fact that dogs correctly followed foot pointing with hands occupied, but not hands free, suggests that they are sensitive to environmental constraints, and use this information to infer rational, goal-directed action. We discuss these results in light of the role of experience in recognizing communicative gestures, as well as the significance of coding criteria for studies of canine competence. Copyright © 2010 Elsevier B.V. All rights reserved.

Human Mitochondrial RNA Polymerase: Evaluation of the Single-Nucleotide-Addition Cycle on Synthetic RNA/DNA Scaffolds

PubMed Central

Smidansky, Eric D.; Arnold, Jamie J.; Reynolds, Shelley L.; Cameron, Craig E.

2013-01-01

The human mitochondrial RNA polymerase (h-mtRNAP) serves as both the transcriptase for expression and the primase for replication of mitochondrial DNA. As such, the enzyme is of fundamental importance to cellular energy metabolism, and defects in its function may be related to human disease states. Here we describe in vitro analysis of the h-mtRNAP kinetic mechanism for single, correct nucleotide incorporation. This was made possible by the development of efficient methods for expression and purification of h-mtRNAP using a bacterial system and by utilization of assays that rely on simple, synthetic RNA/DNA scaffolds without the need for mitochondrial transcription accessory proteins. We find that h-mtRNAP accomplishes single-nucleotide incorporation by using the same core steps, including conformational change steps before and after chemistry, that are prototypical for most types of nucleic acid polymerases. The polymerase binds to scaffolds via a two-step mechanism consisting of a fast initial-encounter step followed by a much slower isomerization that leads to catalytic competence. A substantial solvent deuterium kinetic isotope effect was observed for the forward reaction, but none was detectable for the reverse reaction, suggesting that chemistry is at least partially rate-limiting in the forward direction but not in the reverse. h-mtRNAP appears to exercise much more stringent surveillance over base than over sugar in determining the correctness of a nucleotide. The utility of developing the robust in vitro assays described here and of establishing a baseline of kinetic performance for the wild-type enzyme is that biological questions concerning h-mtRNAP may now begin to be addressed. PMID:21548588

Leaching of biocides from building facades: Upscaling of a local two-region leaching model to the city scale

NASA Astrophysics Data System (ADS)

Coutu, S.; Rota, C.; Rossi, L.; Barry, D. A.

2011-12-01

Facades are protected by paints that contain biocides as protection against degradation. These biocides are leached by rainfall (albeit at low concentrations). At the city scale, however, the surface area of building facades is significant, and leached biocides are a potential environmental risk to receiving waters. A city-scale biocide-leaching model was developed based on two main steps. In the first step, laboratory experiments on a single facade were used to calibrate and validate a 1D, two-region phenomenological model of biocide leaching. The same data set was analyzed independently by another research group who found empirically that biocide leachate breakthrough curves were well represented by a sum of two exponentials. Interestingly, the two-region model was found analytically to reproduce this functional form as a special case. The second step in the method is site-specific, and involves upscaling the validated single facade model to a particular city. In this step, (i) GIS-based estimates of facade heights and areas are deduced using the city's cadastral data, (ii) facade flow is estimated using local meteorological data (rainfall, wind direction) and (iii) paint application rates are modeled as a stochastic process based on manufacturers' recommendations. The methodology was applied to Lausanne, Switzerland, a city of about 200,000 inhabitants. Approximately 30% of the annually applied mass of biocides was estimated to be released to the environment.

An Improved Single-Step Cloning Strategy Simplifies the Agrobacterium tumefaciens-Mediated Transformation (ATMT)-Based Gene-Disruption Method for Verticillium dahliae.

PubMed

Wang, Sheng; Xing, Haiying; Hua, Chenlei; Guo, Hui-Shan; Zhang, Jie

2016-06-01

The soilborne fungal pathogen Verticillium dahliae infects a broad range of plant species to cause severe diseases. The availability of Verticillium genome sequences has provided opportunities for large-scale investigations of individual gene function in Verticillium strains using Agrobacterium tumefaciens-mediated transformation (ATMT)-based gene-disruption strategies. Traditional ATMT vectors require multiple cloning steps and elaborate characterization procedures to achieve successful gene replacement; thus, these vectors are not suitable for high-throughput ATMT-based gene deletion. Several advancements have been made that either involve simplification of the steps required for gene-deletion vector construction or increase the efficiency of the technique for rapid recombinant characterization. However, an ATMT binary vector that is both simple and efficient is still lacking. Here, we generated a USER-ATMT dual-selection (DS) binary vector, which combines both the advantages of the USER single-step cloning technique and the efficiency of the herpes simplex virus thymidine kinase negative-selection marker. Highly efficient deletion of three different genes in V. dahliae using the USER-ATMT-DS vector enabled verification that this newly-generated vector not only facilitates the cloning process but also simplifies the subsequent identification of fungal homologous recombinants. The results suggest that the USER-ATMT-DS vector is applicable for efficient gene deletion and suitable for large-scale gene deletion in V. dahliae.

Surface modification of aramid fibers by bio-inspired poly(dopamine) and epoxy functionalized silane grafting.

PubMed

Sa, Rina; Yan, Yan; Wei, Zhenhai; Zhang, Liqun; Wang, Wencai; Tian, Ming

2014-12-10

A novel biomimetic surface modification method for meta-aramid (MPIA) fibers and the improvement on adhesion with rubber matrix was demonstrated. Inspired by the composition of adhesive proteins in mussels, we used dopamine (DOPA) self-polymerization to form thin, surface-adherent poly(dopamine) (PDA) films onto the surface of MPIA fibers simply by immersing MPIA fibers in a dopamine solution at room temperature. An epoxy functionalized silane (KH560) grafting was then carried out on the surface of the poly(dopamine)-coated MPIA, either by a "one-step" or "two-step" method, to introduce an epoxy group onto the MPIA fiber surface. The surface composition and microstructure of the modified MPIA was characterized by X-ray photoelectron spectroscopy (XPS), attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR), scanning electron microscopy (SEM), and thermogravimetric analysis (TGA). The results indicated successful grafting of KH560 on the PDA-coated MPIA surface. A single-fiber pull-out test was applied to evaluate the adhesion of MPIA fibers with the rubber matrix. Compared with the untreated MPIA fibers, the adhesion strength between the modified MPIA fibers by "one step" method with rubber matrix has an increase of 62.5%.

Metabolic network visualization eliminating node redundance and preserving metabolic pathways

PubMed Central

Bourqui, Romain; Cottret, Ludovic; Lacroix, Vincent; Auber, David; Mary, Patrick; Sagot, Marie-France; Jourdan, Fabien

2007-01-01

Background The tools that are available to draw and to manipulate the representations of metabolism are usually restricted to metabolic pathways. This limitation becomes problematic when studying processes that span several pathways. The various attempts that have been made to draw genome-scale metabolic networks are confronted with two shortcomings: 1- they do not use contextual information which leads to dense, hard to interpret drawings, 2- they impose to fit to very constrained standards, which implies, in particular, duplicating nodes making topological analysis considerably more difficult. Results We propose a method, called MetaViz, which enables to draw a genome-scale metabolic network and that also takes into account its structuration into pathways. This method consists in two steps: a clustering step which addresses the pathway overlapping problem and a drawing step which consists in drawing the clustered graph and each cluster. Conclusion The method we propose is original and addresses new drawing issues arising from the no-duplication constraint. We do not propose a single drawing but rather several alternative ways of presenting metabolism depending on the pathway on which one wishes to focus. We believe that this provides a valuable tool to explore the pathway structure of metabolism. PMID:17608928

Rapid micro-scale proteolysis of proteins for MALDI-MS peptide mapping using immobilized trypsin

NASA Astrophysics Data System (ADS)

Gobom, Johan; Nordhoff, Eckhard; Ekman, Rolf; Roepstorff, Peter

1997-12-01

In this study we present a rapid method for tryptic digestion of proteins using micro-columns with enzyme immobilized on perfusion chromatography media. The performance of the method is exemplified with acyl-CoA-binding protein and reduced carbamidomethylated bovine serum albumin. The method proved to be significantly faster and yielded a better sequence coverage and an improved signal-to-noise ratio for the MALDI-MS peptide maps, compared to in-solution- and on-target digestion. Only a single sample transfer step is required, and therefore sample loss due to adsorption to surfaces is reduced, which is a critical issue when handling low picomole to femtomole amounts of proteins. An example is shown with on-column proteolytic digestion and subsequent elution of the digest into a reversed-phase micro-column. This is useful if the sample contains large amounts of salt or is too diluted for MALDI-MS analysis. Furthermore, by step-wise elution from the reversedphase column, a complex digest can be fractionated, which reduces signal suppression and facilitates data interpretation in the subsequent MS-analysis. The method also proved useful for consecutive digestions with enzymes of different cleavage specificity. This is exemplified with on-column tryptic digestion, followed by reversed-phase step-wise elution, and subsequent on-target V8 protease digestion.

A novel two-step optimization method for tandem and ovoid high-dose-rate brachytherapy treatment for locally advanced cervical cancer.

PubMed

Sharma, Manju; Fields, Emma C; Todor, Dorin A

2015-01-01

To present a novel method allowing fast volumetric optimization of tandem and ovoid high-dose-rate treatments and to quantify its benefits. Twenty-seven CT-based treatment plans from 6 consecutive cervical cancer patients treated with four to five intracavitary tandem and ovoid insertions were used. Initial single-step optimized plans were manually optimized, approved, and delivered plans created with a goal to cover high-risk clinical target volume (HR-CTV) with D90 >90% and minimize rectum, bladder, and sigmoid D2cc. For the two-step optimized (TSO) plan, each single-step optimized plan was replanned adding a structure created from prescription isodose line to the existent physician delineated HR-CTV, rectum, bladder, and sigmoid. New, more rigorous dose-volume histogram constraints for the critical organs at risks (OARs) were used for the optimization. HR-CTV D90 and OAR D2ccs were evaluated in both plans. TSO plans had consistently smaller D2ccs for all three OARs while preserving HR-CTV D90. On plans with "excellent" CTV coverage, average D90 of 96% (91-102%), sigmoid, bladder, and rectum D2cc, respectively, reduced on average by 37% (16-73%), 28% (20-47%), and 27% (15-45%). Similar reductions were obtained on plans with "good" coverage, average D90 of 93% (90-99%). For plans with "inferior" coverage, average D90 of 81%, the coverage increased to 87% with concurrent D2cc reductions of 31%, 18%, and 11% for sigmoid, bladder, and rectum, respectively. The TSO can be added with minimal planning time increase but with the potential of dramatic and systematic reductions in OAR D2ccs and in some cases with concurrent increase in target dose coverage. These single-fraction modifications would be magnified over the course of four to five intracavitary insertions and may have real clinical implications in terms of decreasing both acute and late toxicities. Copyright © 2015 American Brachytherapy Society. Published by Elsevier Inc. All rights reserved.

High quality factor whispering gallery modes from self-assembled hexagonal GaN rods grown by metal-organic vapor phase epitaxy.

PubMed

Tessarek, C; Sarau, G; Kiometzis, M; Christiansen, S

2013-02-11

Self-assembled GaN rods were grown on sapphire by metal-organic vapor phase epitaxy using a simple two-step method that relies first on a nitridation step followed by GaN epitaxy. The mask-free rods formed without any additional catalyst. Most of the vertically aligned rods exhibit a regular hexagonal shape with sharp edges and smooth sidewall facets. Cathodo- and microphotoluminescence investigations were carried out on single GaN rods. Whispering gallery modes with quality factors greater than 4000 were measured demonstrating the high morphological and optical quality of the self-assembled GaN rods.

Optimization of cryoprotectant loading into murine and human oocytes.

PubMed

Karlsson, Jens O M; Szurek, Edyta A; Higgins, Adam Z; Lee, Sang R; Eroglu, Ali

2014-02-01

Loading of cryoprotectants into oocytes is an important step of the cryopreservation process, in which the cells are exposed to potentially damaging osmotic stresses and chemical toxicity. Thus, we investigated the use of physics-based mathematical optimization to guide design of cryoprotectant loading methods for mouse and human oocytes. We first examined loading of 1.5 M dimethyl sulfoxide (Me(2)SO) into mouse oocytes at 23°C. Conventional one-step loading resulted in rates of fertilization (34%) and embryonic development (60%) that were significantly lower than those of untreated controls (95% and 94%, respectively). In contrast, the mathematically optimized two-step method yielded much higher rates of fertilization (85%) and development (87%). To examine the causes for oocyte damage, we performed experiments to separate the effects of cell shrinkage and Me(2)SO exposure time, revealing that neither shrinkage nor Me(2)SO exposure single-handedly impairs the fertilization and development rates. Thus, damage during one-step Me(2)SO addition appears to result from interactions between the effects of Me(2)SO toxicity and osmotic stress. We also investigated Me(2)SO loading into mouse oocytes at 30°C. At this temperature, fertilization rates were again lower after one-step loading (8%) in comparison to mathematically optimized two-step loading (86%) and untreated controls (96%). Furthermore, our computer algorithm generated an effective strategy for reducing Me(2)SO exposure time, using hypotonic diluents for cryoprotectant solutions. With this technique, 1.5 M Me(2)SO was successfully loaded in only 2.5 min, with 92% fertilizability. Based on these promising results, we propose new methods to load cryoprotectants into human oocytes, designed using our mathematical optimization approach. Copyright © 2013 Elsevier Inc. All rights reserved.

Optimization of Cryoprotectant Loading into Murine and Human Oocytes

PubMed Central

Karlsson, Jens O.M.; Szurek, Edyta A.; Higgins, Adam Z.; Lee, Sang R.; Eroglu, Ali

2014-01-01

Loading of cryoprotectants into oocytes is an important step of the cryopreservation process, in which the cells are exposed to potentially damaging osmotic stresses and chemical toxicity. Thus, we investigated the use of physics-based mathematical optimization to guide design of cryoprotectant loading methods for mouse and human oocytes. We first examined loading of 1.5 M dimethylsulfoxide (Me2SO) into mouse oocytes at 23°C. Conventional one-step loading resulted in rates of fertilization (34%) and embryonic development (60%) that were significantly lower than those of untreated controls (95% and 94%, respectively). In contrast, the mathematically optimized two-step method yielded much higher rates of fertilization (85%) and development (87%). To examine the causes for oocyte damage, we performed experiments to separate the effects of cell shrinkage and Me2SO exposure time, revealing that neither shrinkage nor Me2SO exposure single-handedly impairs the fertilization and development rates. Thus, damage during one-step Me2SO addition appears to result from interactions between the effects of Me2SO toxicity and osmotic stress. We also investigated Me2SO loading into mouse oocytes at 30°C. At this temperature, fertilization rates were again lower after one-step loading (8%) in comparison to mathematically optimized two-step loading (86%) and untreated controls (96%). Furthermore, our computer algorithm generated an effective strategy for reducing Me2SO exposure time, using hypotonic diluents for cryoprotectant solutions. With this technique, 1.5 M Me2SO was successfully loaded in only 2.5 min, with 92% fertilizability. Based on these promising results, we propose new methods to load cryoprotectants into human oocytes, designed using our mathematical optimization approach. PMID:24246951

An efficient method for variable region assembly in the construction of scFv phage display libraries using independent strand amplification

PubMed Central

Sotelo, Pablo H.; Collazo, Noberto; Zuñiga, Roberto; Gutiérrez-González, Matías; Catalán, Diego; Ribeiro, Carolina Hager; Aguillón, Juan Carlos; Molina, María Carmen

2012-01-01

Phage display library technology is a common method to produce human antibodies. In this technique, the immunoglobulin variable regions are displayed in a bacteriophage in a way that each filamentous virus displays the product of a single antibody gene on its surface. From the collection of different phages, it is possible to isolate the virus that recognizes specific targets. The most common form in which to display antibody variable regions in the phage is the single chain variable fragment format (scFv), which requires assembly of the heavy and light immunoglobulin variable regions in a single gene. In this work, we describe a simple and efficient method for the assembly of immunoglobulin heavy and light chain variable regions in a scFv format. This procedure involves a two-step reaction: (1) DNA amplification to produce the single strand form of the heavy or light chain gene required for the fusion; and (2) mixture of both single strand products followed by an assembly reaction to construct a complete scFv gene. Using this method, we produced 6-fold more scFv encoding DNA than the commonly used splicing by overlap extension PCR (SOE-PCR) approach. The scFv gene produced by this method also proved to be efficient in generating a diverse scFv phage display library. From this scFv library, we obtained phages that bound several non-related antigens, including recombinant proteins and rotavirus particles. PMID:22692130

A Multiomics Approach to Identify Genes Associated with Childhood Asthma Risk and Morbidity.

PubMed

Forno, Erick; Wang, Ting; Yan, Qi; Brehm, John; Acosta-Perez, Edna; Colon-Semidey, Angel; Alvarez, Maria; Boutaoui, Nadia; Cloutier, Michelle M; Alcorn, John F; Canino, Glorisa; Chen, Wei; Celedón, Juan C

2017-10-01

Childhood asthma is a complex disease. In this study, we aim to identify genes associated with childhood asthma through a multiomics "vertical" approach that integrates multiple analytical steps using linear and logistic regression models. In a case-control study of childhood asthma in Puerto Ricans (n = 1,127), we used adjusted linear or logistic regression models to evaluate associations between several analytical steps of omics data, including genome-wide (GW) genotype data, GW methylation, GW expression profiling, cytokine levels, asthma-intermediate phenotypes, and asthma status. At each point, only the top genes/single-nucleotide polymorphisms/probes/cytokines were carried forward for subsequent analysis. In step 1, asthma modified the gene expression-protein level association for 1,645 genes; pathway analysis showed an enrichment of these genes in the cytokine signaling system (n = 269 genes). In steps 2-3, expression levels of 40 genes were associated with intermediate phenotypes (asthma onset age, forced expiratory volume in 1 second, exacerbations, eosinophil counts, and skin test reactivity); of those, methylation of seven genes was also associated with asthma. Of these seven candidate genes, IL5RA was also significant in analytical steps 4-8. We then measured plasma IL-5 receptor α levels, which were associated with asthma age of onset and moderate-severe exacerbations. In addition, in silico database analysis showed that several of our identified IL5RA single-nucleotide polymorphisms are associated with transcription factors related to asthma and atopy. This approach integrates several analytical steps and is able to identify biologically relevant asthma-related genes, such as IL5RA. It differs from other methods that rely on complex statistical models with various assumptions.

Pre-ordering of interfacial water in the pathway of heterogeneous ice nucleation does not lead to a two-step crystallization mechanism.

PubMed

Lupi, Laura; Peters, Baron; Molinero, Valeria

2016-12-07

According to Classical Nucleation Theory (CNT), the transition from liquid to crystal occurs in a single activated step with a transition state controlled by the size of the crystal embryo. This picture has been challenged in the last two decades by several reports of two-step crystallization processes in which the liquid first produces pre-ordered or dense domains, within which the crystal nucleates in a second step. Pre-ordering preceding crystal nucleation has been recently reported in simulations of ice crystallization, raising the question of whether the mechanism of ice nucleation involves two steps. In this paper, we investigate the heterogeneous nucleation of ice on carbon surfaces. We use molecular simulations with efficient coarse-grained models combined with rare event sampling methods and free energy calculations to elucidate the role of pre-ordering of liquid water at the carbon surface in the reaction coordinate for heterogeneous nucleation. We find that ice nucleation proceeds through a classical mechanism, with a single barrier between liquid and crystal. The reaction coordinate that determines the crossing of the nucleation barrier is the size of the crystal nucleus, as predicted by CNT. Wetting of the critical ice nuclei within pre-ordered domains decreases the nucleation barrier, increasing the nucleation rates. The preferential pathway for crystallization involves the early creation of pre-ordered domains that are the birthplace of the ice crystallites but do not represent a minimum in the free energy pathway from liquid to ice. We conclude that a preferential pathway through an intermediate-order precursor does not necessarily result in a two-step mechanism.

Pressure estimation from single-snapshot tomographic PIV in a turbulent boundary layer

NASA Astrophysics Data System (ADS)

Schneiders, Jan F. G.; Pröbsting, Stefan; Dwight, Richard P.; van Oudheusden, Bas W.; Scarano, Fulvio

2016-04-01

A method is proposed to determine the instantaneous pressure field from a single tomographic PIV velocity snapshot and is applied to a flat-plate turbulent boundary layer. The main concept behind the single-snapshot pressure evaluation method is to approximate the flow acceleration using the vorticity transport equation. The vorticity field calculated from the measured instantaneous velocity is advanced over a single integration time step using the vortex-in-cell (VIC) technique to update the vorticity field, after which the temporal derivative and material derivative of velocity are evaluated. The pressure in the measurement volume is subsequently evaluated by solving a Poisson equation. The procedure is validated considering data from a turbulent boundary layer experiment, obtained with time-resolved tomographic PIV at 10 kHz, where an independent surface pressure fluctuation measurement is made by a microphone. The cross-correlation coefficient of the surface pressure fluctuations calculated by the single-snapshot pressure method with respect to the microphone measurements is calculated and compared to that obtained using time-resolved pressure-from-PIV, which is regarded as benchmark. The single-snapshot procedure returns a cross-correlation comparable to the best result obtained by time-resolved PIV, which uses a nine-point time kernel. When the kernel of the time-resolved approach is reduced to three measurements, the single-snapshot method yields approximately 30 % higher correlation. Use of the method should be cautioned when the contributions to fluctuating pressure from outside the measurement volume are significant. The study illustrates the potential for simplifying the hardware configurations (e.g. high-speed PIV or dual PIV) required to determine instantaneous pressure from tomographic PIV.

Live-Cell Imaging of Early Steps of Single HIV-1 Infection.

PubMed

Francis, Ashwanth C; Melikyan, Gregory B

2018-05-19

Live-cell imaging of single HIV-1 entry offers a unique opportunity to delineate the spatio-temporal regulation of infection. Novel virus labeling and imaging approaches enable the visualization of key steps of HIV-1 entry leading to nuclear import, integration into the host genome, and viral protein expression. Here, we discuss single virus imaging strategies, focusing on live-cell imaging of single virus fusion and productive uncoating that culminates in HIV-1 infection.

Twisting and subunit rotation in single FOF1-ATP synthase

PubMed Central

Sielaff, Hendrik; Börsch, Michael

2013-01-01

FOF1-ATP synthases are ubiquitous proton- or ion-powered membrane enzymes providing ATP for all kinds of cellular processes. The mechanochemistry of catalysis is driven by two rotary nanomotors coupled within the enzyme. Their different step sizes have been observed by single-molecule microscopy including videomicroscopy of fluctuating nanobeads attached to single enzymes and single-molecule Förster resonance energy transfer. Here we review recent developments of approaches to monitor the step size of subunit rotation and the transient elastic energy storage mechanism in single FOF1-ATP synthases. PMID:23267178

Environmentally-friendly lithium recycling from a spent organic li-ion battery.

PubMed

Renault, Stéven; Brandell, Daniel; Edström, Kristina

2014-10-01

A simple and straightforward method using non-polluting solvents and a single thermal treatment step at moderate temperature was investigated as an environmentally-friendly process to recycle lithium from organic electrode materials for secondary lithium batteries. This method, highly dependent on the choice of electrolyte, gives up to 99% of sustained capacity for the recycled materials used in a second life-cycle battery when compared with the original. The best results were obtained using a dimethyl carbonate/lithium bis(trifluoromethane sulfonyl) imide electrolyte that does not decompose in presence of water. The process implies a thermal decomposition step at a moderate temperature of the extracted organic material into lithium carbonate, which is then used as a lithiation agent for the preparation of fresh electrode material without loss of lithium. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

On the error propagation of semi-Lagrange and Fourier methods for advection problems☆

PubMed Central

Einkemmer, Lukas; Ostermann, Alexander

2015-01-01

In this paper we study the error propagation of numerical schemes for the advection equation in the case where high precision is desired. The numerical methods considered are based on the fast Fourier transform, polynomial interpolation (semi-Lagrangian methods using a Lagrange or spline interpolation), and a discontinuous Galerkin semi-Lagrangian approach (which is conservative and has to store more than a single value per cell). We demonstrate, by carrying out numerical experiments, that the worst case error estimates given in the literature provide a good explanation for the error propagation of the interpolation-based semi-Lagrangian methods. For the discontinuous Galerkin semi-Lagrangian method, however, we find that the characteristic property of semi-Lagrangian error estimates (namely the fact that the error increases proportionally to the number of time steps) is not observed. We provide an explanation for this behavior and conduct numerical simulations that corroborate the different qualitative features of the error in the two respective types of semi-Lagrangian methods. The method based on the fast Fourier transform is exact but, due to round-off errors, susceptible to a linear increase of the error in the number of time steps. We show how to modify the Cooley–Tukey algorithm in order to obtain an error growth that is proportional to the square root of the number of time steps. Finally, we show, for a simple model, that our conclusions hold true if the advection solver is used as part of a splitting scheme. PMID:25844018

Direct Observation of Two-Step Photon Absorption in an InAs/GaAs Single Quantum Dot for the Operation of Intermediate-Band Solar Cells.

PubMed

Nozawa, Tomohiro; Takagi, Hiroyuki; Watanabe, Katsuyuki; Arakawa, Yasuhiko

2015-07-08

We present the first direct observation of two-step photon absorption in an InAs/GaAs single quantum dot (QD) using photocurrent spectroscopy with two lasers. The sharp peaks of the photocurrent are shifted due to the quantum confined Stark effect, indicating that the photocurrent from a single QD is obtained. In addition, the intensity of the peaks depends on the power of the secondary laser. These results reveal the direct demonstration of the two-step photon absorption in a single QD. This is an essential result for both the fundamental operation and the realization of ultrahigh solar-electricity energy conversion in quantum dot intermediate-band solar cells.

Composition of single-step media used for human embryo culture.

PubMed

Morbeck, Dean E; Baumann, Nikola A; Oglesbee, Devin

2017-04-01

To determine compositions of commercial single-step culture media and test with a murine model whether differences in composition are biologically relevant. Experimental laboratory study. University-based laboratory. Inbred female mice were superovulated and mated with outbred male mice. Amino acid, organic acid, and ions content were determined for single-step culture media: CSC, Global, G-TL, and 1-Step. To determine whether differences in composition of these media are biologically relevant, mouse one-cell embryos were cultured for 96 hours in each culture media at 5% and 20% oxygen in a time-lapse incubator. Compositions of four culture media were analyzed for concentrations of 30 amino acids, organic acids, and ions. Blastocysts at 96 hours of culture and cell cycle timings were calculated, and experiments were repeated in triplicate. Of the more than 30 analytes, concentrations of glucose, lactate, pyruvate, amino acids, phosphate, calcium, and magnesium varied in concentrations. Mouse embryos were differentially affected by oxygen in G-TL and 1-Step. Four single-step culture media have compositions that vary notably in pyruvate, lactate, and amino acids. Blastocyst development was affected by culture media and its interaction with oxygen concentration. Copyright © 2017 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

Comparison of the DNA extraction methods for polymerase chain reaction amplification from formalin-fixed and paraffin-embedded tissues.

PubMed

Sato, Y; Sugie, R; Tsuchiya, B; Kameya, T; Natori, M; Mukai, K

2001-12-01

To obtain an adequate quality and quantity of DNA from formalin-fixed and paraffin-embedded tissue, six different DNA extraction methods were compared. Four methods used deparaffinization by xylene followed by proteinase K digestion and phenol-chloroform extraction. The temperature of the different steps was changed to obtain higher yields and improved quality of extracted DNA. The remaining two methods used microwave heating for deparaffinization. The best DNA extraction method consisted of deparaffinization by microwave irradiation, protein digestion with proteinase K at 48 degrees C overnight, and no further purification steps. By this method, the highest DNA yield was obtained and the amplification of a 989-base pair beta-globin gene fragment was achieved. Furthermore, DNA extracted by means of this procedure from five gastric carcinomas was successfully used for single strand conformation polymorphism and direct sequencing assays of the beta-catenin gene. Because the microwave-based DNA extraction method presented here is simple, has a lower contamination risk, and results in a higher yield of DNA compared with the ordinary organic chemical reagent-based extraction method, it is considered applicable to various clinical and basic fields.

Pseudo-time methods for constrained optimization problems governed by PDE

NASA Technical Reports Server (NTRS)

Taasan, Shlomo

1995-01-01

In this paper we present a novel method for solving optimization problems governed by partial differential equations. Existing methods are gradient information in marching toward the minimum, where the constrained PDE is solved once (sometimes only approximately) per each optimization step. Such methods can be viewed as a marching techniques on the intersection of the state and costate hypersurfaces while improving the residuals of the design equations per each iteration. In contrast, the method presented here march on the design hypersurface and at each iteration improve the residuals of the state and costate equations. The new method is usually much less expensive per iteration step since, in most problems of practical interest, the design equation involves much less unknowns that that of either the state or costate equations. Convergence is shown using energy estimates for the evolution equations governing the iterative process. Numerical tests show that the new method allows the solution of the optimization problem in a cost of solving the analysis problems just a few times, independent of the number of design parameters. The method can be applied using single grid iterations as well as with multigrid solvers.

Three-axis attitude control by two-step rotations using only magnetic torquers in a low Earth orbit near the magnetic equator

NASA Astrophysics Data System (ADS)

Inamori, Takaya; Otsuki, Kensuke; Sugawara, Yoshiki; Saisutjarit, Phongsatorn; Nakasuka, Shinichi

2016-11-01

This study proposes a novel method for three-axis attitude control using only magnetic torquers (MTQs). Previously, MTQs have been utilized for attitude control in many low Earth orbit satellites. Although MTQs are useful for achieving attitude control at low cost and high reliability without the need for propellant, these electromagnetic coils cannot be used to generate an attitude control torque about the geomagnetic field vector. Thus, conventional attitude control methods using MTQs assume the magnetic field changes in an orbital period so that the satellite can generate a required attitude control torque after waiting for a change in the magnetic field direction. However, in a near magnetic equatorial orbit, the magnetic field does not change in an inertial reference frame. Thus, satellites cannot generate a required attitude control torque in a single orbital period with only MTQs. This study proposes a method for achieving a rotation about the geomagnetic field vector by generating a torque that is perpendicular to it. First, this study shows that the three-axis attitude control using only MTQs is feasible with a two-step rotation. Then, the study proposes a method for controlling the attitude with the two-step rotation using a PD controller. Finally, the proposed method is assessed by examining the results of numerical simulations.

Harmonic source wavefront aberration correction for ultrasound imaging

PubMed Central

Dianis, Scott W.; von Ramm, Olaf T.

2011-01-01

A method is proposed which uses a lower-frequency transmit to create a known harmonic acoustical source in tissue suitable for wavefront correction without a priori assumptions of the target or requiring a transponder. The measurement and imaging steps of this method were implemented on the Duke phased array system with a two-dimensional (2-D) array. The method was tested with multiple electronic aberrators [0.39π to 1.16π radians root-mean-square (rms) at 4.17 MHz] and with a physical aberrator 0.17π radians rms at 4.17 MHz) in a variety of imaging situations. Corrections were quantified in terms of peak beam amplitude compared to the unaberrated case, with restoration between 0.6 and 36.6 dB of peak amplitude with a single correction. Standard phantom images before and after correction were obtained and showed both visible improvement and 14 dB contrast improvement after correction. This method, when combined with previous phase correction methods, may be an important step that leads to improved clinical images. PMID:21303031

Antibiotic Combinations That Enable One-Step, Targeted Mutagenesis of Chromosomal Genes.

PubMed

Lee, Wonsik; Do, Truc; Zhang, Ge; Kahne, Daniel; Meredith, Timothy C; Walker, Suzanne

2018-06-08

Targeted modification of bacterial chromosomes is necessary to understand new drug targets, investigate virulence factors, elucidate cell physiology, and validate results of -omics-based approaches. For some bacteria, reverse genetics remains a major bottleneck to progress in research. Here, we describe a compound-centric strategy that combines new negative selection markers with known positive selection markers to achieve simple, efficient one-step genome engineering of bacterial chromosomes. The method was inspired by the observation that certain nonessential metabolic pathways contain essential late steps, suggesting that antibiotics targeting a late step can be used to select for the absence of genes that control flux into the pathway. Guided by this hypothesis, we have identified antibiotic/counterselectable markers to accelerate reverse engineering of two increasingly antibiotic-resistant pathogens, Staphylococcus aureus and Acinetobacter baumannii. For S. aureus, we used wall teichoic acid biosynthesis inhibitors to select for the absence of tarO and for A. baumannii, we used colistin to select for the absence of lpxC. We have obtained desired gene deletions, gene fusions, and promoter swaps in a single plating step with perfect efficiency. Our method can also be adapted to generate markerless deletions of genes using FLP recombinase. The tools described here will accelerate research on two important pathogens, and the concept we outline can be readily adapted to any organism for which a suitable target pathway can be identified.

SALP, a new single-stranded DNA library preparation method especially useful for the high-throughput characterization of chromatin openness states.

PubMed

Wu, Jian; Dai, Wei; Wu, Lin; Wang, Jinke

2018-02-13

Next-generation sequencing (NGS) is fundamental to the current biological and biomedical research. Construction of sequencing library is a key step of NGS. Therefore, various library construction methods have been explored. However, the current methods are still limited by some shortcomings. This study developed a new NGS library construction method, Single strand Adaptor Library Preparation (SALP), by using a novel single strand adaptor (SSA). SSA is a double-stranded oligonucleotide with a 3' overhang of 3 random nucleotides, which can be efficiently ligated to the 3' end of single strand DNA by T4 DNA ligase. SALP can be started with any denatured DNA fragments such as those sheared by Tn5 tagmentation, enzyme digestion and sonication. When started with Tn5-tagmented chromatin, SALP can overcome a key limitation of ATAC-seq and become a high-throughput NGS library construction method, SALP-seq, which can be used to comparatively characterize the chromatin openness state of multiple cells unbiasly. In this way, this study successfully characterized the comparative chromatin openness states of four different cell lines, including GM12878, HepG2, HeLa and 293T, with SALP-seq. Similarly, this study also successfully characterized the chromatin openness states of HepG2 cells with SALP-seq by using 10 5 to 500 cells. This study developed a new NGS library construction method, SALP, by using a novel kind of single strand adaptor (SSA), which should has wide applications in the future due to its unique performance.