Rapid regulation of nuclear proteins by rapamycin-induced translocation in fission yeast

PubMed Central

Ding, Lin; Laor, Dana; Weisman, Ronit; Forsburg, Susan L

2014-01-01

Genetic analysis of protein function requires a rapid means of inactivating the gene under study. Typically this exploits temperature sensitive mutations, or promoter shut-off techniques. We report the adaptation to Schizosaccharomyces pombe of the Anchor Away technique, originally designed in budding yeast (Haruki et al., 2008a). This method relies on a rapamycin-mediated interaction between the FRB and FKBP12 binding domains, to relocalize nuclear proteins of interest to the cytoplasm. We demonstrate a rapid nuclear depletion of abundant proteins as proof-of-principle. PMID:24733494

Protoplast isolation, transient transformation of leaf mesophyll protoplasts and improved Agrobacterium-mediated leaf disc infiltration of Phaseolus vulgaris: tools for rapid gene expression analysis.

PubMed

Nanjareddy, Kalpana; Arthikala, Manoj-Kumar; Blanco, Lourdes; Arellano, Elizabeth S; Lara, Miguel

2016-06-24

Phaseolus vulgaris is one of the most extensively studied model legumes in the world. The P. vulgaris genome sequence is available; therefore, the need for an efficient and rapid transformation system is more imperative than ever. The functional characterization of P. vulgaris genes is impeded chiefly due to the non-amenable nature of Phaseolus sp. to stable genetic transformation. Transient transformation systems are convenient and versatile alternatives for rapid gene functional characterization studies. Hence, the present work focuses on standardizing methodologies for protoplast isolation from multiple tissues and transient transformation protocols for rapid gene expression analysis in the recalcitrant grain legume P. vulgaris. Herein, we provide methodologies for the high-throughput isolation of leaf mesophyll-, flower petal-, hypocotyl-, root- and nodule-derived protoplasts from P. vulgaris. The highly efficient polyethylene glycol-mannitol magnesium (PEG-MMG)-mediated transformation of leaf mesophyll protoplasts was optimized using a GUS reporter gene. We used the P. vulgaris SNF1-related protein kinase 1 (PvSnRK1) gene as proof of concept to demonstrate rapid gene functional analysis. An RT-qPCR analysis of protoplasts that had been transformed with PvSnRK1-RNAi and PvSnRK1-OE vectors showed the significant downregulation and ectopic constitutive expression (overexpression), respectively, of the PvSnRK1 transcript. We also demonstrated an improved transient transformation approach, sonication-assisted Agrobacterium-mediated transformation (SAAT), for the leaf disc infiltration of P. vulgaris. Interestingly, this method resulted in a 90 % transformation efficiency and transformed 60-85 % of the cells in a given area of the leaf surface. The constitutive expression of YFP further confirmed the amenability of the system to gene functional characterization studies. We present simple and efficient methodologies for protoplast isolation from multiple P. vulgaris tissues. We also provide a high-efficiency and amenable method for leaf mesophyll transformation for rapid gene functional characterization studies. Furthermore, a modified SAAT leaf disc infiltration approach aids in validating genes and their functions. Together, these methods help to rapidly unravel novel gene functions and are promising tools for P. vulgaris research.

Rapid identification of Bacillus anthracis spores in suspicious powder samples by using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS).

PubMed

Dybwad, Marius; van der Laaken, Anton L; Blatny, Janet Martha; Paauw, Armand

2013-09-01

Rapid and reliable identification of Bacillus anthracis spores in suspicious powders is important to mitigate the safety risks and economic burdens associated with such incidents. The aim of this study was to develop and validate a rapid and reliable laboratory-based matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis method for identifying B. anthracis spores in suspicious powder samples. A reference library containing 22 different Bacillus sp. strains or hoax materials was constructed and coupled with a novel classification algorithm and standardized processing protocol for various powder samples. The method's limit of B. anthracis detection was determined to be 2.5 × 10(6) spores, equivalent to a 55-μg sample size of the crudest B. anthracis-containing powder discovered during the 2001 Amerithrax incidents. The end-to-end analysis method was able to successfully discriminate among samples containing B. anthracis spores, closely related Bacillus sp. spores, and commonly encountered hoax materials. No false-positive or -negative classifications of B. anthracis spores were observed, even when the analysis method was challenged with a wide range of other bacterial agents. The robustness of the method was demonstrated by analyzing samples (i) at an external facility using a different MALDI-TOF MS instrument, (ii) using an untrained operator, and (iii) using mixtures of Bacillus sp. spores and hoax materials. Taken together, the observed performance of the analysis method developed demonstrates its potential applicability as a rapid, specific, sensitive, robust, and cost-effective laboratory-based analysis tool for resolving incidents involving suspicious powders in less than 30 min.

Rapid Identification of Bacillus anthracis Spores in Suspicious Powder Samples by Using Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry (MALDI-TOF MS)

PubMed Central

van der Laaken, Anton L.; Blatny, Janet Martha; Paauw, Armand

2013-01-01

Rapid and reliable identification of Bacillus anthracis spores in suspicious powders is important to mitigate the safety risks and economic burdens associated with such incidents. The aim of this study was to develop and validate a rapid and reliable laboratory-based matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) analysis method for identifying B. anthracis spores in suspicious powder samples. A reference library containing 22 different Bacillus sp. strains or hoax materials was constructed and coupled with a novel classification algorithm and standardized processing protocol for various powder samples. The method's limit of B. anthracis detection was determined to be 2.5 × 106 spores, equivalent to a 55-μg sample size of the crudest B. anthracis-containing powder discovered during the 2001 Amerithrax incidents. The end-to-end analysis method was able to successfully discriminate among samples containing B. anthracis spores, closely related Bacillus sp. spores, and commonly encountered hoax materials. No false-positive or -negative classifications of B. anthracis spores were observed, even when the analysis method was challenged with a wide range of other bacterial agents. The robustness of the method was demonstrated by analyzing samples (i) at an external facility using a different MALDI-TOF MS instrument, (ii) using an untrained operator, and (iii) using mixtures of Bacillus sp. spores and hoax materials. Taken together, the observed performance of the analysis method developed demonstrates its potential applicability as a rapid, specific, sensitive, robust, and cost-effective laboratory-based analysis tool for resolving incidents involving suspicious powders in less than 30 min. PMID:23811517

Environmental science applications with Rapid Integrated Mapping and analysis System (RIMS)

NASA Astrophysics Data System (ADS)

Shiklomanov, A.; Prusevich, A.; Gordov, E.; Okladnikov, I.; Titov, A.

2016-11-01

The Rapid Integrated Mapping and analysis System (RIMS) has been developed at the University of New Hampshire as an online instrument for multidisciplinary data visualization, analysis and manipulation with a focus on hydrological applications. Recently it was enriched with data and tools to allow more sophisticated analysis of interdisciplinary data. Three different examples of specific scientific applications with RIMS are demonstrated and discussed. Analysis of historical changes in major components of the Eurasian pan-Arctic water budget is based on historical discharge data, gridded observational meteorological fields, and remote sensing data for sea ice area. Express analysis of the extremely hot and dry summer of 2010 across European Russia is performed using a combination of near-real time and historical data to evaluate the intensity and spatial distribution of this event and its socioeconomic impacts. Integrative analysis of hydrological, water management, and population data for Central Asia over the last 30 years provides an assessment of regional water security due to changes in climate, water use and demography. The presented case studies demonstrate the capabilities of RIMS as a powerful instrument for hydrological and coupled human-natural systems research.

Rapid protein concentration, efficient fluorescence labeling and purification on a micro/nanofluidics chip.

PubMed

Wang, Chen; Ouyang, Jun; Ye, De-Kai; Xu, Jing-Juan; Chen, Hong-Yuan; Xia, Xing-Hua

2012-08-07

Fluorescence analysis has proved to be a powerful detection technique for achieving single molecule analysis. However, it usually requires the labeling of targets with bright fluorescent tags since most chemicals and biomolecules lack fluorescence. Conventional fluorescence labeling methods require a considerable quantity of biomolecule samples, long reaction times and extensive chromatographic purification procedures. Herein, a micro/nanofluidics device integrating a nanochannel in a microfluidics chip has been designed and fabricated, which achieves rapid protein concentration, fluorescence labeling, and efficient purification of product in a miniaturized and continuous manner. As a demonstration, labeling of the proteins bovine serum albumin (BSA) and IgG with fluorescein isothiocyanate (FITC) is presented. Compared to conventional methods, the present micro/nanofluidics device performs about 10(4)-10(6) times faster BSA labeling with 1.6 times higher yields due to the efficient nanoconfinement effect, improved mass, and heat transfer in the chip device. The results demonstrate that the present micro/nanofluidics device promises rapid and facile fluorescence labeling of small amount of reagents such as proteins, nucleic acids and other biomolecules with high efficiency.

Direct rapid analysis of trace bioavailable soil macronutrients by chemometrics-assisted energy dispersive X-ray fluorescence and scattering spectrometry.

PubMed

Kaniu, M I; Angeyo, K H; Mwala, A K; Mangala, M J

2012-06-04

Precision agriculture depends on the knowledge and management of soil quality (SQ), which calls for affordable, simple and rapid but accurate analysis of bioavailable soil nutrients. Conventional SQ analysis methods are tedious and expensive. We demonstrate the utility of a new chemometrics-assisted energy dispersive X-ray fluorescence and scattering (EDXRFS) spectroscopy method we have developed for direct rapid analysis of trace 'bioavailable' macronutrients (i.e. C, N, Na, Mg, P) in soils. The method exploits, in addition to X-ray fluorescence, the scatter peaks detected from soil pellets to develop a model for SQ analysis. Spectra were acquired from soil samples held in a Teflon holder analyzed using (109)Cd isotope source EDXRF spectrometer for 200 s. Chemometric techniques namely principal component analysis (PCA), partial least squares (PLS) and artificial neural networks (ANNs) were utilized for pattern recognition based on fluorescence and Compton scatter peaks regions, and to develop multivariate quantitative calibration models based on Compton scatter peak respectively. SQ analyses were realized with high CMD (R(2)>0.9) and low SEP (0.01% for N and Na, 0.05% for C, 0.08% for Mg and 1.98 μg g(-1) for P). Comparison of predicted macronutrients with reference standards using a one-way ANOVA test showed no statistical difference at 95% confidence level. To the best of the authors' knowledge, this is the first time that an XRF method has demonstrated utility in trace analysis of macronutrients in soil or related matrices. Copyright © 2012 Elsevier B.V. All rights reserved.

Proof of Principle for a Real-Time Pathogen Isolation Media Diagnostic: The Use of Laser-Induced Breakdown Spectroscopy to Discriminate Bacterial Pathogens and Antimicrobial-Resistant Staphylococcus aureus Strains Grown on Blood Agar

PubMed Central

Multari, Rosalie A.; Cremers, David A.; Bostian, Melissa L.; Dupre, Joanne M.

2013-01-01

Laser-Induced Breakdown Spectroscopy (LIBS) is a rapid, in situ, diagnostic technique in which light emissions from a laser plasma formed on the sample are used for analysis allowing automated analysis results to be available in seconds to minutes. This speed of analysis coupled with little or no sample preparation makes LIBS an attractive detection tool. In this study, it is demonstrated that LIBS can be utilized to discriminate both the bacterial species and strains of bacterial colonies grown on blood agar. A discrimination algorithm was created based on multivariate regression analysis of spectral data. The algorithm was deployed on a simulated LIBS instrument system to demonstrate discrimination capability using 6 species. Genetically altered Staphylococcus aureus strains grown on BA, including isogenic sets that differed only by the acquisition of mutations that increase fusidic acid or vancomycin resistance, were also discriminated. The algorithm successfully identified all thirteen cultures used in this study in a time period of 2 minutes. This work provides proof of principle for a LIBS instrumentation system that could be developed for the rapid discrimination of bacterial species and strains demonstrating relatively minor genomic alterations using data collected directly from pathogen isolation media. PMID:24109513

Social learning by following: an analysis1

PubMed Central

Bullock, Daniel; Neuringer, Allen

1977-01-01

Learning by “following”, probably a common means by which behaviors are socially transmitted from adults to young in many species, was analyzed. Pigeons first learned to eat from a human hand. When the hand then approached an operant key and pecked it, the pigeons followed and quickly learned to do the same, thereby demonstrating social learning. When the hand only led the birds to the area of the key, without demonstrating the key-peck response, the birds learned as rapidly as with a key-peck demonstration. Birds also learned, but less reliably and more slowly, when they could observe the hand's responses but were constrained and unable to follow. “Following” was also shown to engender very rapid learning of a more complex, two-member response chain. PMID:16811970

Rapid and accurate detection of urinary pathogens by mobile IMS-based electronic nose: a proof-of-principle study.

PubMed

Roine, Antti; Saviauk, Taavi; Kumpulainen, Pekka; Karjalainen, Markus; Tuokko, Antti; Aittoniemi, Janne; Vuento, Risto; Lekkala, Jukka; Lehtimäki, Terho; Tammela, Teuvo L; Oksala, Niku K J

2014-01-01

Urinary tract infection (UTI) is a common disease with significant morbidity and economic burden, accounting for a significant part of the workload in clinical microbiology laboratories. Current clinical chemisty point-of-care diagnostics rely on imperfect dipstick analysis which only provides indirect and insensitive evidence of urinary bacterial pathogens. An electronic nose (eNose) is a handheld device mimicking mammalian olfaction that potentially offers affordable and rapid analysis of samples without preparation at athmospheric pressure. In this study we demonstrate the applicability of ion mobility spectrometry (IMS) -based eNose to discriminate the most common UTI pathogens from gaseous headspace of culture plates rapidly and without sample preparation. We gathered a total of 101 culture samples containing four most common UTI bacteries: E. coli, S. saprophyticus, E. faecalis, Klebsiella spp and sterile culture plates. The samples were analyzed using ChemPro 100i device, consisting of IMS cell and six semiconductor sensors. Data analysis was conducted by linear discriminant analysis (LDA) and logistic regression (LR). The results were validated by leave-one-out and 5-fold cross validation analysis. In discrimination of sterile and bacterial samples sensitivity of 95% and specificity of 97% were achieved. The bacterial species were identified with sensitivity of 95% and specificity of 96% using eNose as compared to urine bacterial cultures. These findings strongly demonstrate the ability of our eNose to discriminate bacterial cultures and provides a proof of principle to use this method in urinanalysis of UTI.

Supercritical-fluid extraction and chromatography-mass spectrometry for analysis of mycotoxins

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

Smith, R.D.; Udseth, H.R.

1982-07-01

The use of direct supercritical-fluid injection-mass spectrometry for the rapid analysis of mycotoxins of the tricothecene group is demonstrated. A solution containing diacetoxyscirpenol or T-2 toxin is injected into a fluid consisting primarily of pentane or carbon dioxide and is rapidly brought to supercritical conditions. Direct injection of the fluid stream into a chemical ionization source allows thermally labile compounds to be analyzed. Under these conditions trichothecene mass spectra showing significant (M + 1)/sup +/ ions and distinctive fragmentation patterns are obtained. Detection limits are in the subnanogram range. Direct analysis from complex substrates using selective supercritical-fluid extraction is proposed.more » 4 figures.« less

Microgravimetric Analysis Method for Activation-Energy Extraction from Trace-Amount Molecule Adsorption.

PubMed

Xu, Pengcheng; Yu, Haitao; Li, Xinxin

2016-05-03

Activation-energy (Ea) value for trace-amount adsorption of gas molecules on material is rapidly and inexpensively obtained, for the first time, from a microgravimetric analysis experiment. With the material loaded, a resonant microcantilever is used to record in real time the adsorption process at two temperatures. The kinetic parameter Ea is thereby extracted by solving the Arrhenius equation. As an example, two CO2 capture nanomaterials are examined by the Ea extracting method for evaluation/optimization and, thereby, demonstrating the applicability of the microgravimetric analysis method. The achievement helps to solve the absence in rapid quantitative characterization of sorption kinetics and opens a new route to investigate molecule adsorption processes and materials.

META-ANALYSIS OF CYP2D6 METABOLIZER PHENOTYPE AND METOPROLOL PHARMACOKINETICS

PubMed Central

Blake, CM; Kharasch, ED; Schwab, M; Nagele, P

2013-01-01

Metoprolol, a commonly prescribed beta-blocker, is primarily metabolized by cytochrome P450 2D6 (CYP2D6), an enzyme with substantial genetic heterogeneity. Several smaller studies have shown that metoprolol pharmacokinetics is influenced by CYP2D6 genotype and metabolizer phenotype. To increase robustness of metoprolol pharmacokinetic estimates, a systematic review and meta-analysis of pharmacokinetic studies that administered a single oral dose of immediate release metoprolol was performed. Pooled analysis (n= 264) demonstrated differences in peak plasma metoprolol concentration, area under the concentration-time curve, elimination half-life, and apparent oral clearance that were 2.3-, 4.9-, 2.3-, and 5.9-fold between extensive and poor metabolizers, respectively, and 5.3-, 13-, 2.6-, and 15-fold between ultra-rapid and poor metabolizers (all p<0.001). Enantiomer-specific analysis revealed genotype-dependent enantio-selective metabolism, with nearly 40% greater R- vs S-metoprolol metabolism in ultra-rapid and extensive metabolizers. This study demonstrates a marked effect of CYP2D6 metabolizer phenotype on metoprolol pharmacokinetics and confirms enantiomer specific metabolism of metoprolol. PMID:23665868

Scopolamine rapidly increases mTORC1 signaling, synaptogenesis, and antidepressant behavioral responses

PubMed Central

Voleti, Bhavya; Navarria, Andrea; Liu, Rong-Jian; Banasr, Mounira; Li, Nanxin; Terwilliger, Rose; Sanacora, Gerard; Eid, Tore; Aghajanian, George; Duman, Ronald S.

2013-01-01

Background Clinical studies report that scopolamine, an acetylcholine muscarinic receptor antagonist, produces rapid antidepressant effects in depressed patients, but the mechanisms underlying the therapeutic response have not been determined. The present study examines the role of the mammalian target of rapamycin complex 1 (mTORC1) and synaptogenesis, which have been implicated in the rapid actions of NMDA receptor antagonists. Methods The influence of scopolamine on mTORC1 signaling was determined by analysis of the phosphorylated and activated forms of mTORC1 signaling proteins in the prefrontal cortex (PFC). The numbers and function of spine synapses were analyzed by whole cell patch clamp recording and 2-photon image analysis of PFC neurons. The actions of scopolamine were examined in the forced swim test in the absence or presence of selective mTORC1 and AMPA receptor inhibitors. Results The results demonstrate that a single, low dose of scopolamine rapidly increases mTORC1 signaling and the number and function of spine synapses in layer V pyramidal neurons in the PFC. Scopolamine administration also produces an antidepressant response in the forced swim test that is blocked by pretreatment with the mTORC1 inhibitor or by a glutamate AMPA receptor antagonist. Conclusions Taken together, the results demonstrate that the antidepressant actions of scopolamine require mTORC1 signaling and are associated with increased glutamate transmission, and synaptogenesis, similar to NMDA receptor antagonists. These findings provide novel targets for safer and more efficacious rapid acting antidepressant agents. PMID:23751205

Brief functional analysis and treatment of a vocal tic.

PubMed

Watson, T S; Sterling, H E

1998-01-01

This study sought to extend functional methodology to the assessment and treatment of habits. After a descriptive assessment indicated that coughing occurred while eating, a brief functional analysis suggested that social attention was the maintaining variable. Results demonstrated that treatment, derived from the assessment and analysis data, rapidly eliminated the cough. We discuss the appropriateness of using functional analysis procedures for deriving treatments for habits in a clinical setting.

A Business Case Analysis of Pre-Positioned Expeditionary Assistance Kit Joint Capability Technology Demonstration

DTIC Science & Technology

2013-12-01

of power from sunlight or a wind turbine (same solar panel tarps used in NEST Raptor Solar Light Trailer) • Global Positioning System (GPS) devices...satellite-enabled rapid wireless communications to the most critical areas and functions, working with Joint Task Forces. The first priority after the...a rapid response wireless communications system from military, civilian government, and non-government organizations. The tasks performed by HFN

Initial Multidisciplinary Design and Analysis Framework

NASA Technical Reports Server (NTRS)

Ozoroski, L. P.; Geiselhart, K. A.; Padula, S. L.; Li, W.; Olson, E. D.; Campbell, R. L.; Shields, E. W.; Berton, J. J.; Gray, J. S.; Jones, S. M.;

Rapid non-invasive quality control of semi-finished products for the food industry by direct injection mass spectrometry headspace analysis: the case of milk powder, whey powder and anhydrous milk fat.

PubMed

Makhoul, Salim; Yener, Sine; Khomenko, Iuliia; Capozzi, Vittorio; Cappellin, Luca; Aprea, Eugenio; Scampicchio, Matteo; Gasperi, Flavia; Biasioli, Franco

2016-09-01

In this study, we demonstrated the suitability of direct injection mass spectrometry headspace analysis for rapid non-invasive quality control of semi-finished dairy ingredients, such as skim milk powder (SMP), whole milk powder (WMP), whey powder (WP) and anhydrous milk fat (AMF), which are widely used as ingredients in the food industry. In this work, for the first time, we applied proton transfer reaction-mass spectrometry (PTR-MS) with a time-of-flight (ToF) analyzer for the rapid and non-invasive analysis of volatile compounds in different samples of SMP, WMP, WP and AMF. We selected different dairy ingredients in various concrete situations (e.g. same producer and different expiration times, different producers and same days of storage, different producers) based on their sensory evaluation. PTR-ToF-MS allowed the separation and characterization of different samples based on the volatile organic compound (VOC) profiles. Statistically significant differences in VOC content were generally coherent with differences in sensory evaluation, particularly for SMP, WMP and WP. The good separation of SMP samples from WMP samples suggested the possible application of PTR-ToF-MS to detect possible cases of adulteration of dairy ingredients for the food industry. Our findings demonstrate the efficient and rapid differentiation of dairy ingredients on the basis of the released VOCs via PTR-ToF-MS analysis and suggest this method as a versatile tool (1) for the facilitation/optimization of the selection of dairy ingredients in the food industry and (2) and for the prompt innovation in the production of dairy ingredients. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Evaluation guidelines for bus rapid transit demonstration projects

DOT National Transportation Integrated Search

2002-02-01

The Federal Transit Administration's (FTA) Bus Rapid Transit Demonstration Program is supporting demonstrations of Bus Rapid Transit (BRT) in selected cities across the United States. The US BRT Demonstration Program aims to adapt the principles of h...

The application of near infrared (NIR) spectroscopy to inorganic preservative-treated wood

Treesearch

Chi-Leung So; Stan T. Lebow; Leslie H. Groom; Timothy G. Rials

2004-01-01

There is a growing need to find a rapid, inexpensive, and reliable method to distinguish between treated and untreated waste wood. This paper evaluates the ability of near infrared (NIR) spectroscopy with multivariate analysis (MVA) to distinguish preservative types and retentions. It is demonstrated that principal component analysis (PCA) can differentiate lumber...

Tool for Rapid Analysis of Monte Carlo Simulations

NASA Technical Reports Server (NTRS)

Restrepo, Carolina; McCall, Kurt E.; Hurtado, John E.

2011-01-01

Designing a spacecraft, or any other complex engineering system, requires extensive simulation and analysis work. Oftentimes, the large amounts of simulation data generated are very di cult and time consuming to analyze, with the added risk of overlooking potentially critical problems in the design. The authors have developed a generic data analysis tool that can quickly sort through large data sets and point an analyst to the areas in the data set that cause specific types of failures. The Tool for Rapid Analysis of Monte Carlo simulations (TRAM) has been used in recent design and analysis work for the Orion vehicle, greatly decreasing the time it takes to evaluate performance requirements. A previous version of this tool was developed to automatically identify driving design variables in Monte Carlo data sets. This paper describes a new, parallel version, of TRAM implemented on a graphical processing unit, and presents analysis results for NASA's Orion Monte Carlo data to demonstrate its capabilities.

Internet search query analysis can be used to demonstrate the rapidly increasing public awareness of palliative care in the USA.

PubMed

McLean, Sarah; Lennon, Paul; Glare, Paul

2017-01-27

A lack of public awareness of palliative care (PC) has been identified as one of the main barriers to appropriate PC access. Internet search query analysis is a novel methodology, which has been effectively used in surveillance of infectious diseases, and can be used to monitor public awareness of health-related topics. We aimed to demonstrate the utility of internet search query analysis to evaluate changes in public awareness of PC in the USA between 2005 and 2015. Google Trends provides a referenced score for the popularity of a search term, for defined regions over defined time periods. The popularity of the search term 'palliative care' was measured monthly between 1/1/2005 and 31/12/2015 in the USA and in the UK. Results were analysed using independent t-tests and joinpoint analysis. The mean monthly popularity of the search term increased between 2008-2009 (p<0.001), 2011-2012 (p<0.001), 2013-2014 (p=0.004) and 2014-2015 (p=0.002) in the USA. Joinpoint analysis was used to evaluate the monthly percentage change (MPC) in the popularity of the search term. In the USA, the MPC increase was 0.6%/month (p<0.05); in the UK the MPC of 0.05% was non-significant. Although internet search query surveillance is a novel methodology, it is freely accessible and has significant potential to monitor health-seeking behaviour among the public. PC is rapidly growing in the USA, and the rapidly increasing public awareness of PC as demonstrated in this study, in comparison with the UK, where PC is relatively well established is encouraging in increasingly ensuring appropriate PC access for all. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Rapid Analysis of Bisphenol A and Its Analogues in Food Packaging Products by Paper Spray Ionization Mass Spectrometry.

PubMed

Chen, Shuo; Chang, Quanying; Yin, Kai; He, Qunying; Deng, Yongxiu; Chen, Bo; Liu, Chengbin; Wang, Ying; Wang, Liping

2017-06-14

In this study, a paper spray ionization mass spectrometric (PS-MS) method was developed for the rapid in situ screening and simultaneous quantitative analysis of bisphenol A and its analogues, i.e., bisphenol S, bisphenol F, and bisphenol AF, in food packaging products. At the optimal PS-MS conditions, the calibration curves of bisphenols in the range of 1-100 μg/mL were linear. The correlation coefficients were higher than 0.998, and the LODs of the target compounds were 0.1-0.3 μg/mL. After a simple treatment by dichloromethane on the surface, the samples were analyzed by PS-MS in situ for rapid screening without a traditional sample pretreatment procedure, such as powdering, extraction, and enrichment steps. The analytical time of the PS-MS method was less than 1 min. In comparison with conventional HPLC-MS/MS, it was demonstrated that PS-MS was a more effective high-throughput screening and quantitative analysis method.

Demonstration and Evaluation of Solid Phase Microextraction for the Assessment of Bioavailability and Contaminant Mobility. ESTCP Cost and Performance Report

DTIC Science & Technology

2012-08-01

subsequent chemical analysis (into acetonitrile for high-performance liquid chromatography [ HPLC ] analysis or hexane for gas chromatography [GC... analysis ) is rapid and complete. In this work, PAHs were analyzed by Waters 2795 HPLC with fluorescent detection (USEPA Method 8310) and PCBs were...detection limits by direct water injection versus SPME with PDMS and coefficient of variation and correlation coefficient for SPME. Analysis by HPLC

Automated mini-column solid-phase extraction cleanup for high-throughput analysis of chemical contaminants in foods by low-pressure gas chromatography – tandem mass spectrometry

USDA-ARS?s Scientific Manuscript database

This study demonstrated the application of an automated high-throughput mini-cartridge solid-phase extraction (mini-SPE) cleanup for the rapid low-pressure gas chromatography – tandem mass spectrometry (LPGC-MS/MS) analysis of pesticides and environmental contaminants in QuEChERS extracts of foods. ...

Perceived Stress and Use of Coping Strategies as a Response to Rapidly Changing Student Demographics

ERIC Educational Resources Information Center

Lindner, Reinhard W.; Healy, Donald E., Jr.

2004-01-01

The authors present findings from an initial information gathering and analysis of a larger Office of Special Education Programs model demonstration project, "Connections to Success." The article is based on an analysis of a teacher survey conducted at four schools in the project's partner district focused on perceived problems, sources of stress,…

Field transportable beta spectrometer. Innovative technology summary report

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

NONE

1998-12-01

The objective of the Large-Scale Demonstration Project (LSDP) is to select and demonstrate potentially beneficial technologies at the Argonne National Laboratory-East (ANL) Chicago Pile-5 Test Reactor (CP-5). The purpose of the LSDP is to demonstrate that by using innovative and improved deactivation and decommissioning (D and D) technologies from various sources, significant benefits can be achieved when compared to baseline D and D technologies. One such capability being addressed by the D and D Focus Area is rapid characterization for facility contaminants. The technology was field demonstrated during the period January 7 through January 9, 1997, and offers several potentialmore » benefits, including faster turn-around time, cost reduction, and reduction in secondary waste. This report describes a PC controlled, field-transportable beta counter-spectrometer which uses solid scintillation coincident counting and low-noise photomultiplier tubes to count element-selective filters and other solid media. The dry scintillation counter used in combination with an element-selective technology eliminates the mess and disposal costs of liquid scintillation cocktails. Software in the instrument provides real-time spectral analysis. The instrument can detect and measure Tc-99, Sr-90, and other beta emitters reaching detection limits in the 20 pCi range (with shielding). Full analysis can be achieved in 30 minutes. The potential advantages of a field-portable beta counter-spectrometer include the savings gained from field generated results. The basis for decision-making is provided with a rapid turnaround analysis in the field. This technology would be competitive with the radiometric analysis done in fixed laboratories and the associated chain of custody operations.« less

Rapid analysis of Aurantii Fructus Immaturus (Zhishi) using paper spray ionization mass spectrometry.

PubMed

Liu, Xuemei; Gu, Zhixin; Guo, Yuan; Liu, Jingjing; Ma, Ming; Chen, Bo; Wang, Liping

2017-04-15

Paper spray-mass spectrometry (PS-MS) is a rapid, solvent-efficient, and high-throughput analytical method for analyzing complex samples. In this study, a PS-MS method was developed to obtain MS profiles of Aurantii Fructus Immaturus (aka Zhishi in Chinese) in positive and negative ion modes. In combination with multivariate analyses, including principal component analysis and cluster analysis, the PS-MS profiles of 25 batches of Zhishi were discriminated in 25 batches of Citri Reticulatae Pericarpium Viride (aka Qingpi in Chinese; an adulterant of Zhishi). Moreover, a rapid quantitative analysis of synephrine, a prescriptive quality control component of Zhishi listed in the Chinese Pharmacopoeia, was conducted with PS-MS using synephrine-d2 as an internal standard (IS). The linearity range was 1.68-16.8μg/mL (R 2 =0.9985), the limit of quantitation was 0.5μg/mL. Relative standard deviations in the intra- and inter-day precision of the MS were 4.87 and 4.90%, respectively. Compared with HPLC results, there was no significant difference in the quantitation of synephrine. This study demonstrated that the PS-MS method is useful for the rapid discrimination and quality control of Zhishi samples. Copyright © 2017 Elsevier B.V. All rights reserved.

Airplane numerical simulation for the rapid prototyping process

NASA Astrophysics Data System (ADS)

Roysdon, Paul F.

Airplane Numerical Simulation for the Rapid Prototyping Process is a comprehensive research investigation into the most up-to-date methods for airplane development and design. Uses of modern engineering software tools, like MatLab and Excel, are presented with examples of batch and optimization algorithms which combine the computing power of MatLab with robust aerodynamic tools like XFOIL and AVL. The resulting data is demonstrated in the development and use of a full non-linear six-degrees-of-freedom simulator. The applications for this numerical tool-box vary from un-manned aerial vehicles to first-order analysis of manned aircraft. A Blended-Wing-Body airplane is used for the analysis to demonstrate the flexibility of the code from classic wing-and-tail configurations to less common configurations like the blended-wing-body. This configuration has been shown to have superior aerodynamic performance -- in contrast to their classic wing-and-tube fuselage counterparts -- and have reduced sensitivity to aerodynamic flutter as well as potential for increased engine noise abatement. Of course without a classic tail elevator to damp the nose up pitching moment, and the vertical tail rudder to damp the yaw and possible rolling aerodynamics, the challenges in lateral roll and yaw stability, as well as pitching moment are not insignificant. This thesis work applies the tools necessary to perform the airplane development and optimization on a rapid basis, demonstrating the strength of this tool through examples and comparison of the results to similar airplane performance characteristics published in literature.

Development of a rapid 21-plex autosomal STR typing system for forensic applications.

PubMed

Yang, Meng; Yin, Caiyong; Lv, Yuexin; Yang, Yaran; Chen, Jing; Yu, Zailiang; Liu, Xu; Xu, Meibo; Chen, Feng; Wu, Huijuan; Yan, Jiangwei

2016-10-01

DNA-STR genotyping technology has been widely used in forensic investigations. Even with such success, there is a great need to reduce the analysis time. In this study, we established a new rapid 21-plex STR typing system, including 13 CODIS loci, Penta D, Penta E, D12S391, D2S1338, D6S1043, D19S433, D2S441 and Amelogenin loci. This system could shorten the amplification time to a minimum of 90 min and does not require DNA extraction from the samples. Validation of the typing system complied with the Scientific Working Group on DNA Analysis Methods (SWGDAM) and the Chinese National Standard (GA/T815-2009) guidelines. The results demonstrated that this 21-plex STR typing system was a valuable tool for rapid criminal investigation. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Rapid analysis of microbial systems using vibrational spectroscopy and supervised learning methods: application to the discrimination between methicillin-resistant and methicillin-susceptible Staphy

NASA Astrophysics Data System (ADS)

Goodacre, Royston; Rooney, Paul J.; Kell, Douglas B.

1998-04-01

FTIR spectra were obtained from 15 methicillin-resistant and 22 methicillin-susceptible Staphylococcus aureus strains using our DRASTIC approach. Cluster analysis showed that the major source of variation between the IR spectra was not due to their resistance or susceptibility to methicillin; indeed early studies suing pyrolysis mass spectrometry had shown that this unsupervised analysis gave information on the phage group of the bacteria. By contrast, artificial neural networks, based on a supervised learning, could be trained to recognize those aspects of the IR spectra which differentiated methicillin-resistant from methicillin- susceptible strains. These results give the first demonstration that the combination of FTIR with neural networks can provide a very rapid and accurate antibiotic susceptibility testing technique.

SIMS: A Hybrid Method for Rapid Conformational Analysis

PubMed Central

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

2013-01-01

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

Unsupervised Discovery of Demixed, Low-Dimensional Neural Dynamics across Multiple Timescales through Tensor Component Analysis.

PubMed

Williams, Alex H; Kim, Tony Hyun; Wang, Forea; Vyas, Saurabh; Ryu, Stephen I; Shenoy, Krishna V; Schnitzer, Mark; Kolda, Tamara G; Ganguli, Surya

2018-06-27

Perceptions, thoughts, and actions unfold over millisecond timescales, while learned behaviors can require many days to mature. While recent experimental advances enable large-scale and long-term neural recordings with high temporal fidelity, it remains a formidable challenge to extract unbiased and interpretable descriptions of how rapid single-trial circuit dynamics change slowly over many trials to mediate learning. We demonstrate a simple tensor component analysis (TCA) can meet this challenge by extracting three interconnected, low-dimensional descriptions of neural data: neuron factors, reflecting cell assemblies; temporal factors, reflecting rapid circuit dynamics mediating perceptions, thoughts, and actions within each trial; and trial factors, describing both long-term learning and trial-to-trial changes in cognitive state. We demonstrate the broad applicability of TCA by revealing insights into diverse datasets derived from artificial neural networks, large-scale calcium imaging of rodent prefrontal cortex during maze navigation, and multielectrode recordings of macaque motor cortex during brain machine interface learning. Copyright © 2018 Elsevier Inc. All rights reserved.

Genetic Regulation of Development of Thymic Lymphomas Induced by N‐Propyl‐N‐nitrosourea in the Rat

PubMed Central

Fukami, Hiroko; Nishimura, Mayumi; Matsuyama, Mutsushi

1995-01-01

To clarify the linkage between Hbb and Tls‐1 (thymic lymphoma susceptible‐1) loci and to investigate other loci concerned in thymic lymphomagenesis, the BUF/Mna rat, which is highly sensitive to the lymphomagenic activity of N‐propyl‐N‐nitrosourea (PNU), the WKY/NCrj rat, reported to be resistant, and their cross offspring were subjected to genetic analysis. F1 hybrid and backcross generations were raised from the 2 strains, and 6 genetic markers including Hbb were analyzed in individuals of the backcross generation. However, no linkage between Hbb and Tls‐1 loci could be demonstrated since WKY rats also developed a high incidence of thymic lymphomas in response to PNU. Nevertheless, thymic lymphomas developed more rapidly and reached a larger size in the BUF rats. F1 rats expressed a rather rapid and large tumor growth phenotype, while the [(WKY × BUF) × WKY] backcross generation consisted of rats with either rapidly growing or slowly growing tumors. It was thus concluded that rapid development of thymic lymphomas is determined by a gene, provisionally designated Tls‐3. Analysis of the relationship between 6 genetic markers and development of thymic lymphoma in the backcross generation demonstrated that the Tls‐3 locus is loosely linked to the Gc locus, suggesting a possible location on rat chromosome 14. Tls‐3 may not be identical with Tls‐1 and other genes known to be relevant to thymic tumors, but its relationship with Tls‐2 remains obscure. PMID:7559080

A method for rapid sampling and characterization of smokeless powder using sorbent-coated wire mesh and direct analysis in real time - mass spectrometry (DART-MS).

PubMed

Li, Frederick; Tice, Joseph; Musselman, Brian D; Hall, Adam B

2016-09-01

Improvised explosive devices (IEDs) are often used by terrorists and criminals to create public panic and destruction, necessitating rapid investigative information. However, backlogs in many forensic laboratories resulting in part from time-consuming GC-MS and LC-MS techniques prevent prompt analytical information. Direct analysis in real time - mass spectrometry (DART-MS) is a promising analytical technique that can address this challenge in the forensic science community by permitting rapid trace analysis of energetic materials. Therefore, we have designed a qualitative analytical approach that utilizes novel sorbent-coated wire mesh and dynamic headspace concentration to permit the generation of information rich chemical attribute signatures (CAS) for trace energetic materials in smokeless powder with DART-MS. Sorbent-coated wire mesh improves the overall efficiency of capturing trace energetic materials in comparison to swabbing or vacuuming. Hodgdon Lil' Gun smokeless powder was used to optimize the dynamic headspace parameters. This method was compared to traditional GC-MS methods and validated using the NIST RM 8107 smokeless powder reference standard. Additives and energetic materials, notably nitroglycerin, were rapidly and efficiently captured by the Carbopack X wire mesh, followed by detection and identification using DART-MS. This approach has demonstrated the capability of generating comparable results with significantly reduced analysis time in comparison to GC-MS. All targeted components that can be detected by GC-MS were detected by DART-MS in less than a minute. Furthermore, DART-MS offers the advantage of detecting targeted analytes that are not amenable to GC-MS. The speed and efficiency associated with both the sample collection technique and DART-MS demonstrate an attractive and viable potential alternative to conventional techniques. Copyright © 2016 The Chartered Society of Forensic Sciences. Published by Elsevier Ireland Ltd. All rights reserved.

Analysis of Rapid Multi-Focal Zone ARFI Imaging

PubMed Central

Rosenzweig, Stephen; Palmeri, Mark; Nightingale, Kathryn

2015-01-01

Acoustic radiation force impulse (ARFI) imaging has shown promise for visualizing structure and pathology within multiple organs; however, because the contrast depends on the push beam excitation width, image quality suffers outside of the region of excitation. Multi-focal zone ARFI imaging has previously been used to extend the region of excitation (ROE), but the increased acquisition duration and acoustic exposure have limited its utility. Supersonic shear wave imaging has previously demonstrated that through technological improvements in ultrasound scanners and power supplies, it is possible to rapidly push at multiple locations prior to tracking displacements, facilitating extended depth of field shear wave sources. Similarly, ARFI imaging can utilize these same radiation force excitations to achieve tight pushing beams with a large depth of field. Finite element method simulations and experimental data are presented demonstrating that single- and rapid multi-focal zone ARFI have comparable image quality (less than 20% loss in contrast), but the multi-focal zone approach has an extended axial region of excitation. Additionally, as compared to single push sequences, the rapid multi-focal zone acquisitions improve the contrast to noise ratio by up to 40% in an example 4 mm diameter lesion. PMID:25643078

Validity and Reliability of the Brazilian Version of the Rapid Estimate of Adult Literacy in Dentistry--BREALD-30.

PubMed

Junkes, Monica C; Fraiz, Fabian C; Sardenberg, Fernanda; Lee, Jessica Y; Paiva, Saul M; Ferreira, Fernanda M

2015-01-01

The aim of the present study was to translate, perform the cross-cultural adaptation of the Rapid Estimate of Adult Literacy in Dentistry to Brazilian-Portuguese language and test the reliability and validity of this version. After translation and cross-cultural adaptation, interviews were conducted with 258 parents/caregivers of children in treatment at the pediatric dentistry clinics and health units in Curitiba, Brazil. To test the instrument's validity, the scores of Brazilian Rapid Estimate of Adult Literacy in Dentistry (BREALD-30) were compared based on occupation, monthly household income, educational attainment, general literacy, use of dental services and three dental outcomes. The BREALD-30 demonstrated good internal reliability. Cronbach's alpha ranged from 0.88 to 0.89 when words were deleted individually. The analysis of test-retest reliability revealed excellent reproducibility (intraclass correlation coefficient = 0.983 and Kappa coefficient ranging from moderate to nearly perfect). In the bivariate analysis, BREALD-30 scores were significantly correlated with the level of general literacy (rs = 0.593) and income (rs = 0.327) and significantly associated with occupation, educational attainment, use of dental services, self-rated oral health and the respondent's perception regarding his/her child's oral health. However, only the association between the BREALD-30 score and the respondent's perception regarding his/her child's oral health remained significant in the multivariate analysis. The BREALD-30 demonstrated satisfactory psychometric properties and is therefore applicable to adults in Brazil.

Validity and Reliability of the Brazilian Version of the Rapid Estimate of Adult Literacy in Dentistry – BREALD-30

PubMed Central

Junkes, Monica C.; Fraiz, Fabian C.; Sardenberg, Fernanda; Lee, Jessica Y.; Paiva, Saul M.; Ferreira, Fernanda M.

2015-01-01

Objective The aim of the present study was to translate, perform the cross-cultural adaptation of the Rapid Estimate of Adult Literacy in Dentistry to Brazilian-Portuguese language and test the reliability and validity of this version. Methods After translation and cross-cultural adaptation, interviews were conducted with 258 parents/caregivers of children in treatment at the pediatric dentistry clinics and health units in Curitiba, Brazil. To test the instrument's validity, the scores of Brazilian Rapid Estimate of Adult Literacy in Dentistry (BREALD-30) were compared based on occupation, monthly household income, educational attainment, general literacy, use of dental services and three dental outcomes. Results The BREALD-30 demonstrated good internal reliability. Cronbach’s alpha ranged from 0.88 to 0.89 when words were deleted individually. The analysis of test-retest reliability revealed excellent reproducibility (intraclass correlation coefficient = 0.983 and Kappa coefficient ranging from moderate to nearly perfect). In the bivariate analysis, BREALD-30 scores were significantly correlated with the level of general literacy (rs = 0.593) and income (rs = 0.327) and significantly associated with occupation, educational attainment, use of dental services, self-rated oral health and the respondent’s perception regarding his/her child's oral health. However, only the association between the BREALD-30 score and the respondent’s perception regarding his/her child's oral health remained significant in the multivariate analysis. Conclusion The BREALD-30 demonstrated satisfactory psychometric properties and is therefore applicable to adults in Brazil. PMID:26158724

Bisphosphonates in the Prevention of Post-Traumatic Osteoarthritis

DTIC Science & Technology

David, et al . 2017 J Ortho Res. - Histological analysis of mouse joints following DMM demonstrated rapid (within 3-day of injury), and focal (spatially...Medial Meniscus in Mice (David, et al . 2018 In Preparation) - The present study has shown that repeated i. a. injection of ZA into the murine knee

Optofluidic refractive-index sensors employing bent waveguide structures for low-cost, rapid chemical and biomedical sensing.

PubMed

Liu, I-Chen; Chen, Pin-Chuan; Chau, Lai-Kwan; Chang, Guo-En

2018-01-08

We propose and develop an intensity-detection-based refractive-index (RI) sensor for low-cost, rapid RI sensing. The sensor is composed of a polymer bent ridge waveguide (BRWG) structure on a low-cost glass substrate and is integrated with a microfluidic channel. Different-RI solutions flowing through the BRWG sensing region induce output optical power variations caused by optical bend losses, enabling simple and real-time RI detection. Additionally, the sensors are fabricated using rapid and cost-effective vacuum-less processes, attaining the low cost and high throughput required for mass production. A good RI solution of 5.31 10 -4 × RIU -1 is achieved from the RI experiments. This study demonstrates mass-producible and compact RI sensors for rapid and sensitive chemical analysis and biomedical sensing.

Raman spectral analysis for rapid screening of dengue infection

NASA Astrophysics Data System (ADS)

Mahmood, T.; Nawaz, H.; Ditta, A.; Majeed, M. I.; Hanif, M. A.; Rashid, N.; Bhatti, H. N.; Nargis, H. F.; Saleem, M.; Bonnier, F.; Byrne, H. J.

2018-07-01

Infection with the dengue virus is currently clinically detected according to different biomarkers in human blood plasma, commonly measured by enzyme linked immunosorbent assays, including non-structural proteins (Ns1), immunoglobulin M (IgM) and immunoglobulin G (IgG). However, there is little or no mutual correlation between the biomarkers, as demonstrated in this study by a comparison of their levels in samples from 17 patients. As an alternative, the label free, rapid screening technique, Raman spectroscopy has been used for the characterisation/diagnosis of healthy and dengue infected human blood plasma samples. In dengue positive samples, changes in specific Raman spectral bands associated with lipidic and amino acid/protein content are observed and assigned based on literature and these features can be considered as markers associated with dengue development. Based on the spectroscopic analysis of the current, albeit limited, cohort of samples, Principal Components Analysis (PCA) coupled Factorial Discriminant Analysis, yielded values of 97.95% sensitivity and 95.40% specificity for identification of dengue infection. Furthermore, in a comparison of the normal samples to the patient samples which scored low for only one of the biomarker tests, but high or medium for either or both of the other two, PCA-FDA demonstrated a sensitivity of 97.38% and specificity of 86.18%, thus providing an unambiguous screening technology.

Proflavine Hemisulfate as a Fluorescent Contrast Agent for Point-of-Care Cytology

PubMed Central

Prieto, Sandra P.; Powless, Amy J.; Boice, Jackson W.; Sharma, Shree G.; Muldoon, Timothy J.

2015-01-01

Proflavine hemisulfate, an acridine-derived fluorescent dye, can be used as a rapid stain for cytologic examination of biological specimens. Proflavine fluorescently stains cell nuclei and cytoplasmic structures, owing to its small amphipathic structure and ability to intercalate DNA. In this manuscript, we demonstrated the use of proflavine as a rapid cytologic dye on a number of specimens, including normal exfoliated oral squamous cells, cultured human oral squamous carcinoma cells, and leukocytes derived from whole blood specimens using a custom-built, portable, LED-illuminated fluorescence microscope. No incubation time was needed after suspending cells in 0.01% (w/v) proflavine diluted in saline. Images of proflavine stained oral cells had clearly visible nuclei as well as granular cytoplasm, while stained leukocytes exhibited bright nuclei, and highlighted the multilobar nature of nuclei in neutrophils. We also demonstrated the utility of quantitative analysis of digital images of proflavine stained cells, which can be used to detect significant morphological differences between different cell types. Proflavine stained oral cells have well-defined nuclei and cell membranes which allowed for quantitative analysis of nuclear to cytoplasmic ratios, as well as image texture analysis to extract quantitative image features. PMID:25962131

Proflavine Hemisulfate as a Fluorescent Contrast Agent for Point-of-Care Cytology.

PubMed

Prieto, Sandra P; Powless, Amy J; Boice, Jackson W; Sharma, Shree G; Muldoon, Timothy J

2015-01-01

Proflavine hemisulfate, an acridine-derived fluorescent dye, can be used as a rapid stain for cytologic examination of biological specimens. Proflavine fluorescently stains cell nuclei and cytoplasmic structures, owing to its small amphipathic structure and ability to intercalate DNA. In this manuscript, we demonstrated the use of proflavine as a rapid cytologic dye on a number of specimens, including normal exfoliated oral squamous cells, cultured human oral squamous carcinoma cells, and leukocytes derived from whole blood specimens using a custom-built, portable, LED-illuminated fluorescence microscope. No incubation time was needed after suspending cells in 0.01% (w/v) proflavine diluted in saline. Images of proflavine stained oral cells had clearly visible nuclei as well as granular cytoplasm, while stained leukocytes exhibited bright nuclei, and highlighted the multilobar nature of nuclei in neutrophils. We also demonstrated the utility of quantitative analysis of digital images of proflavine stained cells, which can be used to detect significant morphological differences between different cell types. Proflavine stained oral cells have well-defined nuclei and cell membranes which allowed for quantitative analysis of nuclear to cytoplasmic ratios, as well as image texture analysis to extract quantitative image features.

Comparison of orbital volume obtained by tomography and rapid prototyping.

PubMed

Roça, Guilherme Berto; Foggiatto, José Aguiomar; Ono, Maria Cecilia Closs; Ono, Sergio Eiji; da Silva Freitas, Renato

2013-11-01

This study aims to compare orbital volume obtained by helical tomography and rapid prototyping. The study sample was composed of 6 helical tomography scans. Eleven healthy orbits were identified to have their volumes measured. The volumetric analysis with the helical tomography utilized the same protocol developed by the Plastic Surgery Unit of the Federal University of Paraná. From the CT images, 11 prototypes were created, and their respective volumes were analyzed in 2 ways: using software by SolidWorks and by direct analysis, when the prototype was filled with saline solution. For statistical analysis, the results of the volumes of the 11 orbits were considered independent. The average orbital volume measurements obtained by the method of Ono et al was 20.51 cm, the average obtained by the SolidWorks program was 20.64 cm, and the average measured using the prototype method was 21.81 cm. The 3 methods demonstrated a strong correlation between the measurements. The right and left orbits of each patient had similar volumes. The tomographic method for the analysis of orbital volume using the Ono protocol yielded consistent values, and by combining this method with rapid prototyping, both reliability validations of results were enhanced.

[Rapid multi-elemental analysis on four precious Tibetan medicines based on LIBS technique].

PubMed

Liu, Xiao-na; Shi, Xin-yuan; Jia, Shuai-yun; Zhao, Na; Wu, Zhi-sheng; Qiao, Yan-jiang

2015-06-01

The laser-induced breakdown spectroscopy (LIBS) was applied to perform a qualitative elementary analysis on four precious Tibetan medicines, i. e. Renqing Mangjue, Renqing Changjue, 25-herb coral pills and 25-herb pearl pills. The specific spectra of the four Tibetan medicines were established. In the experiment, Nd: YAG and 1 064 nm-baseband pulse laser were adopted to collect the spectra. A laser beam focused on the surface of the samples to generate plasma. Its spectral signal was detected by using spectrograph. Based on the National Institute of Standard and Technology (NIST) database, LIBS spectral lines were indentified. The four Tibetan medicines mainly included Ca, Na, K, Mg and other elements and C-N molecular band. Specifically, Fe was detected in Renqing Changjue and 25-herb pearl pills; heavy mental elements Hg and Cu were shown in Renqing Mangjue and Renqing Changjue; Ag was found in Renqing Changjue. The results demonstrated that LIBS is a reliable and rapid multi-element analysis on the four Tibetan medicines. With Real-time, rapid and nondestructive advantages, LIBS has a wide application prospect in the element analysis on ethnic medicines.

Analysis of Rare Earth Elements in Uranium Using Handheld Laser-Induced Breakdown Spectroscopy (HH LIBS)

DOE PAGES

Manard, Benjamin T.; Wylie, E. Miller; Willson, Stephen P.

2018-05-22

In this paper, a portable handheld laser-induced breakdown spectroscopy (HH LIBS) instrument was evaluated as a rapid method to qualitatively analyze rare earth elements in a uranium oxide matrix. This research is motivated by the need for development of a method to perform rapid, at-line chemical analysis in a nuclear facility, particularly to provide a rapid first pass analysis to determine if additional actions or measurements are warranted. This will result in the minimization of handling and transport of radiological and nuclear material and subsequent exposure to their associated hazards. In this work, rare earth elements (Eu, Nd, and Yb)more » were quantitatively spiked into a uranium oxide powder and analyzed by the HH LIBS instrumentation. This method demonstrates the ability to rapidly identify elemental constituents in sub-percent levels in a uranium matrix. Preliminary limits of detection (LODs) were determined with values on the order of hundredths of a percent. Validity of this methodology was explored by employing a National Institute of Standards and Technology (NIST) standard reference materials (SRM) 610 and 612 (Trace Elements in Glass). Finally, it was determined that the HH LIBS method was able to clearly discern the rare earths elements of interest in the glass or uranium matrices.« less

Analysis of Rare Earth Elements in Uranium Using Handheld Laser-Induced Breakdown Spectroscopy (HH LIBS)

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

Manard, Benjamin T.; Wylie, E. Miller; Willson, Stephen P.

In this paper, a portable handheld laser-induced breakdown spectroscopy (HH LIBS) instrument was evaluated as a rapid method to qualitatively analyze rare earth elements in a uranium oxide matrix. This research is motivated by the need for development of a method to perform rapid, at-line chemical analysis in a nuclear facility, particularly to provide a rapid first pass analysis to determine if additional actions or measurements are warranted. This will result in the minimization of handling and transport of radiological and nuclear material and subsequent exposure to their associated hazards. In this work, rare earth elements (Eu, Nd, and Yb)more » were quantitatively spiked into a uranium oxide powder and analyzed by the HH LIBS instrumentation. This method demonstrates the ability to rapidly identify elemental constituents in sub-percent levels in a uranium matrix. Preliminary limits of detection (LODs) were determined with values on the order of hundredths of a percent. Validity of this methodology was explored by employing a National Institute of Standards and Technology (NIST) standard reference materials (SRM) 610 and 612 (Trace Elements in Glass). Finally, it was determined that the HH LIBS method was able to clearly discern the rare earths elements of interest in the glass or uranium matrices.« less

Analysis of Rare Earth Elements in Uranium Using Handheld Laser-Induced Breakdown Spectroscopy (HH LIBS).

PubMed

Manard, Benjamin T; Wylie, E Miller; Willson, Stephen P

2018-01-01

A portable handheld laser-induced breakdown spectroscopy (HH LIBS) instrument was evaluated as a rapid method to qualitatively analyze rare earth elements in a uranium oxide matrix. This research is motivated by the need for development of a method to perform rapid, at-line chemical analysis in a nuclear facility, particularly to provide a rapid first pass analysis to determine if additional actions or measurements are warranted. This will result in the minimization of handling and transport of radiological and nuclear material and subsequent exposure to their associated hazards. In this work, rare earth elements (Eu, Nd, and Yb) were quantitatively spiked into a uranium oxide powder and analyzed by the HH LIBS instrumentation. This method demonstrates the ability to rapidly identify elemental constituents in sub-percent levels in a uranium matrix. Preliminary limits of detection (LODs) were determined with values on the order of hundredths of a percent. Validity of this methodology was explored by employing a National Institute of Standards and Technology (NIST) standard reference materials (SRM) 610 and 612 (Trace Elements in Glass). It was determined that the HH LIBS method was able to clearly discern the rare earths elements of interest in the glass or uranium matrices.

Ambient Mass Spectrometry in Cancer Research.

PubMed

Takats, Z; Strittmatter, N; McKenzie, J S

2017-01-01

Ambient ionization mass spectrometry was developed as a sample preparation-free alternative to traditional MS-based workflows. Desorption electrospray ionization (DESI)-MS methods were demonstrated to allow the direct analysis of a broad range of samples including unaltered biological tissue specimens. In contrast to this advantageous feature, nowadays DESI-MS is almost exclusively used for sample preparation intensive mass spectrometric imaging (MSI) in the area of cancer research. As an alternative to MALDI, DESI-MSI offers matrix deposition-free experiment with improved signal in the lower (<500m/z) range. DESI-MSI enables the spatial mapping of tumor metabolism and has been broadly demonstrated to offer an alternative to frozen section histology for intraoperative tissue identification and surgical margin assessment. Rapid evaporative ionization mass spectrometry (REIMS) was developed exclusively for the latter purpose by the direct combination of electrosurgical devices and mass spectrometry. In case of the REIMS technology, aerosol particles produced by electrosurgical dissection are subjected to MS analysis, providing spectral information on the structural lipid composition of tissues. REIMS technology was demonstrated to give real-time information on the histological nature of tissues being dissected, deeming it an ideal tool for intraoperative tissue identification including surgical margin control. More recently, the method has also been used for the rapid lipidomic phenotyping of cancer cell lines as it was demonstrated in case of the NCI-60 cell line collection. © 2017 Elsevier Inc. All rights reserved.

A homotopy analysis method for the nonlinear partial differential equations arising in engineering

NASA Astrophysics Data System (ADS)

Hariharan, G.

2017-05-01

In this article, we have established the homotopy analysis method (HAM) for solving a few partial differential equations arising in engineering. This technique provides the solutions in rapid convergence series with computable terms for the problems with high degree of nonlinear terms appearing in the governing differential equations. The convergence analysis of the proposed method is also discussed. Finally, we have given some illustrative examples to demonstrate the validity and applicability of the proposed method.

Rapid detection of bacterial contamination in cell or tissue cultures based on Raman spectroscopy

NASA Astrophysics Data System (ADS)

Bolwien, Carsten; Sulz, Gerd; Becker, Sebastian; Thielecke, Hagen; Mertsching, Heike; Koch, Steffen

2008-02-01

Monitoring the sterility of cell or tissue cultures is an essential task, particularly in the fields of regenerative medicine and tissue engineering when implanting cells into the human body. We present a system based on a commercially available microscope equipped with a microfluidic cell that prepares the particles found in the solution for analysis, a Raman-spectrometer attachment optimized for non-destructive, rapid recording of Raman spectra, and a data acquisition and analysis tool for identification of the particles. In contrast to conventional sterility testing in which samples are incubated over weeks, our system is able to analyze milliliters of supernatant or cell suspension within hours by filtering relevant particles and placing them on a Raman-friendly substrate in the microfluidic cell. Identification of critical particles via microscopic imaging and subsequent image analysis is carried out before micro-Raman analysis of those particles is then carried out with an excitation wavelength of 785 nm. The potential of this setup is demonstrated by results of artificial contamination of samples with a pool of bacteria, fungi, and spores: single-channel spectra of the critical particles are automatically baseline-corrected without using background data and classified via hierarchical cluster analysis, showing great promise for accurate and rapid detection and identification of contaminants.

Fuji apple storage time rapid determination method using Vis/NIR spectroscopy.

PubMed

Liu, Fuqi; Tang, Xuxiang

2015-01-01

Fuji apple storage time rapid determination method using visible/near-infrared (Vis/NIR) spectroscopy was studied in this paper. Vis/NIR diffuse reflection spectroscopy responses to samples were measured for 6 days. Spectroscopy data were processed by stochastic resonance (SR). Principal component analysis (PCA) was utilized to analyze original spectroscopy data and SNR eigen value. Results demonstrated that PCA could not totally discriminate Fuji apples using original spectroscopy data. Signal-to-noise ratio (SNR) spectrum clearly classified all apple samples. PCA using SNR spectrum successfully discriminated apple samples. Therefore, Vis/NIR spectroscopy was effective for Fuji apple storage time rapid discrimination. The proposed method is also promising in condition safety control and management for food and environmental laboratories.

Rapid Transfer of Abstract Rules to Novel Contexts in Human Lateral Prefrontal Cortex

PubMed Central

Cole, Michael W.; Etzel, Joset A.; Zacks, Jeffrey M.; Schneider, Walter; Braver, Todd S.

2011-01-01

Flexible, adaptive behavior is thought to rely on abstract rule representations within lateral prefrontal cortex (LPFC), yet it remains unclear how these representations provide such flexibility. We recently demonstrated that humans can learn complex novel tasks in seconds. Here we hypothesized that this impressive mental flexibility may be possible due to rapid transfer of practiced rule representations within LPFC to novel task contexts. We tested this hypothesis using functional MRI and multivariate pattern analysis, classifying LPFC activity patterns across 64 tasks. Classifiers trained to identify abstract rules based on practiced task activity patterns successfully generalized to novel tasks. This suggests humans can transfer practiced rule representations within LPFC to rapidly learn new tasks, facilitating cognitive performance in novel circumstances. PMID:22125519

Fuji apple storage time rapid determination method using Vis/NIR spectroscopy

PubMed Central

Liu, Fuqi; Tang, Xuxiang

2015-01-01

Fuji apple storage time rapid determination method using visible/near-infrared (Vis/NIR) spectroscopy was studied in this paper. Vis/NIR diffuse reflection spectroscopy responses to samples were measured for 6 days. Spectroscopy data were processed by stochastic resonance (SR). Principal component analysis (PCA) was utilized to analyze original spectroscopy data and SNR eigen value. Results demonstrated that PCA could not totally discriminate Fuji apples using original spectroscopy data. Signal-to-noise ratio (SNR) spectrum clearly classified all apple samples. PCA using SNR spectrum successfully discriminated apple samples. Therefore, Vis/NIR spectroscopy was effective for Fuji apple storage time rapid discrimination. The proposed method is also promising in condition safety control and management for food and environmental laboratories. PMID:25874818

Applications of Response Surface-Based Methods to Noise Analysis in the Conceptual Design of Revolutionary Aircraft

NASA Technical Reports Server (NTRS)

Hill, Geoffrey A.; Olson, Erik D.

2004-01-01

Due to the growing problem of noise in today's air transportation system, there have arisen needs to incorporate noise considerations in the conceptual design of revolutionary aircraft. Through the use of response surfaces, complex noise models may be converted into polynomial equations for rapid and simplified evaluation. This conversion allows many of the commonly used response surface-based trade space exploration methods to be applied to noise analysis. This methodology is demonstrated using a noise model of a notional 300 passenger Blended-Wing-Body (BWB) transport. Response surfaces are created relating source noise levels of the BWB vehicle to its corresponding FAR-36 certification noise levels and the resulting trade space is explored. Methods demonstrated include: single point analysis, parametric study, an optimization technique for inverse analysis, sensitivity studies, and probabilistic analysis. Extended applications of response surface-based methods in noise analysis are also discussed.

Optimization of ultrahigh-speed multiplex PCR for forensic analysis.

PubMed

Gibson-Daw, Georgiana; Crenshaw, Karin; McCord, Bruce

2018-01-01

In this paper, we demonstrate the design and optimization of an ultrafast PCR amplification technique, used with a seven-locus multiplex that is compatible with conventional capillary electrophoresis systems as well as newer microfluidic chip devices. The procedure involves the use of a high-speed polymerase and a rapid cycling protocol to permit multiplex PCR amplification of forensic short tandem repeat loci in 6.5 min. We describe the selection and optimization of master mix reagents such as enzyme, buffer, MgCl 2 , and dNTPs, as well as primer ratios, total volume, and cycle conditions, in order to get the best profile in the shortest time possible. Sensitivity and reproducibility studies are also described. The amplification process utilizes a small high-speed thermocycler and compact laptop, making it portable and potentially useful for rapid, inexpensive on-site genotyping. The seven loci of the multiplex were taken from conventional STR genotyping kits and selected for their size and lack of overlap. Analysis was performed using conventional capillary electrophoresis and microfluidics with fluorescent detection. Overall, this technique provides a more rapid method for rapid sample screening of suspects and victims. Graphical abstract Rapid amplification of forensic DNA using high speed thermal cycling followed by capillary or microfluidic electrophoresis.

Rapid fingerprinting and classification of extra virgin olive oil by microjet sampling and extractive electrospray ionization mass spectrometry.

PubMed

Law, Wai Siang; Chen, Huan Wen; Balabin, Roman; Berchtold, Christian; Meier, Lukas; Zenobi, Renato

2010-04-01

Microjet sampling in combination with extractive electrospray ionization (EESI) mass spectrometry (MS) was applied to the rapid characterization and classification of extra virgin olive oil (EVOO) without any sample pretreatment. When modifying the composition of the primary ESI spray solvent, mass spectra of an identical EVOO sample showed differences. This demonstrates the capability of this technique to extract molecules with varying polarities, hence generating rich molecular information of the EVOO. Moreover, with the aid of microjet sampling, compounds of different volatilities (e.g.E-2-hexenal, trans-trans-2,4-heptadienal, tyrosol and caffeic acid) could be sampled simultaneously. EVOO data was also compared with that of other edible oils. Principal Component Analysis (PCA) was performed to discriminate EVOO and EVOO adulterated with edible oils. Microjet sampling EESI-MS was found to be a simple, rapid (less than 2 min analysis time per sample) and powerful method to obtain MS fingerprints of EVOO without requiring any complicated sample pretreatment steps.

Rapid, High-Resolution Detection of Environmental Change over Continental Scales from Satellite Data - the Earth Observation Data Cube

NASA Technical Reports Server (NTRS)

Lewis, Adam; Lymburner, Leo; Purss, Matthew B. J.; Brooke, Brendan; Evans, Ben; Ip, Alex; Dekker, Arnold G.; Irons, James R.; Minchin, Stuart; Mueller, Norman

2015-01-01

The effort and cost required to convert satellite Earth Observation (EO) data into meaningful geophysical variables has prevented the systematic analysis of all available observations. To overcome these problems, we utilise an integrated High Performance Computing and Data environment to rapidly process, restructure and analyse the Australian Landsat data archive. In this approach, the EO data are assigned to a common grid framework that spans the full geospatial and temporal extent of the observations - the EO Data Cube. This approach is pixel-based and incorporates geometric and spectral calibration and quality assurance of each Earth surface reflectance measurement. We demonstrate the utility of the approach with rapid time-series mapping of surface water across the entire Australian continent using 27 years of continuous, 25 m resolution observations. Our preliminary analysis of the Landsat archive shows how the EO Data Cube can effectively liberate high-resolution EO data from their complex sensor-specific data structures and revolutionise our ability to measure environmental change.

Millimeter-wave optical double resonance schemes for rapid assignment of perturbed spectra, with applications to the C{sup ~} {sup 1}B{sub 2} state of SO{sub 2}

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

Park, G. Barratt, E-mail: barratt@mit.edu, E-mail: barratt.park@gmail.com; Womack, Caroline C.; Jiang, Jun

2015-04-14

Millimeter-wave detected, millimeter-wave optical double resonance (mmODR) spectroscopy is a powerful tool for the analysis of dense, complicated regions in the optical spectra of small molecules. The availability of cavity-free microwave and millimeter wave spectrometers with frequency-agile generation and detection of radiation (required for chirped-pulse Fourier-transform spectroscopy) opens up new schemes for double resonance experiments. We demonstrate a multiplexed population labeling scheme for rapid acquisition of double resonance spectra, probing multiple rotational transitions simultaneously. We also demonstrate a millimeter-wave implementation of the coherence-converted population transfer scheme for background-free mmODR, which provides a ∼10-fold sensitivity improvement over the population labeling scheme.more » We analyze perturbations in the C{sup ~} state of SO{sub 2}, and we rotationally assign a b{sub 2} vibrational level at 45 328 cm{sup −1} that borrows intensity via a c-axis Coriolis interaction. We also demonstrate the effectiveness of our multiplexed mmODR scheme for rapid acquisition and assignment of three predissociated vibrational levels of the C{sup ~} state of SO{sub 2} between 46 800 and 47 650 cm{sup −1}.« less

Rapid determination of trace nitrophenolic organics in water by combining solid-phase extraction with surface-assisted laser desorption/ionization time-of-flight mass spectrometry.

PubMed

Chen, Y C; Shiea, J; Sunner, J

2000-01-01

A rapid technique for the screening of trace compounds in water by combining solid-phase extraction (SPE) with activated carbon surface-assisted laser desorption/ionization (SALDI) time-of-flight mass spectrometry is demonstrated. Activated carbon is used both as the sorbent in SPE and as the solid in the SALDI matrix system. This eliminates the need for an SPE elution process. After the analytes have been adsorbed on the surfaces of the activated carbon during SPE extraction, the activated carbon is directly mixed with the SALDI liquid and mass spectrometric analysis is performed. Trace phenolic compounds in water were used to demonstrate the effectiveness of the method. The detection limit for these compounds is in the ppb to ppt range. Copyright 2000 John Wiley & Sons, Ltd.

Final Progress Report: Isotope Identification Algorithm for Rapid and Accurate Determination of Radioisotopes Feasibility Study

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

Rawool-Sullivan, Mohini; Bounds, John Alan; Brumby, Steven P.

2012-04-30

This is the final report of the project titled, 'Isotope Identification Algorithm for Rapid and Accurate Determination of Radioisotopes,' PMIS project number LA10-HUMANID-PD03. The goal of the work was to demonstrate principles of emulating a human analysis approach towards the data collected using radiation isotope identification devices (RIIDs). It summarizes work performed over the FY10 time period. The goal of the work was to demonstrate principles of emulating a human analysis approach towards the data collected using radiation isotope identification devices (RIIDs). Human analysts begin analyzing a spectrum based on features in the spectrum - lines and shapes that aremore » present in a given spectrum. The proposed work was to carry out a feasibility study that will pick out all gamma ray peaks and other features such as Compton edges, bremsstrahlung, presence/absence of shielding and presence of neutrons and escape peaks. Ultimately success of this feasibility study will allow us to collectively explain identified features and form a realistic scenario that produced a given spectrum in the future. We wanted to develop and demonstrate machine learning algorithms that will qualitatively enhance the automated identification capabilities of portable radiological sensors that are currently being used in the field.« less

Dissecting Online Control in Developmental Coordination Disorder: A Kinematic Analysis of Double-Step Reaching

ERIC Educational Resources Information Center

Hyde, Christian; Wilson, Peter H.

2011-01-01

In a recent study, children with movement clumsiness (or Developmental Coordination Disorder--DCD) were shown to have difficulties making rapid online corrections when reaching, demonstrated by slower and less accurate movements to double-step targets (Hyde & Wilson, 2011). These results suggest that children with DCD have difficulty using…

Groundwater flow system under a rapidly urbanizing coastal city as determined by hydrogeochemistry

NASA Astrophysics Data System (ADS)

Kagabu, Makoto; Shimada, Jun; Delinom, Robert; Tsujimura, Maki; Taniguchi, Makoto

2011-01-01

In the Jakarta area (Indonesia), excessive groundwater pumping due to the rapidly increasing population has caused groundwater-related problems such as brackish water contamination in coastal areas and land subsidence. In this study, we adopted multiple hydrogeochemical techniques to demonstrate the groundwater flow system in the Jakarta area. Although almost all groundwater existing in the Jakarta basin is recharged at similar elevations, the water quality and residence time demonstrates a clear difference between the shallow and deep aquifers. Due to the rapid decrease in the groundwater potential in urban areas, we found that the seawater intrusion and the shallow and deep groundwaters are mixing, a conclusion confirmed by major ions, Br -:Cl - ratios, and chlorofluorocarbon (CFC)-12 analysis. Spring water and groundwater samples collected from the southern mountainside area show younger age characteristics with high concentrations of 14C and Ca-HCO 3 type water chemistry. We estimated the residence times of these groundwaters within 45 years under piston flow conditions by tritium analysis. Also, these groundwater ages can be limited to 20-30 years with piston flow evaluated by CFCs. Moreover, due to the magnitude of the CFC-12 concentration, we can use a pseudo age indicator in this field study, because we found a positive correlation between the major type of water chemistry and the CFC-12 concentration.

A rapid, one step preparation for measuring selected free plus SO2-bound wine carbonyls by HPLC-DAD/MS.

PubMed

Han, Guomin; Wang, Hua; Webb, Michael R; Waterhouse, Andrew L

2015-03-01

Carbonyl compounds are produced during fermentation and chemical oxidation during wine making and aging, and they are important to wine flavor and color stability. Since wine also contains these compounds as α-hydroxysulfonates as a result of their reaction with sulfur dioxide, an alkaline pre-treatment requiring oxygen exclusion has been used to release these bound carbonyls for analysis. By modifying the method to hydrolyze the hydroxysulfonates with heating and acid in the presence of 2,4-dinitrophenylhydrazine (DNPH), the carbonyl compounds are simultaneously and quickly released and derivatized, resulting in a simpler and more rapid method. In addition, the method avoids air exclusion complications during hydrolysis by the addition of sulfur dioxide. The method was optimized for temperature, reaction time, and the concentrations of DNPH, sulfur dioxide and acid. The hydrazones were shown to be stable for 10 h, adequate time for chromatographic analysis by HPLC-DAD/MS. This method is demonstrated for 2-ketoglutaric acid, pyruvic acid, acetoin and acetaldehyde, wine carbonyls of very different reactivities, and it offers good specificity, high recovery and low limits of detection. This new rapid, simple method is demonstrated for the measurement of carbonyl compounds in a range of wines of different ages and grape varieties. Copyright © 2014 Elsevier B.V. All rights reserved.

Rapid and nondestructive method for evaluation of embryo culture media using drop coating deposition Raman spectroscopy

NASA Astrophysics Data System (ADS)

Huang, Zufang; Sun, Yan; Wang, Jing; Du, Shengrong; Li, Yongzeng; Lin, Juqiang; Feng, Shangyuan; Lei, Jinping; Lin, Hongxin; Chen, Rong; Zeng, Haishan

2013-12-01

In this study, a rapid and simple method which combines drop coating deposition and Raman spectroscopy (DCDR) was developed to characterize the dry embryo culture media (ECM) droplet. We demonstrated that Raman spectra obtained from the droplet edge presented useful and characteristic signatures for protein and amino acids assessment. Using a different analytical method, scanning electron microscopy coupled with energy dispersive X-ray analysis, we further confirmed that Na, K, and Cl were mainly detected in the central area of the dry ECM droplet while sulphur, an indicative of the presence of macromolecules such as proteins, was mainly found at the periphery of the droplet. In addition, to reduce sample preparation time, different temperatures for drying the droplets were tested. The results showed that drying temperature at 50°C can effectively reduce the sample preparation time to 6 min (as compared to 50 min for drying at room temperature, ˜25°C) without inducing thermal damage to the proteins. This work demonstrated that DCDR has potential for rapid and reliable metabolomic profiling of ECM in clinical applications.

Bus Rapid Transit Demonstration Program

DOT National Transportation Integrated Search

1998-12-31

This report was prepared by the Federal Transit Administration's (FTA) Office of Research, Demonstration and Innovation. It describes the FTA's Bus Rapid Transit Demonstration Program, designed to provide funding and support to transit agencies engag...

Integrated Modeling, Mapping, and Simulation (IMMS) framework for planning exercises.

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

Friedman-Hill, Ernest J.; Plantenga, Todd D.

2010-06-01

The Integrated Modeling, Mapping, and Simulation (IMMS) program is designing and prototyping a simulation and collaboration environment for linking together existing and future modeling and simulation tools to enable analysts, emergency planners, and incident managers to more effectively, economically, and rapidly prepare, analyze, train, and respond to real or potential incidents. When complete, the IMMS program will demonstrate an integrated modeling and simulation capability that supports emergency managers and responders with (1) conducting 'what-if' analyses and exercises to address preparedness, analysis, training, operations, and lessons learned, and (2) effectively, economically, and rapidly verifying response tactics, plans and procedures.

Rapid and Sensitive Detection of Protein Biomarker Using a Portable Fluorescence Biosensor based on Quantum Dots and a Lateral Flow Test Strip

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

Li, Zhaohui; Wang, Ying; Wang, Jun

2010-08-15

A portable fluorescence biosensor with rapid and ultrasensitive response for trace protein has been built up with quantum dots and lateral flow test strip. The superior signal brightness and high photostability of quantum dots are combined with the promising advantages of lateral flow test strip and resulted in high sensitivity, selectivity and speedy for protein detection. Nitrated ceruloplasmin, a significant biomarker for cardiovascular disease, lung cancer and stress response to smoking, was used as model protein to demonstrate the good performances of this proposed Qdot-based lateral flow test strip. Quantitative detection of nitrated ceruloplasmin was realized by recording the fluorescencemore » intensity of quantum dots captured on the test line. Under optimal conditions, this portable fluorescence biosensor displays rapid responses for nitrated ceruloplasmin in wide dynamic range with a detection limit of 0.1ng/mL (S/N=3). Furthermore, the biosensor was successfully utilized for spiked human plasma sample detection with the concentration as low as 1ng/mL. The results demonstrate that the quantum dot-based lateral flow test strip is capable for rapid, sensitive, and quantitative detection of nitrated ceruloplasmin and hold a great promise for point-of-care and in field analysis of other protein biomarkers.« less

Alternatives to current flow cytometry data analysis for clinical and research studies.

PubMed

Gondhalekar, Carmen; Rajwa, Bartek; Patsekin, Valery; Ragheb, Kathy; Sturgis, Jennifer; Robinson, J Paul

2018-02-01

Flow cytometry has well-established methods for data analysis based on traditional data collection techniques. These techniques typically involved manual insertion of tube samples into an instrument that, historically, could only measure 1-3 colors. The field has since evolved to incorporate new technologies for faster and highly automated sample preparation and data collection. For example, the use of microwell plates on benchtop instruments is now a standard on virtually every new instrument, and so users can easily accumulate multiple data sets quickly. Further, because the user must carefully define the layout of the plate, this information is already defined when considering the analytical process, expanding the opportunities for automated analysis. Advances in multi-parametric data collection, as demonstrated by the development of hyperspectral flow-cytometry, 20-40 color polychromatic flow cytometry, and mass cytometry (CyTOF), are game-changing. As data and assay complexity increase, so too does the complexity of data analysis. Complex data analysis is already a challenge to traditional flow cytometry software. New methods for reviewing large and complex data sets can provide rapid insight into processes difficult to define without more advanced analytical tools. In settings such as clinical labs where rapid and accurate data analysis is a priority, rapid, efficient and intuitive software is needed. This paper outlines opportunities for analysis of complex data sets using examples of multiplexed bead-based assays, drug screens and cell cycle analysis - any of which could become integrated into the clinical environment. Copyright © 2017. Published by Elsevier Inc.

Cost-effective and Rapid Blood Analysis on a Cell-phone

PubMed Central

Zhu, Hongying; Sencan, Ikbal; Wong, Justin; Dimitrov, Stoyan; Tseng, Derek; Nagashima, Keita; Ozcan, Aydogan

2013-01-01

We demonstrate a compact and cost-effective imaging cytometry platform installed on a cell-phone for the measurement of the density of red and white blood cells as well as hemoglobin concentration in human blood samples. Fluorescent and bright-field images of blood samples are captured using separate optical attachments to the cell-phone and are rapidly processed through a custom-developed smart application running on the phone for counting of blood cells and determining hemoglobin density. We evaluated the performance of this cell-phone based blood analysis platform using anonymous human blood samples and achieved comparable results to a standard bench-top hematology analyser. Test results can either be stored on the cell-phone memory or be transmitted to a central server, providing remote diagnosis opportunities even in field settings. PMID:23392286

Cost-effective and rapid blood analysis on a cell-phone.

PubMed

Zhu, Hongying; Sencan, Ikbal; Wong, Justin; Dimitrov, Stoyan; Tseng, Derek; Nagashima, Keita; Ozcan, Aydogan

2013-04-07

We demonstrate a compact and cost-effective imaging cytometry platform installed on a cell-phone for the measurement of the density of red and white blood cells as well as hemoglobin concentration in human blood samples. Fluorescent and bright-field images of blood samples are captured using separate optical attachments to the cell-phone and are rapidly processed through a custom-developed smart application running on the phone for counting of blood cells and determining hemoglobin density. We evaluated the performance of this cell-phone based blood analysis platform using anonymous human blood samples and achieved comparable results to a standard bench-top hematology analyser. Test results can either be stored on the cell-phone memory or be transmitted to a central server, providing remote diagnosis opportunities even in field settings.

Rapid screening of illicit additives in weight loss dietary supplements with desorption corona beam ionisation (DCBI) mass spectrometry.

PubMed

Wang, H; Wu, Y; Zhao, Y; Sun, W; Ding, L; Guo, B; Chen, B

2012-08-01

Desorption corona beam ionisation (DCBI), the relatively novel ambient mass spectrometry (MS) technique, was utilised to screen for illicit additives in weight-loss food. The five usually abused chemicals - fenfluramine, N-di-desmethyl sibutramine, N-mono-desmethyl sibutramine, sibutramine and phenolphthalein - were detected with the proposed DCBI-MS method. Fast single-sample and high-throughput analysis was demonstrated. Semi-quantification was accomplished based on peak areas in the ion chromatograms. Four illicit additives were identified and semi-quantified in commercial samples. As there was no tedious sample pre-treatment compared with conventional HPLC methods, high-throughput analysis was achieved with DCBI. The results proved that DCBI-MS is a powerful tool for the rapid screening of illicit additives in weight-loss dietary supplements.

Direct Detection of Pharmaceuticals and Personal Care Products from Aqueous Samples with Thermally-Assisted Desorption Electrospray Ionization Mass Spectrometry

NASA Astrophysics Data System (ADS)

Campbell, Ian S.; Ton, Alain T.; Mulligan, Christopher C.

2011-07-01

An ambient mass spectrometric method based on desorption electrospray ionization (DESI) has been developed to allow rapid, direct analysis of contaminated water samples, and the technique was evaluated through analysis of a wide array of pharmaceutical and personal care product (PPCP) contaminants. Incorporating direct infusion of aqueous sample and thermal assistance into the source design has allowed low ppt detection limits for the target analytes in drinking water matrices. With this methodology, mass spectral information can be collected in less than 1 min, consuming ~100 μL of total sample. Quantitative ability was also demonstrated without the use of an internal standard, yielding decent linearity and reproducibility. Initial results suggest that this source configuration is resistant to carryover effects and robust towards multi-component samples. The rapid, continuous analysis afforded by this method offers advantages in terms of sample analysis time and throughput over traditional hyphenated mass spectrometric techniques.

Direct detection of pharmaceuticals and personal care products from aqueous samples with thermally-assisted desorption electrospray ionization mass spectrometry.

PubMed

Campbell, Ian S; Ton, Alain T; Mulligan, Christopher C

2011-07-01

An ambient mass spectrometric method based on desorption electrospray ionization (DESI) has been developed to allow rapid, direct analysis of contaminated water samples, and the technique was evaluated through analysis of a wide array of pharmaceutical and personal care product (PPCP) contaminants. Incorporating direct infusion of aqueous sample and thermal assistance into the source design has allowed low ppt detection limits for the target analytes in drinking water matrices. With this methodology, mass spectral information can be collected in less than 1 min, consuming ~100 μL of total sample. Quantitative ability was also demonstrated without the use of an internal standard, yielding decent linearity and reproducibility. Initial results suggest that this source configuration is resistant to carryover effects and robust towards multi-component samples. The rapid, continuous analysis afforded by this method offers advantages in terms of sample analysis time and throughput over traditional hyphenated mass spectrometric techniques.

Classification of Fusarium-Infected Korean Hulled Barley Using Near-Infrared Reflectance Spectroscopy and Partial Least Squares Discriminant Analysis

PubMed Central

Lim, Jongguk; Kim, Giyoung; Mo, Changyeun; Oh, Kyoungmin; Yoo, Hyeonchae; Ham, Hyeonheui; Kim, Moon S.

2017-01-01

The purpose of this study is to use near-infrared reflectance (NIR) spectroscopy equipment to nondestructively and rapidly discriminate Fusarium-infected hulled barley. Both normal hulled barley and Fusarium-infected hulled barley were scanned by using a NIR spectrometer with a wavelength range of 1175 to 2170 nm. Multiple mathematical pretreatments were applied to the reflectance spectra obtained for Fusarium discrimination and the multivariate analysis method of partial least squares discriminant analysis (PLS-DA) was used for discriminant prediction. The PLS-DA prediction model developed by applying the second-order derivative pretreatment to the reflectance spectra obtained from the side of hulled barley without crease achieved 100% accuracy in discriminating the normal hulled barley and the Fusarium-infected hulled barley. These results demonstrated the feasibility of rapid discrimination of the Fusarium-infected hulled barley by combining multivariate analysis with the NIR spectroscopic technique, which is utilized as a nondestructive detection method. PMID:28974012

Rapid LC-MS/MS quantification of the major benzodiazepines and their metabolites on dried blood spots using a simple and cost-effective sample pretreatment.

PubMed

Déglon, Julien; Versace, François; Lauer, Estelle; Widmer, Christèle; Mangin, Patrice; Thomas, Aurélien; Staub, Christian

2012-06-01

Dried blood spots (DBS) sampling has gained popularity in the bioanalytical community as an alternative to conventional plasma sampling, as it provides numerous benefits in terms of sample collection and logistics. The aim of this work was to show that these advantages can be coupled with a simple and cost-effective sample pretreatment, with subsequent rapid LC-MS/MS analysis for quantitation of 15 benzodiazepines, six metabolites and three Z-drugs. For this purpose, a simplified offline procedure was developed that consisted of letting a 5-µl DBS infuse directly into 100 µl of MeOH, in a conventional LC vial. The parameters related to the DBS pretreatment, such as extraction time or internal standard addition, were investigated and optimized, demonstrating that passive infusion in a regular LC vial was sufficient to quantitatively extract the analytes of interest. The method was validated according to international criteria in the therapeutic concentration ranges of the selected compounds. The presented strategy proved to be efficient for the rapid analysis of the selected drugs. Indeed, the offline sample preparation was reduced to a minimum, using a small amount of organic solvent and consumables, without affecting the accuracy of the method. Thus, this approach enables simple and rapid DBS analysis, even when using a non-DBS-dedicated autosampler, while lowering the costs and environmental impact.

Statistical Analysis for Collision-free Boson Sampling.

PubMed

Huang, He-Liang; Zhong, Han-Sen; Li, Tan; Li, Feng-Guang; Fu, Xiang-Qun; Zhang, Shuo; Wang, Xiang; Bao, Wan-Su

2017-11-10

Boson sampling is strongly believed to be intractable for classical computers but solvable with photons in linear optics, which raises widespread concern as a rapid way to demonstrate the quantum supremacy. However, due to its solution is mathematically unverifiable, how to certify the experimental results becomes a major difficulty in the boson sampling experiment. Here, we develop a statistical analysis scheme to experimentally certify the collision-free boson sampling. Numerical simulations are performed to show the feasibility and practicability of our scheme, and the effects of realistic experimental conditions are also considered, demonstrating that our proposed scheme is experimentally friendly. Moreover, our broad approach is expected to be generally applied to investigate multi-particle coherent dynamics beyond the boson sampling.

DRAQ5 and Eosin (‘D&E’) as an Analog to Hematoxylin and Eosin for Rapid Fluorescence Histology of Fresh Tissues

PubMed Central

Elfer, Katherine N.; Sholl, Andrew B.; Wang, Mei; Tulman, David B.; Mandava, Sree H.; Lee, Benjamin R.; Brown, J. Quincy

2016-01-01

Real-time on-site histopathology review of biopsy tissues at the point-of-procedure has great potential for significant clinical value and improved patient care. For instance, on-site review can aid in rapid screening of diagnostic biopsies to reduce false-negative results, or in quantitative assessment of biospecimen quality to increase the efficacy of downstream laboratory and histopathology analysis. However, the only currently available rapid pathology method, frozen section analysis (FSA), is too time- and labor-intensive for use in screening large quantities of biopsy tissues and is too destructive for maximum tissue conservation in multiple small needle core biopsies. In this work we demonstrate the spectrally-compatible combination of the nuclear stain DRAQ5 and the anionic counterstain eosin as a dual-component fluorescent staining analog to hematoxylin and eosin intended for use on fresh, unsectioned tissues. Combined with optical sectioning fluorescence microscopy and pseudo-coloring algorithms, DRAQ5 and eosin (“D&E”) enables very fast, non-destructive psuedohistological imaging of tissues at the point-of-acquisition with minimal tissue handling and processing. D&E was validated against H&E on a one-to-one basis on formalin-fixed paraffin-embedded and frozen section tissues of various human organs using standard epi-fluorescence microscopy, demonstrating high fidelity of the staining mechanism as an H&E analog. The method was then applied to fresh, whole 18G renal needle core biopsies and large needle core prostate biospecimen biopsies using fluorescence structured illumination optical sectioning microscopy. We demonstrate the ability to obtain high-resolution histology-like images of unsectioned, fresh tissues similar to subsequent H&E staining of the tissue. The application of D&E does not interfere with subsequent standard-of-care H&E staining and imaging, preserving the integrity of the tissue for thorough downstream analysis. These results indicate that this dual-stain pseudocoloring method could provide a real-time histology-like image at the time of acquisition and valuable objective tissue analysis for the clinician at the time of service. PMID:27788264

Rapid phenotypic antimicrobial susceptibility testing using nanoliter arrays.

PubMed

Avesar, Jonathan; Rosenfeld, Dekel; Truman-Rosentsvit, Marianna; Ben-Arye, Tom; Geffen, Yuval; Bercovici, Moran; Levenberg, Shulamit

2017-07-18

Antibiotic resistance is a major global health concern that requires action across all sectors of society. In particular, to allow conservative and effective use of antibiotics clinical settings require better diagnostic tools that provide rapid determination of antimicrobial susceptibility. We present a method for rapid and scalable antimicrobial susceptibility testing using stationary nanoliter droplet arrays that is capable of delivering results in approximately half the time of conventional methods, allowing its results to be used the same working day. In addition, we present an algorithm for automated data analysis and a multiplexing system promoting practicality and translatability for clinical settings. We test the efficacy of our approach on numerous clinical isolates and demonstrate a 2-d reduction in diagnostic time when testing bacteria isolated directly from urine samples.

Getting something for nothing: Regeneration of peptide signals from apparently exhausted MALDI samples by “waterboarding"

USDA-ARS?s Scientific Manuscript database

An often cited advantage of MALDI-MS is the ability to archive and reuse sample plates after the initial analysis is complete. However, experience demonstrates that the peptide ion signals decay rapidly as the number of laser shots becomes large. Thus, the signal level obtainable from an archived sa...

Air Force Manufacturing Technology. Year 2000 Project Book

DTIC Science & Technology

2000-01-01

Electronic Warfare Component Manufacturing 13 National Center for Manufacturing Science 14 Product Research Market Analysis System 15 Electronics Acoustic...other agile organizations that can respond to rapidly changing market demands. Approach This program demonstrated and evaluated the advanced design...production worker contact with customers and suppliers; shopfloor identification of new technologies, markets , and products; and strategic planning to assure

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

PubMed Central

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

2013-01-01

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

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

PubMed

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

2013-01-01

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

Mechanical Stress Induces Biotic and Abiotic Stress Responses via a Novel cis-Element

PubMed Central

Walley, Justin W; Coughlan, Sean; Hudson, Matthew E; Covington, Michael F; Kaspi, Roy; Banu, Gopalan; Harmer, Stacey L; Dehesh, Katayoon

2007-01-01

Plants are continuously exposed to a myriad of abiotic and biotic stresses. However, the molecular mechanisms by which these stress signals are perceived and transduced are poorly understood. To begin to identify primary stress signal transduction components, we have focused on genes that respond rapidly (within 5 min) to stress signals. Because it has been hypothesized that detection of physical stress is a mechanism common to mounting a response against a broad range of environmental stresses, we have utilized mechanical wounding as the stress stimulus and performed whole genome microarray analysis of Arabidopsis thaliana leaf tissue. This led to the identification of a number of rapid wound responsive (RWR) genes. Comparison of RWR genes with published abiotic and biotic stress microarray datasets demonstrates a large overlap across a wide range of environmental stresses. Interestingly, RWR genes also exhibit a striking level and pattern of circadian regulation, with induced and repressed genes displaying antiphasic rhythms. Using bioinformatic analysis, we identified a novel motif overrepresented in the promoters of RWR genes, herein designated as the Rapid Stress Response Element (RSRE). We demonstrate in transgenic plants that multimerized RSREs are sufficient to confer a rapid response to both biotic and abiotic stresses in vivo, thereby establishing the functional involvement of this motif in primary transcriptional stress responses. Collectively, our data provide evidence for a novel cis-element that is distributed across the promoters of an array of diverse stress-responsive genes, poised to respond immediately and coordinately to stress signals. This structure suggests that plants may have a transcriptional network resembling the general stress signaling pathway in yeast and that the RSRE element may provide the key to this coordinate regulation. PMID:17953483

Rapid, Reliable Shape Setting of Superelastic Nitinol for Prototyping Robots

PubMed Central

Gilbert, Hunter B.; Webster, Robert J.

2016-01-01

Shape setting Nitinol tubes and wires in a typical laboratory setting for use in superelastic robots is challenging. Obtaining samples that remain superelastic and exhibit desired precurvatures currently requires many iterations, which is time consuming and consumes a substantial amount of Nitinol. To provide a more accurate and reliable method of shape setting, in this paper we propose an electrical technique that uses Joule heating to attain the necessary shape setting temperatures. The resulting high power heating prevents unintended aging of the material and yields consistent and accurate results for the rapid creation of prototypes. We present a complete algorithm and system together with an experimental analysis of temperature regulation. We experimentally validate the approach on Nitinol tubes that are shape set into planar curves. We also demonstrate the feasibility of creating general space curves by shape setting a helical tube. The system demonstrates a mean absolute temperature error of 10°C. PMID:27648473

Rapid, Reliable Shape Setting of Superelastic Nitinol for Prototyping Robots.

PubMed

Gilbert, Hunter B; Webster, Robert J

Shape setting Nitinol tubes and wires in a typical laboratory setting for use in superelastic robots is challenging. Obtaining samples that remain superelastic and exhibit desired precurvatures currently requires many iterations, which is time consuming and consumes a substantial amount of Nitinol. To provide a more accurate and reliable method of shape setting, in this paper we propose an electrical technique that uses Joule heating to attain the necessary shape setting temperatures. The resulting high power heating prevents unintended aging of the material and yields consistent and accurate results for the rapid creation of prototypes. We present a complete algorithm and system together with an experimental analysis of temperature regulation. We experimentally validate the approach on Nitinol tubes that are shape set into planar curves. We also demonstrate the feasibility of creating general space curves by shape setting a helical tube. The system demonstrates a mean absolute temperature error of 10°C.

TMV-Gate vectors: Gateway compatible tobacco mosaic virus based expression vectors for functional analysis of proteins

PubMed Central

Kagale, Sateesh; Uzuhashi, Shihomi; Wigness, Merek; Bender, Tricia; Yang, Wen; Borhan, M. Hossein; Rozwadowski, Kevin

2012-01-01

Plant viral expression vectors are advantageous for high-throughput functional characterization studies of genes due to their capability for rapid, high-level transient expression of proteins. We have constructed a series of tobacco mosaic virus (TMV) based vectors that are compatible with Gateway technology to enable rapid assembly of expression constructs and exploitation of ORFeome collections. In addition to the potential of producing recombinant protein at grams per kilogram FW of leaf tissue, these vectors facilitate either N- or C-terminal fusions to a broad series of epitope tag(s) and fluorescent proteins. We demonstrate the utility of these vectors in affinity purification, immunodetection and subcellular localisation studies. We also apply the vectors to characterize protein-protein interactions and demonstrate their utility in screening plant pathogen effectors. Given its broad utility in defining protein properties, this vector series will serve as a useful resource to expedite gene characterization efforts. PMID:23166857

A rapid, naked-eye detection of hypochlorite and bisulfite using a robust and highly-photostable indicator dye Quinaldine Red in aqueous medium

NASA Astrophysics Data System (ADS)

Dutta, Tanoy; Chandra, Falguni; Koner, Apurba L.

2018-02-01

A ;naked-eye; detection of health hazardous bisulfite (HSO3-) and hypochlorite (ClO-) using an indicator dye (Quinaldine Red, QR) in a wide range of pH is demonstrated. The molecule contains a quinoline moiety linked to an N,N-dimethylaniline moiety with a conjugated double bond. Treatment of QR with HSO3- and ClO-, in aqueous solution at near-neutral pH, resulted in a colorless product with high selectivity and sensitivity. The detection limit was 47.8 μM and 0.2 μM for HSO3- and ClO- respectively. However, ClO- was 50 times more sensitive and with 2 times faster response compared to HSO3-. The detail characterization and related analysis demonstrate the potential of QR for a rapid, robust and highly efficient colorimetric sensor for the practical applications to detect hypochlorite in water samples.

Evaluation of Flow-Injection Tandem Mass Spectrometry for Rapid and High-Throughput Quantitative Determination of B-Vitamins in Nutritional Supplements

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

Bhandari, Deepak; Van Berkel, Gary J

2012-01-01

The use of flow-injection electrospray ionization tandem mass spectrometry for rapid and high-throughput mass spectral analysis of selected B-vitamins, viz. B1, B2, B3, B5, and B6, in nutritional formulations was demonstrated. A simple and rapid (~5 min) in-tube sample preparation was performed by adding extraction solvent to a powdered sample aliquot followed by agitation, centrifugation, and filtration to recover an extract for analysis. Automated flow injection introduced 1 L of the extracts directly into the mass spectrometer ion source without chromatographic separation. Sample-to-sample analysis time was 60 s representing significant improvement over conventional liquid chromatography approaches which typically require 25-45more » min, and often require more significant sample preparation procedures. Quantitative capabilities of the flow-injection analysis were tested using the method of standard additions and NIST standard reference material (SRM 3280) multivitamin/multielement tablets. The quantity determined for each B-vitamin in SRM 3280 was within the statistical range provided for the respective certified values. The same sample preparation and analysis approach was also applied to two different commercial vitamin supplement tablets and proved to be successful in the quantification of the selected B-vitamins as evidenced by an agreement with the labels values and the results obtained using isotope dilution liquid chromatography/mass spectrometry.« less

Laser induced breakdown spectroscopy (LIBS) as a rapid tool for material analysis

NASA Astrophysics Data System (ADS)

Hussain, T.; Gondal, M. A.

2013-06-01

Laser induced breakdown spectroscopy (LIBS) is a novel technique for elemental analysis based on laser-generated plasma. In this technique, laser pulses are applied for ablation of the sample, resulting in the vaporization and ionization of sample in hot plasma which is finally analyzed by the spectrometer. The elements are identified by their unique spectral signatures. LIBS system was developed for elemental analysis of solid and liquid samples. The developed system was applied for qualitative as well as quantitative measurement of elemental concentration present in iron slag and open pit ore samples. The plasma was generated by focusing a pulsed Nd:YAG laser at 1064 nm on test samples to study the capabilities of LIBS as a rapid tool for material analysis. The concentrations of various elements of environmental significance such as cadmium, calcium, magnesium, chromium, manganese, titanium, barium, phosphorus, copper, iron, zinc etc., in these samples were determined. Optimal experimental conditions were evaluated for improving the sensitivity of developed LIBS system through parametric dependence study. The laser-induced breakdown spectroscopy (LIBS) results were compared with the results obtained using standard analytical technique such as inductively couple plasma emission spectroscopy (ICP). Limit of detection (LOD) of our LIBS system were also estimated for the above mentioned elements. This study demonstrates that LIBS could be highly appropriate for rapid online analysis of iron slag and open pit waste.

Simultaneous injection-effective mixing analysis of palladium.

PubMed

Teshima, Norio; Noguchi, Daisuke; Joichi, Yasutaka; Lenghor, Narong; Ohno, Noriko; Sakai, Tadao; Motomizu, Shoji

2010-01-01

A novel concept of simultaneous injection-effective mixing analysis (SIEMA) is proposed, and a SIEMA method applied to the spectrophotometric determination of palladium using a water-soluble chromogenic reagent has been demonstrated. The flow configuration of SIEMA is a hybrid format of flow injection analysis (FIA), sequential injection analysis (SIA) and multicommutation in flow-based analysis. Sample and reagent solutions are aspirated into each holding coil through each solenoid valve by a syringe pump, and then the zones are simultaneously dispensed (injected) into a mixing coil by reversed flow toward a detector through a confluence point. This results in effective mixing and rapid detection with low reagent consumption.

Droplet-based microfluidic analysis and screening of single plant cells.

PubMed

Yu, Ziyi; Boehm, Christian R; Hibberd, Julian M; Abell, Chris; Haseloff, Jim; Burgess, Steven J; Reyna-Llorens, Ivan

2018-01-01

Droplet-based microfluidics has been used to facilitate high-throughput analysis of individual prokaryote and mammalian cells. However, there is a scarcity of similar workflows applicable to rapid phenotyping of plant systems where phenotyping analyses typically are time-consuming and low-throughput. We report on-chip encapsulation and analysis of protoplasts isolated from the emergent plant model Marchantia polymorpha at processing rates of >100,000 cells per hour. We use our microfluidic system to quantify the stochastic properties of a heat-inducible promoter across a population of transgenic protoplasts to demonstrate its potential for assessing gene expression activity in response to environmental conditions. We further demonstrate on-chip sorting of droplets containing YFP-expressing protoplasts from wild type cells using dielectrophoresis force. This work opens the door to droplet-based microfluidic analysis of plant cells for applications ranging from high-throughput characterisation of DNA parts to single-cell genomics to selection of rare plant phenotypes.

Validation of a Rapid Bacteria Endospore Enumeration System for Planetary Protection Application

NASA Astrophysics Data System (ADS)

Chen, Fei; Kern, Roger; Kazarians, Gayane; Venkateswaran, Kasthuri

NASA monitors spacecraft surfaces to assure that the presence of bacterial endospores meets strict criteria at launch, to minimize the risk of inadvertent contamination of the surface of Mars. Currently, the only approved method for enumerating the spores is a culture based assay that requires three days to produce results. In order to meet the demanding schedules of spacecraft assembly, a more rapid spore detection assay is being considered as an alternate method to the NASA standard culture-based assay. The Millipore Rapid Microbiology Detection System (RMDS) has been used successfully for rapid bioburden enumeration in the pharmaceutical and food industries. The RMDS is rapid and simple, shows high sensitivity (to 1 colony forming unit [CFU]/sample), and correlates well with traditional culture-based methods. It combines membrane filtration, adenosine triphosphate (ATP) bioluminescence chemistry, and image analysis based on photon detection with a Charge Coupled Device (CCD) camera. In this study, we have optimized the assay conditions and evaluated the use of the RMDS as a rapid spore detection tool for NASA applications. In order to select for spores, the samples were subjected to a heat shock step before proceeding with the RMDS incubation protocol. Seven species of Bacillus (nine strains) that have been repeatedly isolated from clean room environments were assayed. All strains were detected by the RMDS in 5 hours and these assay times were repeatedly demonstrated along with low image background noise. Validation experiments to compare the Rapid Sore Assay (RSA) and NASA standard assay (NSA) were also performed. The evaluation criteria were modeled after the FDA Guideline of Process Validation, and Analytical Test Methods. This body of research demonstrates that the Rapid Spore Assay (RSA) is quick, and of equivalent sensitivity to the NASA standard assay, potentially reducing the assay time for bacterial endospores from over 72 hours to less than 8 hours. Accordingly, JPL has produced a report recommending that NASA adopt the RSA method as a suitable alternative to the NASA standard assay.

Gold nanoparticle-sensitized quartz crystal microbalance sensor for rapid and highly selective determination of Cu(II) ions.

PubMed

Jin, Yulong; Huang, Yanyan; Liu, Guoquan; Zhao, Rui

2013-09-21

A novel quartz crystal microbalance (QCM) sensor for rapid, highly selective and sensitive detection of copper ions was developed. As a signal amplifier, gold nanoparticles (Au NPs) were self-assembled onto the surface of the sensor. A simple dip-and-dry method enabled the whole detection procedure to be accomplished within 20 min. High selectivity of the sensor towards copper ions is demonstrated by both individual and coexisting assays with interference ions. This gold nanoparticle mediated amplification allowed a detection limit down to 3.1 μM. Together with good repeatability and regeneration, the QCM sensor was also applied to the analysis of copper contamination in drinking water. This work provides a flexible method for fabricating QCM sensors for the analysis of important small molecules in environmental and biological samples.

Label-free and amplified quantitation of proteins in complex mixtures using diffractive optics technology.

PubMed

Cleverley, Steve; Chen, Irene; Houle, Jean-François

2010-01-15

Immunoaffinity approaches remain invaluable tools for characterization and quantitation of biopolymers. Their application in separation science is often limited due to the challenges of immunoassay development. Typical end-point immunoassays require time consuming and labor-intensive approaches for optimization. Real-time label-free analysis using diffractive optics technology (dot) helps guide a very effective iterative process for rapid immunoassay development. Both label-free and amplified approaches can be used throughout feasibility testing and ultimately in the final assay, providing a robust platform for biopolymer analysis over a very broad dynamic range. We demonstrate the use of dot in rapidly developing assays for quantitating (1) human IgG in complex media, (2) a fusion protein in production media and (3) protein A contamination in purified immunoglobulin preparations. 2009 Elsevier B.V. All rights reserved.

OpenNFT: An open-source Python/Matlab framework for real-time fMRI neurofeedback training based on activity, connectivity and multivariate pattern analysis.

PubMed

Koush, Yury; Ashburner, John; Prilepin, Evgeny; Sladky, Ronald; Zeidman, Peter; Bibikov, Sergei; Scharnowski, Frank; Nikonorov, Artem; De Ville, Dimitri Van

2017-08-01

Neurofeedback based on real-time functional magnetic resonance imaging (rt-fMRI) is a novel and rapidly developing research field. It allows for training of voluntary control over localized brain activity and connectivity and has demonstrated promising clinical applications. Because of the rapid technical developments of MRI techniques and the availability of high-performance computing, new methodological advances in rt-fMRI neurofeedback become possible. Here we outline the core components of a novel open-source neurofeedback framework, termed Open NeuroFeedback Training (OpenNFT), which efficiently integrates these new developments. This framework is implemented using Python and Matlab source code to allow for diverse functionality, high modularity, and rapid extendibility of the software depending on the user's needs. In addition, it provides an easy interface to the functionality of Statistical Parametric Mapping (SPM) that is also open-source and one of the most widely used fMRI data analysis software. We demonstrate the functionality of our new framework by describing case studies that include neurofeedback protocols based on brain activity levels, effective connectivity models, and pattern classification approaches. This open-source initiative provides a suitable framework to actively engage in the development of novel neurofeedback approaches, so that local methodological developments can be easily made accessible to a wider range of users. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Rapid wide-field Mueller matrix polarimetry imaging based on four photoelastic modulators with no moving parts.

PubMed

Alali, Sanaz; Gribble, Adam; Vitkin, I Alex

2016-03-01

A new polarimetry method is demonstrated to image the entire Mueller matrix of a turbid sample using four photoelastic modulators (PEMs) and a charge coupled device (CCD) camera, with no moving parts. Accurate wide-field imaging is enabled with a field-programmable gate array (FPGA) optical gating technique and an evolutionary algorithm (EA) that optimizes imaging times. This technique accurately and rapidly measured the Mueller matrices of air, polarization elements, and turbid phantoms. The system should prove advantageous for Mueller matrix analysis of turbid samples (e.g., biological tissues) over large fields of view, in less than a second.

Fabricated nanogap-rich plasmonic nanostructures through an optothermal surface bubble in a droplet.

PubMed

Karim, Farzia; Vasquez, Erick S; Zhao, Chenglong

2018-01-15

A rapid and cost-effective method for the fabrication of nanogap-rich structures is demonstrated in this Letter. The method utilizes the Marangoni convection around an optothermal surface bubble inside a liquid droplet with a nanoliter volume. The liquid droplet containing metallic nanoparticles reduces the sample consumption and confines the liquid flow. The optothermal surface bubble creates a strong convective flow that allows for the rapid deposition of the metallic nanoparticles to form nanogap-rich structures on any substrate under ambient conditions. This method will enable a broad range of applications such as biosensing, environmental analysis, and nonlinear optics.

A Rapid and Efficient Method for Evaluation of Suspect Testimony: Palynological Scanning.

PubMed

Wiltshire, Patricia E J; Hawksworth, David L; Edwards, Kevin J

2015-11-01

A rapid method for evaluating suspect testimony is valuable at any stage in an inquiry and can result in a change of direction in an investigation. Rape cases, in particular, can present problems where a defendant renders DNA analysis redundant by claiming that the claimant consented to have sexual relations. Forensic palynology is valuable in confirming or eliminating locations as being crime scenes, thus checking the testimony of both parties. In contrast to some forensic disciplines, forensic palynology can provide critical information without time-consuming full analysis. Two cases are described where the palynological assemblages from comparator samples of pertinent places were compared with those obtained from clothing of claimants and defendants. The results of rapid microscopical scanning of relevant preparations led to early confessions, thus obviating the need for costly analyses and protracted court proceedings. A third case demonstrates the unbiased nature of this technique where a man, although innocent of any offense, lied about having visited the crime scene for fear of prosecution. This highlights the need for sensitive policing in claims of rape. © 2015 American Academy of Forensic Sciences.

Rapid detection of α-thalassaemia alleles of --(SEA)/, -α(3.7)/ and -α(4.2)/ using a dual labelling, self-quenching hybridization probe/melting curve analysis.

PubMed

Gao, Lan; Liu, Yanhui; Sun, Manna; Zhao, Ying; Xie, Rungui; He, Yi; Xu, Wanfang; Liu, Jianxin; Lin, Yangyang; Lou, Jiwu

2015-12-01

The aim of the study was to set up an alternative automatic molecular diagnostic method for deletional α-thalassaemia mutations without gel electrophoresis. Based on the sequence variation within the two Z boxes and melting curve analysis of dually labelled probes, a real-time PCR assay was developed and validated for the rapid detection of major α-genotypes (--(SEA)/αα, --(SEA)/-α(3.7), --(SEA)/-α(4.2), --(SEA)/--(SEA), -α(3.7)/-α(3.7) and -α(4.2)/-α(4.2)). Samples with the -α(3.7)/-α(3.7), -α(4.2)/-α(4.2), --(SEA)/αα, --(SEA)/-α(3.7), --(SEA)/-α(4.2), and --(SEA)/--(SEA) genotypes could be clearly distinguished. The accuracy of this technique for these samples was 100% sensitivity and specificity. This technique is rapid and reliable, demonstrating feasibility for use in large-scale population screening and prenatal diagnosis of deletional Hb H disease and Hb Bart's hydrops fetalis. Copyright © 2015 Elsevier Ltd. All rights reserved.

Rapid determination of trace copper in animal feed based on micro-plate colorimetric reaction and statistical partitioning correction.

PubMed

Niu, Yiming; Wang, Jiayi; Zhang, Chi; Chen, Yiqiang

2017-04-15

The objective of this study was to develop a micro-plate based colorimetric assay for rapid and high-throughput detection of copper in animal feed. Copper ion in animal feed was extracted by trichloroacetic acid solution and reduced to cuprous ion by hydroxylamine. The cuprous ion can chelate with 2,2'-bicinchoninic acid to form a Cu-BCA complex which was detected with high sensitivity by micro-plate reader at 354nm. The whole assay procedure can be completed within 20min. To eliminate matrix interference, a statistical partitioning correction approach was proposed, which makes the detection of copper in complex samples possible. The limit of detection was 0.035μg/mL and the detection range was 0.1-10μg/mL of copper in buffer solution. Actual sample analysis indicated that this colorimetric assay produced results consistent with atomic absorption spectrometry analysis. These results demonstrated that the developed assay can be used for rapid determination of copper in animal feed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Assessment of the diagnostic value of a urinary adipsin rapid strip test for pre-eclampsia: A prospective multicenter study.

PubMed

Peng, Bing; Zhang, Li; Yan, Jianying; Qi, Hongbo; Zhang, Weiyuan; Fan, Ling; Hu, Yayi; Lin, Li; Li, Xiaotian; Hu, Rong; Xie, Lan; Zhang, Jianping; Wu, Yanqiao; Li, Li; Zhou, Rong

2017-01-01

The purpose of the present study was to evaluate the clinical value of the rapid strip test of urinary adipsin for the quick diagnosis of pre-eclampsia. In a multicenter diagnostic test study, we studied the diagnostic accuracy of the rapid strip test of urinary adipsin in women presenting with pre-eclampsia. A total of 204 pre-eclampsia patients and 254 healthy pregnant women were recruited for this study, respectively. The rapid strip test of urinary adipsin was used to detect the adipsin in the urine of each patient. The diagnostic value of the rapid strip test of urinary adipsin for pre-eclampsia was demonstrated by its high sensitivity and specificity (95.10% and 97.64%, respectively). The diagnostic accuracy was 96.51%. The consistency analysis showed that the kappa value was 0.93 compared with the gold standard diagnosis of pre-eclampsia. The rapid strip test of urinary adipsin is a non-invasive test for the diagnosis of pre-eclampsia with high sensitivity and specificity. It could help the quick diagnosis of pre-eclampsia in clinical practice greatly. © 2016 Japan Society of Obstetrics and Gynecology.

Achieving Dramatic School Improvement: An Exploratory Study. A Cross-Site Analysis from the Evaluation of Comprehensive School Reform Program Implementation and Outcomes Study

ERIC Educational Resources Information Center

Aladjem, Daniel K.; Birman, Beatrice F.; Orland, Martin; Harr-Robins, Jenifer; Heredia, Alberto; Parrish, Thomas B.; Ruffini, Stephen J.

2010-01-01

This exploratory study describes approaches to improving schools through retrospective, in-depth qualitative case studies. To select schools to be examined, the authors sought to identify Comprehensive School Reform (CSR) schools demonstrating two distinctive patterns of improved student achievement between 2000 and 2005, rapid-improvement (i.e.,…

Quantitative analysis of NMR spectra with chemometrics

NASA Astrophysics Data System (ADS)

Winning, H.; Larsen, F. H.; Bro, R.; Engelsen, S. B.

2008-01-01

The number of applications of chemometrics to series of NMR spectra is rapidly increasing due to an emerging interest for quantitative NMR spectroscopy e.g. in the pharmaceutical and food industries. This paper gives an analysis of advantages and limitations of applying the two most common chemometric procedures, Principal Component Analysis (PCA) and Multivariate Curve Resolution (MCR), to a designed set of 231 simple alcohol mixture (propanol, butanol and pentanol) 1H 400 MHz spectra. The study clearly demonstrates that the major advantage of chemometrics is the visualisation of larger data structures which adds a new exploratory dimension to NMR research. While robustness and powerful data visualisation and exploration are the main qualities of the PCA method, the study demonstrates that the bilinear MCR method is an even more powerful method for resolving pure component NMR spectra from mixtures when certain conditions are met.

Sex differences in objective measures of sleep in post-traumatic stress disorder and healthy control subjects.

PubMed

Richards, Anne; Metzler, Thomas J; Ruoff, Leslie M; Inslicht, Sabra S; Rao, Madhu; Talbot, Lisa S; Neylan, Thomas C

2013-12-01

A growing literature shows prominent sex effects for risk for post-traumatic stress disorder and associated medical comorbid burden. Previous research indicates that post-traumatic stress disorder is associated with reduced slow wave sleep, which may have implications for overall health, and abnormalities in rapid eye movement sleep, which have been implicated in specific post-traumatic stress disorder symptoms, but most research has been conducted in male subjects. We therefore sought to compare objective measures of sleep in male and female post-traumatic stress disorder subjects with age- and sex-matched control subjects. We used a cross-sectional, 2 × 2 design (post-traumatic stress disorder/control × female/male) involving83 medically healthy, non-medicated adults aged 19-39 years in the inpatient sleep laboratory. Visual electroencephalographic analysis demonstrated that post-traumatic stress disorder was associated with lower slow wave sleep duration (F(3,82)  = 7.63, P = 0.007) and slow wave sleep percentage (F(3,82)  = 6.11, P = 0.016). There was also a group × sex interaction effect for rapid eye movement sleep duration (F(3,82)  = 4.08, P = 0.047) and rapid eye movement sleep percentage (F(3,82)  = 4.30, P = 0.041), explained by greater rapid eye movement sleep in post-traumatic stress disorder females compared to control females, a difference not seen in male subjects. Quantitative electroencephalography analysis demonstrated that post-traumatic stress disorder was associated with lower energy in the delta spectrum (F(3,82)  = 6.79, P = 0.011) in non-rapid eye movement sleep. Slow wave sleep and delta findings were more pronounced in males. Removal of post-traumatic stress disorder subjects with comorbid major depressive disorder, who had greater post-traumatic stress disorder severity, strengthened delta effects but reduced rapid eye movement effects to non-significance. These findings support previous evidence that post-traumatic stress disorder is associated with impairment in the homeostatic function of sleep, especially in men with the disorder. These findings suggest that group × sex interaction effects on rapid eye movement may occur with more severe post-traumatic stress disorder or with post-traumatic stress disorder comorbid with major depressive disorder. © 2013 European Sleep Research Society.

Rapid extraction and assay of uranium from environmental surface samples

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

Barrett, Christopher A.; Chouyyok, Wilaiwan; Speakman, Robert J.

Extraction methods enabling faster removal and concentration of uranium compounds for improved trace and low-level assay are demonstrated for standard surface sampling material in support of nuclear safeguards efforts, health monitoring, and other nuclear analysis applications. A key problem with the existing surface sampling swipes is the requirement for complete digestion of sample and sampling matrix. This is a time-consuming and labour-intensive process that limits laboratory throughput, elevates costs, and increases background levels. Various extraction methods are explored for their potential to quickly and efficiently remove different chemical forms of uranium from standard surface sampling material. A combination of carbonatemore » and peroxide solutions is shown to give the most rapid and complete form of uranyl compound extraction and dissolution. This rapid extraction process is demonstrated to be compatible with standard inductive coupled plasma mass spectrometry methods for uranium isotopic assay as well as screening techniques such as x-ray fluorescence. The general approach described has application beyond uranium to other analytes of nuclear forensic interest (e.g., rare earth elements and plutonium) as well as heavy metals for environmental and industrial hygiene monitoring.« less

Rapid, all-optical crystal orientation imaging of two-dimensional transition metal dichalcogenide monolayers

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

David, Sabrina N.; Zhai, Yao; van der Zande, Arend M.

Two-dimensional (2D) atomic materials such as graphene and transition metal dichalcogenides (TMDCs) have attracted significant research and industrial interest for their electronic, optical, mechanical, and thermal properties. While large-area crystal growth techniques such as chemical vapor deposition have been demonstrated, the presence of grain boundaries and orientation of grains arising in such growths substantially affect the physical properties of the materials. There is currently no scalable characterization method for determining these boundaries and orientations over a large sample area. We here present a second-harmonic generation based microscopy technique for rapidly mapping grain orientations and boundaries of 2D TMDCs. We experimentallymore » demonstrate the capability to map large samples to an angular resolution of ±1° with minimal sample preparation and without involved analysis. A direct comparison of the all-optical grain orientation maps against results obtained by diffraction-filtered dark-field transmission electron microscopy plus selected-area electron diffraction on identical TMDC samples is provided. This rapid and accurate tool should enable large-area characterization of TMDC samples for expedited studies of grain boundary effects and the efficient characterization of industrial-scale production techniques.« less

Reliable clinical serum analysis with reusable electrochemical sensor: Toward point-of-care measurement of the antipsychotic medication clozapine.

PubMed

Kang, Mijeong; Kim, Eunkyoung; Winkler, Thomas E; Banis, George; Liu, Yi; Kitchen, Christopher A; Kelly, Deanna L; Ghodssi, Reza; Payne, Gregory F

2017-09-15

Clozapine is one of the most promising medications for managing schizophrenia but it is under-utilized because of the challenges of maintaining serum levels in a safe therapeutic range (1-3μM). Timely measurement of serum clozapine levels has been identified as a barrier to the broader use of clozapine, which is however challenging due to the complexity of serum samples. We demonstrate a robust and reusable electrochemical sensor with graphene-chitosan composite for rapidly measuring serum levels of clozapine. Our electrochemical measurements in clinical serum from clozapine-treated and clozapine-untreated schizophrenia groups are well correlated to centralized laboratory analysis for the readily detected uric acid and for the clozapine which is present at 100-fold lower concentration. The benefits of our electrochemical measurement approach for serum clozapine monitoring are: (i) rapid measurement (≈20min) without serum pretreatment; (ii) appropriate selectivity and sensitivity (limit of detection 0.7μM); (iii) reusability of an electrode over several weeks; and (iv) rapid reliability testing to detect common error-causing problems. This simple and rapid electrochemical approach for serum clozapine measurements should provide clinicians with the timely point-of-care information required to adjust dosages and personalize the management of schizophrenia. Copyright © 2017 Elsevier B.V. All rights reserved.

Rapid screening of 35 new psychoactive substances by ion mobility spectrometry (IMS) and direct analysis in real time (DART) coupled to quadrupole time-of-flight mass spectrometry (QTOF-MS).

PubMed

Gwak, Seongshin; Almirall, Jose R

2015-10-01

The recent propagation of new psychoactive substances (NPS) has led to the development of new techniques for the rapid characterization of controlled substances in this category. A commercial bench-top ion mobility spectrometer (IMS) with a (63) Ni ionization source and a direct analysis in real time (DART) coupled to quadrupole time-of-flight (QTOF) were used for the rapid characterization of 35 NPS. The advantages of these techniques are fast response, ease of operation, and minimal sample preparation. The characteristic reduced mobilities of each substance are reported as are the mass spectra of the 35 compounds. The acquired product ion scan mass spectra were also compared to a library database constructed by QTOF with a electrospray ionization (ESI) source and showed a consistent relative abundance for each peak over time. A total of four seized drug samples provided by the local forensic laboratory were analyzed in order to demonstrate the utility of this approach. The results of this study suggest that both IMS and DART-QTOF are promising alternatives for the rapid screening and characterization of these new psychoactive substances. Copyright © 2015 John Wiley & Sons, Ltd.

Rapid prototyping of nanofluidic systems using size-reduced electrospun nanofibers for biomolecular analysis.

PubMed

Park, Seung-Min; Huh, Yun Suk; Szeto, Kylan; Joe, Daniel J; Kameoka, Jun; Coates, Geoffrey W; Edel, Joshua B; Erickson, David; Craighead, Harold G

2010-11-05

Biomolecular transport in nanofluidic confinement offers various means to investigate the behavior of biomolecules in their native aqueous environments, and to develop tools for diverse single-molecule manipulations. Recently, a number of simple nanofluidic fabrication techniques has been demonstrated that utilize electrospun nanofibers as a backbone structure. These techniques are limited by the arbitrary dimension of the resulting nanochannels due to the random nature of electrospinning. Here, a new method for fabricating nanofluidic systems from size-reduced electrospun nanofibers is reported and demonstrated. As it is demonstrated, this method uses the scanned electrospinning technique for generation of oriented sacrificial nanofibers and exposes these nanofibers to harsh, but isotropic etching/heating environments to reduce their cross-sectional dimension. The creation of various nanofluidic systems as small as 20 nm is demonstrated, and practical examples of single biomolecular handling, such as DNA elongation in nanochannels and fluorescence correlation spectroscopic analysis of biomolecules passing through nanochannels, are provided.

Rapid screening and quantification of residual pesticides and illegal adulterants in red wine by direct analysis in real time mass spectrometry.

PubMed

Guo, Tianyang; Fang, Pingping; Jiang, Juanjuan; Zhang, Feng; Yong, Wei; Liu, Jiahui; Dong, Yiyang

2016-11-04

A rapid method to screen and quantify multi-class analytic targets in red wine has been developed by direct analysis in real time (DART) coupled with triple quadruple tandem mass spectrometry (QqQ-MS). A modified QuEChERS (Quick, Easy, Cheap, Effective, Rugged, and Safe) procedure was used for increasing analytical speed and reducing matrix effect, and the multiple reaction monitoring (MRM) in DART-MS/MS ensured accurate analysis. One bottle of wine containing 50 pesticides and 12 adulterants, i.e., preservatives, antioxidant, sweeteners, and azo dyes, could be totally determined less than 12min. This method exhibited proper linearity (R 2 ≥0.99) in the range of 1-1000ng/mL for pesticides and 10-5000ng/mL for adulterants. The limits of detection (LODs) were obtained in a 0.5-50ng/mL range for pesticides and 5-50ng/mL range for adulterants, and the limits of quantification (LOQs) were in a 1-100ng/mL range for pesticides and 10-250ng/mL range for adulterants. Three spiked levels for each analyte in wine were evaluated, and the recoveries were in a scope of 75-120%. The results demonstrated DART-MS/MS was a rapid and simple method, and could be applied to rapid analyze residual pesticides and illegal adulterants in a large quantities of red wine. Copyright © 2016 Elsevier B.V. All rights reserved.

Rapid characterization of transgenic and non-transgenic soybean oils by chemometric methods using NIR spectroscopy

NASA Astrophysics Data System (ADS)

Luna, Aderval S.; da Silva, Arnaldo P.; Pinho, Jéssica S. A.; Ferré, Joan; Boqué, Ricard

Near infrared (NIR) spectroscopy and multivariate classification were applied to discriminate soybean oil samples into non-transgenic and transgenic. Principal Component Analysis (PCA) was applied to extract relevant features from the spectral data and to remove the anomalous samples. The best results were obtained when with Support Vectors Machine-Discriminant Analysis (SVM-DA) and Partial Least Squares-Discriminant Analysis (PLS-DA) after mean centering plus multiplicative scatter correction. For SVM-DA the percentage of successful classification was 100% for the training group and 100% and 90% in validation group for non transgenic and transgenic soybean oil samples respectively. For PLS-DA the percentage of successful classification was 95% and 100% in training group for non transgenic and transgenic soybean oil samples respectively and 100% and 80% in validation group for non transgenic and transgenic respectively. The results demonstrate that NIR spectroscopy can provide a rapid, nondestructive and reliable method to distinguish non-transgenic and transgenic soybean oils.

Application of a voltammetric electronic tongue and near infrared spectroscopy for a rapid umami taste assessment.

PubMed

Bagnasco, Lucia; Cosulich, M Elisabetta; Speranza, Giovanna; Medini, Luca; Oliveri, Paolo; Lanteri, Silvia

2014-08-15

The relationships between sensory attribute and analytical measurements, performed by electronic tongue (ET) and near-infrared spectroscopy (NIRS), were investigated in order to develop a rapid method for the assessment of umami taste. Commercially available umami products and some aminoacids were submitted to sensory analysis. Results were analysed in comparison with the outcomes of analytical measurements. Multivariate exploratory analysis was performed by principal component analysis (PCA). Calibration models for prediction of the umami taste on the basis of ET and NIR signals were obtained using partial least squares (PLS) regression. Different approaches for merging data from the two different analytical instruments were considered. Both of the techniques demonstrated to provide information related with umami taste. In particular, ET signals showed the higher correlation with umami attribute. Data fusion was found to be slightly beneficial - not so significantly as to justify the coupled use of the two analytical techniques. Copyright © 2014 Elsevier Ltd. All rights reserved.

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.

A real time metabolomic profiling approach to detecting fish fraud using rapid evaporative ionisation mass spectrometry.

PubMed

Black, Connor; Chevallier, Olivier P; Haughey, Simon A; Balog, Julia; Stead, Sara; Pringle, Steven D; Riina, Maria V; Martucci, Francesca; Acutis, Pier L; Morris, Mike; Nikolopoulos, Dimitrios S; Takats, Zoltan; Elliott, Christopher T

2017-01-01

Fish fraud detection is mainly carried out using a genomic profiling approach requiring long and complex sample preparations and assay running times. Rapid evaporative ionisation mass spectrometry (REIMS) can circumvent these issues without sacrificing a loss in the quality of results. To demonstrate that REIMS can be used as a fast profiling technique capable of achieving accurate species identification without the need for any sample preparation. Additionally, we wanted to demonstrate that other aspects of fish fraud other than speciation are detectable using REIMS. 478 samples of five different white fish species were subjected to REIMS analysis using an electrosurgical knife. Each sample was cut 8-12 times with each one lasting 3-5 s and chemometric models were generated based on the mass range m/z 600-950 of each sample. The identification of 99 validation samples provided a 98.99% correct classification in which species identification was obtained near-instantaneously (≈ 2 s) unlike any other form of food fraud analysis. Significant time comparisons between REIMS and polymerase chain reaction (PCR) were observed when analysing 6 mislabelled samples demonstrating how REIMS can be used as a complimentary technique to detect fish fraud. Additionally, we have demonstrated that the catch method of fish products is capable of detection using REIMS, a concept never previously reported. REIMS has been proven to be an innovative technique to help aid the detection of fish fraud and has the potential to be utilised by fisheries to conduct their own quality control (QC) checks for fast accurate results.

Enhancing Next-Generation Sequencing-Guided Cancer Care Through Cognitive Computing.

PubMed

Patel, Nirali M; Michelini, Vanessa V; Snell, Jeff M; Balu, Saianand; Hoyle, Alan P; Parker, Joel S; Hayward, Michele C; Eberhard, David A; Salazar, Ashley H; McNeillie, Patrick; Xu, Jia; Huettner, Claudia S; Koyama, Takahiko; Utro, Filippo; Rhrissorrakrai, Kahn; Norel, Raquel; Bilal, Erhan; Royyuru, Ajay; Parida, Laxmi; Earp, H Shelton; Grilley-Olson, Juneko E; Hayes, D Neil; Harvey, Stephen J; Sharpless, Norman E; Kim, William Y

2018-02-01

Using next-generation sequencing (NGS) to guide cancer therapy has created challenges in analyzing and reporting large volumes of genomic data to patients and caregivers. Specifically, providing current, accurate information on newly approved therapies and open clinical trials requires considerable manual curation performed mainly by human "molecular tumor boards" (MTBs). The purpose of this study was to determine the utility of cognitive computing as performed by Watson for Genomics (WfG) compared with a human MTB. One thousand eighteen patient cases that previously underwent targeted exon sequencing at the University of North Carolina (UNC) and subsequent analysis by the UNCseq informatics pipeline and the UNC MTB between November 7, 2011, and May 12, 2015, were analyzed with WfG, a cognitive computing technology for genomic analysis. Using a WfG-curated actionable gene list, we identified additional genomic events of potential significance (not discovered by traditional MTB curation) in 323 (32%) patients. The majority of these additional genomic events were considered actionable based upon their ability to qualify patients for biomarker-selected clinical trials. Indeed, the opening of a relevant clinical trial within 1 month prior to WfG analysis provided the rationale for identification of a new actionable event in nearly a quarter of the 323 patients. This automated analysis took <3 minutes per case. These results demonstrate that the interpretation and actionability of somatic NGS results are evolving too rapidly to rely solely on human curation. Molecular tumor boards empowered by cognitive computing could potentially improve patient care by providing a rapid, comprehensive approach for data analysis and consideration of up-to-date availability of clinical trials. The results of this study demonstrate that the interpretation and actionability of somatic next-generation sequencing results are evolving too rapidly to rely solely on human curation. Molecular tumor boards empowered by cognitive computing can significantly improve patient care by providing a fast, cost-effective, and comprehensive approach for data analysis in the delivery of precision medicine. Patients and physicians who are considering enrollment in clinical trials may benefit from the support of such tools applied to genomic data. © AlphaMed Press 2017.

Predictors of rapid spontaneous resolution of acute subdural hematoma.

PubMed

Fujimoto, Kenji; Otsuka, Tadahiro; Yoshizato, Kimio; Kuratsu, Jun-ichi

2014-03-01

Acute subdural hematoma (ASDH) usually requires emergency surgical decompression, but rare cases exhibit rapid spontaneous resolution. The aim of this retrospective study was to identify factors predictive of spontaneous ASDH resolution. A total of 366 consecutive patients with ASDH treated between January 2006 and September 2012 were identified in our hospital database. Patients with ASDH clot thickness >10mm in the frontoparietotemporal region and showing a midline shift >10mm on the initial computed tomography (CT) scan were divided into two groups according to subsequent spontaneous resolution. Univariate and multivariate logistic regression analyses were used to identify factors predictive of rapid spontaneous ASDH resolution. Fifty-six ASDH patients met study criteria and 18 demonstrated rapid spontaneous resolution (32%). Majority of these patients were not operated because of poor prognosis/condition and in accordance to family wishes. Univariate analysis revealed significant differences in use of antiplatelet agents before head injury and in the incidence of a low-density band between the hematoma and inner wall of the skull bone on the initial CT. Use of antiplatelet agents before head injury (OR 19.6, 95% CI 1.5-260.1, p=0.02) and the low-density band on CT images (OR 40.3, 95% CI 3.1-520.2, p=0.005) were identified as independent predictive factors by multivariate analysis. Our analysis suggested that use of antiplatelet agents before head injury and a low-density band between the hematoma and inner skull bone on CT images (indicative of cerebrospinal fluid infusion into the subdural space) increase the probability of rapid spontaneous resolution. Copyright © 2013 Elsevier B.V. All rights reserved.

Laser-induced breakdown spectroscopy in industrial and security applications

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

Bol'shakov, Alexander A.; Yoo, Jong H.; Liu Chunyi

2010-05-01

Laser-induced breakdown spectroscopy (LIBS) offers rapid, localized chemical analysis of solid or liquid materials with high spatial resolution in lateral and depth profiling, without the need for sample preparation. Principal component analysis and partial least squares algorithms were applied to identify a variety of complex organic and inorganic samples. This work illustrates how LIBS analyzers can answer a multitude of real-world needs for rapid analysis, such as determination of lead in paint and children's toys, analysis of electronic and solder materials, quality control of fiberglass panels, discrimination of coffee beans from different vendors, and identification of generic versus brand-name drugs.more » Lateral and depth profiling was performed on children's toys and paint layers. Traditional one-element calibration or multivariate chemometric procedures were applied for elemental quantification, from single laser shot determination of metal traces at {approx}10 {mu}g/g to determination of halogens at 90 {mu}g/g using 50-shot spectral accumulation. The effectiveness of LIBS for security applications was demonstrated in the field by testing the 50-m standoff LIBS rasterizing detector.« less

Direct analysis of six antibiotics in wastewater samples using rapid high-performance liquid chromatography coupled with diode array detector: a chemometric study towards green analytical chemistry.

PubMed

Vosough, Maryam; Rashvand, Masoumeh; Esfahani, Hadi M; Kargosha, Kazem; Salemi, Amir

2015-04-01

In this work, a rapid HPLC-DAD method has been developed for the analysis of six antibiotics (amoxicillin, metronidazole, sulfamethoxazole, ofloxacine, sulfadiazine and sulfamerazine) in the sewage treatment plant influent and effluent samples. Decreasing the chromatographic run time to less than 4 min as well as lowering the cost per analysis, were achieved through direct injection of the samples into the HPLC system followed by chemometric analysis. The problem of the complete separation of the analytes from each other and/or from the matrix ingredients was resolved as a posteriori. The performance of MCR/ALS and U-PLS/RBL, as second-order algorithms, was studied and comparable results were obtained from implication of these modeling methods. It was demonstrated that the proposed methods could be used promisingly as green analytical strategies for detection and quantification of the targeted pollutants in wastewater samples while avoiding the more complicated high cost instrumentations. Copyright © 2014 Elsevier B.V. All rights reserved.

Androgen Receptor Functional Analyses by High Throughput Imaging: Determination of Ligand, Cell Cycle, and Mutation-Specific Effects

PubMed Central

Szafran, Adam T.; Szwarc, Maria; Marcelli, Marco; Mancini, Michael A.

2008-01-01

Background Understanding how androgen receptor (AR) function is modulated by exposure to steroids, growth factors or small molecules can have important mechanistic implications for AR-related disease therapies (e.g., prostate cancer, androgen insensitivity syndrome, AIS), and in the analysis of environmental endocrine disruptors. Methodology/Principal Findings We report the development of a high throughput (HT) image-based assay that quantifies AR subcellular and subnuclear distribution, and transcriptional reporter gene activity on a cell-by-cell basis. Furthermore, simultaneous analysis of DNA content allowed determination of cell cycle position and permitted the analysis of cell cycle dependent changes in AR function in unsynchronized cell populations. Assay quality for EC50 coefficients of variation were 5–24%, with Z' values reaching 0.91. This was achieved by the selective analysis of cells expressing physiological levels of AR, important because minor over-expression resulted in elevated nuclear speckling and decreased transcriptional reporter gene activity. A small screen of AR-binding ligands, including known agonists, antagonists, and endocrine disruptors, demonstrated that nuclear translocation and nuclear “speckling” were linked with transcriptional output, and specific ligands were noted to differentially affect measurements for wild type versus mutant AR, suggesting differing mechanisms of action. HT imaging of patient-derived AIS mutations demonstrated a proof-of-principle personalized medicine approach to rapidly identify ligands capable of restoring multiple AR functions. Conclusions/Significance HT imaging-based multiplex screening will provide a rapid, systems-level analysis of compounds/RNAi that may differentially affect wild type AR or clinically relevant AR mutations. PMID:18978937

Rapid increase of health care utilization and cost due to benign prostatic hyperplasia in Korean men: retrospective population-based analysis using the Health Insurance Review and Assessment service data.

PubMed

Son, Hwancheol; Park, Juhyun; Song, Sang Hoon; Kang, Jung Yoon; Hong, Sung Kyu; Lee, Hyun Moo; Kim, Sun-Hee; Park, Byung-Joo; Lee, Hyung-Lae; Lee, Kyung Seop

2015-02-01

Using the Korean public health insurance database, we analyzed patients diagnosed as benign prostatic hyperplasia (BPH) from 2004 to 2008. Age and year-specific amount and seasonal variation of hospital visits (HV), duration of treatment (DT), the total and per capita amount of insurance payment (TAIP, PCIP) were evaluated. A total of 12,088,995 HV were studied. Total HV increased 1.7 times and DT almost doubled in 2008 compared to those in 2004. HV, DT, and TAIP showed linearly increasing patterns year by year. In a time series analysis, HV increased in winter and demonstrated seasonality in a 12-month cycle. In a Poisson regression analysis, the annual variations of HV, DT, TAIP, and PCIP were different by age groups. In patients older than 40 yr, HV significantly increased 1.10-1.16 times compared to that of the previous year. DT markedly increased in their 60s and 80s patients. The rate of increase in PCIP was steeper in patients 50 yr and older than in the others.Health care utilization due to BPH was rapidly increasing in Korea and it was remarkable in the elderly population. Seasonal variation of HV demonstrated that health care utilization increased in winter.

The MSFC Collaborative Engineering Process for Preliminary Design and Concept Definition Studies

NASA Technical Reports Server (NTRS)

Mulqueen, Jack; Jones, David; Hopkins, Randy

2011-01-01

This paper describes a collaborative engineering process developed by the Marshall Space Flight Center's Advanced Concepts Office for performing rapid preliminary design and mission concept definition studies for potential future NASA missions. The process has been developed and demonstrated for a broad range of mission studies including human space exploration missions, space transportation system studies and in-space science missions. The paper will describe the design team structure and specialized analytical tools that have been developed to enable a unique rapid design process. The collaborative engineering process consists of integrated analysis approach for mission definition, vehicle definition and system engineering. The relevance of the collaborative process elements to the standard NASA NPR 7120.1 system engineering process will be demonstrated. The study definition process flow for each study discipline will be will be outlined beginning with the study planning process, followed by definition of ground rules and assumptions, definition of study trades, mission analysis and subsystem analyses leading to a standardized set of mission concept study products. The flexibility of the collaborative engineering design process to accommodate a wide range of study objectives from technology definition and requirements definition to preliminary design studies will be addressed. The paper will also describe the applicability of the collaborative engineering process to include an integrated systems analysis approach for evaluating the functional requirements of evolving system technologies and capabilities needed to meet the needs of future NASA programs.

Acute toxicity of excess mercury on the photosynthetic performance of cyanobacterium, S. platensis--assessment by chlorophyll fluorescence analysis.

PubMed

Lu, C M; Chau, C W; Zhang, J H

2000-07-01

Measurement of chlorophyll fluorescence has been shown to be a rapid, non-invasive, and reliable method to assess photosynthetic performance in a changing environment. In this study, acute toxicity of excess Hg on the photosynthetic performance of the cyanobacterium S. platensis, was investigated by use of chlorophyll fluorescence analysis after cells were exposed to excess Hg (up to 20 microM) for 2 h. The results determined from the fast fluorescence kinetics showed that Hg induced a significant increase in the proportion of the Q(B)-non-reducing PSII reaction centers. The fluorescence parameters measured under the steady state of photosynthesis demonstrated that the increase of Hg concentration led to a decrease in the maximal efficiency of PSII photochemistry, the efficiency of excitation energy capture by the open PSII reaction centers, and the quantum yield of PSII electron transport. Mercury also resulted in a decrease in the coefficients of photochemical and non-photochemical quenching. Mercury may have an acute toxicity on cyanobacteria by inhibiting the quantum yield of photosynthesis sensitively and rapidly. Such changes occurred before any other visible damages that may be evaluated by other conventional measurements. Our results also demonstrated that chlorophyll fluorescence analysis can be used as a useful physiological tool to assess early stages of change in photosynthetic performance of algae in response to heavy metal pollution.

Geologic controls on the formation and evolution of quaternary coastal deposits of the northern Gulf of Mexico

USGS Publications Warehouse

Williams, S.J.; Penland, S.; Sallenger, A.H.; McBride, R.A.; Kindlinger, J.L.

1991-01-01

A study of the barrier islands and wetlands in the deltaic plain of Louisiana is presented. Its purpose was to document rapid changes and to learn more about the processes responsible and the geologic framework within which they operate. It included systematic collection and analysis of precision nearshore hydrographic data, high resolution seismic profiles, surface sediment samples, continuous vibracores, digital shoreline plots, records of storm overwash events, and analysis of tide gage records to quantify the rise in relative sea level. Results from these studies demonstrate that deltaic progradation, river channel switching, and subsequent rapid erosion accompanying the marine transgression are regular and predictable events along the Mississippi River delta plain and will likely continue in the future. Mitigation measures, such as shoreline nourishment and barrier restoration, that mimic the natural processes may slow the land loss.

Classification of smoke tainted wines using mid-infrared spectroscopy and chemometrics.

PubMed

Fudge, Anthea L; Wilkinson, Kerry L; Ristic, Renata; Cozzolino, Daniel

2012-01-11

In this study, the suitability of mid-infrared (MIR) spectroscopy, combined with principal component analysis (PCA) and linear discriminant analysis (LDA), was evaluated as a rapid analytical technique to identify smoke tainted wines. Control (i.e., unsmoked) and smoke-affected wines (260 in total) from experimental and commercial sources were analyzed by MIR spectroscopy and chemometrics. The concentrations of guaiacol and 4-methylguaiacol were also determined using gas chromatography-mass spectrometry (GC-MS), as markers of smoke taint. LDA models correctly classified 61% of control wines and 70% of smoke-affected wines. Classification rates were found to be influenced by the extent of smoke taint (based on GC-MS and informal sensory assessment), as well as qualitative differences in wine composition due to grape variety and oak maturation. Overall, the potential application of MIR spectroscopy combined with chemometrics as a rapid analytical technique for screening smoke-affected wines was demonstrated.

Revealing the glass transition in shape memory polymers using Brillouin spectroscopy.

PubMed

Steelman, Zachary A; Weems, Andrew C; Traverso, Andrew J; Szafron, Jason M; Maitland, Duncan J; Yakovlev, Vladislav V

2017-12-11

Emerging medical devices which employ shape memory polymers (SMPs) require precise measurements of the glass transition temperature (T g ) to ensure highly controlled shape recovery kinetics. Conventional techniques like differential scanning calorimetry (DSC) and dynamic mechanical analysis (DMA) have limitations that prevent utilization for certain devices, including limited accuracy and the need for sacrificial samples. In this report, we employ an approach based on Brillouin spectroscopy to probe the glass transition of SMPs rapidly, remotely, and nondestructively. Further, we compare the T g obtained from Brillouin scattering with DMA- and DSC-measured T g to demonstrate the accuracy of Brillouin scattering for this application. We conclude that Brillouin spectroscopy is an accurate technique for obtaining the glass transition temperature of SMPs, aligning closely with the most common laboratory standards while providing a rapid, remote, and nondestructive method for the analysis of unique polymeric medical devices.

Laser-induced breakdown spectroscopy (LIBS): an overview of recent progress and future potential for biomedical applications.

PubMed

Rehse, S J; Salimnia, H; Miziolek, A W

2012-02-01

The recent progress made in developing laser-induced breakdown spectroscopy (LIBS) has transformed LIBS from an elemental analysis technique to one that can be applied for the reagentless analysis of molecularly complex biological materials or clinical specimens. Rapid advances in the LIBS technology have spawned a growing number of recently published articles in peer-reviewed journals which have consistently demonstrated the capability of LIBS to rapidly detect, biochemically characterize and analyse, and/or accurately identify various biological, biomedical or clinical samples. These analyses are inherently real-time, require no sample preparation, and offer high sensitivity and specificity. This overview of the biomedical applications of LIBS is meant to summarize the research that has been performed to date, as well as to suggest to health care providers several possible specific future applications which, if successfully implemented, would be significantly beneficial to humankind.

Revealing the glass transition in shape memory polymers using Brillouin spectroscopy

NASA Astrophysics Data System (ADS)

Steelman, Zachary A.; Weems, Andrew C.; Traverso, Andrew J.; Szafron, Jason M.; Maitland, Duncan J.; Yakovlev, Vladislav V.

2017-12-01

Emerging medical devices which employ shape memory polymers (SMPs) require precise measurements of the glass transition temperature (Tg) to ensure highly controlled shape recovery kinetics. Conventional techniques like differential scanning calorimetry (DSC) and dynamic mechanical analysis (DMA) have limitations that prevent utilization for certain devices, including limited accuracy and the need for sacrificial samples. In this report, we employ an approach based on Brillouin spectroscopy to probe the glass transition of SMPs rapidly, remotely, and nondestructively. Further, we compare the Tg obtained from Brillouin scattering with DMA- and DSC-measured Tg to demonstrate the accuracy of Brillouin scattering for this application. We conclude that Brillouin spectroscopy is an accurate technique for obtaining the glass transition temperature of SMPs, aligning closely with the most common laboratory standards while providing a rapid, remote, and nondestructive method for the analysis of unique polymeric medical devices.

An Analysis of Test And Evaluation in Rapid Acquisition Programs

DTIC Science & Technology

2015-12-01

program manager is assigned the requirement and allocated resources to carry out with an acquisition plan. 2. Role of Test and Evaluation Test and...Manual, verify the Maintenance Allocation Chart, and ensure the completeness of the System Support Package. The Maintainability Demonstration measured...additional outside personnel that require additional logistics support, such as security, facilitates, and berthing placing additional strain on units. CLS

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

NASA Astrophysics Data System (ADS)

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

2017-11-01

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

Direct, rapid, and label-free detection of enzyme-substrate interactions in physiological buffers using CMOS-compatible nanoribbon sensors.

PubMed

Mu, Luye; Droujinine, Ilia A; Rajan, Nitin K; Sawtelle, Sonya D; Reed, Mark A

2014-09-10

We demonstrate the versatility of Al2O3-passivated Si nanowire devices ("nanoribbons") in the analysis of enzyme-substrate interactions via the monitoring of pH change. Our approach is shown to be effective through the detection of urea in phosphate buffered saline (PBS), and penicillinase in PBS and urine, at limits of detection of <200 μM and 0.02 units/mL, respectively. The ability to extract accurate enzyme kinetics and the Michaelis-Menten constant (Km) from the acetylcholine-acetylcholinesterase reaction is also demonstrated.

Analysis Of Volatile Fingerprints: A Rapid Screening Method For Antifungal Agents For Efficacy Against Dermatophytes

NASA Astrophysics Data System (ADS)

Naraghi, Kamran; Sahgal, Natasha; Adriaans, Beverley; Barr, Hugh; Magan, Naresh

2009-05-01

The potential of using an electronic nose (E. nose) for rapid screening dermatophytes to antifungal agents was studied. In vitro, the 50 and 90% effective concentration (EC) values of five antifungal agents for T. rubrum and T. mentagrophytes were obtained by mycelial growth assays. Then, the qualitative volatile production patterns of the growth responses of these fungi to these values were incorporated into solid medium were analysed after 96-120 hrs incubation at 25° C using headspace analyses. Overall, results, using PCA and CA demonstrated that it is possible to differentiate between various treatments within 96-120 hrs. This study showed that potential exists for using qualitative volatile patterns as a rapid screening method for antifungal agents for microorganism. This approach could also facilitate the monitoring of antimicrobial drug activities and infection control programmes and perhaps drug resistance build up in microbial species.

Rapid Antibiotic Susceptibility Testing of Uropathogenic E. coli by Tracking Submicron Scale Motion of Single Bacterial Cells.

PubMed

Syal, Karan; Shen, Simon; Yang, Yunze; Wang, Shaopeng; Haydel, Shelley E; Tao, Nongjian

2017-08-25

To combat antibiotic resistance, a rapid antibiotic susceptibility testing (AST) technology that can identify resistant infections at disease onset is required. Current clinical AST technologies take 1-3 days, which is often too slow for accurate treatment. Here we demonstrate a rapid AST method by tracking sub-μm scale bacterial motion with an optical imaging and tracking technique. We apply the method to clinically relevant bacterial pathogens, Escherichia coli O157: H7 and uropathogenic E. coli (UPEC) loosely tethered to a glass surface. By analyzing dose-dependent sub-μm motion changes in a population of bacterial cells, we obtain the minimum bactericidal concentration within 2 h using human urine samples spiked with UPEC. We validate the AST method using the standard culture-based AST methods. In addition to population studies, the method allows single cell analysis, which can identify subpopulations of resistance strains within a sample.

Induction of atherosclerosis in mice and hamsters without germline genetic engineering.

PubMed

Bjørklund, Martin Maeng; Hollensen, Anne Kruse; Hagensen, Mette Kallestrup; Dagnaes-Hansen, Frederik; Christoffersen, Christina; Mikkelsen, Jacob Giehm; Bentzon, Jacob Fog

2014-05-23

Atherosclerosis can be achieved in animals by germline genetic engineering, leading to hypercholesterolemia, but such models are constrained to few species and strains, and they are difficult to combine with other powerful techniques involving genetic manipulation or variation. To develop a method for induction of atherosclerosis without germline genetic engineering. Recombinant adeno-associated viral vectors were engineered to encode gain-of-function proprotein convertase subtilisin/kexin type 9 mutants, and mice were given a single intravenous vector injection followed by high-fat diet feeding. Plasma proprotein convertase subtilisin/kexin type 9 and total cholesterol increased rapidly and were maintained at high levels, and after 12 weeks, mice had atherosclerotic lesions in the aorta. Histology of the aortic root showed progression of lesions to the fibroatheromatous stage. To demonstrate the applicability of this method for rapid analysis of the atherosclerosis susceptibility of a mouse strain and for providing temporal control over disease induction, we demonstrated the accelerated atherosclerosis of mature diabetic Akita mice. Furthermore, the versatility of this approach for creating atherosclerosis models also in nonmurine species was demonstrated by inducing hypercholesterolemia and early atherosclerosis in Golden Syrian hamsters. Single injections of proprotein convertase subtilisin/kexin type 9-encoding recombinant adeno-associated viral vectors are a rapid and versatile method to induce atherosclerosis in animals. This method should prove useful for experiments that are high-throughput or involve genetic techniques, strains, or species that do not combine well with current genetically engineered models. © 2014 American Heart Association, Inc.

Demonstrating Change with Astronaut Photography Using Object Based Image Analysis

NASA Technical Reports Server (NTRS)

Hollier, Andi; Jagge, Amy

2017-01-01

Every day, hundreds of images of Earth flood the Crew Earth Observations database as astronauts use hand held digital cameras to capture spectacular frames from the International Space Station. The variety of resolutions and perspectives provide a template for assessing land cover change over decades. We will focus on urban growth in the second fastest growing city in the nation, Houston, TX, using Object-Based Image Analysis. This research will contribute to the land change science community, integrated resource planning, and monitoring of the rapid rate of urban sprawl.

Developmental validation of the DNAscan™ Rapid DNA Analysis™ instrument and expert system for reference sample processing.

PubMed

Della Manna, Angelo; Nye, Jeffrey V; Carney, Christopher; Hammons, Jennifer S; Mann, Michael; Al Shamali, Farida; Vallone, Peter M; Romsos, Erica L; Marne, Beth Ann; Tan, Eugene; Turingan, Rosemary S; Hogan, Catherine; Selden, Richard F; French, Julie L

2016-11-01

Since the implementation of forensic DNA typing in labs more than 20 years ago, the analysis procedures and data interpretation have always been conducted in a laboratory by highly trained and qualified scientific personnel. Rapid DNA technology has the potential to expand testing capabilities within forensic laboratories and to allow forensic STR analysis to be performed outside the physical boundaries of the traditional laboratory. The developmental validation of the DNAscan/ANDE Rapid DNA Analysis System was completed using a BioChipSet™ Cassette consumable designed for high DNA content samples, such as single source buccal swabs. A total of eight laboratories participated in the testing which totaled over 2300 swabs, and included nearly 1400 unique individuals. The goal of this extensive study was to obtain, document, analyze, and assess DNAscan and its internal Expert System to reliably genotype reference samples in a manner compliant with the FBI's Quality Assurance Standards (QAS) and the NDIS Operational Procedures. The DNAscan System provided high quality, concordant results for reference buccal swabs, including automated data analysis with an integrated Expert System. Seven external laboratories and NetBio, the developer of the technology, participated in the validation testing demonstrating the reproducibility and reliability of the system and its successful use in a variety of settings by numerous operators. The DNAscan System demonstrated limited cross reactivity with other species, was resilient in the presence of numerous inhibitors, and provided reproducible results for both buccal and purified DNA samples with sensitivity at a level appropriate for buccal swabs. The precision and resolution of the system met industry standards for detection of micro-variants and displayed single base resolution. PCR-based studies provided confidence that the system was robust and that the amplification reaction had been optimized to provide high quality results. The DNAscan integrated Expert System was examined as part of the Developmental Validation and successfully interpreted the over 2000 samples tested with over 99.998% concordant alleles. The system appropriately flagged samples for human review and failed both mixed samples and samples with insufficient genetic information. These results demonstrated the integrated Expert System makes correct allele calls without human intervention. Copyright © 2016 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Integrated on-chip derivatization and electrophoresis for the rapid analysis of biogenic amines.

PubMed

Beard, Nigel P; Edel, Joshua B; deMello, Andrew J

2004-07-01

We demonstrate the monolithic integration of a chemical reactor with a capillary electrophoresis device for the rapid and sensitive analysis of biogenic amines. Fluorescein isothiocyanate (FITC) is widely employed for the analysis of amino-group containing analytes. However, the slow reaction kinetics hinders the use of this dye for on-chip labeling applications. Other alternatives are available such as o-phthaldehyde (OPA), however, the inferior photophysical properties and the UV lambdamax present difficulties when using common excitation sources leading to a disparity in sensitivity. Consequently, we present for the first time the use of dichlorotriazine fluorescein (DTAF) as a superior in situ derivatizing agent for biogenic amines in microfluidic devices. The developed microdevice employs both hydrodynamic and electroosmotic flow, facilitating the creation of a polymeric microchip to perform both precolumn derivatization and electrophoretic analysis. The favorable photophysical properties of the DTAF and its fast reaction kinetics provide detection limits down to 1 nM and total analysis times (including on-chip mixing and reaction) of <60 s. The detection limits are two orders of magnitude lower than current limits obtained with both FITC and OPA. The optimized microdevice is also employed to probe biogenic amines in real samples.

Rapid bacterial colonization of low-density polyethylene microplastics in coastal sediment microcosms.

PubMed

Harrison, Jesse P; Schratzberger, Michaela; Sapp, Melanie; Osborn, A Mark

2014-09-23

Synthetic microplastics (≤5-mm fragments) are emerging environmental contaminants that have been found to accumulate within coastal marine sediments worldwide. The ecological impacts and fate of microplastic debris are only beginning to be revealed, with previous research into these topics having primarily focused on higher organisms and/or pelagic environments. Despite recent research into plastic-associated microorganisms in seawater, the microbial colonization of microplastics in benthic habitats has not been studied. Therefore, we employed a 14-day microcosm experiment to investigate bacterial colonization of low-density polyethylene (LDPE) microplastics within three types of coastal marine sediment from Spurn Point, Humber Estuary, U.K. Bacterial attachment onto LDPE within sediments was demonstrated by scanning electron microscopy and catalyzed reporter deposition fluorescence in situ hybridisation (CARD-FISH). Log-fold increases in the abundance of 16S rRNA genes from LDPE-associated bacteria occurred within 7 days with 16S rRNA gene numbers on LDPE surfaces differing significantly across sediment types, as shown by quantitative PCR. Terminal-restriction fragment length polymorphism (T-RFLP) analysis demonstrated rapid selection of LDPE-associated bacterial assemblages whose structure and composition differed significantly from those in surrounding sediments. Additionally, T-RFLP analysis revealed successional convergence of the LDPE-associated communities from the different sediments over the 14-day experiment. Sequencing of cloned 16S rRNA genes demonstrated that these communities were dominated after 14 days by the genera Arcobacter and Colwellia (totalling 84-93% of sequences). Attachment by Colwellia spp. onto LDPE within sediments was confirmed by CARD-FISH. These results demonstrate that bacteria within coastal marine sediments can rapidly colonize LDPE microplastics, with evidence for the successional formation of plastisphere-specific bacterial assemblages. Although the taxonomic compositions of these assemblages are likely to differ between marine sediments and the water column, both Arcobacter and Colwellia spp. have previously been affiliated with the degradation of hydrocarbon contaminants within low-temperature marine environments. Since hydrocarbon-degrading bacteria have also been discovered on plastic fragments in seawater, our data suggest that recruitment of hydrocarbonoclastic bacteria on microplastics is likely to represent a shared feature between both benthic and pelagic marine habitats.

NASA'S SERVIR Gulf of Mexico Project: The Gulf of Mexico Regional Collaborative (GoMRC)

NASA Technical Reports Server (NTRS)

Quattrochi, Dale A.; Irwin, Daniel; Presson, Joan; Estes, Maury; Estes, Sue; Judd, Kathleen

2006-01-01

The Gulf of Mexico Regional Collaborative (GoMRC) is a NASA-funded project that has as its goal to develop an integrated, working, prototype IT infrastructure for Earth science data, knowledge and models for the five Gulf U.S. states and Mexico, and to demonstrate its ability to help decision-makers better understand critical Gulf-scale issues. Within this preview, the mission of this project is to provide cross cutting solution network and rapid prototyping capability for the Gulf of Mexico region, in order to demonstrate substantial, collaborative, multi-agency research and transitional capabilities using unique NASA data sets and models to address regional problems. SERVIR Mesoamerica is seen as an excellent existing framework that can be used to integrate observational and GIs data bases, provide a sensor web interface, visualization and interactive analysis tools, archival functions, data dissemination and product generation within a Rapid Prototyping concept to assist decision-makers in better understanding Gulf-scale environmental issues.

Bioprinting of Cartilage and Skin Tissue Analogs Utilizing a Novel Passive Mixing Unit Technique for Bioink Precellularization

PubMed Central

Thayer, Patrick Scott; Orrhult, Linnea Stridh; Martínez, Héctor

2018-01-01

Bioprinting is a powerful technique for the rapid and reproducible fabrication of constructs for tissue engineering applications. In this study, both cartilage and skin analogs were fabricated after bioink pre-cellularization utilizing a novel passive mixing unit technique. This technique was developed with the aim to simplify the steps involved in the mixing of a cell suspension into a highly viscous bioink. The resolution of filaments deposited through bioprinting necessitates the assurance of uniformity in cell distribution prior to printing to avoid the deposition of regions without cells or retention of large cell clumps that can clog the needle. We demonstrate the ability to rapidly blend a cell suspension with a bioink prior to bioprinting of both cartilage and skin analogs. Both tissue analogs could be cultured for up to 4 weeks. Histological analysis demonstrated both cell viability and deposition of tissue specific extracellular matrix (ECM) markers such as glycosaminoglycans (GAGs) and collagen I respectively. PMID:29364216

Identification of vegetable oil botanical speciation in refined vegetable oil blends using an innovative combination of chromatographic and spectroscopic techniques.

PubMed

Osorio, Maria Teresa; Haughey, Simon A; Elliott, Christopher T; Koidis, Anastasios

2015-12-15

European Regulation 1169/2011 requires producers of foods that contain refined vegetable oils to label the oil types. A novel rapid and staged methodology has been developed for the first time to identify common oil species in oil blends. The qualitative method consists of a combination of a Fourier Transform Infrared (FTIR) spectroscopy to profile the oils and fatty acid chromatographic analysis to confirm the composition of the oils when required. Calibration models and specific classification criteria were developed and all data were fused into a simple decision-making system. The single lab validation of the method demonstrated the very good performance (96% correct classification, 100% specificity, 4% false positive rate). Only a small fraction of the samples needed to be confirmed with the majority of oils identified rapidly using only the spectroscopic procedure. The results demonstrate the huge potential of the methodology for a wide range of oil authenticity work. Copyright © 2014 Elsevier Ltd. All rights reserved.

New LightCycler PCR for Rapid and Sensitive Quantification of Parvovirus B19 DNA Guides Therapeutic Decision-Making in Relapsing Infections

PubMed Central

Harder, Timm C.; Hufnagel, Markus; Zahn, Katrin; Beutel, Karin; Schmitt, Heinz-Josef; Ullmann, Uwe; Rautenberg, Peter

2001-01-01

Detection of parvovirus B19 DNA offers diagnostic advantages over serology, particularly in persistent infections of immunocompromised patients. A rapid, novel method of B19 DNA detection and quantification is introduced. This method, a quantitative PCR assay, is based on real-time glass capillary thermocycling (LightCycler [LC]) and fluorescence resonance energy transfer (FRET). The PCR assay allowed quantification over a dynamic range of over 7 logs and could quantify as little as 250 B19 genome equivalents (geq) per ml as calculated for plasmid DNA (i.e., theoretically ≥5 geq per assay). Interrater agreement analysis demonstrated equivalence of LC-FRET PCR and conventional nested PCR in the diagnosis of an active B19 infection (kappa coefficient = 0.83). The benefit of the new method was demonstrated in an immunocompromised child with a relapsing infection, who required an attenuation of the immunosuppressive therapy in addition to repeated doses of immunoglobulin to eliminate the virus. PMID:11724854

Rapidly prototyped three-dimensional nanofluidic channel networks in glass substrates.

PubMed

Ke, Kevin; Hasselbrink, Ernest F; Hunt, Alan J

2005-08-15

Microfluidic and nanofluidic technologies have long sought a fast, reliable method to overcome the creative limitations of planar fabrication methods, the resolution limits of lithography, and the materials limitations for fast prototyping. In the present work, we demonstrate direct 3D machining of submicrometer diameter, subsurface fluidic channels in glass, via optical breakdown near critical intensity, using a femtosecond pulsed laser. No postexposure etching or bonding is required; the channel network (or almost any arbitrary-shaped cavity below the surface) is produced directly from "art-to-part". The key to this approach is to use very low energy, highly focused, pulses in the presence of liquid. Microbubbles that result from laser energy deposition gently expand and extrude machining debris from the channels. These bubbles are in a highly damped, low Reynolds number regime, implying that surface spalling due to bubble collapse is unimportant. We demonstrate rapid prototyping of three-dimensional "jumpers", mixers, and other key components of complex 3D microscale analysis systems in glass substrates.

Design of a rapid magnetic microfluidic mixer

NASA Astrophysics Data System (ADS)

Ballard, Matthew; Owen, Drew; Mills, Zachary Grant; Hanasoge, Srinivas; Hesketh, Peter; Alexeev, Alexander

2015-11-01

Using three-dimensional simulations and experiments, we demonstrate rapid mixing of fluid streams in a microchannel using orbiting magnetic microbeads. We use a lattice Boltzmann model coupled to a Brownian dynamics model to perform numerical simulations that study in depth the effect of system parameters such as channel configuration and fluid and bead velocities. We use our findings to aid the design of an experimental micromixer. Using this experimental device, we demonstrate rapid microfluidic mixing over a compact channel length, and validate our numerical simulation results. Finally, we use numerical simulations to study the physical mechanisms leading to microfluidic mixing in our system. Our findings demonstrate a promising method of rapid microfluidic mixing over a short distance, with applications in lab-on-a-chip sample testing.

Gold nanoparticle-based optical microfluidic sensors for analysis of environmental pollutants.

PubMed

Lafleur, Josiane P; Senkbeil, Silja; Jensen, Thomas G; Kutter, Jörg P

2012-11-21

Conventional methods of environmental analysis can be significantly improved by the development of portable microscale technologies for direct in-field sensing at remote locations. This report demonstrates the vast potential of gold nanoparticle-based microfluidic sensors for the rapid, in-field, detection of two important classes of environmental contaminants - heavy metals and pesticides. Using gold nanoparticle-based microfluidic sensors linked to a simple digital camera as the detector, detection limits as low as 0.6 μg L(-1) and 16 μg L(-1) could be obtained for the heavy metal mercury and the dithiocarbamate pesticide ziram, respectively. These results demonstrate that the attractive optical properties of gold nanoparticle probes combine synergistically with the inherent qualities of microfluidic platforms to offer simple, portable and sensitive sensors for environmental contaminants.

Surgically assisted rapid palatal expansion. An acoustic rhinometric, morphometric and sonographic investigation.

PubMed

Wriedt, S; Kunkel, M; Zentner, A; Wahlmann, U W

2001-03-01

This study aimed to evaluate the effect of surgically assisted rapid palatal expansion on the skeletal structures of the midface. Ten patients (mean age 28.5 years) were investigated by means of acoustic rhinometry, study model analysis and sonography before and after the procedure of surgically assisted rapid palatal expansion. The measurements revealed that surgically assisted rapid palatal expansion not only resulted in transverse expansion of the maxilla, providing dental arch space for lining up the teeth; the procedure also caused a substantial enlargement of the maxillary apical base and of the palatal vault, providing space for the tongue for correct swallowing and thus preventing relapse. There was a distinct subjective improvement in nasal breathing associated with enlargement of the nasal valve towards normal values and with an increase of nasal volume in all compartments. The measurements showed a marked influence of surgically assisted rapid palatal expansion on the skeletal structures of the midface. The significant widening can be demonstrated by non-invasive examination. Success of the osteotomy procedure can be readily monitored by sonographic examination of the expansion and the subsequent ossification, which allows individually adjusted retention periods and avoids frequent radiation exposure.

Interaction of pseudolaric acid B with the colchicine site of tubulin.

PubMed

Sarkar, Taradas; Nguyen, Tam Luong; Su, Zhi-Wei; Hao, Jun; Bai, Ruoli; Gussio, Rick; Qiu, Samuel X; Hamel, Ernest

2012-08-15

We purified pseudolaric acid B (PAB) from the root and stem bark of Pseudolarix kaempferi (Lindl.) Gorden. Confirming previous findings, we found that the compound had high nanomolar IC₅₀ antiproliferative effects in several cultured cell lines, causing mitotic arrest and the disappearance of intracellular microtubules. PAB strongly inhibited tubulin assembly (IC₅₀, 1.1 μM) but weakly inhibited the binding of colchicine to tubulin, as demonstrated by fluorescence and with [³H]colchicine. Kinetic analysis demonstrated that the mechanism of inhibition was competitive, with an apparent K(i) of 12-15 μM. Indirect studies demonstrated that PAB bound rapidly to tubulin and dissociated more rapidly from tubulin than the colchicine analog 2-methoxy-5-(2',3',4'-trimethoxyphenyl)tropone, whose complex with tubulin is known to have a half-life of 17s at 37 °C. We modeled PAB into the colchicine site of tubulin, using the crystal structure 1SA0 that contains two αβ-tubulin heterodimers, both bound to a colchicinoid and to a stathmin fragment. The binding model of PAB revealed common pharmacophoric features between PAB and colchicinoids, not readily apparent from their chemical structures. Published by Elsevier Inc.

Monte Carlo based, patient-specific RapidArc QA using Linac log files.

PubMed

Teke, Tony; Bergman, Alanah M; Kwa, William; Gill, Bradford; Duzenli, Cheryl; Popescu, I Antoniu

2010-01-01

A Monte Carlo (MC) based QA process to validate the dynamic beam delivery accuracy for Varian RapidArc (Varian Medical Systems, Palo Alto, CA) using Linac delivery log files (DynaLog) is presented. Using DynaLog file analysis and MC simulations, the goal of this article is to (a) confirm that adequate sampling is used in the RapidArc optimization algorithm (177 static gantry angles) and (b) to assess the physical machine performance [gantry angle and monitor unit (MU) delivery accuracy]. Ten clinically acceptable RapidArc treatment plans were generated for various tumor sites and delivered to a water-equivalent cylindrical phantom on the treatment unit. Three Monte Carlo simulations were performed to calculate dose to the CT phantom image set: (a) One using a series of static gantry angles defined by 177 control points with treatment planning system (TPS) MLC control files (planning files), (b) one using continuous gantry rotation with TPS generated MLC control files, and (c) one using continuous gantry rotation with actual Linac delivery log files. Monte Carlo simulated dose distributions are compared to both ionization chamber point measurements and with RapidArc TPS calculated doses. The 3D dose distributions were compared using a 3D gamma-factor analysis, employing a 3%/3 mm distance-to-agreement criterion. The dose difference between MC simulations, TPS, and ionization chamber point measurements was less than 2.1%. For all plans, the MC calculated 3D dose distributions agreed well with the TPS calculated doses (gamma-factor values were less than 1 for more than 95% of the points considered). Machine performance QA was supplemented with an extensive DynaLog file analysis. A DynaLog file analysis showed that leaf position errors were less than 1 mm for 94% of the time and there were no leaf errors greater than 2.5 mm. The mean standard deviation in MU and gantry angle were 0.052 MU and 0.355 degrees, respectively, for the ten cases analyzed. The accuracy and flexibility of the Monte Carlo based RapidArc QA system were demonstrated. Good machine performance and accurate dose distribution delivery of RapidArc plans were observed. The sampling used in the TPS optimization algorithm was found to be adequate.

Romer Labs RapidChek®Listeria monocytogenes Test System for the Detection of L. monocytogenes on Selected Foods and Environmental Surfaces.

PubMed

Juck, Gregory; Gonzalez, Verapaz; Allen, Ann-Christine Olsson; Sutzko, Meredith; Seward, Kody; Muldoon, Mark T

2018-04-27

The Romer Labs RapidChek ® Listeria monocytogenes test system (Performance Tested Method ℠ 011805) was validated against the U.S. Department of Agriculture-Food Safety and Inspection Service Microbiology Laboratory Guidebook (USDA-FSIS/MLG), U.S. Food and Drug Association Bacteriological Analytical Manual (FDA/BAM), and AOAC Official Methods of Analysis ℠ (AOAC/OMA) cultural reference methods for the detection of L. monocytogenes on selected foods including hot dogs, frozen cooked breaded chicken, frozen cooked shrimp, cured ham, and ice cream, and environmental surfaces including stainless steel and plastic in an unpaired study design. The RapidChek method uses a proprietary enrichment media system, a 44-48 h enrichment at 30 ± 1°C, and detects L. monocytogenes on an immunochromatographic lateral flow device within 10 min. Different L. monocytogenes strains were used to spike each of the matrixes. Samples were confirmed based on the reference method confirmations and an alternate confirmation method. A total of 140 low-level spiked samples were tested by the RapidChek method after enrichment for 44-48 h in parallel with the cultural reference method. There were 88 RapidChek presumptive positives. One of the presumptive positives was not confirmed culturally. Additionally, one of the culturally confirmed samples did not exhibit a presumptive positive. No difference between the alternate confirmation method and reference confirmation method was observed. The respective cultural reference methods (USDA-FSIS/MLG, FDA/BAM, and AOAC/OMA) produced a total of 63 confirmed positive results. Nonspiked samples from all foods were reported as negative for L. monocytogenes by all methods. Probability of detection analysis demonstrated no significant differences in the number of positive samples detected by the RapidChek method and the respective cultural reference method.

Rapid, portable and cost-effective yeast cell viability and concentration analysis using lensfree on-chip microscopy and machine learning.

PubMed

Feizi, Alborz; Zhang, Yibo; Greenbaum, Alon; Guziak, Alex; Luong, Michelle; Chan, Raymond Yan Lok; Berg, Brandon; Ozkan, Haydar; Luo, Wei; Wu, Michael; Wu, Yichen; Ozcan, Aydogan

2016-11-01

Monitoring yeast cell viability and concentration is important in brewing, baking and biofuel production. However, existing methods of measuring viability and concentration are relatively bulky, tedious and expensive. Here we demonstrate a compact and cost-effective automatic yeast analysis platform (AYAP), which can rapidly measure cell concentration and viability. AYAP is based on digital in-line holography and on-chip microscopy and rapidly images a large field-of-view of 22.5 mm 2 . This lens-free microscope weighs 70 g and utilizes a partially-coherent illumination source and an opto-electronic image sensor chip. A touch-screen user interface based on a tablet-PC is developed to reconstruct the holographic shadows captured by the image sensor chip and use a support vector machine (SVM) model to automatically classify live and dead cells in a yeast sample stained with methylene blue. In order to quantify its accuracy, we varied the viability and concentration of the cells and compared AYAP's performance with a fluorescence exclusion staining based gold-standard using regression analysis. The results agree very well with this gold-standard method and no significant difference was observed between the two methods within a concentration range of 1.4 × 10 5 to 1.4 × 10 6 cells per mL, providing a dynamic range suitable for various applications. This lensfree computational imaging technology that is coupled with machine learning algorithms would be useful for cost-effective and rapid quantification of cell viability and density even in field and resource-poor settings.

Rapid Quantification of Melamine in Different Brands/Types of Milk Powders Using Standard Addition Net Analyte Signal and Near-Infrared Spectroscopy

PubMed Central

2016-01-01

Multivariate calibration (MVC) and near-infrared (NIR) spectroscopy have demonstrated potential for rapid analysis of melamine in various dairy products. However, the practical application of ordinary MVC can be largely restricted because the prediction of a new sample from an uncalibrated batch would be subject to a significant bias due to matrix effect. In this study, the feasibility of using NIR spectroscopy and the standard addition (SA) net analyte signal (NAS) method (SANAS) for rapid quantification of melamine in different brands/types of milk powders was investigated. In SANAS, the NAS vector of melamine in an unknown sample as well as in a series of samples added with melamine standards was calculated and then the Euclidean norms of series standards were used to build a straightforward univariate regression model. The analysis results of 10 different brands/types of milk powders with melamine levels 0~0.12% (w/w) indicate that SANAS obtained accurate results with the root mean squared error of prediction (RMSEP) values ranging from 0.0012 to 0.0029. An additional advantage of NAS is to visualize and control the possible unwanted variations during standard addition. The proposed method will provide a practically useful tool for rapid and nondestructive quantification of melamine in different brands/types of milk powders. PMID:27525154

Rapid synthesis of graft copolymers from natural cellulose fibers.

PubMed

Thakur, Vijay Kumar; Thakur, Manju Kumari; Gupta, Raju Kumar

2013-10-15

Cellulose is the most abundant natural polysaccharide polymer, which is used as such or its derivatives in a number of advanced applications, such as in paper, packaging, biosorption, and biomedical. In present communication, in an effort to develop a proficient way to rapidly synthesize poly(methyl acrylate)-graft-cellulose (PMA-g-cellulose) copolymers, rapid graft copolymerization synthesis was carried out under microwave conditions using ferrous ammonium sulfate-potassium per sulfate (FAS-KPS) as redox initiator. Different reaction parameters such as microwave radiation power, ratio of monomer, solvent and initiator concentrations were optimized to get the highest percentage of grafting. Grafting percentage was found to increase with increase in microwave power up to 70%, and maximum 36.73% grafting was obtained after optimization of all parameters. Fourier transforms infrared spectroscopy (FT-IR), scanning electron microscopy (SEM) and thermogravimetric analysis (TGA/DTA/DTG) analysis were used to confirm the graft copolymerization of poly(methyl acrylate) (PMA) onto the mercerized cellulose. The grafted cellulosic polymers were subsequently subjected to the evaluation of different physico-chemical properties in order to access their application in everyday life, in a direction toward green environment. The grafted copolymers demonstrated increased chemical resistance, and higher thermal stability. Published by Elsevier Ltd.

Effect of visual and tactile feedback on kinematic synergies in the grasping hand.

PubMed

Patel, Vrajeshri; Burns, Martin; Vinjamuri, Ramana

2016-08-01

The human hand uses a combination of feedforward and feedback mechanisms to accomplish high degree of freedom in grasp control efficiently. In this study, we used a synergy-based control model to determine the effect of sensory feedback on kinematic synergies in the grasping hand. Ten subjects performed two types of grasps: one that included feedback (real) and one without feedback (memory-guided), at two different speeds (rapid and natural). Kinematic synergies were extracted from rapid real and rapid memory-guided grasps using principal component analysis. Synergies extracted from memory-guided grasps revealed greater preservation of natural inter-finger relationships than those found in corresponding synergies extracted from real grasps. Reconstruction of natural real and natural memory-guided grasps was used to test performance and generalizability of synergies. A temporal analysis of reconstruction patterns revealed the differing contribution of individual synergies in real grasps versus memory-guided grasps. Finally, the results showed that memory-guided synergies could not reconstruct real grasps as accurately as real synergies could reconstruct memory-guided grasps. These results demonstrate how visual and tactile feedback affects a closed-loop synergy-based motor control system.

Applications of breath gas analysis in medicine

NASA Astrophysics Data System (ADS)

Amann, Anton; Poupart, Guy; Telser, Stefan; Ledochowski, Maximilian; Schmid, Alex; Mechtcheriakov, Sergei

2004-12-01

Volatile organic compounds (VOCs) in exhaled breath gas provide valuable information about the subjects' physiological and pathophysiological condition. Proton-transfer-reaction mass spectrometry (PTR-MS) allows rapid and online measurements of these substances. We present results of three studies illustrating the potential of breath gas analysis by PTR-MS in various contexts: long-time online monitoring of VOCs in sleeping subjects suggests that VOC profiles are related to sleep stages. Analysis of VOC concentrations in the breath of carbohydrate malabsorbers emphasizes the role played by bacteria in the gut. Finally, we demonstrate the large intra- and intersubject concentration variability of VOCs by considering one particular mass.

Flash (Ultra-Rapid) Spark-Plasma Sintering of Silicon Carbide

PubMed Central

Olevsky, Eugene A.; Rolfing, Stephen M.; Maximenko, Andrey L.

2016-01-01

A new ultra-rapid process of flash spark plasma sintering is developed. The idea of flash spark plasma sintering (or flash hot pressing - FHP) stems from the conducted theoretical analysis of the role of thermal runaway phenomena for material processing by flash sintering. The major purpose of the present study is to theoretically analyze the thermal runaway nature of flash sintering and to experimentally address the challenge of uncontrollable thermal conditions by the stabilization of the flash sintering process through the application of the external pressure. The effectiveness of the developed FHP technique is demonstrated by the few seconds–long consolidation of SiC powder in an industrial spark plasma sintering device. Specially designed sacrificial dies heat the pre-compacted SiC powder specimens to a critical temperature before applying any voltage to the powder volume and allowing the electrode-punches of the SPS device setup to contact the specimens and pass electric current through them under elevated temperatures. The experimental results demonstrate that flash sintering phenomena can be realized using conventional SPS devices. The usage of hybrid heating SPS devices is pointed out as the mainstream direction for the future studies and utilization of the new flash hot pressing (ultra-rapid spark plasma sintering) technique. PMID:27624641

Flash (Ultra-Rapid) Spark-Plasma Sintering of Silicon Carbide

DOE PAGES

Olevsky, Eugene A.; Rolfing, Stephen M.; Maximenko, Andrey L.

2016-09-14

A new ultra-rapid process of flash spark plasma sintering is developed. The idea of flash spark plasma sintering (or flash hot pressing - FHP) stems from the conducted theoretical analysis of the role of thermal runaway phenomena for material processing by flash sintering. The major purpose of the present study is to theoretically analyze the thermal runaway nature of flash sintering and to experimentally address the challenge of uncontrollable thermal conditions by the stabilization of the flash sintering process through the application of the external pressure. The effectiveness of the developed FHP technique is demonstrated by the few seconds–long consolidationmore » of SiC powder in an industrial spark plasma sintering device. Specially designed sacrificial dies heat the pre-compacted SiC powder specimens to a critical temperature before applying any voltage to the powder volume and allowing the electrode-punches of the SPS device setup to contact the specimens and pass electric current through them under elevated temperatures. The experimental results demonstrate that flash sintering phenomena can be realized using conventional SPS devices. The usage of hybrid heating SPS devices is pointed out as the mainstream direction for the future studies and utilization of the new flash hot pressing (ultra-rapid spark plasma sintering) technique.« less

Rapid determination of nanowires electrical properties using a dielectrophoresis-well based system

NASA Astrophysics Data System (ADS)

Constantinou, Marios; Hoettges, Kai F.; Krylyuk, Sergiy; Katz, Michael B.; Davydov, Albert; Rigas, Grigorios-Panagiotis; Stolojan, Vlad; Hughes, Michael P.; Shkunov, Maxim

2017-03-01

The use of high quality semiconducting nanomaterials for advanced device applications has been hampered by the unavoidable growth variability of electrical properties of one-dimensional nanomaterials, such as nanowires and nanotubes, thus highlighting the need for the characterization of efficient semiconducting nanomaterials. In this study, we demonstrate a low-cost, industrially scalable dielectrophoretic (DEP) nanowire assembly method for the rapid analysis of the electrical properties of inorganic single crystalline nanowires, by identifying key features in the DEP frequency response spectrum from 1 kHz to 20 MHz in just 60 s. Nanowires dispersed in anisole were characterized using a three-dimensional DEP chip (3DEP), and the resultant spectrum demonstrated a sharp change in nanowire response to DEP signal in 1-20 MHz frequency range. The 3DEP analysis, directly confirmed by field-effect transistor data, indicates that nanowires of higher quality are collected at high DEP signal frequency range above 10 MHz, whereas lower quality nanowires, with two orders of magnitude lower current per nanowire, are collected at lower DEP signal frequencies. These results show that the 3DEP platform can be used as a very efficient characterization tool of the electrical properties of rod-shaped nanoparticles to enable dielectrophoretic selective deposition of nanomaterials with superior conductivity properties.

Use of Standing Gold Nanorods for Detection of Malachite Green and Crystal Violet in Fish by SERS.

PubMed

Chen, Xiaowei; Nguyen, Trang H D; Gu, Liqun; Lin, Mengshi

2017-07-01

With growing consumption of aquaculture products, there is increasing demand on rapid and sensitive techniques that can detect prohibited substances in the seafood products. This study aimed to develop a novel surface-enhanced Raman spectroscopy (SERS) method coupled with simplified extraction protocol and novel gold nanorod (AuNR) substrates to detect banned aquaculture substances (malachite green [MG] and crystal violet [CV]) and their mixture (1:1) in aqueous solution and fish samples. Multivariate statistical tools such as principal component analysis (PCA) and partial least squares regression (PLSR) were used in data analysis. PCA results demonstrate that SERS can distinguish MG, CV and their mixture (1:1) in aqueous solution and in fish samples. The detection limit of SERS coupled with standing AuNR substrates is 1 ppb for both MG and CV in fish samples. A good linear relationship between the actual concentration and predicted concentration of analytes based on PLSR models with R 2 values from 0.87 to 0.99 were obtained, indicating satisfactory quantification results of this method. These results demonstrate that the SERS method coupled with AuNR substrates can be used for rapid and accurate detection of MG and CV in fish samples. © 2017 Institute of Food Technologists®.

Using the iPhone as a device for a rapid quantitative analysis of trinitrotoluene in soil.

PubMed

Choodum, Aree; Kanatharana, Proespichaya; Wongniramaikul, Worawit; Daeid, Niamh Nic

2013-10-15

Mobile 'smart' phones have become almost ubiquitous in society and are typically equipped with a high-resolution digital camera which can be used to produce an image very conveniently. In this study, the built-in digital camera of a smart phone (iPhone) was used to capture the results from a rapid quantitative colorimetric test for trinitrotoluene (TNT) in soil. The results were compared to those from a digital single-lens reflex (DSLR) camera. The colored product from the selective test for TNT was quantified using an innovative application of photography where the relationships between the Red Green Blue (RGB) values and the concentrations of colorimetric product were exploited. The iPhone showed itself to be capable of being used more conveniently than the DSLR while providing similar analytical results with increased sensitivity. The wide linear range and low detection limits achieved were comparable with those from spectrophotometric quantification methods. Low relative errors in the range of 0.4 to 6.3% were achieved in the analysis of control samples and 0.4-6.2% for spiked soil extracts with good precision (2.09-7.43% RSD) for the analysis over 4 days. The results demonstrate that the iPhone provides the potential to be used as an ideal novel platform for the development of a rapid on site semi quantitative field test for the analysis of explosives. © 2013 Elsevier B.V. All rights reserved.

Rapid DNA analysis for automated processing and interpretation of low DNA content samples.

PubMed

Turingan, Rosemary S; Vasantgadkar, Sameer; Palombo, Luke; Hogan, Catherine; Jiang, Hua; Tan, Eugene; Selden, Richard F

2016-01-01

Short tandem repeat (STR) analysis of casework samples with low DNA content include those resulting from the transfer of epithelial cells from the skin to an object (e.g., cells on a water bottle, or brim of a cap), blood spatter stains, and small bone and tissue fragments. Low DNA content (LDC) samples are important in a wide range of settings, including disaster response teams to assist in victim identification and family reunification, military operations to identify friend or foe, criminal forensics to identify suspects and exonerate the innocent, and medical examiner and coroner offices to identify missing persons. Processing LDC samples requires experienced laboratory personnel, isolated workstations, and sophisticated equipment, requires transport time, and involves complex procedures. We present a rapid DNA analysis system designed specifically to generate STR profiles from LDC samples in field-forward settings by non-technical operators. By performing STR in the field, close to the site of collection, rapid DNA analysis has the potential to increase throughput and to provide actionable information in real time. A Low DNA Content BioChipSet (LDC BCS) was developed and manufactured by injection molding. It was designed to function in the fully integrated Accelerated Nuclear DNA Equipment (ANDE) instrument previously designed for analysis of buccal swab and other high DNA content samples (Investigative Genet. 4(1):1-15, 2013). The LDC BCS performs efficient DNA purification followed by microfluidic ultrafiltration of the purified DNA, maximizing the quantity of DNA available for subsequent amplification and electrophoretic separation and detection of amplified fragments. The system demonstrates accuracy, precision, resolution, signal strength, and peak height ratios appropriate for casework analysis. The LDC rapid DNA analysis system is effective for the generation of STR profiles from a wide range of sample types. The technology broadens the range of sample types that can be processed and minimizes the time between sample collection, sample processing and analysis, and generation of actionable intelligence. The fully integrated Expert System is capable of interpreting a wide range or sample types and input DNA quantities, allowing samples to be processed and interpreted without a technical operator.

Quantity of dates trumps quality of dates for dense Bayesian radiocarbon sediment chronologies - Gas ion source 14C dating instructed by simultaneous Bayesian accumulation rate modeling

NASA Astrophysics Data System (ADS)

Rosenheim, B. E.; Firesinger, D.; Roberts, M. L.; Burton, J. R.; Khan, N.; Moyer, R. P.

2016-12-01

Radiocarbon (14C) sediment core chronologies benefit from a high density of dates, even when precision of individual dates is sacrificed. This is demonstrated by a combined approach of rapid 14C analysis of CO2 gas generated from carbonates and organic material coupled with Bayesian statistical modeling. Analysis of 14C is facilitated by the gas ion source on the Continuous Flow Accelerator Mass Spectrometry (CFAMS) system at the Woods Hole Oceanographic Institution's National Ocean Sciences Accelerator Mass Spectrometry facility. This instrument is capable of producing a 14C determination of +/- 100 14C y precision every 4-5 minutes, with limited sample handling (dissolution of carbonates and/or combustion of organic carbon in evacuated containers). Rapid analysis allows over-preparation of samples to include replicates at each depth and/or comparison of different sample types at particular depths in a sediment or peat core. Analysis priority is given to depths that have the least chronologic precision as determined by Bayesian modeling of the chronology of calibrated ages. Use of such a statistical approach to determine the order in which samples are run ensures that the chronology constantly improves so long as material is available for the analysis of chronologic weak points. Ultimately, accuracy of the chronology is determined by the material that is actually being dated, and our combined approach allows testing of different constituents of the organic carbon pool and the carbonate minerals within a core. We will present preliminary results from a deep-sea sediment core abundant in deep-sea foraminifera as well as coastal wetland peat cores to demonstrate statistical improvements in sediment- and peat-core chronologies obtained by increasing the quantity and decreasing the quality of individual dates.

Characterizing of tissue microstructure with single-detector polarization-sensitive optical coherence tomography

NASA Astrophysics Data System (ADS)

Liu, Bin; Harman, Michelle; Giattina, Susanne; Stamper, Debra L.; Demakis, Charles; Chilek, Mark; Raby, Stephanie; Brezinski, Mark E.

2006-06-01

Assessing tissue birefringence with imaging modality polarization-sensitive optical coherence tomography (PS-OCT) could improve the characterization of in vivo tissue pathology. Among the birefringent components, collagen may provide invaluable clinical information because of its alteration in disorders ranging from myocardial infarction to arthritis. But the features required of clinical imaging modality in these areas usually include the ability to assess the parameter of interest rapidly and without extensive data analysis, the characteristics that single-detector PS-OCT demonstrates. But beyond detecting organized collagen, which has been previously demonstrated and confirmed with the appropriate histological techniques, additional information can potentially be gained with PS-OCT, including collagen type, form versus intrinsic birefringence, the collagen angle, and the presence of multiple birefringence materials. In part I, we apply the simple but powerful fast-Fourier transform (FFT) to both PS-OCT mathematical modeling and in vitro bovine meniscus for improved PS-OCT data analysis. The FFT analysis yields, in a rapid, straightforward, and easily interpreted manner, information on the presence of multiple birefringent materials, distinguishing the true anatomical structure from patterns in image resulting from alterations in the polarization state and identifying the tissue/phantom optical axes. Therefore the use of the FFT analysis of PS-OCT data provides information on tissue composition beyond identifying the presence of organized collagen in real time and directly from the image without extensive mathematical manipulation or data analysis. In part II, Helistat phantoms (collagen type I) are analyzed with the ultimate goal of improved tissue characterization. This study, along with the data in part I, advance the insights gained from PS-OCT images beyond simply determining the presence or absence of birefringence.

Association between N-acetyltransferase 2 polymorphisms and pancreatic cancer risk: a meta-analysis.

PubMed

Liang, J X; Gao, W; Liang, Y; Zhou, X M

2015-12-17

N-acetyltransferase 2 (NAT2) is an essential phase II enzyme in the metabolism of aromatic and heterocyclic amines and of hydrazines. NAT2 activity can be divided into three phenotypes: rapid, intermediate, and slow. Studies identifying an association between NAT2 polymorphism and the risk of pancreatic cancer have shown conflicting results. In order to assess this relationship comprehensively, we performed a meta-analysis that involved 1607 patients with pancreatic cancer and 1682 controls from six studies, which were selected from a group of ten, identified by a search of PubMed and Embase databases up to July 2014. Relative risks (RRs) with 95% confidence intervals (CIs) were used to evaluate the relationships. In the overall analysis, no significant associations between NAT2 rapid acetylation genotypes and pancreatic cancer risk (RR = 0.93, 95%CI = 0.73-1.19) were found; however, the results showed significant heterogeneity (I2 = 55.0%). The results from subgroup analysis suggested that the rapid genotypes might decrease the risk of pancreatic cancer (RR = 0.56, 95%CI = 0.38-0.84) in Turkey, although the association was not significant in the United States population (RR = 0.97, 95%CI = 0.71-1.34) or in the multi-center studies (RR = 1.10, 95%CI = 0.90-1.34). Analysis of the slow acetylation genotypes demonstrated the converse outcomes. In conclusion, the results of our study suggested that the NAT2 slow acetylation genotypes might increase the susceptibility to pancreatic cancer in Europe but that these have no significant effects in the United States and multi-center populations.

The cost-effectiveness of predonation screening for transfusion transmissible infections using rapid test kits in a hospital-based blood transfusion centre.

PubMed

Dosunmu, Adedoyin Owolabi; Akinbami, Akinsegun Abduljaleel; Ismail, Ayobami Kamal; Olaiya, Modupe Adebimpe; Uche, Ebele Ifeyinwa; Aile, Igbinoba Kingsley

2017-01-01

Blood transfusion practice emphasises safety, efficacy and appropriate use. These require cost-effective programme management. This study focused on the cost of screening for transfusion transmissible infections (TTI). This was a 1 year (2016) analysis of screening in a hospital-based transfusion centre. The cost of screening all blood donors by ELISA was compared to the cost of serial screening starting from rapid kit, taking into account, the estimated cost of blood bags prevented from discard after ELISA screening (attributable cost). The cost of voluntary donor drive plus cost of ELISA screening was compared with the present cost of screening. A total of 5591 donors were screened for HIV, hepatitis B and C using the rapid kit, 291 donors were deferred (5.2%). A total of 5300 units were further screened by ELISA. A total of 435 blood units (8.2%) were discarded due to TTI positivity. TTI positivity rate was 12.98%. Only 2.36% were voluntary donors and among these 9.1% were TTI positive. The attributable cost of serial screening was 55,653.5 USD while that of screening by ELISA only was 55,910 USD. The attributable cost of rapid screening for only hepatitis B and then ELISA was 53,313.9 USD taking into consideration that 187 blood units would be prevented from undue discard. This analysis demonstrated that with proper donor selection, rapid screening for hepatitis B virus only before ELISA screening is more cost-effective. This will also reduce the waiting time for donors and counselling if HIV positive.

Characterizing the Frequency and Elevation of Rapid Drainage Events in West Greenland

NASA Astrophysics Data System (ADS)

Cooley, S.; Christoffersen, P.

2016-12-01

Rapid drainage of supraglacial lakes on the Greenland Ice Sheet is critical for the establishment of surface-to-bed hydrologic connections and the subsequent transfer of water from surface to bed. Yet, estimates of the number and spatial distribution of rapidly draining lakes vary widely due to limitations in the temporal frequency of image collection and obscureness by cloud. So far, no study has assessed the impact of these observation biases. In this study, we examine the frequency and elevation of rapidly draining lakes in central West Greenland, from 68°N to 72.6°N, and we make a robust statistical analysis to estimate more accurately the likelihood of lakes draining rapidly. Using MODIS imagery and a fully automated lake detection method, we map more than 500 supraglacial lakes per year over a 63000 km2 study area from 2000-2015. Through testing four different definitions of rapidly draining lakes from previously published studies, we find that the number of rapidly draining lakes varies from 3% to 38%. Logistic regression between rapid drainage events and image sampling frequency demonstrates that the number of rapid drainage events is strongly dependent on cloud-free observation percentage. We then develop three new drainage criteria and apply an observation bias correction that suggests a true rapid drainage probability between 36% and 45%, considerably higher than previous studies without bias assessment have reported. We find rapid-draining lakes are on average larger and disappear earlier than slow-draining lakes, and we also observe no elevation differences for the lakes detected as rapidly draining. We conclude a) that methodological problems in rapid drainage research caused by observation bias and varying detection methods have obscured large-scale rapid drainage characteristics and b) that the lack of evidence for an elevation limit on rapid drainage suggests surface-to-bed hydrologic connections may continue to propagate inland as climate warms.

On-line characterization of monoclonal antibody variants by liquid chromatography-mass spectrometry operating in a two-dimensional format.

PubMed

Alvarez, Melissa; Tremintin, Guillaume; Wang, Jennifer; Eng, Marian; Kao, Yung-Hsiang; Jeong, Justin; Ling, Victor T; Borisov, Oleg V

2011-12-01

Recombinant monoclonal antibodies (MAbs) have become one of the most rapidly growing classes of biotherapeutics in the treatment of human disease. MAbs are highly heterogeneous proteins, thereby requiring a battery of analytical technologies for their characterization. However, incompatibility between separation and subsequent detection is often encountered. Here we demonstrate the utility of a generic on-line liquid chromatography-mass spectrometry (LC-MS) method operated in a two-dimensional format toward the rapid characterization of MAb charge and size variants. Using a single chromatographic system capable of running two independent gradients, up to six fractions of interest from an ion exchange (IEC) or size exclusion (SEC) separation can be identified by trapping and desalting the fractions onto a series of reversed phase trap cartridges with subsequent on-line analysis by mass spectrometry. Analysis of poorly resolved and low-level peaks in the IEC or SEC profile was facilitated by preconcentrating fractions on the traps using multiple injections. An on-line disulfide reduction step was successfully incorporated into the workflow, allowing more detailed characterization of modified MAbs by providing chain-specific information. The system is fully automated, thereby enabling high-throughput analysis with minimal sample handling. This technology provides rapid data turnaround time, a much needed feature during product characterization and development of multiple biotherapeutic proteins. Copyright © 2011 Elsevier Inc. All rights reserved.

The Java Image Science Toolkit (JIST) for rapid prototyping and publishing of neuroimaging software.

PubMed

Lucas, Blake C; Bogovic, John A; Carass, Aaron; Bazin, Pierre-Louis; Prince, Jerry L; Pham, Dzung L; Landman, Bennett A

2010-03-01

Non-invasive neuroimaging techniques enable extraordinarily sensitive and specific in vivo study of the structure, functional response and connectivity of biological mechanisms. With these advanced methods comes a heavy reliance on computer-based processing, analysis and interpretation. While the neuroimaging community has produced many excellent academic and commercial tool packages, new tools are often required to interpret new modalities and paradigms. Developing custom tools and ensuring interoperability with existing tools is a significant hurdle. To address these limitations, we present a new framework for algorithm development that implicitly ensures tool interoperability, generates graphical user interfaces, provides advanced batch processing tools, and, most importantly, requires minimal additional programming or computational overhead. Java-based rapid prototyping with this system is an efficient and practical approach to evaluate new algorithms since the proposed system ensures that rapidly constructed prototypes are actually fully-functional processing modules with support for multiple GUI's, a broad range of file formats, and distributed computation. Herein, we demonstrate MRI image processing with the proposed system for cortical surface extraction in large cross-sectional cohorts, provide a system for fully automated diffusion tensor image analysis, and illustrate how the system can be used as a simulation framework for the development of a new image analysis method. The system is released as open source under the Lesser GNU Public License (LGPL) through the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC).

The Java Image Science Toolkit (JIST) for Rapid Prototyping and Publishing of Neuroimaging Software

PubMed Central

Lucas, Blake C.; Bogovic, John A.; Carass, Aaron; Bazin, Pierre-Louis; Prince, Jerry L.; Pham, Dzung

2010-01-01

Non-invasive neuroimaging techniques enable extraordinarily sensitive and specific in vivo study of the structure, functional response and connectivity of biological mechanisms. With these advanced methods comes a heavy reliance on computer-based processing, analysis and interpretation. While the neuroimaging community has produced many excellent academic and commercial tool packages, new tools are often required to interpret new modalities and paradigms. Developing custom tools and ensuring interoperability with existing tools is a significant hurdle. To address these limitations, we present a new framework for algorithm development that implicitly ensures tool interoperability, generates graphical user interfaces, provides advanced batch processing tools, and, most importantly, requires minimal additional programming or computational overhead. Java-based rapid prototyping with this system is an efficient and practical approach to evaluate new algorithms since the proposed system ensures that rapidly constructed prototypes are actually fully-functional processing modules with support for multiple GUI's, a broad range of file formats, and distributed computation. Herein, we demonstrate MRI image processing with the proposed system for cortical surface extraction in large cross-sectional cohorts, provide a system for fully automated diffusion tensor image analysis, and illustrate how the system can be used as a simulation framework for the development of a new image analysis method. The system is released as open source under the Lesser GNU Public License (LGPL) through the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC). PMID:20077162

Selective One-Dimensional Total Correlation Spectroscopy Nuclear Magnetic Resonance Experiments for a Rapid Identification of Minor Components in the Lipid Fraction of Milk and Dairy Products: Toward Spin Chromatography?

PubMed

Papaemmanouil, Christina; Tsiafoulis, Constantinos G; Alivertis, Dimitrios; Tzamaloukas, Ouranios; Miltiadou, Despoina; Tzakos, Andreas G; Gerothanassis, Ioannis P

2015-06-10

We report a rapid, direct, and unequivocal spin-chromatographic separation and identification of minor components in the lipid fraction of milk and common dairy products with the use of selective one-dimensional (1D) total correlation spectroscopy (TOCSY) nuclear magnetic resonance (NMR) experiments. The method allows for the complete backbone spin-coupling network to be elucidated even in strongly overlapped regions and in the presence of major components from 4 × 10(2) to 3 × 10(3) stronger NMR signal intensities. The proposed spin-chromatography method does not require any derivatization steps for the lipid fraction, is selective with excellent resolution, is sensitive with quantitation capability, and compares favorably to two-dimensional (2D) TOCSY and gas chromatography-mass spectrometry (GC-MS) methods of analysis. The results of the present study demonstrated that the 1D TOCSY NMR spin-chromatography method can become a procedure of primary interest in food analysis and generally in complex mixture analysis.

Situation exploration in a persistent surveillance system with multidimensional data

NASA Astrophysics Data System (ADS)

Habibi, Mohammad S.

2013-03-01

There is an emerging need for fusing hard and soft sensor data in an efficient surveillance system to provide accurate estimation of situation awareness. These mostly abstract, multi-dimensional and multi-sensor data pose a great challenge to the user in performing analysis of multi-threaded events efficiently and cohesively. To address this concern an interactive Visual Analytics (VA) application is developed for rapid assessment and evaluation of different hypotheses based on context-sensitive ontology spawn from taxonomies describing human/human and human/vehicle/object interactions. A methodology is described here for generating relevant ontology in a Persistent Surveillance System (PSS) and demonstrates how they can be utilized in the context of PSS to track and identify group activities pertaining to potential threats. The proposed VA system allows for visual analysis of raw data as well as metadata that have spatiotemporal representation and content-based implications. Additionally in this paper, a technique for rapid search of tagged information contingent to ranking and confidence is explained for analysis of multi-dimensional data. Lastly the issue of uncertainty associated with processing and interpretation of heterogeneous data is also addressed.

Miniaturized sample preparation needle: a versatile design for the rapid analysis of smoking-related compounds in hair and air samples.

PubMed

Saito, Yoshihiro; Ueta, Ikuo; Ogawa, Mitsuhiro; Hayashida, Makiko; Jinno, Kiyokatsu

2007-05-09

Miniaturized needle extraction device has been developed as a versatile sample preparation device designed for the rapid and simple analysis of smoking-related compounds in smokers' hair samples and environmental tobacco smoke. Packed with polymeric particle, the resulting particle-packed needle was employed as a miniaturized sample preparation device for the analysis of typical volatile organic compounds in tobacco smoke. Introducing a bundle of polymer-coated filaments as the extraction medium, the needle was further applied as a novel sample preparation device containing simultaneous derivatization/extraction process of volatile aldehydes. Formaldehyde (FA) and acetaldehyde (AA) in smoker's breath during the smoking were successfully derivatized with two derivatization reagents in the polymer-coated fiber-packed needle device followed by the separation and determination in gas chromatography (GC). Smokers' hair samples were also packed into the needle, allowing the direct extraction of nicotine from the hair sample in a conventional GC injector. Optimizing the main experimental parameters for each technique, successful determination of several smoking-related compounds with these needle extraction methods has been demonstrated.

Catharanthus roseus: a natural source for the synthesis of silver nanoparticles

PubMed Central

Mukunthan, KS; Elumalai, EK; Patel, Trupti N; Murty, V Ramachandra

2011-01-01

Objective To develop a simple rapid procedure for bioreduction of silver nanoparticles (AgNPs) using aqueous leaves extracts of Catharanthus roseus (C. roseus). Methods Characterization were determined by using UV-Vis spectrophotometry, scanning electron microscopy (SEM), energy dispersive X-ray and X-ray diffraction. Results SEM showed the formation of silver nanoparticles with an average size of 67 nm to 48 nm. X-ray diffraction analysis showed that the particles were crystalline in nature with face centered cubic geometry. Conclusions C. roseus demonstrates strong potential for synthesis of silver nanoparticles by rapid reduction of silver ions (Ag+ to Ag0). This study provides evidence for developing large scale commercial production of value-added products for biomedical/nanotechnology-based industries. PMID:23569773

Cellufine sulfate column chromatography as a simple, rapid, and effective method to purify dengue virus.

PubMed

Kanlaya, Rattiyaporn; Thongboonkerd, Visith

2016-08-01

Conventional method to purify/concentrate dengue virus (DENV) is time-consuming with low virus recovery yield. Herein, we applied cellufine sulfate column chromatography to purify/concentrate DENV based on the mimicry between heparan sulfate and DENV envelope protein. Comparative analysis demonstrated that this new method offered higher purity (as determined by less contamination of bovine serum albumin) and recovery yield (as determined by greater infectivity). Moreover, overall duration used for cellufine sulfate column chromatography to purify/concentrate DENV was approximately 1/20 of that of conventional method. Therefore, cellufine sulfate column chromatography serves as a simple, rapid, and effective alternative method for DENV purification/concentration. Copyright © 2016 Elsevier B.V. All rights reserved.

Microfluidic study of fast gas-liquid reactions.

PubMed

Li, Wei; Liu, Kun; Simms, Ryan; Greener, Jesse; Jagadeesan, Dinesh; Pinto, Sascha; Günther, Axel; Kumacheva, Eugenia

2012-02-15

We present a new concept for studies of the kinetics of fast gas-liquid reactions. The strategy relies on the microfluidic generation of highly monodisperse gas bubbles in the liquid reaction medium and subsequent analysis of time-dependent changes in bubble dimensions. Using reactions of CO(2) with secondary amines as an exemplary system, we demonstrate that the method enables rapid determination of reaction rate constant and conversion, and comparison of various binding agents. The proposed approach addresses two challenges in studies of gas-liquid reactions: a mass-transfer limitation and a poorly defined gas-liquid interface. The proposed strategy offers new possibilities in studies of the fundamental aspects of rapid multiphase reactions, and can be combined with throughput optimization of reaction conditions.

Field Demonstration of a Multiplexed Point-of-Care Diagnostic Platform for Plant Pathogens.

PubMed

Lau, Han Yih; Wang, Yuling; Wee, Eugene J H; Botella, Jose R; Trau, Matt

2016-08-16

Effective disease management strategies to prevent catastrophic crop losses require rapid, sensitive, and multiplexed detection methods for timely decision making. To address this need, a rapid, highly specific and sensitive point-of-care method for multiplex detection of plant pathogens was developed by taking advantage of surface-enhanced Raman scattering (SERS) labeled nanotags and recombinase polymerase amplification (RPA), which is a rapid isothermal amplification method with high specificity. In this study, three agriculturally important plant pathogens (Botrytis cinerea, Pseudomonas syringae, and Fusarium oxysporum) were used to demonstrate potential translation into the field. The RPA-SERS method was faster, more sensitive than polymerase chain reaction, and could detect as little as 2 copies of B. cinerea DNA. Furthermore, multiplex detection of the three pathogens was demonstrated for complex systems such as the Arabidopsis thaliana plant and commercial tomato crops. To demonstrate the potential for on-site field applications, a rapid single-tube RPA/SERS assay was further developed and successfully performed for a specific target outside of a laboratory setting.

Tool for Rapid Analysis of Monte Carlo Simulations

NASA Technical Reports Server (NTRS)

Restrepo, Carolina; McCall, Kurt E.; Hurtado, John E.

2013-01-01

Designing a spacecraft, or any other complex engineering system, requires extensive simulation and analysis work. Oftentimes, the large amounts of simulation data generated are very difficult and time consuming to analyze, with the added risk of overlooking potentially critical problems in the design. The authors have developed a generic data analysis tool that can quickly sort through large data sets and point an analyst to the areas in the data set that cause specific types of failures. The first version of this tool was a serial code and the current version is a parallel code, which has greatly increased the analysis capabilities. This paper describes the new implementation of this analysis tool on a graphical processing unit, and presents analysis results for NASA's Orion Monte Carlo data to demonstrate its capabilities.

Coupled Solid Rocket Motor Ballistics and Trajectory Modeling for Higher Fidelity Launch Vehicle Design

NASA Technical Reports Server (NTRS)

Ables, Brett

2014-01-01

Multi-stage launch vehicles with solid rocket motors (SRMs) face design optimization challenges, especially when the mission scope changes frequently. Significant performance benefits can be realized if the solid rocket motors are optimized to the changing requirements. While SRMs represent a fixed performance at launch, rapid design iterations enable flexibility at design time, yielding significant performance gains. The streamlining and integration of SRM design and analysis can be achieved with improved analysis tools. While powerful and versatile, the Solid Performance Program (SPP) is not conducive to rapid design iteration. Performing a design iteration with SPP and a trajectory solver is a labor intensive process. To enable a better workflow, SPP, the Program to Optimize Simulated Trajectories (POST), and the interfaces between them have been improved and automated, and a graphical user interface (GUI) has been developed. The GUI enables real-time visual feedback of grain and nozzle design inputs, enforces parameter dependencies, removes redundancies, and simplifies manipulation of SPP and POST's numerous options. Automating the analysis also simplifies batch analyses and trade studies. Finally, the GUI provides post-processing, visualization, and comparison of results. Wrapping legacy high-fidelity analysis codes with modern software provides the improved interface necessary to enable rapid coupled SRM ballistics and vehicle trajectory analysis. Low cost trade studies demonstrate the sensitivities of flight performance metrics to propulsion characteristics. Incorporating high fidelity analysis from SPP into vehicle design reduces performance margins and improves reliability. By flying an SRM designed with the same assumptions as the rest of the vehicle, accurate comparisons can be made between competing architectures. In summary, this flexible workflow is a critical component to designing a versatile launch vehicle model that can accommodate a volatile mission scope.

Characterizing Orthostatic Tremor Using a Smartphone Application.

PubMed

Balachandar, Arjun; Fasano, Alfonso

2017-01-01

Orthostatic tremor is one of the few tremor conditions requiring an electromyogram for definitive diagnosis since leg tremor might not be visible to the naked eye. An iOS application (iSeismometer, ObjectGraph LLC, New York) using an Apple iPhone 5 (Cupertino, CA, USA) inserted into the patient's sock detected a tremor with a frequency of 16.4 Hz on both legs. The rapid and straightforward accelerometer-based recordings accomplished in this patient demonstrate the ease with which quantitative analysis of orthostatic tremor can be conducted and, importantly, demonstrates the potential application of this approach in the assessment of any lower limb tremor.

Quantitative model of diffuse speckle contrast analysis for flow measurement.

PubMed

Liu, Jialin; Zhang, Hongchao; Lu, Jian; Ni, Xiaowu; Shen, Zhonghua

2017-07-01

Diffuse speckle contrast analysis (DSCA) is a noninvasive optical technique capable of monitoring deep tissue blood flow. However, a detailed study of the speckle contrast model for DSCA has yet to be presented. We deduced the theoretical relationship between speckle contrast and exposure time and further simplified it to a linear approximation model. The feasibility of this linear model was validated by the liquid phantoms which demonstrated that the slope of this linear approximation was able to rapidly determine the Brownian diffusion coefficient of the turbid media at multiple distances using multiexposure speckle imaging. Furthermore, we have theoretically quantified the influence of optical property on the measurements of the Brownian diffusion coefficient which was a consequence of the fact that the slope of this linear approximation was demonstrated to be equal to the inverse of correlation time of the speckle.

Multivariate analysis of nystatin and metronidazole in a semi-solid matrix by means of diffuse reflectance NIR spectroscopy and PLS regression.

PubMed

Baratieri, Sabrina C; Barbosa, Juliana M; Freitas, Matheus P; Martins, José A

2006-01-23

A multivariate method of analysis of nystatin and metronidazole in a semi-solid matrix, based on diffuse reflectance NIR measurements and partial least squares regression, is reported. The product, a vaginal cream used in the antifungal and antibacterial treatment, is usually, quantitatively analyzed through microbiological tests (nystatin) and HPLC technique (metronidazole), according to pharmacopeial procedures. However, near infrared spectroscopy has demonstrated to be a valuable tool for content determination, given the rapidity and scope of the method. In the present study, it was successfully applied in the prediction of nystatin (even in low concentrations, ca. 0.3-0.4%, w/w, which is around 100,000 IU/5g) and metronidazole contents, as demonstrated by some figures of merit, namely linearity, precision (mean and repeatability) and accuracy.

A Demonstration and Analysis of Requirements for Maritime Navigation Planning.

DTIC Science & Technology

1998-03-01

it the highest and 0-4 and above the lowest. Once again, the value added by grouping the data and comparing may be nothing...purpose behind a prototype is to ascertain user requirements. It should be created rapidly to speed up the system development life cycle ( SDLC ). Since...system is contained in Chapter II, Section B. 3. Internet to Sea (SEANET) Program The SeaNet Project is a collaborative effort to bring the

Comparative Demonstration of Active and Semi-Passive In Situ Bioremediation Approaches for Perchlorate-Impacted Groundwater at Longhorn Army Ammunitions Plant

DTIC Science & Technology

2009-01-01

lactate, citric acid , or ethanol have been used in field applications. Biomass grows rapidly during the active phase when high concentrations of...6.7.4 Results of Oxidation Reduction Potential (ORP) Monitoring.............39 6.7.5 Results of Volatile Fatty Acids (VFA) Analysis...trinitrotoluene USEPA U.S. Environmental Protection Agency VC vinyl chloride VFA volatile fatty acid VOC volatile organic compounds Technical

WPSS: watching people security services

NASA Astrophysics Data System (ADS)

Bouma, Henri; Baan, Jan; Borsboom, Sander; van Zon, Kasper; Luo, Xinghan; Loke, Ben; Stoeller, Bram; van Kuilenburg, Hans; Dijk, Judith

2013-10-01

To improve security, the number of surveillance cameras is rapidly increasing. However, the number of human operators remains limited and only a selection of the video streams are observed. Intelligent software services can help to find people quickly, evaluate their behavior and show the most relevant and deviant patterns. We present a software platform that contributes to the retrieval and observation of humans and to the analysis of their behavior. The platform consists of mono- and stereo-camera tracking, re-identification, behavioral feature computation, track analysis, behavior interpretation and visualization. This system is demonstrated in a busy shopping mall with multiple cameras and different lighting conditions.

The physics of a popsicle stick bomb

NASA Astrophysics Data System (ADS)

Sautel, Jérémy; Bourges, Andréane; Caussarieu, Aude; Plihon, Nicolas; Taberlet, Nicolas

2017-10-01

Popsicle sticks can be interlocked in the so-called "cobra weave" to form a chain under tension. When one end of the chain is released, the sticks rapidly disentangle, forming a traveling wave that propagates down the chain. In this paper, the properties of the traveling front are studied experimentally, and classical results from the theory of elasticity allow for a dimensional analysis of the height and speed of the traveling wave. The study presented here can help undergraduate students familiarize themselves with experimental techniques of image processing, and it also demonstrates the power of dimensional analysis and scaling laws.

Principal component analysis of bacteria using surface-enhanced Raman spectroscopy

NASA Astrophysics Data System (ADS)

Guicheteau, Jason; Christesen, Steven D.

2006-05-01

Surface-enhanced Raman scattering (SERS) provides rapid fingerprinting of biomaterial in a non-destructive manner. The problem of tissue fluorescence, which can overwhelm a normal Raman signal from biological samples, is largely overcome by treatment of biomaterials with colloidal silver. This work presents a study into the applicability of qualitative SER spectroscopy with principal component analysis (PCA) for the discrimination of four biological threat simulants; Bacillus globigii, Pantoea agglomerans, Brucella noetomae, and Yersinia rohdei. We also demonstrate differentiation of gram-negative and gram-positive species and as well as spores and vegetative cells of Bacillus globigii.

Rapid analysis of abietanes in conifers.

PubMed

Kersten, P J; Kopper, B J; Raffa, K F; Illman, B L

2006-12-01

Diterpene resin acids are major constituents of conifer oleoresin and play important roles in tree defense against insects and microbial pathogens. The tricyclic C-20 carboxylic acids are generally classified into two groups, the abietanes and the pimaranes. The abietanes have conjugated double bonds and exhibit characteristic UV spectra. Here, we report the analysis of abietanes by reversed-phase high-performance liquid chromatography using multiwavelength detection to optimize quantification of underivatized abietic, neoabietic, palustric, levopimaric, and dehydroabietic acids. The utility of the method is demonstrated with methanol extracts of white spruce (Picea glauca) phloem, and representative concentrations are reported.

Direct analysis of volatile organic compounds in foods by headspace extraction atmospheric pressure chemical ionisation mass spectrometry.

PubMed

Perez-Hurtado, P; Palmer, E; Owen, T; Aldcroft, C; Allen, M H; Jones, J; Creaser, C S; Lindley, M R; Turner, M A; Reynolds, J C

2017-11-30

The rapid screening of volatile organic compounds (VOCs) by direct analysis has potential applications in the areas of food and flavour science. Currently, the technique of choice for VOC analysis is gas chromatography/mass spectrometry (GC/MS). However, the long chromatographic run times and elaborate sample preparation associated with this technique have led a movement towards direct analysis techniques, such as selected ion flow tube mass spectrometry (SIFT-MS), proton transfer reaction mass spectrometry (PTR-MS) and electronic noses. The work presented here describes the design and construction of a Venturi jet-pump-based modification for a compact mass spectrometer which enables the direct introduction of volatiles for qualitative and quantitative analysis. Volatile organic compounds were extracted from the headspace of heated vials into the atmospheric pressure chemical ionization source of a quadrupole mass spectrometer using a Venturi pump. Samples were analysed directly with no prior sample preparation. Principal component analysis (PCA) was used to differentiate between different classes of samples. The interface is shown to be able to routinely detect problem analytes such as fatty acids and biogenic amines without the requirement of a derivatisation step, and is shown to be able to discriminate between four different varieties of cheese with good intra and inter-day reproducibility using an unsupervised PCA model. Quantitative analysis is demonstrated using indole standards with limits of detection and quantification of 0.395 μg/mL and 1.316 μg/mL, respectively. The described methodology can routinely detect highly reactive analytes such as volatile fatty acids and diamines without the need for a derivatisation step or lengthy chromatographic separations. The capability of the system was demonstrated by discriminating between different varieties of cheese and monitoring the spoilage of meats. © 2017 The Authors. Rapid Communications in Mass Spectrometry Published by John Wiley & Sons Ltd.

Rapid and non-destructive identification of water-injected beef samples using multispectral imaging analysis.

PubMed

Liu, Jinxia; Cao, Yue; Wang, Qiu; Pan, Wenjuan; Ma, Fei; Liu, Changhong; Chen, Wei; Yang, Jianbo; Zheng, Lei

2016-01-01

Water-injected beef has aroused public concern as a major food-safety issue in meat products. In the study, the potential of multispectral imaging analysis in the visible and near-infrared (405-970 nm) regions was evaluated for identifying water-injected beef. A multispectral vision system was used to acquire images of beef injected with up to 21% content of water, and partial least squares regression (PLSR) algorithm was employed to establish prediction model, leading to quantitative estimations of actual water increase with a correlation coefficient (r) of 0.923. Subsequently, an optimized model was achieved by integrating spectral data with feature information extracted from ordinary RGB data, yielding better predictions (r = 0.946). Moreover, the prediction equation was transferred to each pixel within the images for visualizing the distribution of actual water increase. These results demonstrate the capability of multispectral imaging technology as a rapid and non-destructive tool for the identification of water-injected beef. Copyright © 2015 Elsevier Ltd. All rights reserved.

Rapid Prototyping Technology for Manufacturing GTE Turbine Blades

NASA Astrophysics Data System (ADS)

Balyakin, A. V.; Dobryshkina, E. M.; Vdovin, R. A.; Alekseev, V. P.

2018-03-01

The conventional approach to manufacturing turbine blades by investment casting is expensive and time-consuming, as it takes a lot of time to make geometrically precise and complex wax patterns. Turbine blade manufacturing in pilot production can be sped up by accelerating the casting process while keeping the geometric precision of the final product. This paper compares the rapid prototyping method (casting the wax pattern composition into elastic silicone molds) to the conventional technology. Analysis of the size precision of blade casts shows that silicon-mold casting features sufficient geometric precision. Thus, this method for making wax patterns can be a cost-efficient solution for small-batch or pilot production of turbine blades for gas-turbine units (GTU) and gas-turbine engines (GTE). The paper demonstrates how additive technology and thermographic analysis can speed up the cooling of wax patterns in silicone molds. This is possible at an optimal temperature and solidification time, which make the process more cost-efficient while keeping the geometric quality of the final product.

Emergence and global spread of epidemic healthcare-associated Clostridium difficile

PubMed Central

He, Miao; Miyajima, Fabio; Roberts, Paul; Ellison, Louise; Pickard, Derek J.; Martin, Melissa J.; Connor, Thomas R.; Harris, Simon R.; Fairley, Derek; Bamford, Kathleen B.; D’Arc, Stephanie; Brazier, Jon; Brown, Derek; Coia, John E.; Douce, Gill; Gerding, Dale; Kim, Hee Jung; Koh, Tse Hsien; Kato, Haru; Senoh, Mitsutoshi; Louie, Tom; Michell, Stephen; Butt, Emma; Peacock, Sharon J.; Brown, Nick M.; Riley, Tom; Songer, Glen; Wilcox, Mark; Pirmohamed, Munir; Kuijper, Ed; Hawkey, Peter; Wren, Brendan W.; Dougan, Gordon; Parkhill, Julian; Lawley, Trevor D.

2012-01-01

Epidemic Clostridium difficile (027/BI/NAP1) rapidly emerged in the past decade as the leading cause of antibiotic-associated diarrhea worldwide. However, the key moments in the evolutionary history leading to its emergence and subsequent patterns of global spread remain unknown. Here we define the global population structure of C. difficile 027/BI/NAP1 based on whole-genome sequencing and phylogenetic analysis. We demonstrate that two distinct epidemic lineages, FQR1 and FQR2, not one as previously thought, emerged in North America within a relatively short period after acquiring the same fluoroquinolone resistance mutation and a highly-related conjugative transposon. The two epidemic lineages displayed distinct patterns of global spread, and the FQR2 lineage spread more widely leading to healthcare outbreaks in the UK, continental Europe and Australia. Our analysis identifies key genetic changes linked to the rapid trans-continental dissemination of epidemic C. difficile 027/BI/NAP1 and highlights the routes by which it spreads through the global healthcare system. PMID:23222960

Mid-infrared absorption spectroscopy using quantum cascade lasers

NASA Astrophysics Data System (ADS)

Haibach, Fred; Erlich, Adam; Deutsch, Erik

2011-06-01

Block Engineering has developed an absorption spectroscopy system based on widely tunable Quantum Cascade Lasers (QCL). The QCL spectrometer rapidly cycles through a user-selected range in the mid-infrared spectrum, between 6 to 12 μm (1667 to 833 cm-1), to detect and identify substances on surfaces based on their absorption characteristics from a standoff distance of up to 2 feet with an eye-safe laser. It can also analyze vapors and liquids in a single device. For military applications, the QCL spectrometer has demonstrated trace explosive, chemical warfare agent (CWA), and toxic industrial chemical (TIC) detection and analysis. The QCL's higher power density enables measurements from diffuse and highly absorbing materials and substrates. Other advantages over Fourier Transform Infrared (FTIR) spectroscopy include portability, ruggedness, rapid analysis, and the ability to function from a distance through free space or a fiber optic probe. This paper will discuss the basic technology behind the system and the empirical data on various safety and security applications.

Determination of rice syrup adulterant concentration in honey using three-dimensional fluorescence spectra and multivariate calibrations

NASA Astrophysics Data System (ADS)

Chen, Quansheng; Qi, Shuai; Li, Huanhuan; Han, Xiaoyan; Ouyang, Qin; Zhao, Jiewen

2014-10-01

To rapidly and efficiently detect the presence of adulterants in honey, three-dimensional fluorescence spectroscopy (3DFS) technique was employed with the help of multivariate calibration. The data of 3D fluorescence spectra were compressed using characteristic extraction and the principal component analysis (PCA). Then, partial least squares (PLS) and back propagation neural network (BP-ANN) algorithms were used for modeling. The model was optimized by cross validation, and its performance was evaluated according to root mean square error of prediction (RMSEP) and correlation coefficient (R) in prediction set. The results showed that BP-ANN model was superior to PLS models, and the optimum prediction results of the mixed group (sunflower ± longan ± buckwheat ± rape) model were achieved as follow: RMSEP = 0.0235 and R = 0.9787 in the prediction set. The study demonstrated that the 3D fluorescence spectroscopy technique combined with multivariate calibration has high potential in rapid, nondestructive, and accurate quantitative analysis of honey adulteration.

Study on the echinococcosis blood serum detection based on Raman spectroscopy combined with neural network

NASA Astrophysics Data System (ADS)

Cheng, Jin-ying; Xu, Liang; Lü, Guo-dong; Tang, Jun; Mo, Jia-qing; Lü, Xiao-yi; Gao, Zhi-xian

2017-01-01

A Raman spectroscopy method combined with neural network is used for the invasive and rapid detection of echinococcosis. The Raman spectroscopy measurements are performed on two groups of blood serum samples, which are from 28 echinococcosis patients and 38 healthy persons, respectively. The normalized Raman reflection spectra show that the reflectivity of the echinococcosis blood serum is higher than that of the normal human blood serum in the wavelength ranges of 101—175 nm and 1 801—2 701 nm. Then the principal component analysis (PCA) and back propagation neural network (BPNN) model are used to obtain the diagnosis results. The diagnosis rates for healthy persons and echinococcosis persons are 93.333 3% and 90.909 1%, respectively, so the average final diagnosis rate is 92.121 2%. The results demonstrate that the Raman spectroscopy analysis of blood serum combined with PCA-BPNN has considerable potential for the non-invasive and rapid detection of echinococcosis.

Velocity Mapping Toolbox (VMT): a processing and visualization suite for moving-vessel ADCP measurements

USGS Publications Warehouse

Parsons, D.R.; Jackson, P.R.; Czuba, J.A.; Engel, F.L.; Rhoads, B.L.; Oberg, K.A.; Best, J.L.; Mueller, D.S.; Johnson, K.K.; Riley, J.D.

2013-01-01

The use of acoustic Doppler current profilers (ADCP) for discharge measurements and three-dimensional flow mapping has increased rapidly in recent years and has been primarily driven by advances in acoustic technology and signal processing. Recent research has developed a variety of methods for processing data obtained from a range of ADCP deployments and this paper builds on this progress by describing new software for processing and visualizing ADCP data collected along transects in rivers or other bodies of water. The new utility, the Velocity Mapping Toolbox (VMT), allows rapid processing (vector rotation, projection, averaging and smoothing), visualization (planform and cross-section vector and contouring), and analysis of a range of ADCP-derived datasets. The paper documents the data processing routines in the toolbox and presents a set of diverse examples that demonstrate its capabilities. The toolbox is applicable to the analysis of ADCP data collected in a wide range of aquatic environments and is made available as open-source code along with this publication.

Rapid In Situ Profiling of Lipid C═C Location Isomers in Tissue Using Ambient Mass Spectrometry with Photochemical Reactions.

PubMed

Tang, Fei; Guo, Chengan; Ma, Xiaoxiao; Zhang, Jian; Su, Yuan; Tian, Ran; Shi, Riyi; Xia, Yu; Wang, Xiaohao; Ouyang, Zheng

2018-05-01

Rapid and in situ profiling of lipids using ambient mass spectrometry (AMS) techniques has great potential for clinical diagnosis, biological studies, and biomarker discovery. In this study, the online photochemical reaction involving carbon-carbon double bonds was coupled with a surface sampling technique to develop a direct tissue-analysis method with specificity to lipid C═C isomers. This method enabled the in situ analysis of lipids from the surface of various tissues or tissue sections, which allowed the structural characterization of lipid isomers within 2 min. Under optimized reaction conditions, we have established a method for the relative quantitation of lipid C═C location isomers by comparing the abundances of the diagnostic ions arising from each isomer, which has been proven effective through the established linear relationship ( R 2 = 0.999) between molar ratio and diagnostic ion ratio of the FA 18:1 C═C location isomers. This method was then used for the rapid profiling of unsaturated lipid C═C isomers in the sections of rat brain, lung, liver, spleen, and kidney, as well as in normal and diseased rat tissues. Quantitative information on FA 18:1 and PC 16:0-18:1 C═C isomers was obtained, and significant differences were observed between different samples. To the best of our knowledge, this is the first study to report the direct analysis of lipid C═C isomers in tissues using AMS. Our results demonstrated that this method can serve as a rapid analytical approach for the profiling of unsaturated lipid C═C isomers in biological tissues and should contribute to functional lipidomics and clinical diagnosis.

Rapid Quantitative Analysis of Microcystins in Raw Surface Waters with MALDI MS Utilizing Easily Synthesized Internal Standards

PubMed Central

Roegner, Amber F.; Schirmer, Macarena Pírez; Puschner, Birgit; Brena, Beatriz; Gonzalez-Sapienza, Gualberto

2014-01-01

The freshwater cyanotoxins, microcystins (MCs), pose a global public health threat as potent hepatotoxins in cyanobacterial blooms; their persistence in drinking and recreational water has been associated with potential chronic effects in addition to acute intoxications. Rapid and accurate detection of the over 80 structural congeners is challenged by the rigorous and time consuming clean up required to overcome interference found in raw water samples. MALDI-MS has shown promise for rapid quantification of individual congeners in raw water samples, with very low operative cost, but so far limited sensitivity and lack of available and versatile internal standards (ISs) has limited its use. Two easily synthesized S-hydroxyethyl–Cys(7)-MC-LR and –RR ISs were used to generate linear standard curves in a reflectron MALDI instrument, reproducible across several orders of magnitude for MC –LR, - RR and –YR. Minimum quantification limits in direct water samples with no clean up or concentration step involved were consistently below 7 μg/L, with recoveries from spiked samples between 80 and 119%. This method improves sensitivity by 30 fold over previous reports of quantitative MALDI-TOF applications to MCs and provides a salient option for rapid throughput analysis for multiple MC congeners in untreated raw surface water blooms as a means to identify source public health threats and target intervention strategies within a watershed. As demonstrated by analysis of a set of samples from Uruguay, utilizing the reaction of different MC congeners with alternate sulfhydryl compounds, the m/z of the IS can be customized to avoid overlap with interfering compounds in local surface water samples. PMID:24388801

The use of interpractive graphic displays for interpretation of surface design parameters

NASA Technical Reports Server (NTRS)

Talcott, N. A., Jr.

1981-01-01

An interactive computer graphics technique known as the Graphic Display Data method has been developed to provide a convenient means for rapidly interpreting large amounts of surface design data. The display technique should prove valuable in such disciplines as aerodynamic analysis, structural analysis, and experimental data analysis. To demonstrate the system's features, an example is presented of the Graphic Data Display method used as an interpretive tool for radiation equilibrium temperature distributions over the surface of an aerodynamic vehicle. Color graphic displays were also examined as a logical extension of the technique to improve its clarity and to allow the presentation of greater detail in a single display.

Consolidation quality and mechanical performance of stamp formed tailored blanks produced by rapid AFP

NASA Astrophysics Data System (ADS)

Slange, T. K.; Warnet, L. L.; Grouve, W. J. B.; Akkerman, R.

2018-05-01

Stamp forming is a rapid manufacturing technology used to shape flat blanks of thermoplastic composite material into three-dimensional components. The combination with rapid AFP as blank manufacturing technology can further extend the applicability of stamp forming by allowing rapid lay-up of tailored blanks and offering partial preconsolidation. In an experimental study it is demonstrated that high quality laminates with good flexural strength can be obtained by following this process route. The consolidation of ply-drop regions is demonstrated by flat laminates with a thickness step. The influence of fiber orientations, blank-tooling misalignments and AFP tolerances is investigated.

Rapid underway profiling of water quality in Queensland estuaries.

PubMed

Hodge, Jonathan; Longstaff, Ben; Steven, Andy; Thornton, Phillip; Ellis, Peter; McKelvie, Ian

2005-01-01

We present an overview of a portable underway water quality monitoring system (RUM-Rapid Underway Monitoring), developed by integrating several off-the-shelf water quality instruments to provide rapid, comprehensive, and spatially referenced 'snapshots' of water quality conditions. We demonstrate the utility of the system from studies in the Northern Great Barrier Reef (Daintree River) and the Moreton Bay region. The Brisbane dataset highlights RUM's utility in characterising plumes as well as its ability to identify the smaller scale structure of large areas. RUM is shown to be particularly useful when measuring indicators with large small-scale variability such as turbidity and chlorophyll-a. Additionally, the Daintree dataset shows the ability to integrate other technologies, resulting in a more comprehensive analysis, whilst sampling offshore highlights some of the analytical issues required for sampling low concentration data. RUM is a low cost, highly flexible solution that can be modified for use in any water type, on most vessels and is only limited by the available monitoring technologies.

Hyperspectral Imaging and SPA-LDA Quantitative Analysis for Detection of Colon Cancer Tissue

NASA Astrophysics Data System (ADS)

Yuan, X.; Zhang, D.; Wang, Ch.; Dai, B.; Zhao, M.; Li, B.

2018-05-01

Hyperspectral imaging (HSI) has been demonstrated to provide a rapid, precise, and noninvasive method for cancer detection. However, because HSI contains many data, quantitative analysis is often necessary to distill information useful for distinguishing cancerous from normal tissue. To demonstrate that HSI with our proposed algorithm can make this distinction, we built a Vis-NIR HSI setup and made many spectral images of colon tissues, and then used a successive projection algorithm (SPA) to analyze the hyperspectral image data of the tissues. This was used to build an identification model based on linear discrimination analysis (LDA) using the relative reflectance values of the effective wavelengths. Other tissues were used as a prediction set to verify the reliability of the identification model. The results suggest that Vis-NIR hyperspectral images, together with the spectroscopic classification method, provide a new approach for reliable and safe diagnosis of colon cancer and could lead to advances in cancer diagnosis generally.

A rapid HPLC method for simultaneous determination of tretinoin and isotretinoin in dermatological formulations.

PubMed

Tashtoush, Bassam M; Jacobson, Elaine L; Jacobson, Myron K

2007-02-19

A rapid method using an isocratic high-pressure liquid chromatography and UV detection for determination of both all-trans retinoic acid (tretinoin) and 13-cis retinoic acid (isotretinoin) in dermatological preparations is presented. Tretinoin and isotretinoin samples were extracted with acetonitrile by a procedure that can be completed in less than 10 min. Subsequent separation and quantification of amounts as low as 10 pmol was accomplished in less than 15 min using reversed-phase HPLC with isocratic elution with 0.01% trifluoroacetic acid (TFA)/acetonitrile (15:85, v/v). Validation experiments confirmed the precision and accuracy of the method. When applied to commercial tretinoin samples, recoveries of 104.9% for cream formulations and 107.7% for gel formulations were obtained. Application of the method for analysis of a tretinoin cream exposed to solar simulated light (SSL) demonstrated detection of the major photoisomerization product isotretinoin as well as 9-cis retinoic acid, demonstrating the utility of the method for studies of tretinoin photostability. The method should also facilitate studies of the formulation compatibility and photocompatibility of tretinoin with agents that may improve its clinical tolerability.

Assessing blood vessel perfusion and vital signs through retinal imaging photoplethysmography.

PubMed

Hassan, Harnani; Jaidka, Sheila; Dwyer, Vincent M; Hu, Sijung

2018-05-01

One solution to the global challenge of increasing ocular disease is a cost-effective technique for rapid screening and assessment. Current ophthalmic imaging techniques, e.g. scanning and ocular blood flow systems, are expensive, complex to operate and utilize invasive contrast agents during assessment. The work presented here demonstrates a simple retinal imaging photoplethysmography (iPPG) system with the potential to provide screening, diagnosis, monitoring and assessment that is non-invasive, painless and radiationless. Time series of individual retinal blood vessel images, captured with an eye fundus camera, are processed using standard filtering, amplitude demodulation and principle component analysis (PCA) methods to determine the values of the heart rate (HR) and respiration rate (RR), which are in compliance with simultaneously obtained measurements using commercial pulse oximetry. It also seems possible that some information on the dynamic changes in oxygen saturation levels ( SpO 2 ) in a retinal blood vessel may also be obtained. As a consequence, the retinal iPPG modality system demonstrates a potential avenue for rapid ophthalmic screening, and even early diagnosis, against ocular disease without the need for fluorescent or contrast agents.

Microwave energy fixation for electron microscopy.

PubMed Central

Login, G. R.; Dvorak, A. M.

1985-01-01

We have demonstrated that microwave energy (MW) can be used in conjunction with chemical cross-linking agents in order to rapidly fix cell suspensions and tissue blocks for electron microscopy in 7-9 seconds. The optimal MW fixation method involved immersing tissues up to 1 cu cm in dilute aldehyde fixation and immediately irradiating the specimens in a conventional microwave oven for 9 seconds to 50 C. Ultrastructural preservation of samples irradiated by MW energy was comparable to that of the control samples immersed in aldehyde fixative for 2 hours at 25 C. Stereologic analysis showed that tissue blocks fixed by the MW fixation method did not cause organelles such as liver mitochondria and salivary gland granules to shrink or to swell. Potential applications for this new fixation technology include the investigation of rapid intracellular processes (eg, vesicular transport) and preservation of proteins that are difficult to demonstrate with routine fixation methods (eg, antigens and enzymes). Images Figure 4 Figure 5 Figure 2 Figure 3 Figure 6 Figure 7 Figure 8 Figure 9 Figure 10 Figure 11 PMID:3927740

Joint Rapid Airfield Construction (JRAC) 2007 Technology Demonstration

DTIC Science & Technology

2008-07-01

ER D C/ G SL T R- 08 -1 7 Joint Rapid Airfield Construction (JRAC) 2007 Technology Demonstration Gary L. Anderton, Ernest S. Berney IV...Technology Demonstration Gary L. Anderton, Ernest S. Berney IV, Travis A. Mann, J. Kent Newman, E. Alex Baylot, Daniel K. Miller, and Quint Mason... Berney IV, Dr. J. Kent Newman, Daniel K. Miller, Quint Mason, Airfields and Pavements Branch (APB), and E. Alex Baylot, Mobility Systems Branch. The

Redistribution of hematoma to spinal subdural space as a mechanism for the rapid spontaneous resolution of posttraumatic intracranial acute subdural hematoma: case report.

PubMed

Wong, Sui To; Yuen, Ming Keung; Fok, Kam Fuk; Yuen, Shing Chau; Yam, Kwong Yui; Fong, Dawson

2009-01-01

Rapid spontaneous resolution of posttraumatic intracranial ASDH has been reported in the literature since 1986. We report a case to demonstrate that redistribution of hematoma to the spinal subdural space is a mechanism for the rapid spontaneous resolution of posttraumatic intracranial ASDH. A 73-year-old woman with a slipped-and-fell injury had a worst GCS score of 8/15. Computerized tomography of the brain demonstrated a large intracranial ASDH with mass effect. Conservative management was decided because of her poor premorbid general condition. Rapid clinical improvement was observed within 5 hours after the CT. Progress CT of the brain at 45 hours postinjury showed that the size of the intracranial ASDH was markedly diminished. The CT findings apparently demonstrated a caudal distribution of the intracranial ASDH over the tentorium and then into the posterior fossa. To investigate this further, an MRI of the spine was performed, which showed that there was spinal SDH in the cervical and thoracic spine. This is the first report demonstrating that redistribution of posttraumatic intracranial ASDH to the spinal subdural space is one of the mechanisms behind the rapid spontaneous resolution of posttraumatic intracranial ASDH in the acute phase.

Rapid Disaster Damage Estimation

NASA Astrophysics Data System (ADS)

Vu, T. T.

2012-07-01

The experiences from recent disaster events showed that detailed information derived from high-resolution satellite images could accommodate the requirements from damage analysts and disaster management practitioners. Richer information contained in such high-resolution images, however, increases the complexity of image analysis. As a result, few image analysis solutions can be practically used under time pressure in the context of post-disaster and emergency responses. To fill the gap in employment of remote sensing in disaster response, this research develops a rapid high-resolution satellite mapping solution built upon a dual-scale contextual framework to support damage estimation after a catastrophe. The target objects are building (or building blocks) and their condition. On the coarse processing level, statistical region merging deployed to group pixels into a number of coarse clusters. Based on majority rule of vegetation index, water and shadow index, it is possible to eliminate the irrelevant clusters. The remaining clusters likely consist of building structures and others. On the fine processing level details, within each considering clusters, smaller objects are formed using morphological analysis. Numerous indicators including spectral, textural and shape indices are computed to be used in a rule-based object classification. Computation time of raster-based analysis highly depends on the image size or number of processed pixels in order words. Breaking into 2 level processing helps to reduce the processed number of pixels and the redundancy of processing irrelevant information. In addition, it allows a data- and tasks- based parallel implementation. The performance is demonstrated with QuickBird images captured a disaster-affected area of Phanga, Thailand by the 2004 Indian Ocean tsunami are used for demonstration of the performance. The developed solution will be implemented in different platforms as well as a web processing service for operational uses.

Rapid prototyping of microfluidic systems using a PDMS/polymer tape composite.

PubMed

Kim, Jungkyu; Surapaneni, Rajesh; Gale, Bruce K

2009-05-07

Rapid prototyping of microfluidic systems using a combination of double-sided tape and PDMS (polydimethylsiloxane) is introduced. PDMS is typically difficult to bond using adhesive tapes due to its hydrophobic nature and low surface energy. For this reason, PDMS is not compatible with the xurography method, which uses a knife plotter and various adhesive coated polymer tapes. To solve these problems, a PDMS/tape composite was developed and demonstrated in microfluidic applications. The PDMS/tape composite was created by spinning it to make a thin layer of PDMS over double-sided tape. Then the PDMS/tape composite was patterned to create channels using xurography, and bonded to a PDMS slab. After removing the backing paper from the tape, a complete microfluidic system could be created by placing the construct onto nearly any substrate; including glass, plastic or metal-coated glass/silicon substrates. The bond strength was shown to be sufficient for the pressures that occur in typical microfluidic channels used for chemical or biological analysis. This method was demonstrated in three applications: standard microfluidic channels and reactors, a microfluidic system with an integrated membrane, and an electrochemical biosensor. The PDMS/tape composite rapid prototyping technique provides a fast and cost effective fabrication method and can provide easy integration of microfluidic channels with sensors and other components without the need for a cleanroom facility.

Fundamentals of rapid injection molding for microfluidic cell-based assays.

PubMed

Lee, Ulri N; Su, Xiaojing; Guckenberger, David J; Dostie, Ashley M; Zhang, Tianzi; Berthier, Erwin; Theberge, Ashleigh B

2018-01-30

Microscale cell-based assays have demonstrated unique capabilities in reproducing important cellular behaviors for diagnostics and basic biological research. As these assays move beyond the prototyping stage and into biological and clinical research environments, there is a need to produce microscale culture platforms more rapidly, cost-effectively, and reproducibly. 'Rapid' injection molding is poised to meet this need as it enables some of the benefits of traditional high volume injection molding at a fraction of the cost. However, rapid injection molding has limitations due to the material and methods used for mold fabrication. Here, we characterize advantages and limitations of rapid injection molding for microfluidic device fabrication through measurement of key features for cell culture applications including channel geometry, feature consistency, floor thickness, and surface polishing. We demonstrate phase contrast and fluorescence imaging of cells grown in rapid injection molded devices and provide design recommendations to successfully utilize rapid injection molding methods for microscale cell-based assay development in academic laboratory settings.

Rapid prediction of ochratoxin A-producing strains of Penicillium on dry-cured meat by MOS-based electronic nose.

PubMed

Lippolis, Vincenzo; Ferrara, Massimo; Cervellieri, Salvatore; Damascelli, Anna; Epifani, Filomena; Pascale, Michelangelo; Perrone, Giancarlo

2016-02-02

The availability of rapid diagnostic methods for monitoring ochratoxigenic species during the seasoning processes for dry-cured meats is crucial and constitutes a key stage in order to prevent the risk of ochratoxin A (OTA) contamination. A rapid, easy-to-perform and non-invasive method using an electronic nose (e-nose) based on metal oxide semiconductors (MOS) was developed to discriminate dry-cured meat samples in two classes based on the fungal contamination: class P (samples contaminated by OTA-producing Penicillium strains) and class NP (samples contaminated by OTA non-producing Penicillium strains). Two OTA-producing strains of Penicillium nordicum and two OTA non-producing strains of Penicillium nalgiovense and Penicillium salamii, were tested. The feasibility of this approach was initially evaluated by e-nose analysis of 480 samples of both Yeast extract sucrose (YES) and meat-based agar media inoculated with the tested Penicillium strains and incubated up to 14 days. The high recognition percentages (higher than 82%) obtained by Discriminant Function Analysis (DFA), either in calibration and cross-validation (leave-more-out approach), for both YES and meat-based samples demonstrated the validity of the used approach. The e-nose method was subsequently developed and validated for the analysis of dry-cured meat samples. A total of 240 e-nose analyses were carried out using inoculated sausages, seasoned by a laboratory-scale process and sampled at 5, 7, 10 and 14 days. DFA provided calibration models that permitted discrimination of dry-cured meat samples after only 5 days of seasoning with mean recognition percentages in calibration and cross-validation of 98 and 88%, respectively. A further validation of the developed e-nose method was performed using 60 dry-cured meat samples produced by an industrial-scale seasoning process showing a total recognition percentage of 73%. The pattern of volatile compounds of dry-cured meat samples was identified and characterized by a developed HS-SPME/GC-MS method. Seven volatile compounds (2-methyl-1-butanol, octane, 1R-α-pinene, d-limonene, undecane, tetradecanal, 9-(Z)-octadecenoic acid methyl ester) allowed discrimination between dry-cured meat samples of classes P and NP. These results demonstrate that MOS-based electronic nose can be a useful tool for a rapid screening in preventing OTA contamination in the cured meat supply chain. Copyright © 2015 Elsevier B.V. All rights reserved.

Rapid detection and typing of pathogenic nonpneumophila Legionella spp. isolates using a multiplex real-time PCR assay.

PubMed

Benitez, Alvaro J; Winchell, Jonas M

2016-04-01

We developed a single tube multiplex real-time PCR assay that allows for the rapid detection and typing of 9 nonpneumophila Legionella spp. isolates that are clinically relevant. The multiplex assay is capable of simultaneously detecting and discriminating L. micdadei, L. bozemanii, L. dumoffii, L. longbeachae, L. feeleii, L. anisa, L. parisiensis, L. tucsonensis serogroup (sg) 1 and 3, and L. sainthelensis sg 1 and 2 isolates. Evaluation of the assay with nucleic acid from each of these species derived from both clinical and environmental isolates and typing strains demonstrated 100% sensitivity and 100% specificity when tested against 43 other Legionella spp. Typing of L. anisa, L. parisiensis, and L. tucsonensis sg 1 and 3 isolates was accomplished by developing a real-time PCR assay followed by high-resolution melt (HRM) analysis targeting the ssrA gene. Further typing of L. bozemanii, L. longbeachae, and L. feeleii isolates to the serogroup level was accomplished by developing a real-time PCR assay followed by HRM analysis targeting the mip gene. When used in conjunction with other currently available diagnostic tests, these assays may aid in rapidly identifying specific etiologies associated with Legionella outbreaks, clusters, sporadic cases, and potential environmental sources. Published by Elsevier Inc.

Rapid identification of Enterobacter hormaechei and Enterobacter cloacae genetic cluster III.

PubMed

Ohad, S; Block, C; Kravitz, V; Farber, A; Pilo, S; Breuer, R; Rorman, E

2014-05-01

Enterobacter cloacae complex bacteria are of both clinical and environmental importance. Phenotypic methods are unable to distinguish between some of the species in this complex, which often renders their identification incomplete. The goal of this study was to develop molecular assays to identify Enterobacter hormaechei and Ent. cloacae genetic cluster III which are relatively frequently encountered in clinical material. The molecular assays developed in this study are qPCR technology based and served to identify both Ent. hormaechei and Ent. cloacae genetic cluster III. qPCR results were compared to hsp60 sequence analysis. Most clinical isolates were assigned to Ent. hormaechei subsp. steigerwaltii and Ent. cloacae genetic cluster III. The latter was proportionately more frequently isolated from bloodstream infections than from other material (P < 0·05). The qPCR assays detecting Ent. hormaechei and Ent. cloacae genetic cluster III demonstrated high sensitivity and specificity. The presented qPCR assays allow accurate and rapid identification of clinical isolates of the Ent. cloacae complex. The improved identifications obtained can specifically assist analysis of Ent. hormaechei and Ent. cloacae genetic cluster III in nosocomial outbreaks and can promote rapid environmental monitoring. An association was observed between Ent. cloacae cluster III and systemic infection that deserves further attention. © 2014 The Society for Applied Microbiology.

Rapid Holocene coastal change revealed by high-resolution micropaleontological analysis, Pamlico Sound, North Carolina, USA

USGS Publications Warehouse

Grand, Pre C.; Culver, S.J.; Mallinson, D.J.; Farrell, K.M.; Corbett, D.R.; Horton, B.P.; Hillier, C.; Riggs, S.R.; Snyder, S.W.; Buzas, M.A.

2011-01-01

Foraminiferal analyses of 404 contiguous samples, supported by diatom, lithologic, geochronologic and seismic data, reveal both rapid and gradual Holocene paleoenvironmental changes in an 8.21-m vibracore taken from southern Pamlico Sound, North Carolina. Data record initial flooding of a latest Pleistocene river drainage and the formation of an estuary 9000. yr ago. Estuarine conditions were punctuated by two intervals of marine influence from approximately 4100 to 3700 and 1150 to 500. cal. yr BP. Foraminiferal assemblages in the muddy sand facies that accumulated during these intervals contain many well-preserved benthic foraminiferal species, which occur today in open marine settings as deep as the mid shelf, and significant numbers of well-preserved planktonic foraminifera, some typical of Gulf Stream waters. We postulate that these marine-influenced units resulted from temporary destruction of the southern Outer Banks barrier islands by hurricanes. The second increase in marine influence is coeval with increased rate of sea-level rise and a peak in Atlantic tropical cyclone activity during the Medieval Climate Anomaly. This high-resolution analysis demonstrates the range of environmental variability and the rapidity of coastal change that can result from the interplay of changing climate, sea level and geomorphology in an estuarine setting. ?? 2011 University of Washington.

Gradient elution moving boundary electrophoresis enables rapid analysis of acids in complex biomass-derived streams

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

Munson, Matthew S.; Karp, Eric M.; Nimlos, Claire T.

Biomass conversion processes such as pretreatment, liquefaction, and pyrolysis often produce complex mixtures of intermediates that are a substantial challenge to analyze rapidly and reliably. To characterize these streams more comprehensively and efficiently, new techniques are needed to track species through biomass deconstruction and conversion processes. Here, we present the application of an emerging analytical method, gradient elution moving boundary electrophoresis (GEMBE), to quantify a suite of acids in a complex, biomass-derived streams from alkaline pretreatment of corn stover. GEMBE offers distinct advantages over common chromatography-spectrometry analytical approaches in terms of analysis time, sample preparation requirements, and cost of equipment.more » As demonstrated here, GEMBE is able to track 17 distinct compounds (oxalate, formate, succinate, malate, acetate, glycolate, protocatechuate, 3-hydroxypropanoate, lactate, glycerate, 2-hydroxybutanoate, 4-hydroxybenzoate, vanillate, p-coumarate, ferulate, sinapate, and acetovanillone). The lower limit of detection was compound dependent and ranged between 0.9 and 3.5 umol/L. Results from GEMBE were similar to recent results from an orthogonal method based on GCxGC-TOF/MS. Altogether, GEMBE offers a rapid, robust approach to analyze complex biomass-derived samples, and given the ease and convenience of deployment, may offer an analytical solution for online tracking of multiple types of biomass streams.« less

Flux qubit interaction with rapid single-flux quantum logic circuits: Control and readout

NASA Astrophysics Data System (ADS)

Klenov, N. V.; Kuznetsov, A. V.; Soloviev, I. I.; Bakurskiy, S. V.; Denisenko, M. V.; Satanin, A. M.

2017-07-01

We present the results of an analytical study and numerical simulation of the dynamics of a superconducting three-Josephson-junction (3JJ) flux qubit magnetically coupled with rapid single-flux quantum (RSFQ) logic circuit, which demonstrate the fundamental possibility of implementing the simplest logic operations at picosecond times, as well as rapid non-destructive readout. It is shown that when solving optimization problems, the qubit dynamics can be conveniently interpreted as a precession of the magnetic moment vector around the direction of the magnetic field. In this case, the role of magnetic field components is played by combinations of the Hamiltonian matrix elements, and the role of the magnetic moment is played by the Bloch vector. Features of the 3JJ qubit model are discussed during the analysis of how the qubit is affected by exposure to a short control pulse, as are the similarities between the Bloch and Landau-Lifshitz-Gilbert equations. An analysis of solutions to the Bloch equations made it possible to develop recommendations for the use of readout RSFQ circuits in implementing an optimal interface between the classical and quantum parts of the computer system, as well as to justify the use of single-quantum logic in order to control superconducting quantum circuits on a chip.

Gradient elution moving boundary electrophoresis enables rapid analysis of acids in complex biomass-derived streams

DOE PAGES

Munson, Matthew S.; Karp, Eric M.; Nimlos, Claire T.; ...

2016-09-27

Biomass conversion processes such as pretreatment, liquefaction, and pyrolysis often produce complex mixtures of intermediates that are a substantial challenge to analyze rapidly and reliably. To characterize these streams more comprehensively and efficiently, new techniques are needed to track species through biomass deconstruction and conversion processes. Here, we present the application of an emerging analytical method, gradient elution moving boundary electrophoresis (GEMBE), to quantify a suite of acids in a complex, biomass-derived streams from alkaline pretreatment of corn stover. GEMBE offers distinct advantages over common chromatography-spectrometry analytical approaches in terms of analysis time, sample preparation requirements, and cost of equipment.more » As demonstrated here, GEMBE is able to track 17 distinct compounds (oxalate, formate, succinate, malate, acetate, glycolate, protocatechuate, 3-hydroxypropanoate, lactate, glycerate, 2-hydroxybutanoate, 4-hydroxybenzoate, vanillate, p-coumarate, ferulate, sinapate, and acetovanillone). The lower limit of detection was compound dependent and ranged between 0.9 and 3.5 umol/L. Results from GEMBE were similar to recent results from an orthogonal method based on GCxGC-TOF/MS. Altogether, GEMBE offers a rapid, robust approach to analyze complex biomass-derived samples, and given the ease and convenience of deployment, may offer an analytical solution for online tracking of multiple types of biomass streams.« less

Rapid Operational Access and Maneuver Support (ROAMS) Platform for Improved Military Logistics Lines of Communication and Operational Vessel Routing

DTIC Science & Technology

2017-06-01

case study in a northeastern American metropolitan area. METHODOLOGY : The ROAMS platform provides expanded analysis, model automation, and enhanced...shoals. An initial route for such operations is selected much like the military logistics case . Subsequent adjustments to routes may be done on an ad...IX-45 June 2017 8 CASE STUDY: The ROAMS platform was applied to a large, northeast American metropolitan region to demonstrate the capability of

Rapid antigen tests for dengue virus serotypes and Zika virus in patient serum.

PubMed

Bosch, Irene; de Puig, Helena; Hiley, Megan; Carré-Camps, Marc; Perdomo-Celis, Federico; Narváez, Carlos F; Salgado, Doris M; Senthoor, Dewahar; O'Grady, Madeline; Phillips, Elizabeth; Durbin, Ann; Fandos, Diana; Miyazaki, Hikaru; Yen, Chun-Wan; Gélvez-Ramírez, Margarita; Warke, Rajas V; Ribeiro, Lucas S; Teixeira, Mauro M; Almeida, Roque P; Muñóz-Medina, José E; Ludert, Juan E; Nogueira, Mauricio L; Colombo, Tatiana E; Terzian, Ana C B; Bozza, Patricia T; Calheiros, Andrea S; Vieira, Yasmine R; Barbosa-Lima, Giselle; Vizzoni, Alexandre; Cerbino-Neto, José; Bozza, Fernando A; Souza, Thiago M L; Trugilho, Monique R O; de Filippis, Ana M B; de Sequeira, Patricia C; Marques, Ernesto T A; Magalhaes, Tereza; Díaz, Francisco J; Restrepo, Berta N; Marín, Katerine; Mattar, Salim; Olson, Daniel; Asturias, Edwin J; Lucera, Mark; Singla, Mohit; Medigeshi, Guruprasad R; de Bosch, Norma; Tam, Justina; Gómez-Márquez, Jose; Clavet, Charles; Villar, Luis; Hamad-Schifferli, Kimberly; Gehrke, Lee

2017-09-27

The recent Zika virus (ZIKV) outbreak demonstrates that cost-effective clinical diagnostics are urgently needed to detect and distinguish viral infections to improve patient care. Unlike dengue virus (DENV), ZIKV infections during pregnancy correlate with severe birth defects, including microcephaly and neurological disorders. Because ZIKV and DENV are related flaviviruses, their homologous proteins and nucleic acids can cause cross-reactions and false-positive results in molecular, antigenic, and serologic diagnostics. We report the characterization of monoclonal antibody pairs that have been translated into rapid immunochromatography tests to specifically detect the viral nonstructural 1 (NS1) protein antigen and distinguish the four DENV serotypes (DENV1-4) and ZIKV without cross-reaction. To complement visual test analysis and remove user subjectivity in reading test results, we used image processing and data analysis for data capture and test result quantification. Using a 30-μl serum sample, the sensitivity and specificity values of the DENV1-4 tests and the pan-DENV test, which detects all four dengue serotypes, ranged from 0.76 to 1.00. Sensitivity/specificity for the ZIKV rapid test was 0.81/0.86, respectively, using a 150-μl serum input. Serum ZIKV NS1 protein concentrations were about 10-fold lower than corresponding DENV NS1 concentrations in infected patients; moreover, ZIKV NS1 protein was not detected in polymerase chain reaction-positive patient urine samples. Our rapid immunochromatography approach and reagents have immediate application in differential clinical diagnosis of acute ZIKV and DENV cases, and the platform can be applied toward developing rapid antigen diagnostics for emerging viruses. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Discrete elements for 3D microfluidics.

PubMed

Bhargava, Krisna C; Thompson, Bryant; Malmstadt, Noah

2014-10-21

Microfluidic systems are rapidly becoming commonplace tools for high-precision materials synthesis, biochemical sample preparation, and biophysical analysis. Typically, microfluidic systems are constructed in monolithic form by means of microfabrication and, increasingly, by additive techniques. These methods restrict the design and assembly of truly complex systems by placing unnecessary emphasis on complete functional integration of operational elements in a planar environment. Here, we present a solution based on discrete elements that liberates designers to build large-scale microfluidic systems in three dimensions that are modular, diverse, and predictable by simple network analysis techniques. We develop a sample library of standardized components and connectors manufactured using stereolithography. We predict and validate the flow characteristics of these individual components to design and construct a tunable concentration gradient generator with a scalable number of parallel outputs. We show that these systems are rapidly reconfigurable by constructing three variations of a device for generating monodisperse microdroplets in two distinct size regimes and in a high-throughput mode by simple replacement of emulsifier subcircuits. Finally, we demonstrate the capability for active process monitoring by constructing an optical sensing element for detecting water droplets in a fluorocarbon stream and quantifying their size and frequency. By moving away from large-scale integration toward standardized discrete elements, we demonstrate the potential to reduce the practice of designing and assembling complex 3D microfluidic circuits to a methodology comparable to that found in the electronics industry.

Faster Array Training and Rapid Analysis for a Sensor Array Intended for an Event Monitor in Air

NASA Technical Reports Server (NTRS)

Homer, Margie L.; Shevade, A. V.; Fonollosa, J.; Huerta, R.

2013-01-01

Environmental monitoring, in particular, air monitoring, is a critical need for human space flight. Both monitoring and life support systems have needs for closed loop process feedback and quality control for environmental factors. Monitoring protects the air environment and water supply for the astronaut crew and different sensors help ensure that the habitat falls within acceptable limits, and that the life support system is functioning properly and efficiently. The longer the flight duration and the farther the destination, the more critical it becomes to have carefully monitored and automated control systems for life support. There is an acknowledged need for an event monitor which samples the air continuously and provides near real-time information on changes in the air. Past experiments with the JPL ENose have demonstrated a lifetime of the sensor array, with the software, of around 18 months. We are working on a sensor array and new algorithms that will incorporate transient sensor responses in the analysis. Preliminary work has already showed more rapid quantification and identification of analytes and the potential for faster training time of the array. We will look at some of the factors that contribute to demonstrating faster training time for the array. Faster training will decrease the integrated sensor exposure to training analytes, which will also help extend sensor lifetime.

Effects of partial sleep deprivation on slow waves during non-rapid eye movement sleep: A high density EEG investigation.

PubMed

Plante, David T; Goldstein, Michael R; Cook, Jesse D; Smith, Richard; Riedner, Brady A; Rumble, Meredith E; Jelenchick, Lauren; Roth, Andrea; Tononi, Giulio; Benca, Ruth M; Peterson, Michael J

2016-02-01

Changes in slow waves during non-rapid eye movement (NREM) sleep in response to acute total sleep deprivation are well-established measures of sleep homeostasis. This investigation utilized high-density electroencephalography (hdEEG) to examine topographic changes in slow waves during repeated partial sleep deprivation. Twenty-four participants underwent a 6-day sleep restriction protocol. Spectral and period-amplitude analyses of sleep hdEEG data were used to examine changes in slow wave energy, count, amplitude, and slope relative to baseline. Changes in slow wave energy were dependent on the quantity of NREM sleep utilized for analysis, with widespread increases during sleep restriction and recovery when comparing data from the first portion of the sleep period, but restricted to recovery sleep if the entire sleep episode was considered. Period-amplitude analysis was less dependent on the quantity of NREM sleep utilized, and demonstrated topographic changes in the count, amplitude, and distribution of slow waves, with frontal increases in slow wave amplitude, numbers of high-amplitude waves, and amplitude/slopes of low amplitude waves resulting from partial sleep deprivation. Topographic changes in slow waves occur across the course of partial sleep restriction and recovery. These results demonstrate a homeostatic response to partial sleep loss in humans. Copyright © 2015 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

Electro-focusing liquid extractive surface analysis (EF-LESA) coupled to mass spectrometry.

PubMed

Brenton, A Gareth; Godfrey, A Ruth

2014-04-01

Analysis of the chemical composition of surfaces by liquid sampling devices interfaced to mass spectrometry is attractive as the sample stream can be continuously monitored at good sensitivity and selectivity. A sampling probe has been constructed that takes discrete liquid samples (typically <100 nL) of a surface. It incorporates an electrostatic lens system, comprising three electrodes, to which static and pulsed voltages are applied to form a conical "liquid tip", employed to dissolve analytes at a surface. A prototype system demonstrates spatial resolution of 0.093 mm(2). Time of contact between the liquid tip and the surface is controlled to standardize extraction. Calibration graphs of different analyte concentrations on a stainless surface have been measured, together with the probe's reproducibility, carryover, and recovery. A leucine enkephalin-coated surface demonstrated good linearity (R(2) = 0.9936), with a recovery of 90% and a limit of detection of 38 fmol per single spot sampled. The probe is compact and can be fitted into automated sample analysis equipment having potential for rapid analysis of surfaces at a good spatial resolution.

Electro-Focusing Liquid Extractive Surface Analysis (EF-LESA) Coupled to Mass Spectrometry

PubMed Central

2014-01-01

Analysis of the chemical composition of surfaces by liquid sampling devices interfaced to mass spectrometry is attractive as the sample stream can be continuously monitored at good sensitivity and selectivity. A sampling probe has been constructed that takes discrete liquid samples (typically <100 nL) of a surface. It incorporates an electrostatic lens system, comprising three electrodes, to which static and pulsed voltages are applied to form a conical “liquid tip”, employed to dissolve analytes at a surface. A prototype system demonstrates spatial resolution of 0.093 mm2. Time of contact between the liquid tip and the surface is controlled to standardize extraction. Calibration graphs of different analyte concentrations on a stainless surface have been measured, together with the probe’s reproducibility, carryover, and recovery. A leucine enkephalin-coated surface demonstrated good linearity (R2 = 0.9936), with a recovery of 90% and a limit of detection of 38 fmol per single spot sampled. The probe is compact and can be fitted into automated sample analysis equipment having potential for rapid analysis of surfaces at a good spatial resolution. PMID:24597530

The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes.

PubMed

Treangen, Todd J; Ondov, Brian D; Koren, Sergey; Phillippy, Adam M

2014-01-01

Whole-genome sequences are now available for many microbial species and clades, however existing whole-genome alignment methods are limited in their ability to perform sequence comparisons of multiple sequences simultaneously. Here we present the Harvest suite of core-genome alignment and visualization tools for the rapid and simultaneous analysis of thousands of intraspecific microbial strains. Harvest includes Parsnp, a fast core-genome multi-aligner, and Gingr, a dynamic visual platform. Together they provide interactive core-genome alignments, variant calls, recombination detection, and phylogenetic trees. Using simulated and real data we demonstrate that our approach exhibits unrivaled speed while maintaining the accuracy of existing methods. The Harvest suite is open-source and freely available from: http://github.com/marbl/harvest.

CGP stain: An inexpensive, odorless, rapid, sensitive, and in principle in vitro methylation-free Coomassie Brilliant Blue stain.

PubMed

Yasumitsu, Hidetaro; Ozeki, Yasuhiro; Kawsar, Sarkar M A; Toda, Tosifusa; Kanaly, Robert

2010-11-01

Coomassie Brilliant Blue (CBB) protein stains are inexpensive but detect proteins at only at microgram levels. Because of acetic acid and methanol, they cause skin irritation and reduce work motivation by malodor. Recent mass spectrometric (MS) analyses demonstrated that nanogram-sensitive colloidal CBB staining resulted in in vitro methylations of proteins. We propose a rapid, inexpensive, sensitive, odorless, less harsh, and in vitro methylation-free CBB stain. CGP uses three components: citric acid, CBB G-250, and polyvinylpyrrolidone. CGP detects proteins at 12ng within 45min, and because it is nonalcohol, in principle in vitro methylation would be eliminated. Indeed, MS analysis of CGP-stained bands confirmed a lack of methylation. 2010 Elsevier Inc. All rights reserved.

Large-scale Parallel Unstructured Mesh Computations for 3D High-lift Analysis

NASA Technical Reports Server (NTRS)

Mavriplis, Dimitri J.; Pirzadeh, S.

1999-01-01

A complete "geometry to drag-polar" analysis capability for the three-dimensional high-lift configurations is described. The approach is based on the use of unstructured meshes in order to enable rapid turnaround for complicated geometries that arise in high-lift configurations. Special attention is devoted to creating a capability for enabling analyses on highly resolved grids. Unstructured meshes of several million vertices are initially generated on a work-station, and subsequently refined on a supercomputer. The flow is solved on these refined meshes on large parallel computers using an unstructured agglomeration multigrid algorithm. Good prediction of lift and drag throughout the range of incidences is demonstrated on a transport take-off configuration using up to 24.7 million grid points. The feasibility of using this approach in a production environment on existing parallel machines is demonstrated, as well as the scalability of the solver on machines using up to 1450 processors.

Desorption atmospheric pressure photoionization.

PubMed

Haapala, Markus; Pól, Jaroslav; Saarela, Ville; Arvola, Ville; Kotiaho, Tapio; Ketola, Raimo A; Franssila, Sami; Kauppila, Tiina J; Kostiainen, Risto

2007-10-15

An ambient ionization technique for mass spectrometry, desorption atmospheric pressure photoionization (DAPPI), is presented, and its application to the rapid analysis of compounds of various polarities on surfaces is demonstrated. The DAPPI technique relies on a heated nebulizer microchip delivering a heated jet of vaporized solvent, e.g., toluene, and a photoionization lamp emitting 10-eV photons. The solvent jet is directed toward sample spots on a surface, causing the desorption of analytes from the surface. The photons emitted by the lamp ionize the analytes, which are then directed into the mass spectrometer. The limits of detection obtained with DAPPI were in the range of 56-670 fmol. Also, the direct analysis of pharmaceuticals from a tablet surface was successfully demonstrated. A comparison of the performance of DAPPI with that of the popular desorption electrospray ionization method was done with four standard compounds. DAPPI was shown to be equally or more sensitive especially in the case of less polar analytes.

Argon direct analysis in real time mass spectrometry in conjunction with makeup solvents: a method for analysis of labile compounds.

PubMed

Yang, Hongmei; Wan, Debin; Song, Fengrui; Liu, Zhiqiang; Liu, Shuying

2013-02-05

Helium direct analysis in real time (He-DART) mass spectrometry (MS) analysis of labile compounds usually tends to be challenging because of the occurrence of prominent fragmentation, which obscures the assigning of an ion to an independent species or merely a fragment in a mixture. In the present work, argon DART (Ar-DART) MS in conjunction with makeup solvents has been demonstrated to analyze a variety of labile compounds including nucleosides, alkaloids, glucose, and other small molecules. The results presented here confirm that Ar-DART can generate significantly less energetic ions than conventional He-DART and is able to produce the intact molecular ions with little or no fragmentation in both positive and negative ion modes. Adding a makeup solvent (absolute ethyl alcohol, methanol, fluorobenzene, or acetone) to the argon gas stream at the exit of the DART ion source can result in 1-2 orders of magnitude increase in detection signals. The sensitivity attainable by Ar-DART was found to be comparable to that by He-DART. The investigation of influence of solvents improves our understanding of the fundamental desorption and ionization processes in DART. The practical application of this rapid and high throughput method is demonstrated by the successful analysis of a natural product (Crude Kusnezoff Monkshood) extract, demonstrating the great potential in mixture research.

A highly sensitive and specific capacitive aptasensor for rapid and label-free trace analysis of Bisphenol A (BPA) in canned foods.

PubMed

Mirzajani, Hadi; Cheng, Cheng; Wu, Jayne; Chen, Jiangang; Eda, Shigotoshi; Najafi Aghdam, Esmaeil; Badri Ghavifekr, Habib

2017-03-15

A rapid, highly sensitive, specific and low-cost capacitive affinity biosensor is presented here for label-free and single step detection of Bisphenol A (BPA). The sensor design allows rapid prototyping at low-cost using printed circuit board material by benchtop equipment. High sensitivity detection is achieved through the use of a BPA-specific aptamer as probe molecule and large electrodes to enhance AC-electroelectrothermal effect for long-range transport of BPA molecules toward electrode surface. Capacitive sensing technique is used to determine the bounded BPA level by measuring the sample/electrode interfacial capacitance of the sensor. The developed biosensor can detect BPA level in 20s and exhibits a large linear range from 1 fM to 10 pM, with a limit of detection (LOD) of 152.93 aM. This biosensor was applied to test BPA in canned food samples and could successfully recover the levels of spiked BPA. This sensor technology is demonstrated to be highly promising and reliable for rapid, sensitive and on-site monitoring of BPA in food samples. Copyright © 2016 Elsevier B.V. All rights reserved.

Rapid Spontaneously Resolving Acute Subdural Hematoma

PubMed Central

Gan, Qi; Zhao, Hexiang; Zhang, Hanmei; You, Chao

2017-01-01

Introduction: This study reports a rare patient of a rapid spontaneously resolving acute subdural hematoma. In addition, an analysis of potential clues for the phenomenon is presented with a review of the literature. Patient Presentation: A 1-year-and-2-month-old boy fell from a height of approximately 2 m. The patient was in a superficial coma with a Glasgow Coma Scale of 8 when he was transferred to the authors’ hospital. Computed tomography revealed the presence of an acute subdural hematoma with a midline shift beyond 1 cm. His guardians refused invasive interventions and chose conservative treatment. Repeat imaging after 15 hours showed the evident resolution of the hematoma and midline reversion. Progressive magnetic resonance imaging demonstrated the complete resolution of the hematoma, without redistribution to a remote site. Conclusions: Even though this phenomenon has a low incidence, the probability of a rapid spontaneously resolving acute subdural hematoma should be considered when patients present with the following characteristics: children or elderly individuals suffering from mild to moderate head trauma; stable or rapidly recovered consciousness; and simple acute subdural hematoma with a moderate thickness and a particularly low-density band in computed tomography scans. PMID:28468224

Rapid formation and evolution of an extreme haze episode in Northern China during winter 2015

PubMed Central

Sun, Yele; Chen, Chen; Zhang, Yingjie; Xu, Weiqi; Zhou, Libo; Cheng, Xueling; Zheng, Haitao; Ji, Dongsheng; Li, Jie; Tang, Xiao; Fu, Pingqing; Wang, Zifa

2016-01-01

We investigate the rapid formation and evolutionary mechanisms of an extremely severe and persistent haze episode that occurred in northern China during winter 2015 using comprehensive ground and vertical measurements, along with receptor and dispersion model analysis. Our results indicate that the life cycle of a severe winter haze episode typically consists of four stages: (1) rapid formation initiated by sudden changes in meteorological parameters and synchronous increases in most aerosol species, (2) persistent evolution with relatively constant variations in secondary inorganic aerosols and secondary organic aerosols, (3) further evolution associated with fog processing and significantly enhanced sulfate levels, and (4) clearing due to dry, cold north-northwesterly winds. Aerosol composition showed substantial changes during the formation and evolution of the haze episode but was generally dominated by regional secondary aerosols (53–67%). Our results demonstrate the important role of regional transport, largely from the southwest but also from the east, and of coal combustion emissions for winter haze formation in Beijing. Also, we observed an important downward mixing pathway during the severe haze in 2015 that can lead to rapid increases in certain aerosol species. PMID:27243909

Generation of anisotropy in turbulent flows subjected to rapid distortion

NASA Astrophysics Data System (ADS)

Clark, Timothy T.; Kurien, Susan; Rubinstein, Robert

2018-01-01

A computational tool for the anisotropic time-evolution of the spectral velocity correlation tensor is presented. We operate in the linear, rapid distortion limit of the mean-field-coupled equations. Each term of the equations is written in the form of an expansion to arbitrary order in the basis of irreducible representations of the SO(3) symmetry group. The computational algorithm for this calculation solves a system of coupled equations for the scalar weights of each generated anisotropic mode. The analysis demonstrates that rapid distortion rapidly but systematically generates higher-order anisotropic modes. To maintain a tractable computation, the maximum number of rotational modes to be used in a given calculation is specified a priori. The computed Reynolds stress converges to the theoretical result derived by Batchelor and Proudman [Quart. J. Mech. Appl. Math. 7, 83 (1954), 10.1093/qjmam/7.1.83] if a sufficiently large maximum number of rotational modes is utilized; more modes are required to recover the solution at later times. The emergence and evolution of the underlying multidimensional space of functions is presented here using a 64-mode calculation. Alternative implications for modeling strategies are discussed.

Rapid 3D Refractive‐Index Imaging of Live Cells in Suspension without Labeling Using Dielectrophoretic Cell Rotation

PubMed Central

Habaza, Mor; Kirschbaum, Michael; Guernth‐Marschner, Christian; Dardikman, Gili; Barnea, Itay; Korenstein, Rafi; Duschl, Claus

2016-01-01

A major challenge in the field of optical imaging of live cells is achieving rapid, 3D, and noninvasive imaging of isolated cells without labeling. If successful, many clinical procedures involving analysis and sorting of cells drawn from body fluids, including blood, can be significantly improved. A new label‐free tomographic interferometry approach is presented. This approach provides rapid capturing of the 3D refractive‐index distribution of single cells in suspension. The cells flow in a microfluidic channel, are trapped, and then rapidly rotated by dielectrophoretic forces in a noninvasive and precise manner. Interferometric projections of the rotated cell are acquired and processed into the cellular 3D refractive‐index map. Uniquely, this approach provides full (360°) coverage of the rotation angular range around any axis, and knowledge on the viewing angle. The experimental demonstrations presented include 3D, label‐free imaging of cancer cells and three types of white blood cells. This approach is expected to be useful for label‐free cell sorting, as well as for detection and monitoring of pathological conditions resulting in cellular morphology changes or occurrence of specific cell types in blood or other body fluids. PMID:28251046

Sensor-triggered sampling to determine instantaneous airborne vapor exposure concentrations.

PubMed

Smith, Philip A; Simmons, Michael K; Toone, Phillip

2018-06-01

It is difficult to measure transient airborne exposure peaks by means of integrated sampling for organic chemical vapors, even with very short-duration sampling. Selection of an appropriate time to measure an exposure peak through integrated sampling is problematic, and short-duration time-weighted average (TWA) values obtained with integrated sampling are not likely to accurately determine actual peak concentrations attained when concentrations fluctuate rapidly. Laboratory analysis for integrated exposure samples is preferred from a certainty standpoint over results derived in the field from a sensor, as a sensor user typically must overcome specificity issues and a number of potential interfering factors to obtain similarly reliable data. However, sensors are currently needed to measure intra-exposure period concentration variations (i.e., exposure peaks). In this article, the digitized signal from a photoionization detector (PID) sensor triggered collection of whole-air samples when toluene or trichloroethylene vapors attained pre-determined levels in a laboratory atmosphere generation system. Analysis by gas chromatography-mass spectrometry of whole-air samples (with both 37 and 80% relative humidity) collected using the triggering mechanism with rapidly increasing vapor concentrations showed good agreement with the triggering set point values. Whole-air samples (80% relative humidity) in canisters demonstrated acceptable 17-day storage recoveries, and acceptable precision and bias were obtained. The ability to determine exceedance of a ceiling or peak exposure standard by laboratory analysis of an instantaneously collected sample, and to simultaneously provide a calibration point to verify the correct operation of a sensor was demonstrated. This latter detail may increase the confidence in reliability of sensor data obtained across an entire exposure period.

Potential of mid IR spectroscopy in the rapid label free identification of skin malignancies

NASA Astrophysics Data System (ADS)

Kastl, Lena; Kemper, Björn; Lloyd, Gavin R.; Nallala, Jayakrupakar; Stone, Nick; Naranjo, Valery; Penaranda, Francisco; Schnekenburger, Jürgen

2016-03-01

The rapid inspection of suspicious skin lesions for pathological cell types is the objective of optical point of care diagnostics technologies. A marker free fast diagnosis of skin malignancies would overcome the limitations of the current gold standard surgical biopsy. The time consuming and costly biopsy procedure requires the inspection of each sample by a trained pathologist, which limits the analysis of potentially malignant lesions. Optical technologies like RAMAN or infrared spectroscopy, which provide both, localization and chemical information, can be used to differentiate malignant from healthy tissue by the analysis of multi cell structures and cell type specific spectra. We here report the application of midIR spectroscopy towards fast and reliable skin diagnostics. Within the European research project MINERVA we developed standardized in vitro skin systems with increasing complexity, from single skin cell types as fibroblasts, keratinocytes and melanoma cells, to mixtures of these and finally three dimensional human skin equivalents. The standards were characterized in the established midIR range and also with newly developed systems for fast imaging up to 12 μm. The analysis of the spectra by novel data processing algorithms demonstrated the clear separation of all cell types, especially the tumor cells. The signals from single cell layers were sufficient for cell type differentiation. We have compared different midIR systems and found all of them suitable for specific cell type identification. Our data demonstrate the potential of midIR spectroscopy for fast image acquisition and an improved data processing as sensitive and specific optical biopsy technology.

Design and optimization of the micro-engine turbine rotor manufacturing using the rapid prototyping technology

NASA Astrophysics Data System (ADS)

Vdovin, R. A.; Smelov, V. G.

2017-02-01

This work describes the experience in manufacturing the turbine rotor for the micro-engine. It demonstrates the design principles for the complex investment casting process combining the use of the ProCast software and the rapid prototyping techniques. At the virtual modelling stage, in addition to optimized process parameters, the casting structure was improved to obtain the defect-free section. The real production stage allowed demonstrating the performance and fitness of rapid prototyping techniques for the manufacture of geometrically-complex engine-building parts.

International trades, local spread and viral evolution: the case of porcine circovirus type 2 (PCV2) strains heterogeneity in Italy.

PubMed

Franzo, Giovanni; Tucciarone, Claudia M; Dotto, Giorgia; Gigli, Alessandra; Ceglie, Letizia; Drigo, Michele

2015-06-01

Porcine circovirus type 2 is one of the most widespread and economically relevant infections of swine. Four genotypes have been recognized, but currently, only three (PCV2a, PCV2b and PCV2d) are effectively circulating. The widespread livestock trade and rapid viral evolution have contributed to determining the high heterogeneity of PCV2 and the dispersal of potentially more virulent strains. Italian swine farming and the related processing industry are relevant in the national economy. Despite the noteworthy losses associated with direct and control measure costs, no data are currently available on the molecular epidemiology of PCV2 in Italy. Our study, which was intended to fill this gap, considered 75 completed genome PCV2 sequences, which were obtained from samples collected from the highly densely populated area of Northern Italy between 2007 and 2014. Phylogenetic analysis and comparison with reference sequences demonstrated the co-circulation, with different prevalences, of PCV2a, PCV2b and PCV2d within the national borders, with PCV2b being the most prevalent. Recombination between different genotypes was also proven to be frequent. Phylogeographic analysis demonstrated that the marked variability of Italian PCV2 strains can be attributable to multiple introduction events. The comparison of the phylogenetic analysis results, the location of different haplotypes and the international commercial routs of live pigs allow the speculation of several links as well as the role of Italy as both an importer and exporter of PCV2 haplotypes, mainly from and to European and Asian countries. A similarly intricate contact network was demonstrated within national borders, with different haplotypes being detected in the same province and different provinces harbouring the same haplotype. Overall, this paper represents the first description of PCV2 in Italy and demonstrates that the high variability of circulating Italian strains is due to multiple introduction events, wide circulation within national boundaries and rapid viral evolution. Copyright © 2015 Elsevier B.V. All rights reserved.

Strain-Level Metagenomic Analysis of the Fermented Dairy Beverage Nunu Highlights Potential Food Safety Risks

PubMed Central

Walsh, Aaron M.; Crispie, Fiona; Daari, Kareem; O'Sullivan, Orla; Martin, Jennifer C.; Arthur, Cornelius T.; Claesson, Marcus J.; Scott, Karen P.

2017-01-01

ABSTRACT The rapid detection of pathogenic strains in food products is essential for the prevention of disease outbreaks. It has already been demonstrated that whole-metagenome shotgun sequencing can be used to detect pathogens in food but, until recently, strain-level detection of pathogens has relied on whole-metagenome assembly, which is a computationally demanding process. Here we demonstrated that three short-read-alignment-based methods, i.e., MetaMLST, PanPhlAn, and StrainPhlAn, could accurately and rapidly identify pathogenic strains in spinach metagenomes that had been intentionally spiked with Shiga toxin-producing Escherichia coli in a previous study. Subsequently, we employed the methods, in combination with other metagenomics approaches, to assess the safety of nunu, a traditional Ghanaian fermented milk product that is produced by the spontaneous fermentation of raw cow milk. We showed that nunu samples were frequently contaminated with bacteria associated with the bovine gut and, worryingly, we detected putatively pathogenic E. coli and Klebsiella pneumoniae strains in a subset of nunu samples. Ultimately, our work establishes that short-read-alignment-based bioinformatics approaches are suitable food safety tools, and we describe a real-life example of their utilization. IMPORTANCE Foodborne pathogens are responsible for millions of illnesses each year. Here we demonstrate that short-read-alignment-based bioinformatics tools can accurately and rapidly detect pathogenic strains in food products by using shotgun metagenomics data. The methods used here are considerably faster than both traditional culturing methods and alternative bioinformatics approaches that rely on metagenome assembly; therefore, they can potentially be used for more high-throughput food safety testing. Overall, our results suggest that whole-metagenome sequencing can be used as a practical food safety tool to prevent diseases or to link outbreaks to specific food products. PMID:28625983

Nanoparticles and Ocean Optics

DTIC Science & Technology

2006-01-01

could control in- fection by the dilution process. Subsequent dilution experiments have included eukaryotic hosts ( Emiliania huxleyi) and its... Emiliania huxleyi, at a rapid rate that we have never observed in a eukaryotic virus. Optical experiments demonstrated major optical changes on the time...Results of infection of eukaryotic coccolithophorid, Emiliania huxleyi, with new virus isolate ø 43, which demonstrates rapid optical changes

ISPAN (Interactive Stiffened Panel Analysis): A tool for quick concept evaluation and design trade studies

NASA Technical Reports Server (NTRS)

Hairr, John W.; Dorris, William J.; Ingram, J. Edward; Shah, Bharat M.

1993-01-01

Interactive Stiffened Panel Analysis (ISPAN) modules, written in FORTRAN, were developed to provide an easy to use tool for creating finite element models of composite material stiffened panels. The modules allow the user to interactively construct, solve and post-process finite element models of four general types of structural panel configurations using only the panel dimensions and properties as input data. Linear, buckling and post-buckling solution capability is provided. This interactive input allows rapid model generation and solution by non finite element users. The results of a parametric study of a blade stiffened panel are presented to demonstrate the usefulness of the ISPAN modules. Also, a non-linear analysis of a test panel was conducted and the results compared to measured data and previous correlation analysis.

Detection of caffeine in tea, instant coffee, green tea beverage, and soft drink by direct analysis in real time (DART) source coupled to single-quadrupole mass spectrometry.

PubMed

Wang, Lei; Zhao, Pengyue; Zhang, Fengzu; Bai, Aijuan; Pan, Canping

2013-01-01

Ambient ionization direct analysis in real time (DART) coupled to single-quadrupole MS (DART-MS) was evaluated for rapid detection of caffeine in commercial samples without chromatographic separation or sample preparation. Four commercial samples were examined: tea, instant coffee, green tea beverage, and soft drink. The response-related parameters were optimized for the DART temperature and MS fragmentor. Under optimal conditions, the molecular ion (M+H)+ was the major ion for identification of caffeine. The results showed that DART-MS is a promising tool for the quick analysis of important marker molecules in commercial samples. Furthermore, this system has demonstrated significant potential for high sample throughput and real-time analysis.

A membrane-separator interface for mass-spectrometric analysis of blood plasma

NASA Astrophysics Data System (ADS)

Elizarov, A. Yu.; Gerasimov, D. G.

2014-09-01

We demonstrate the possibility of rapid mass-spectrometric determination of the content of anesthetic agents in blood plasma with the aid of a membrane-separator interface. The interface employs a hydrophobic selective membrane that is capable of separating various anesthetic drugs (including inhalation anesthetic sevofluran, noninhalation anesthetic thiopental, hypnotic propofol, and opioid analgesic fentanyl) from the blood plasma and introducing samples into a mass spectrometer. Analysis of the blood plasma was not accompanied by the memory effect and did not lead to membrane degradation. Results of clinical investigation of the concentration of anesthetics in the blood plasma of patients are presented.

Parallel human genome analysis: microarray-based expression monitoring of 1000 genes.

PubMed Central

Schena, M; Shalon, D; Heller, R; Chai, A; Brown, P O; Davis, R W

1996-01-01

Microarrays containing 1046 human cDNAs of unknown sequence were printed on glass with high-speed robotics. These 1.0-cm2 DNA "chips" were used to quantitatively monitor differential expression of the cognate human genes using a highly sensitive two-color hybridization assay. Array elements that displayed differential expression patterns under given experimental conditions were characterized by sequencing. The identification of known and novel heat shock and phorbol ester-regulated genes in human T cells demonstrates the sensitivity of the assay. Parallel gene analysis with microarrays provides a rapid and efficient method for large-scale human gene discovery. Images Fig. 1 Fig. 2 Fig. 3 PMID:8855227

High-resolution melting PCR analysis for rapid genotyping of Burkholderia mallei.

PubMed

Girault, G; Wattiau, P; Saqib, M; Martin, B; Vorimore, F; Singha, H; Engelsma, M; Roest, H J; Spicic, S; Grunow, R; Vicari, N; De Keersmaecker, S C J; Roosens, N H C; Fabbi, M; Tripathi, B N; Zientara, S; Madani, N; Laroucau, K

2018-05-08

Burkholderia (B.) mallei is the causative agent of glanders. A previous work conducted on single-nucleotide polymorphisms (SNP) extracted from the whole genome sequences of 45 B. mallei isolates identified 3 lineages for this species. In this study, we designed a high-resolution melting (HRM) method for the screening of 15 phylogenetically informative SNPs within the genome of B. mallei that subtype the species into 3 lineages and 12 branches/sub-branches/groups. The present results demonstrate that SNP-based genotyping represent an interesting approach for the molecular epidemiology analysis of B. mallei. Copyright © 2018 Elsevier B.V. All rights reserved.

Optical detection of radon decay in air

PubMed Central

Sand, Johan; Ihantola, Sakari; Peräjärvi, Kari; Toivonen, Harri; Toivonen, Juha

2016-01-01

An optical radon detection method is presented. Radon decay is directly measured by observing the secondary radiolumines cence light that alpha particles excite in air, and the selectivity of coincident photon detection is further enhanced with online pulse-shape analysis. The sensitivity of a demonstration device was 6.5 cps/Bq/l and the minimum detectable concentration was 12 Bq/m3 with a 1 h integration time. The presented technique paves the way for optical approaches in rapid radon detec tion, and it can be applied beyond radon to the analysis of any alpha-active sample which can be placed in the measurement chamber. PMID:26867800

Photocleavable DNA barcode-antibody conjugates allow sensitive and multiplexed protein analysis in single cells.

PubMed

Agasti, Sarit S; Liong, Monty; Peterson, Vanessa M; Lee, Hakho; Weissleder, Ralph

2012-11-14

DNA barcoding is an attractive technology, as it allows sensitive and multiplexed target analysis. However, DNA barcoding of cellular proteins remains challenging, primarily because barcode amplification and readout techniques are often incompatible with the cellular microenvironment. Here we describe the development and validation of a photocleavable DNA barcode-antibody conjugate method for rapid, quantitative, and multiplexed detection of proteins in single live cells. Following target binding, this method allows DNA barcodes to be photoreleased in solution, enabling easy isolation, amplification, and readout. As a proof of principle, we demonstrate sensitive and multiplexed detection of protein biomarkers in a variety of cancer cells.

A novel microreactor approach for analysis of ketones and aldehydes in breath.

PubMed

Fu, Xiao-An; Li, Mingxiao; Biswas, Souvik; Nantz, Michael H; Higashi, Richard M

2011-11-21

We report a fabricated microreactor with thousands of micropillars in channels. Each micropillar surface is chemically functionalized to selectively preconcentrate gaseous ketones and aldehydes of exhaled breath and to enhance ultra-trace, rapid analysis by direct-infusion Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometry (MS). The micropillar reactive coating contains the quaternary ammonium aminooxy salt 2-(aminooxy)ethyl-N,N,N-trimethylammonium iodide (ATM) for capturing trace carbonyl VOCs by means of an oximation reaction. We demonstrate the utility of this approach for detection of C(1) to C(12) aldehydes and ketones in exhaled breath, but the approach is applicable to any gaseous sample.

Enhanced Microbial Detection Capabilities by a Rapid Portable Instrument

NASA Technical Reports Server (NTRS)

Morris, Heather; Monaco, Lisa; Wainwright, Norm; Steele, Andrew; Damon, Michael; Schenk, Alison; Stimpson, Eric; Maule, Jake; Effinger, Michael

2010-01-01

We present data describing a progression of continuing technology development - from expanding the detection capabilities of the current PTS unit to re-outfitting the instrument with a protein microarray increasing the number of detectable compounds. To illustrate the adaptability of the cartridge format, on-orbit operations data from the ISS demonstrate the detection of the fungal cell wall compound beta-glucan using applicable LOCAD-PTS cartridges. LOCAD-PTS is a handheld device consisting of a spectrophotometer, an onboard pumping mechanism, and data storage capabilities. A suite of interchangeable cartridges lined with four distinct capillaries allow a hydrated sample to mix with necessary reagents in the channels before being pumped to the optical well for spectrophotometric analysis. The reagents housed in one type of cartridge trigger a reaction based on the Limulus Amebocyte Lysate (LAL) assay, which results in the release of paranitroaniline dye. The dye is measured using a 395 nm filter. The LAL assay detects the Gram-negative bacterial cell wall molecule, endotoxin or lipopolysaccharide (LPS). The more dye released, the greater the concentration of endotoxin in the sample. Sampling, quantitative analysis, and data retrieval require less than 20 minutes. This is significantly faster than standard culture-based methods, which require at least a 24 hour incubation period.Using modified cartridges, we demonstrate the detection of Gram negative bacteria with protein microarray technology. Additionally, we provide data from multiple field tests where both standard and advanced PTS technologies were used. These tests investigate the transfer of target microbial molecules from one surface to another. Collectively, these data demonstrate that the new cartridges expand the number of compounds detected by LOCAD-PTS, while maintaining the rapid, in situ analysis characteristic of the instrument. The unit provides relevant data for verifying sterile sample collection protocols, which are critical for conducting accurate scientific experiments during future missions to the Moon and Mars.

RAPID3 scores and hand outcome measurements in RA patients: a preliminary study.

PubMed

Qorolli, Merita; Hundozi-Hysenaj, Hajrije; Rexhepi, Sylejman; Rehxepi, Blerta; Grazio, Simeon

2017-06-01

The Routine Assessment of Patient Index Data 3 (RAPID3) is a patient-reported disease activity measure used to assess physical function, pain, and global health in patients with rheumatoid arthritis (RA) without formal joint counts. Since hand involvement and its decreased function are hallmarks of RA, the aim of our study was to investigate the performance of RAPID3 scores with regard to hand function and to confirm previous findings that the RAPID3 score as a disease activity measure is strongly correlated with the DAS28 score. Sixty-eight consecutive patients with RA (85% female), aged 18-75 years, were included in the study and were recruited during their outpatient visit. Apart from demographic and clinical data, the obtained parameters of interest included RAPID3 scores and assessments of the function of the hand, namely, the signal of functional impairment (SOFI)-hand, grip strength, and pulp-to-palm distance, as well the Health Assessment Questionnaire- Disability Index (HAQ-DI) and DAS28 scores. Pearson's correlation coefficient, Student's t test and linear regression were used in the statistical analysis of the results. The significance was set to p < 0.05. A positive correlation was found between RAPID3 scores and HAQ-DI scores, SOFI-hand scores, and pulp-to-palm distance, and negative correlation was observed between RAPID3 scores and grip strength. The order regarding the strength of correlations between RAPID3 scores and other variables (from the strongest to the weakest) was as follows: HAQ-DI, grip strength, SOFI-hand and pulp-to-palm distance. The hand assessment variables had stronger correlations with RAPID3 scores than with DAS28 scores. Our preliminary study showed that RAPID3 scores were strongly correlated with measurements of the functional ability of the hand, demonstrating that RAPID3 can be used as a measure of disease activity in clinical practice and to characterize hand function. Further studies are needed to confirm this result.

Feasibility of utilizing the SD BIOLINE Onchocerciasis IgG4 rapid test in onchocerciasis surveillance in Senegal.

PubMed

Dieye, Yakou; Storey, Helen L; Barrett, Kelsey L; Gerth-Guyette, Emily; Di Giorgio, Laura; Golden, Allison; Faulx, Dunia; Kalnoky, Michael; Ndiaye, Marie Khemesse Ngom; Sy, Ngayo; Mané, Malang; Faye, Babacar; Sarr, Mamadou; Dioukhane, Elhadji Mamadou; Peck, Roger B; Guinot, Philippe; de Los Santos, Tala

2017-10-01

As effective onchocerciasis control efforts in Africa transition to elimination efforts, different diagnostic tools are required to support country programs. Senegal, with its long standing, successful control program, is transitioning to using the SD BIOLINE Onchocerciasis IgG4 (Ov16) rapid test over traditional skin snip microscopy. The aim of this study is to demonstrate the feasibility of integrating the Ov16 rapid test into onchocerciasis surveillance activities in Senegal, based on the following attributes of acceptability, usability, and cost. A cross-sectional study was conducted in 13 villages in southeastern Senegal in May 2016. Individuals 5 years and older were invited to participate in a demographic questionnaire, an Ov16 rapid test, a skin snip biopsy, and an acceptability interview. Rapid test technicians were interviewed and a costing analysis was conducted. Of 1,173 participants, 1,169 (99.7%) agreed to the rapid test while 383 (32.7%) agreed to skin snip microscopy. The sero-positivity rate of the rapid test among those tested was 2.6% with zero positives 10 years and younger. None of the 383 skin snips were positive for Ov microfilaria. Community members appreciated that the rapid test was performed quickly, was not painful, and provided reliable results. The total costs for this surveillance activity was $22,272.83, with a cost per test conducted at $3.14 for rapid test, $7.58 for skin snip microscopy, and $13.43 for shared costs. If no participants had refused skin snip microscopy, the total cost per method with shared costs would have been around $16 per person tested. In this area with low onchocerciasis sero-positivity, there was high acceptability and perceived value of the rapid test by community members and technicians. This study provides evidence of the feasibility of implementing the Ov16 rapid test in Senegal and may be informative to other country programs transitioning to Ov16 serologic tools.

Feasibility of utilizing the SD BIOLINE Onchocerciasis IgG4 rapid test in onchocerciasis surveillance in Senegal

PubMed Central

Dieye, Yakou; Barrett, Kelsey L.; Gerth-Guyette, Emily; Di Giorgio, Laura; Golden, Allison; Faulx, Dunia; Kalnoky, Michael; Ndiaye, Marie Khemesse Ngom; Sy, Ngayo; Mané, Malang; Faye, Babacar; Sarr, Mamadou; Dioukhane, Elhadji Mamadou; Peck, Roger B.; Guinot, Philippe; de los Santos, Tala

2017-01-01

As effective onchocerciasis control efforts in Africa transition to elimination efforts, different diagnostic tools are required to support country programs. Senegal, with its long standing, successful control program, is transitioning to using the SD BIOLINE Onchocerciasis IgG4 (Ov16) rapid test over traditional skin snip microscopy. The aim of this study is to demonstrate the feasibility of integrating the Ov16 rapid test into onchocerciasis surveillance activities in Senegal, based on the following attributes of acceptability, usability, and cost. A cross-sectional study was conducted in 13 villages in southeastern Senegal in May 2016. Individuals 5 years and older were invited to participate in a demographic questionnaire, an Ov16 rapid test, a skin snip biopsy, and an acceptability interview. Rapid test technicians were interviewed and a costing analysis was conducted. Of 1,173 participants, 1,169 (99.7%) agreed to the rapid test while 383 (32.7%) agreed to skin snip microscopy. The sero-positivity rate of the rapid test among those tested was 2.6% with zero positives 10 years and younger. None of the 383 skin snips were positive for Ov microfilaria. Community members appreciated that the rapid test was performed quickly, was not painful, and provided reliable results. The total costs for this surveillance activity was $22,272.83, with a cost per test conducted at $3.14 for rapid test, $7.58 for skin snip microscopy, and $13.43 for shared costs. If no participants had refused skin snip microscopy, the total cost per method with shared costs would have been around $16 per person tested. In this area with low onchocerciasis sero-positivity, there was high acceptability and perceived value of the rapid test by community members and technicians. This study provides evidence of the feasibility of implementing the Ov16 rapid test in Senegal and may be informative to other country programs transitioning to Ov16 serologic tools. PMID:28972982

Multi-hazard risk analysis using the FP7 RASOR Platform

NASA Astrophysics Data System (ADS)

Koudogbo, Fifamè N.; Duro, Javier; Rossi, Lauro; Rudari, Roberto; Eddy, Andrew

2014-10-01

Climate change challenges our understanding of risk by modifying hazards and their interactions. Sudden increases in population and rapid urbanization are changing exposure to risk around the globe, making impacts harder to predict. Despite the availability of operational mapping products, there is no single tool to integrate diverse data and products across hazards, update exposure data quickly and make scenario-based predictions to support both short and long-term risk-related decisions. RASOR (Rapid Analysis and Spatialization Of Risk) will develop a platform to perform multi-hazard risk analysis for the full cycle of disaster management, including targeted support to critical infrastructure monitoring and climate change impact assessment. A scenario-driven query system simulates future scenarios based on existing or assumed conditions and compares them with historical scenarios. RASOR will thus offer a single work environment that generates new risk information across hazards, across data types (satellite EO, in-situ), across user communities (global, local, climate, civil protection, insurance, etc.) and across the world. Five case study areas are considered within the project, located in Haiti, Indonesia, Netherlands, Italy and Greece. Initially available over those demonstration areas, RASOR will ultimately offer global services to support in-depth risk assessment and full-cycle risk management.

Lab-on-a-Drone: Toward Pinpoint Deployment of Smartphone-Enabled Nucleic Acid-Based Diagnostics for Mobile Health Care

PubMed Central

2016-01-01

We introduce a portable biochemical analysis platform for rapid field deployment of nucleic acid-based diagnostics using consumer-class quadcopter drones. This approach exploits the ability to isothermally perform the polymerase chain reaction (PCR) with a single heater, enabling the system to be operated using standard 5 V USB sources that power mobile devices (via battery, solar, or hand crank action). Time-resolved fluorescence detection and quantification is achieved using a smartphone camera and integrated image analysis app. Standard sample preparation is enabled by leveraging the drone’s motors as centrifuges via 3D printed snap-on attachments. These advancements make it possible to build a complete DNA/RNA analysis system at a cost of ∼$50 ($US). Our instrument is rugged and versatile, enabling pinpoint deployment of sophisticated diagnostics to distributed field sites. This capability is demonstrated by successful in-flight replication of Staphylococcus aureus and λ-phage DNA targets in under 20 min. The ability to perform rapid in-flight assays with smartphone connectivity eliminates delays between sample collection and analysis so that test results can be delivered in minutes, suggesting new possibilities for drone-based systems to function in broader and more sophisticated roles beyond cargo transport and imaging. PMID:26898247

Lab-on-a-Drone: Toward Pinpoint Deployment of Smartphone-Enabled Nucleic Acid-Based Diagnostics for Mobile Health Care.

PubMed

Priye, Aashish; Wong, Season; Bi, Yuanpeng; Carpio, Miguel; Chang, Jamison; Coen, Mauricio; Cope, Danielle; Harris, Jacob; Johnson, James; Keller, Alexandra; Lim, Richard; Lu, Stanley; Millard, Alex; Pangelinan, Adriano; Patel, Neal; Smith, Luke; Chan, Kamfai; Ugaz, Victor M

2016-05-03

We introduce a portable biochemical analysis platform for rapid field deployment of nucleic acid-based diagnostics using consumer-class quadcopter drones. This approach exploits the ability to isothermally perform the polymerase chain reaction (PCR) with a single heater, enabling the system to be operated using standard 5 V USB sources that power mobile devices (via battery, solar, or hand crank action). Time-resolved fluorescence detection and quantification is achieved using a smartphone camera and integrated image analysis app. Standard sample preparation is enabled by leveraging the drone's motors as centrifuges via 3D printed snap-on attachments. These advancements make it possible to build a complete DNA/RNA analysis system at a cost of ∼$50 ($US). Our instrument is rugged and versatile, enabling pinpoint deployment of sophisticated diagnostics to distributed field sites. This capability is demonstrated by successful in-flight replication of Staphylococcus aureus and λ-phage DNA targets in under 20 min. The ability to perform rapid in-flight assays with smartphone connectivity eliminates delays between sample collection and analysis so that test results can be delivered in minutes, suggesting new possibilities for drone-based systems to function in broader and more sophisticated roles beyond cargo transport and imaging.

Fourier Transform Infrared Spectroscopy (FT-IR) and Simple Algorithm Analysis for Rapid and Non-Destructive Assessment of Developmental Cotton Fibers.

PubMed

Liu, Yongliang; Kim, Hee-Jin

2017-06-22

With cotton fiber growth or maturation, cellulose content in cotton fibers markedly increases. Traditional chemical methods have been developed to determine cellulose content, but it is time-consuming and labor-intensive, mostly owing to the slow hydrolysis process of fiber cellulose components. As one approach, the attenuated total reflection Fourier transform infrared (ATR FT-IR) spectroscopy technique has also been utilized to monitor cotton cellulose formation, by implementing various spectral interpretation strategies of both multivariate principal component analysis (PCA) and 1-, 2- or 3-band/-variable intensity or intensity ratios. The main objective of this study was to compare the correlations between cellulose content determined by chemical analysis and ATR FT-IR spectral indices acquired by the reported procedures, among developmental Texas Marker-1 (TM-1) and immature fiber ( im ) mutant cotton fibers. It was observed that the R value, CI IR , and the integrated intensity of the 895 cm -1 band exhibited strong and linear relationships with cellulose content. The results have demonstrated the suitability and utility of ATR FT-IR spectroscopy, combined with a simple algorithm analysis, in assessing cotton fiber cellulose content, maturity, and crystallinity in a manner which is rapid, routine, and non-destructive.

Rapid Analysis, Self-Calibrating Array for Air Monitoring

NASA Technical Reports Server (NTRS)

Homer, Margie L.; Shevade, Abhijit V.; Lara, Liana; Huerta, Ramon; Vergara, Alexander; Muezzinoglua, Mehmet K.

2012-01-01

Human space missions have critical needs for monitoring and control for life support systems. These systems have monitoring needs that include feedback for closed loop processes and quality control for environmental factors. Sensors and monitoring technologies assure that the air environment and water supply for the astronaut crew habitat fall within acceptable limits, and that the life support system is functioning properly and efficiently. The longer the flight duration and the more distant the destination, the more critical it becomes to have carefully monitored and automated control systems for life support. Past experiments with the JPL ENose have demonstrated a lifetime of the sensor array, with the software, of around 18 months. The lifetime of the calibration, for some analytes, was as long as 24 months. We are working on a sensor array and new algorithms that will include sensor response time in the analysis. The preliminary array analysis for two analytes shows that the analysis time, of an event, can be dropped from 45 minutes to less than10 minutes and array training time can be cut substantially. We will describe the lifetime testing of an array and show lifetime data on individual sensors. This progress will lead to more rapid identification of analytes, and faster training time of the array.

Extracting neuronal functional network dynamics via adaptive Granger causality analysis.

PubMed

Sheikhattar, Alireza; Miran, Sina; Liu, Ji; Fritz, Jonathan B; Shamma, Shihab A; Kanold, Patrick O; Babadi, Behtash

2018-04-24

Quantifying the functional relations between the nodes in a network based on local observations is a key challenge in studying complex systems. Most existing time series analysis techniques for this purpose provide static estimates of the network properties, pertain to stationary Gaussian data, or do not take into account the ubiquitous sparsity in the underlying functional networks. When applied to spike recordings from neuronal ensembles undergoing rapid task-dependent dynamics, they thus hinder a precise statistical characterization of the dynamic neuronal functional networks underlying adaptive behavior. We develop a dynamic estimation and inference paradigm for extracting functional neuronal network dynamics in the sense of Granger, by integrating techniques from adaptive filtering, compressed sensing, point process theory, and high-dimensional statistics. We demonstrate the utility of our proposed paradigm through theoretical analysis, algorithm development, and application to synthetic and real data. Application of our techniques to two-photon Ca 2+ imaging experiments from the mouse auditory cortex reveals unique features of the functional neuronal network structures underlying spontaneous activity at unprecedented spatiotemporal resolution. Our analysis of simultaneous recordings from the ferret auditory and prefrontal cortical areas suggests evidence for the role of rapid top-down and bottom-up functional dynamics across these areas involved in robust attentive behavior.

Summary Report on Phase I and Phase II Results From the 3D Printing in Zero-G Technology Demonstration Mission. Volume II

NASA Technical Reports Server (NTRS)

Prater, T. J.; Werkheiser, N. J.; Ledbetter, F. E., III

2018-01-01

In-space manufacturing seeks to develop the processes, skill sets, and certification architecture needed to provide a rapid response manufacturing capability on long-duration exploration missions. The first 3D printer on the Space Station was developed by Made in Space, Inc. and completed two rounds of operation on orbit as part of the 3D Printing in Zero-G Technology Demonstration Mission. This Technical Publication provides a comprehensive overview of the technical objections of the mission, the two phases of hardware operation conducted on orbit, and the subsequent detailed analysis of specimens produced. No engineering significant evidence of microgravity effects on material outcomes was noted. This technology demonstration mission represents the first step in developing a suite of manufacturing capabilities to meet future mission needs.

Molecular definition of the identity and activation of natural killer cells.

PubMed

Bezman, Natalie A; Kim, Charles C; Sun, Joseph C; Min-Oo, Gundula; Hendricks, Deborah W; Kamimura, Yosuke; Best, J Adam; Goldrath, Ananda W; Lanier, Lewis L

2012-10-01

Using whole-genome microarray data sets of the Immunological Genome Project, we demonstrate a closer transcriptional relationship between NK cells and T cells than between any other leukocytes, distinguished by their shared expression of genes encoding molecules with similar signaling functions. Whereas resting NK cells are known to share expression of a few genes with cytotoxic CD8(+) T cells, our transcriptome-wide analysis demonstrates that the commonalities extend to hundreds of genes, many encoding molecules with unknown functions. Resting NK cells demonstrate a 'preprimed' state compared with naive T cells, which allows NK cells to respond more rapidly to viral infection. Collectively, our data provide a global context for known and previously unknown molecular aspects of NK cell identity and function by delineating the genome-wide repertoire of gene expression of NK cells in various states.

[Development of sample pretreatment techniques-rapid detection coupling methods for food security analysis].

PubMed

Huang, Yichun; Ding, Weiwei; Zhang, Zhuomin; Li, Gongke

2013-07-01

This paper summarizes the recent developments of the rapid detection methods for food security, such as sensors, optical techniques, portable spectral analysis, enzyme-linked immunosorbent assay, portable gas chromatograph, etc. Additionally, the applications of these rapid detection methods coupled with sample pretreatment techniques in real food security analysis are reviewed. The coupling technique has the potential to provide references to establish the selective, precise and quantitative rapid detection methods in food security analysis.

Rapid direct methods for enumeration of specific, active bacteria in water and biofilms

NASA Technical Reports Server (NTRS)

McFeters, G. A.; Pyle, B. H.; Lisle, J. T.; Broadaway, S. C.

1999-01-01

Conventional methods for detecting indicator and pathogenic bacteria in water may underestimate the actual population due to sublethal environmental injury, inability of the target bacteria to take up nutrients and other physiological factors which reduce bacterial culturability. Rapid and direct methods are needed to more accurately detect and enumerate active bacteria. Such a methodological advance would provide greater sensitivity in assessing the microbiological safety of water and food. The principle goal of this presentation is to describe novel approaches we have formulated for the rapid and simultaneous detection of bacteria plus the determination of their physiological activity in water and other environmental samples. The present version of our method involves the concentration of organisms by membrane filtration or immunomagnetic separation and combines an intracellular fluorochrome (CTC) for assessment of respiratory activity plus fluorescent-labelled antibody detection of specific bacteria. This approach has also been successfully used to demonstrate spatial and temporal heterogeneities of physiological activities in biofilms when coupled with cryosectioning. Candidate physiological stains include those capable of determining respiratory activity, membrane potential, membrane integrity, growth rate and cellular enzymatic activities. Results obtained thus far indicate that immunomagnetic separation can provide a high degree of sensitivity in the recovery of seeded target bacteria (Escherichia coli O157:H7) in water and hamburger. The captured and stained target bacteria are then enumerated by either conventional fluorescence microscopy or ChemScan(R), a new instrument that is very sensitive and rapid. The ChemScan(R) laser scanning instrument (Chemunex, Paris, France) provides the detection of individual fluorescently labelled bacterial cells using three emission channels in less than 5 min. A high degree of correlation has been demonstrated between results obtained with the ChemScan and traditional plate counts of mixed natural bacterial populations in water. The continuing evolution of these methods will be valuable in the rapid and accurate analysis of environmental samples.

CoBOP: Electro-Optic Identification Laser Line Sean Sensors

DTIC Science & Technology

1998-01-01

Electro - Optic Identification Sensors Project[1] is to develop and demonstrate high resolution underwater electro - optic (EO) imaging sensors, and associated image processing/analysis methods, for rapid visual identification of mines and mine-like contacts (MLCs). Identification of MLCs is a pressing Fleet need. During MCM operations, sonar contacts are classified as mine-like if they are sufficiently similar to signatures of mines. Each contact classified as mine-like must be identified as a mine or not a mine. During MCM operations in littoral areas,

High-throughput analysis of spatio-temporal dynamics in Dictyostelium

PubMed Central

Sawai, Satoshi; Guan, Xiao-Juan; Kuspa, Adam; Cox, Edward C

2007-01-01

We demonstrate a time-lapse video approach that allows rapid examination of the spatio-temporal dynamics of Dictyostelium cell populations. Quantitative information was gathered by sampling life histories of more than 2,000 mutant clones from a large mutagenesis collection. Approximately 4% of the clonal lines showed a mutant phenotype at one stage. Many of these could be ordered by clustering into functional groups. The dataset allows one to search and retrieve movies on a gene-by-gene and phenotype-by-phenotype basis. PMID:17659086

Robust Selection Algorithm (RSA) for Multi-Omic Biomarker Discovery; Integration with Functional Network Analysis to Identify miRNA Regulated Pathways in Multiple Cancers.

PubMed

Sehgal, Vasudha; Seviour, Elena G; Moss, Tyler J; Mills, Gordon B; Azencott, Robert; Ram, Prahlad T

2015-01-01

MicroRNAs (miRNAs) play a crucial role in the maintenance of cellular homeostasis by regulating the expression of their target genes. As such, the dysregulation of miRNA expression has been frequently linked to cancer. With rapidly accumulating molecular data linked to patient outcome, the need for identification of robust multi-omic molecular markers is critical in order to provide clinical impact. While previous bioinformatic tools have been developed to identify potential biomarkers in cancer, these methods do not allow for rapid classification of oncogenes versus tumor suppressors taking into account robust differential expression, cutoffs, p-values and non-normality of the data. Here, we propose a methodology, Robust Selection Algorithm (RSA) that addresses these important problems in big data omics analysis. The robustness of the survival analysis is ensured by identification of optimal cutoff values of omics expression, strengthened by p-value computed through intensive random resampling taking into account any non-normality in the data and integration into multi-omic functional networks. Here we have analyzed pan-cancer miRNA patient data to identify functional pathways involved in cancer progression that are associated with selected miRNA identified by RSA. Our approach demonstrates the way in which existing survival analysis techniques can be integrated with a functional network analysis framework to efficiently identify promising biomarkers and novel therapeutic candidates across diseases.

Analysis of cocoa flavanols and procyanidins (DP 1-10) in cocoa-containing ingredients and products by rapid resolution liquid chromatography: single-laboratory validation.

PubMed

Machonis, Philip R; Jones, Matthew A; Kwik-Uribe, Catherine

2014-01-01

Recently, a multilaboratory validation (MLV) of AOAC Official Method 2012.24 for the determination of cocoa flavanols and procyanidins (CF-CP) in cocoa-based ingredients and products determined that the method was robust, reliable, and transferrable. Due to the complexity of the CF-CP molecules, this method required a run time exceeding 1 h to achieve acceptable separations. To address this issue, a rapid resolution normal phase LC method was developed, and a single-laboratory validation (SLV) study conducted. Flavanols and procyanidins with a degree of polymerization (DP) up to 10 were eluted in 15 min using a binary gradient applied to a diol stationary phase, detected using fluorescence detection, and reported as a total sum of DP 1-10. Quantification was achieved using (-)-epicatechin-based relative response factors for DP 2-10. Spike recovery samples and seven different types of cocoa-based samples were analyzed to evaluate the accuracy, precision, LOD, LOQ, and linearity of the method. The within-day precision of the reported content for the samples was 1.15-5.08%, and overall precision was 3.97-13.61%. Spike-recovery experiments demonstrated recoveries of over 98%. The results of this SLV were compared to those previously obtained in the MLV and found to be consistent. The translation to rapid resolution LC allowed for an 80% reduction in analysis time and solvent usage, while retaining the accuracy and reliability of the original method. The savings in both cost and time of this rapid method make it well-suited for routine laboratory use.

Feasibility of rapid discharge after transoral robotic surgery of the oropharynx.

PubMed

Richmon, Jeremy D; Feng, Allen L; Yang, Wuyang; Starmer, Heather; Quon, Harry; Gourin, Christine G

2014-11-01

To investigate the use of an algorithm for rapid discharge after transoral robotic surgery (TORS) and its effect on postoperative complications. Retrospective cohort study. A retrospective analysis of TORS cases from September 2009 to February 2013 was conducted. The effect of patient and tumor characteristics on postoperative length of stay (LOS) and complications were analyzed. A total of 91 patients were included; 79 underwent TORS for malignancy and 12 for a benign process. The mean LOS was 1.51 days (range, 1-5 days) with a median of 1 day. The mean time to initiation of oral diet was 1.26 days (range, 1-7 days) with a median of 1 day. Eleven (12%) patients experienced one or more complications during their postoperative course. Multivariate analysis demonstrated a significant association between patient and procedure variables and postoperative complications. TORS base of tongue reduction for obstructive sleep apnea (OSA) was associated with a significantly greater mean incremental time to initiation of oral diet (1.0 days, 95% confidence interval [CI]: 0.4 to 1.7, P < .001). A significantly greater mean incremental LOS was observed for patients with advanced comorbidity and a delay in initiation of oral diet beyond 24 hours. Rapid initiation of oral diet and rapid discharge home is feasible and not associated with postoperative complications. Similarly, the performance of a concurrent neck dissection does not contribute to LOS or the development of postoperative complications. Patients undergoing TORS for OSA are at greater risk of delay in initiation of oral diet and increased LOS. 4 © 2014 The American Laryngological, Rhinological and Otological Society, Inc.

Rapid detection of Pseudomonas aeruginosa biomarkers in biological fluids using surface-enhanced Raman scattering

NASA Astrophysics Data System (ADS)

Wu, Xiaomeng; Chen, Jing; Zhao, Yiping; Zughaier, Susu M.

2014-05-01

Pseudomonas aeruginosa (PA) is an opportunistic pathogen that causes major infection not only in Cystic Fibrosis patients but also in chronic obstructive pulmonary disease and in critically ill patients in intensive care units. Successful antibiotic treatment of the infection relies on accurate and rapid identification of the infectious agents. Conventional microbiological detection methods usually take more than 3 days to obtain accurate results. We have developed a rapid diagnostic technique based on surface-enhanced Raman scattering to directly identify PA from biological fluids. P. aeruginosa strains, PAO1 and PA14, are cultured in lysogeny broth, and the SERS spectra of the broth show the signature Raman peaks from pyocyanin and pyoverdine, two major biomarkers that P. aeruginosa secretes during its growth, as well as lipopolysaccharides. This provides the evidence that the presence of these biomarkers can be used to indicate P. aeruginosa infection. A total of 22 clinical exhaled breath condensates (EBC) samples were obtained from subjects with CF disease and from non-CF healthy donors. SERS spectra of these EBC samples were obtained and further analyzed by both principle component analysis and partial least square-discriminant analysis (PLS-DA). PLS-DA can discriminate the samples with P. aeruginosa infection and the ones without P. aeruginosa infection at 99.3% sensitivity and 99.6% specificity. In addition, this technique can also discriminate samples from subject with CF disease and healthy donor with 97.5% sensitivity and 100% specificity. These results demonstrate the potential of using SERS of EBC samples as a rapid diagnostic tool to detect PA infection.

The use of real-time polymerase chain reaction for rapid diagnosis of skeletal tuberculosis.

PubMed

Kobayashi, Naomi; Fraser, Thomas G; Bauer, Thomas W; Joyce, Michael J; Hall, Gerri S; Tuohy, Marion J; Procop, Gary W

2006-07-01

We identified Mycobacterium tuberculosis DNA using real-time polymerase chain reaction on a specimen from an osteolytic lesion of a femoral condyle, in which the frozen section demonstrated granulomas. The process was much more rapid than is possible with culture. The rapid detection of M tuberculosis and the concomitant exclusion of granulomatous disease caused by nontuberculous mycobacteria or systemic fungi are necessary to appropriately treat skeletal tuberculosis. The detection and identification of M tuberculosis by culture may require several weeks using traditional methods. The real-time polymerase chain reaction method used has been shown to be rapid and reliable, and is able to detect and differentiate both tuberculous and nontuberculous mycobacteria. Real-time polymerase chain reaction may become a diagnostic standard for the evaluation of clinical specimens for the presence of mycobacteria; this case demonstrates the potential utility of this assay for the rapid diagnosis of skeletal tuberculosis.

Differentiation of five enterohepatic Helicobacter species by nested PCR with high-resolution melting curve analysis.

PubMed

Wu, Miaoli; Rao, Dan; Zhu, Yujun; Wang, Jing; Yuan, Wen; Zhang, Yu; Huang, Ren; Guo, Pengju

2017-04-01

Enterohepatic Helicobacter species (EHS) are widespread in rodent species around the world. Several studies have demonstrated that infection with EHS can interfere with the outcomes of animal experiments in cancer research and significantly influence the study results. Therefore, it is essential to establish a rapid detection and identification of EHS for biomedical research using laboratory rodents. Our study aimed to develop a rapid and sensitive method to detect and distinguish five enterohepatic Helicobacter species. Nested PCR followed by high-resolution melting curve analysis (HRM) was developed for identification of H. bilis, H. rodentium, H. muridarum, H. typhlonius, as well as H. hepaticus. To validate the accuracy of nested PCR-HRM analysis, quantitative real-time PCR methods for five different enterohepatic Helicobacter species were developed. A total of 50 cecal samples were tested using both nested PCR-HRM analysis and qPCR method. The nested PCR-HRM method could distinguish five enterohepatic Helicobacter species by different melting temperatures. The melting curve were characterized by peaks of 78.7 ± 0.12°C for H. rodentium, 80.51 ± 0.09°C for H. bilis, 81.6 ± 0.1°C for H. typhlonius, 82.11 ± 0.18°C for H. muridarum, and 82.95 ± 0.09°C for H. hepaticus. The nested PCR-HRM assay is a simple, rapid, and cost-effective assay. This assay could be a useful tool for molecular epidemiology study of enterohepatic Helicobacter infection and an attractive alternative for genotyping of enterohepatic Helicobacter species. © 2016 John Wiley & Sons Ltd.

Mechanisms underlying the rapid effects of estradiol and progesterone on hippocampal memory consolidation in female rodents.

PubMed

Frick, Karyn M; Kim, Jaekyoon

2018-05-09

Although rapid effects of 17β‑estradiol (E 2 ) and progesterone on cellular functions have been observed for several decades, a proliferation of data in recent years has demonstrated the importance of these actions to cognition. In particular, an emerging literature has demonstrated that these hormones promote the consolidation of spatial and object recognition memories in rodents via rapid activation of numerous cellular events including cell signaling, histone modifications, and local protein translation in the hippocampus. This article provides an overview of the evidence demonstrating that E 2 and progesterone enhance hippocampal memory consolidation in female rodents, and then discusses numerous molecular mechanisms thus far shown to mediate the beneficial effects of these hormones on memory formation. Copyright © 2018 Elsevier Inc. All rights reserved.

3D printed microneedles for insulin skin delivery.

PubMed

Pere, Cristiane Patricia Pissinato; Economidou, Sophia N; Lall, Gurprit; Ziraud, Clémentine; Boateng, Joshua S; Alexander, Bruce D; Lamprou, Dimitrios A; Douroumis, Dennis

2018-06-15

In this study, polymeric microneedle patches were fabricated by stereolithography, a 3D printing technique, for the transdermal delivery of insulin. A biocompatible resin was photopolymerized to build pyramid and cone microneedle designs followed by inkjet print coating of insulin formulations. Trehalose, mannitol and xylitol were used as drug carriers with the aim to preserve insulin integrity and stability but also to facilitate rapid release rates. Circular dichroism and Raman analysis demonstrated that all carriers maintained the native form of insulin, with xylitol presenting the best performance. Franz cell release studies were used for in vitro determination of insulin release rates in porcine skin. Insulin was released rapidly within 30 min irrespectively of the microneedle design. 3D printing was proved an effective technology for the fabrication of biocompatible and scalable microneedle patches. Copyright © 2018 Elsevier B.V. All rights reserved.

Sequential microfluidic droplet processing for rapid DNA extraction.

PubMed

Pan, Xiaoyan; Zeng, Shaojiang; Zhang, Qingquan; Lin, Bingcheng; Qin, Jianhua

2011-11-01

This work describes a novel droplet-based microfluidic device, which enables sequential droplet processing for rapid DNA extraction. The microdevice consists of a droplet generation unit, two reagent addition units and three droplet splitting units. The loading/washing/elution steps required for DNA extraction were carried out by sequential microfluidic droplet processing. The movement of superparamagnetic beads, which were used as extraction supports, was controlled with magnetic field. The microdevice could generate about 100 droplets per min, and it took about 1 min for each droplet to perform the whole extraction process. The extraction efficiency was measured to be 46% for λ-DNA, and the extracted DNA could be used in subsequent genetic analysis such as PCR, demonstrating the potential of the device for fast DNA extraction. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Rapid, quantitative and sensitive immunochromatographic assay based on stripping voltammetric detection of a metal ion label

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

Lu, Fang; Wang, Kaihua; Lin, Yuehe

2005-10-10

A novel, sensitive immunochromatographic electrochemical biosensor (IEB) which combines an immunochromatographic strip technique with an electrochemical detection technique is demonstrated. The IEB takes advantages of the speed and low-cost of the conventional immunochromatographic test kits and high-sensitivity of stripping voltammetry. Bismuth ions (Bi3+) have been coupled with the antibody through the bifunctional chelating agent diethylenetriamine pentaacetic acid (DTPA). After immunoreactions, Bi3+ was released and quantified by anodic stripping voltammetry at a built-in single-use screen-printed electrode. As an example for the applications of such novel device, the detection of human chorionic gonadotronphin (HCG) in a specimen was performed. This biosensor providesmore » a more user-friendly, rapid, clinically accurate, and less expensive immunoassay for such analysis in specimens than currently available test kits.« less

Accelerated Cartesian expansions for the rapid solution of periodic multiscale problems

DOE PAGES

Baczewski, Andrew David; Dault, Daniel L.; Shanker, Balasubramaniam

2012-07-03

We present an algorithm for the fast and efficient solution of integral equations that arise in the analysis of scattering from periodic arrays of PEC objects, such as multiband frequency selective surfaces (FSS) or metamaterial structures. Our approach relies upon the method of Accelerated Cartesian Expansions (ACE) to rapidly evaluate the requisite potential integrals. ACE is analogous to FMM in that it can be used to accelerate the matrix vector product used in the solution of systems discretized using MoM. Here, ACE provides linear scaling in both CPU time and memory. Details regarding the implementation of this method within themore » context of periodic systems are provided, as well as results that establish error convergence and scalability. In addition, we also demonstrate the applicability of this algorithm by studying several exemplary electrically dense systems.« less

Multiplex pyrosequencing of InDel markers for forensic DNA analysis.

PubMed

Bus, Magdalena M; Karas, Ognjen; Allen, Marie

2016-12-01

The capillary electrophoresis (CE) technology is commonly used for fragment length separation of markers in forensic DNA analysis. In this study, pyrosequencing technology was used as an alternative and rapid tool for the analysis of biallelic InDel (insertion/deletion) markers for individual identification. The DNA typing is based on a subset of the InDel markers that are included in the Investigator ® DIPplex Kit, which are sequenced in a multiplex pyrosequencing analysis. To facilitate the analysis of degraded DNA, the polymerase chain reaction (PCR) fragments were kept short in the primer design. Samples from individuals of Swedish origin were genotyped using the pyrosequencing strategy and analysis of the Investigator ® DIPplex markers with CE. A comparison between the pyrosequencing and CE data revealed concordant results demonstrating a robust and correct genotyping by pyrosequencing. Using optimal marker combination and a directed dispensation strategy, five markers could be multiplexed and analyzed simultaneously. In this proof-of-principle study, we demonstrate that multiplex InDel pyrosequencing analysis is possible. However, further studies on degraded samples, lower DNA quantities, and mixtures will be required to fully optimize InDel analysis by pyrosequencing for forensic applications. Overall, although CE analysis is implemented in most forensic laboratories, multiplex InDel pyrosequencing offers a cost-effective alternative for some applications. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Rapid culture-independent microbial analysis aboard the international space station (ISS) stage two: quantifying three microbial biomarkers.

PubMed

Morris, Heather C; Damon, Michael; Maule, Jake; Monaco, Lisa A; Wainwright, Norm

2012-09-01

Abstract A portable, rapid, microbial detection unit, the Lab-On-a-Chip Application Development Portable Test System (LOCAD-PTS), was launched to the International Space Station (ISS) as a technology demonstration unit in December 2006. Results from the first series of experiments designed to detect Gram-negative bacteria on ISS surfaces by quantifying a single microbial biomarker lipopolysaccharide (LPS) were reported in a previous article. Herein, we report additional technology demonstration experiments expanding the on-orbit capabilities of the LOCAD-PTS to detecting three different microbial biomarkers on ISS surfaces. Six different astronauts on more than 20 occasions participated in these experiments, which were designed to test the new beta-glucan (fungal cell wall molecule) and lipoteichoic acid (LTA; Gram-positive bacterial cell wall component) cartridges individually and in tandem with the existing Limulus Amebocyte Lysate (LAL; Gram-negative bacterial LPS detection) cartridges. Additionally, we conducted the sampling side by side with the standard culture-based detection method currently used on the ISS. Therefore, we present data on the distribution of three microbial biomarkers collected from various surfaces in every module present on the ISS at the time of sampling. In accordance with our previous experiments, we determined that spacecraft surfaces known to be frequently in contact with crew members demonstrated higher values of all three microbial molecules. Key Words: Planetary protection-Spaceflight-Microbiology-Biosensor. Astrobiology 12, 830-840.

Identification of Salmonella Typhimurium-specific DNA aptamers developed using whole-cell SELEX and FACS analysis.

PubMed

Moon, Jihea; Kim, Giyoung; Lee, Sangdae; Park, Saetbyeol

2013-11-01

Conventional methods for detection of infective organisms, such as Salmonella, are complicated and require multiple steps, and the need for rapid detection has increased. Biosensors show great potential for rapid detection of pathogens. In turn, aptamers have great potential for biosensor assay development, given their small size, ease of synthesis and labeling, lack of immunogenicity, a lower cost of production than antibodies, and high target specificity. In this study, ssDNA aptamers specific to Salmonella Typhimurium were obtained by a whole bacterium-based systematic evolution of ligands by exponential enrichment (SELEX) procedure and applied to probing S. Typhimurium. After 10 rounds of selection with S. Typhimurium as the target and Salmonella Enteritidis, Escherichia coli and Staphylococcus aureus as counter targets, the highly enriched oligonucleic acid pool was sorted using flow cytometry. In total, 12 aptamer candidates from different families were sequenced and grouped. Fluorescent analysis demonstrated that aptamer C4 had particularly high binding affinity and selectivity; this aptamer was then further characterized. © 2013 Elsevier B.V. All rights reserved.

Development of rapid and sensitive high throughput pharmacologic assays for marine phycotoxins.

PubMed

Van Dolah, F M; Finley, E L; Haynes, B L; Doucette, G J; Moeller, P D; Ramsdell, J S

1994-01-01

The lack of rapid, high throughput assays is a major obstacle to many aspects of research on marine phycotoxins. Here we describe the application of microplate scintillation technology to develop high throughput assays for several classes of marine phycotoxin based on their differential pharmacologic actions. High throughput "drug discovery" format microplate receptor binding assays developed for brevetoxins/ciguatoxins and for domoic acid are described. Analysis for brevetoxins/ciguatoxins is carried out by binding competition with [3H] PbTx-3 for site 5 on the voltage dependent sodium channel in rat brain synaptosomes. Analysis of domoic acid is based on binding competition with [3H] kainic acid for the kainate/quisqualate glutamate receptor using frog brain synaptosomes. In addition, a high throughput microplate 45Ca flux assay for determination of maitotoxins is described. These microplate assays can be completed within 3 hours, have sensitivities of less than 1 ng, and can analyze dozens of samples simultaneously. The assays have been demonstrated to be useful for assessing algal toxicity and for assay-guided purification of toxins, and are applicable to the detection of biotoxins in seafood.

Stability indicating simplified HPLC method for simultaneous analysis of resveratrol and quercetin in nanoparticles and human plasma.

PubMed

Kumar, Sandeep; Lather, Viney; Pandita, Deepti

2016-04-15

Resveratrol and quercetin are well-known polyphenolic compounds present in common foods, which have demonstrated enormous potential in the treatment of a wide variety of diseases. Owing to their exciting synergistic potential and combination delivery applications, we developed a simple and rapid RP-HPLC method based on isosbestic point detection. The separation was carried out on phenomenex Synergi 4μ Hydro-RP 80A column using methanol: acetonitrile (ACN): 0.1% phosphoric acid (60:10:30) as mobile phase. The method was able to quantify nanograms of analytes simultaneously on a single wavelength (269 nm), making it highly sensitive, rapid as well as economical. Additionally, forced degradation studies of resveratrol and quercetin were established and the method's applicability was evaluated on PLGA nanoparticles and human plasma. The analytes peaks were found to be well resolved in the presence of degradation products and excipients. The simplicity of the developed method potentializes its suitability for routine in vitro and in vivo analysis of resveratrol and quercetin. Copyright © 2015 Elsevier Ltd. All rights reserved.

Object-Place Recognition Learning Triggers Rapid Induction of Plasticity-Related Immediate Early Genes and Synaptic Proteins in the Rat Dentate Gyrus

PubMed Central

Soulé, Jonathan; Penke, Zsuzsa; Kanhema, Tambudzai; Alme, Maria Nordheim; Laroche, Serge; Bramham, Clive R.

2008-01-01

Long-term recognition memory requires protein synthesis, but little is known about the coordinate regulation of specific genes. Here, we examined expression of the plasticity-associated immediate early genes (Arc, Zif268, and Narp) in the dentate gyrus following long-term object-place recognition learning in rats. RT-PCR analysis from dentate gyrus tissue collected shortly after training did not reveal learning-specific changes in Arc mRNA expression. In situ hybridization and immunohistochemistry were therefore used to assess possible sparse effects on gene expression. Learning about objects increased the density of granule cells expressing Arc, and to a lesser extent Narp, specifically in the dorsal blade of the dentate gyrus, while Zif268 expression was elevated across both blades. Thus, object-place recognition triggers rapid, blade-specific upregulation of plasticity-associated immediate early genes. Furthermore, Western blot analysis of dentate gyrus homogenates demonstrated concomitant upregulation of three postsynaptic density proteins (Arc, PSD-95, and α-CaMKII) with key roles in long-term synaptic plasticity and long-term memory. PMID:19190776

Application of Fourier Transform Infrared (FTIR) Spectroscopy for Rapid Detection of Fumonisin B2 in Raisins.

PubMed

Heperkan, Dilek; Gökmen, Ece

2016-07-01

The aim of this study was to investigate the potential use of FTIR spectroscopy as a rapid screening method to detect fumonisin produced by Aspergillus niger. A. niger spore suspensions isolated from raisins were inoculated in Petri dishes prepared with sultana raisin or black raisin extracts containing agar and malt extract agar (MEA). After 9 days of incubation at 25°C, fumonisin B2 (FB2) production on each agar plate was determined by subjecting the agar plugs to IR spectroscopy. The presence of amino group (at 1636-1639 cm(-1)) was especially indicative of fumonisin production in MEA and the raisin extracts containing agar. The results were confirmed by HPLC analysis of the agar sample extracts after immunoaffinity column cleanup. It was determined that A. niger produced more FB2 in sultana raisins than in MEA, with no FB2 being produced in black raisin extract agar. This study demonstrated that proper sample preparation procedure followed by FTIR analysis is a useful technique for identifying toxigenic molds and their mycotoxin production in agricultural commodities.

Analysis of compositional monosaccharides in fungus polysaccharides by capillary zone electrophoresis.

PubMed

Hu, Yuanyuan; Wang, Tong; Yang, Xingbin; Zhao, Yan

2014-02-15

A rapid analytical method of capillary zone electrophoresis (CZE) was established for the simultaneous separation and determination of 10 monosaccharides (aldoses and uronic acids). The monosaccharides were labeled with 1-phenyl-3-methyl-5-pyrazolone (PMP), and subsequently separated using an uncoated capillary (50 μm i.d. × 58.5 cm) and detected by UV at 245 nm with pH 11.0, 175 mM borate buffer at voltage 20 kV and capillary temperature 25 °C by CZE. The 10 PMP-labeled monosaccharides were rapidly baseline separated within 20 min. The optimized CZE method was successfully applied to the simultaneous separation and identification of the monosaccharide composition in Termitomyces albuminosus polysaccharides (TAPs) and Panus giganteus polysaccharides (PGPs). The quantitative recovery of the component monosaccharides in the fungus polysaccharides was in the range of 92.0-101.0% and the CV value was lower than 3.5%. The results demonstrate that the proposed CZE method is precise and practical for the monosaccharide analysis of fungus polysaccharides. Copyright © 2013 Elsevier Ltd. All rights reserved.

The HIP1 binding site is required for growth regulation of the dihydrofolate reductase gene promoter.

PubMed

Means, A L; Slansky, J E; McMahon, S L; Knuth, M W; Farnham, P J

1992-03-01

The transcription rate of the dihydrofolate reductase (DHFR) gene increases at the G1/S boundary of the proliferative cell cycle. Through analysis of transiently and stably transfected NIH 3T3 cells, we have now demonstrated that DHFR promoter sequences extending from -270 to +20 are sufficient to confer similar regulation on a reporter gene. Mutation of a protein binding site that spans sequences from -16 to +11 in the DHFR promoter resulted in loss of the transcriptional increase at the G1/S boundary. Purification of an activity from HeLa nuclear extract that binds to this region enriched for a 180-kDa polypeptide (HIP1). Using this HIP1 preparation, we have identified specific positions within the binding site that are critical for efficient protein-DNA interactions. An analysis of association and dissociation rates suggests that bound HIP1 protein can exchange rapidly with free protein. This rapid exchange may facilitate the burst of transcriptional activity from the DHFR promoter at the G1/S boundary.

The HIP1 binding site is required for growth regulation of the dihydrofolate reductase gene promoter.

PubMed Central

Means, A L; Slansky, J E; McMahon, S L; Knuth, M W; Farnham, P J

1992-01-01

The transcription rate of the dihydrofolate reductase (DHFR) gene increases at the G1/S boundary of the proliferative cell cycle. Through analysis of transiently and stably transfected NIH 3T3 cells, we have now demonstrated that DHFR promoter sequences extending from -270 to +20 are sufficient to confer similar regulation on a reporter gene. Mutation of a protein binding site that spans sequences from -16 to +11 in the DHFR promoter resulted in loss of the transcriptional increase at the G1/S boundary. Purification of an activity from HeLa nuclear extract that binds to this region enriched for a 180-kDa polypeptide (HIP1). Using this HIP1 preparation, we have identified specific positions within the binding site that are critical for efficient protein-DNA interactions. An analysis of association and dissociation rates suggests that bound HIP1 protein can exchange rapidly with free protein. This rapid exchange may facilitate the burst of transcriptional activity from the DHFR promoter at the G1/S boundary. Images PMID:1545788

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

PubMed

Egorov, A V; Klochkova, N V

2009-01-01

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

Droplet centrifugation, droplet DNA extraction, and rapid droplet thermocycling for simpler and faster PCR assay using wire-guided manipulations

PubMed Central

2012-01-01

A computer numerical control (CNC) apparatus was used to perform droplet centrifugation, droplet DNA extraction, and rapid droplet thermocycling on a single superhydrophobic surface and a multi-chambered PCB heater. Droplets were manipulated using “wire-guided” method (a pipette tip was used in this study). This methodology can be easily adapted to existing commercial robotic pipetting system, while demonstrated added capabilities such as vibrational mixing, high-speed centrifuging of droplets, simple DNA extraction utilizing the hydrophobicity difference between the tip and the superhydrophobic surface, and rapid thermocycling with a moving droplet, all with wire-guided droplet manipulations on a superhydrophobic surface and a multi-chambered PCB heater (i.e., not on a 96-well plate). Serial dilutions were demonstrated for diluting sample matrix. Centrifuging was demonstrated by rotating a 10 μL droplet at 2300 round per minute, concentrating E. coli by more than 3-fold within 3 min. DNA extraction was demonstrated from E. coli sample utilizing the disposable pipette tip to cleverly attract the extracted DNA from the droplet residing on a superhydrophobic surface, which took less than 10 min. Following extraction, the 1500 bp sequence of Peptidase D from E. coli was amplified using rapid droplet thermocycling, which took 10 min for 30 cycles. The total assay time was 23 min, including droplet centrifugation, droplet DNA extraction and rapid droplet thermocycling. Evaporation from of 10 μL droplets was not significant during these procedures, since the longest time exposure to air and the vibrations was less than 5 min (during DNA extraction). The results of these sequentially executed processes were analyzed using gel electrophoresis. Thus, this work demonstrates the adaptability of the system to replace many common laboratory tasks on a single platform (through re-programmability), in rapid succession (using droplets), and with a high level of accuracy and automation. PMID:22947281

Rapid flood loss estimation for large scale floods in Germany

NASA Astrophysics Data System (ADS)

Schröter, Kai; Kreibich, Heidi; Merz, Bruno

2013-04-01

Rapid evaluations of flood events are needed for efficient responses both in emergency management and financial appraisal. Beyond that, closely monitoring and documenting the formation and development of flood events and their impacts allows for an improved understanding and in depth analyses of the interplay between meteorological, hydrological, hydraulic and societal causes leading to flood damage. This contribution focuses on the development of a methodology for the rapid assessment of flood events. In the first place, the focus is on the prediction of damage to residential buildings caused by large scale floods in Germany. For this purpose an operational flood event analysis system is developed. This system has basic spatial thematic data available and supports data capturing about the current flood situation. This includes the retrieval of online gauge data and the integration of remote sensing data. Further, it provides functionalities to evaluate the current flood situation, to assess the hazard extent and intensity and to estimate the current flood impact using the flood loss estimation model FLEMOps+r. The operation of the flood event analysis system will be demonstrated for the past flood event from January 2011 with a focus on the Elbe/Saale region. On this grounds, further requirements and potential for improving the information basis as for instance by including hydrological and /or hydraulic model results as well as information from social sensors will be discussed.

In vitro rapid intraoral adjustment of porcelain prostheses using a high-speed dental handpiece.

PubMed

Song, Xiao-Fei; Yin, Ling; Han, Yi-Gang; Wang, Hui

2008-03-01

In vitro rapid intraoral adjustment of porcelain prostheses was conducted using a high-speed dental handpiece and diamond bur. The adjustment process was characterized by measurement of removal forces and energy, with scanning electron microscopic (SEM) observation of porcelain debris, surfaces and subsurface damage produced as a function of operational feed rate. Finite element analysis (FEA) was applied to evaluate subsurface stress distributions and degrees of subsurface damage. The results show that an increase in feed rate resulted in increases in both tangential and normal forces (analysis of variance (ANOVA), P<0.01). When the feed rate approached the highest rate of 60mm min(-1) at a fixed depth of cut of 100microm, the tangential force was nearly seven times that at the lowest feed rate of 15mm min(-1). Consequently, the specific removal energy increased significantly (ANOVA, P<0.01), and the maximum depth of subsurface damage obtained was approximately 110 and 120microm at the highest feed rate of 60mm min(-1) using SEM and FEA, respectively. The topographies of both the adjusted porcelain surfaces and the debris demonstrate microscopically that porcelain was removed via brittle fracture and plastic deformation. Clinicians must be cautious when pursuing rapid dental adjustments, because high operational energy, larger forces and severe surface and subsurface damage can be induced.

DNA Microarray Gene Expression Profile of Marginal Zone versus Follicular B cells and Idiotype Positive Marginal Zone B cells Before and After Immunization with Streptococcus pneumoniae 1

PubMed Central

Liu, Jiabin; Behrens, Timothy W.; Kearney, John F.

2014-01-01

Marginal Zone (MZ) B cells play an important role in the clearance of blood-borne bacterial infections via rapid T-independent IgM responses. We have previously demonstrated that MZ B cells respond rapidly and robustly to bacterial particulates. To determine the MZ-specific genes that are expressed to allow for this response, MZ and Follicular (FO) B cells were sort-purified and analyzed via DNA microarray analysis. We identified 181 genes that were significantly different between the two B cell populations. 99 genes were more highly expressed in MZ B cells while 82 genes were more highly expressed in FO B cells. To further understand the molecular mechanisms by which MZ B cells respond so rapidly to bacterial challenge, idiotype positive and negative MZ B cells were sort-purified before (0 hour) or after (1 hour) i.v. immunization with heat killed Streptococcus pneumoniae, R36A, and analyzed via DNA microarray analysis. We identified genes specifically up regulated or down regulated at 1 hour following immunization in the idiotype positive MZ B cells. These results give insight into the gene expression pattern in resting MZ vs. FO B cells and the specific regulation of gene expression in antigen-specific MZ B cells following interaction with antigen. PMID:18453586

A rapid generalized least squares model for a genome-wide quantitative trait association analysis in families.

PubMed

Li, Xiang; Basu, Saonli; Miller, Michael B; Iacono, William G; McGue, Matt

2011-01-01

Genome-wide association studies (GWAS) using family data involve association analyses between hundreds of thousands of markers and a trait for a large number of related individuals. The correlations among relatives bring statistical and computational challenges when performing these large-scale association analyses. Recently, several rapid methods accounting for both within- and between-family variation have been proposed. However, these techniques mostly model the phenotypic similarities in terms of genetic relatedness. The familial resemblances in many family-based studies such as twin studies are not only due to the genetic relatedness, but also derive from shared environmental effects and assortative mating. In this paper, we propose 2 generalized least squares (GLS) models for rapid association analysis of family-based GWAS, which accommodate both genetic and environmental contributions to familial resemblance. In our first model, we estimated the joint genetic and environmental variations. In our second model, we estimated the genetic and environmental components separately. Through simulation studies, we demonstrated that our proposed approaches are more powerful and computationally efficient than a number of existing methods are. We show that estimating the residual variance-covariance matrix in the GLS models without SNP effects does not lead to an appreciable bias in the p values as long as the SNP effect is small (i.e. accounting for no more than 1% of trait variance). Copyright © 2011 S. Karger AG, Basel.

Examining the Neurocognitive Profile of Dysnomia: A Comparison of School-Aged Children with and without Dyslexia across the Domains of Expressive Language, Attention/Memory, and Academic Achievement

ERIC Educational Resources Information Center

Howarth, Robyn Ann

2010-01-01

Word-retrieval and rapid naming abilities play an important role in language processing and cognitive development. Researchers have demonstrated that early language difficulties may lead to later reading impairments and several decades of research has convincingly demonstrated that rapid automatized naming is a powerful predictor of concurrent and…

Pathways of Barotrauma in Juvenile Salmonids Exposed to Simulated Hydroturbine Passage: Boyle’s Law vs. Henry’s Law

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

Brown, Richard S.; Pflugrath, Brett D.; Colotelo, Alison HA

2012-06-01

On their seaward migration, juvenile salmonids commonly pass hydroelectric dams. Fish passing by the turbine blade may experience rapid decompression, the severity of which can be highly variable and may result in a number of barotraumas. The mechanisms of these injuries can be due to expansion of existing bubbles or gases coming out of solution; governed by Boyle’s Law and Henry’s Law, respectively. This paper combines re-analysis of published data with new experiments to gain a better understanding of the mechanisms of injury and mortality for fish experiencing rapid decompression associated with hydroturbine passage. From these data it appears thatmore » the majority of decompression related injuries are due to the expansion of existing bubbles in the fish, particularly the expansion and rupture of the swim bladder. This information is particularly useful for fisheries managers and turbine manufacturers, demonstrating that reducing the rate of swim bladder ruptures by reducing the frequency of occurrence and severity of rapid decompression during hydroturbine passage could reduce the rates of injury and mortality for hydroturbine passed juvenile salmonids.« less

Alterations in endogenous circadian rhythm of core temperature in senescent Fischer 344 rats

NASA Technical Reports Server (NTRS)

McDonald, R. B.; Hoban-Higgins, T. M.; Ruhe, R. C.; Fuller, C. A.; Horwitz, B. A.

1999-01-01

We assessed whether alterations in endogenous circadian rhythm of core temperature (CRT) in aging rats are associated with chronological time or with a biological marker of senescence, i.e., spontaneous rapid body weight loss. CRT was measured in male Fischer 344 (F344) rats beginning at age 689 days and then continuously until death. Young rats were also monitored. The rats were housed under constant dim red light at 24-26 degrees C, and core temperature was recorded every 10 min via biotelemetry. The CRT amplitude of the body weight-stable (presenescent) old rats was significantly less than that of young rats at all analysis periods. At the onset of spontaneous rapid weight loss (senescence), all measures of endogenous CRT differed significantly from those in the presenescent period. The suprachiasmatic nucleus (a circadian pacemaker) of the senescent rats maintained its light responsiveness as determined by an increase in c-fos expression after a brief light exposure. These data demonstrate that some characteristics of the CRT are altered slowly with chronological aging, whereas others occur rapidly with the onset of senescence.

Design of Neural Networks for Fast Convergence and Accuracy

NASA Technical Reports Server (NTRS)

Maghami, Peiman G.; Sparks, Dean W., Jr.

1998-01-01

A novel procedure for the design and training of artificial neural networks, used for rapid and efficient controls and dynamics design and analysis for flexible space systems, has been developed. Artificial neural networks are employed to provide a means of evaluating the impact of design changes rapidly. Specifically, two-layer feedforward neural networks are designed to approximate the functional relationship between the component spacecraft design changes and measures of its performance. A training algorithm, based on statistical sampling theory, is presented, which guarantees that the trained networks provide a designer-specified degree of accuracy in mapping the functional relationship. Within each iteration of this statistical-based algorithm, a sequential design algorithm is used for the design and training of the feedforward network to provide rapid convergence to the network goals. Here, at each sequence a new network is trained to minimize the error of previous network. The design algorithm attempts to avoid the local minima phenomenon that hampers the traditional network training. A numerical example is performed on a spacecraft application in order to demonstrate the feasibility of the proposed approach.

Facile and sensitive determination of N-nitrosamines in food samples by high-performance liquid chromatography via combining fluorescent labeling with dispersive liquid-liquid microextraction.

PubMed

Lu, Shuaimin; Wu, Di; Li, Guoliang; Lv, Zhengxian; Gong, Peiwei; Xia, Lian; Sun, Zhiwei; Chen, Guang; Chen, Xuefeng; You, Jinmao; Wu, Yongning

2017-11-01

The intake of N-nitrosamines (NAs) from foodstuffs is considered to be an important influence factor for several cancers. But the rapid and sensitive screening of NAs remains a challenge in the field of food safety. Inspired by that, a sensitive and rapid method was demonstrated for determination of five NAs (Nitrosopyrrolidine, Nitrosodimethylamine, Nitrosodiethylamine, Nitrosodipropylamine and Nitrosodibutylamine) using dispersive liquid-liquid microextraction (DLLME) followed by high-performance liquid chromatography with fluorescence detection (HPLC-FLD). The NAs were firstly denitrosated and labeled by 2-(11H-benzo[a]carbazol-11-yl) ethyl carbonochloridate (BCEC-Cl) and finally enriched by DLLME. Furthermore, the main DLLME conditions were optimized systematically. Under the optimal conditions, satisfactory limits of detection (LODs) were obtained with a range of 0.01-0.07ngg -1 , which were significantly lower than the reported methods. The developed method showed many merits including rapidity, simplicity, high sensitivity and excellent selectivity, which shows a broad prospect in food safety analysis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Rapid electrostatics-assisted layer-by-layer assembly of near-infrared-active colloidal photonic crystals.

PubMed

Askar, Khalid; Leo, Sin-Yen; Xu, Can; Liu, Danielle; Jiang, Peng

2016-11-15

Here we report a rapid and scalable bottom-up technique for layer-by-layer (LBL) assembling near-infrared-active colloidal photonic crystals consisting of large (⩾1μm) silica microspheres. By combining a new electrostatics-assisted colloidal transferring approach with spontaneous colloidal crystallization at an air/water interface, we have demonstrated that the crystal transfer speed of traditional Langmuir-Blodgett-based colloidal assembly technologies can be enhanced by nearly 2 orders of magnitude. Importantly, the crystalline quality of the resultant photonic crystals is not compromised by this rapid colloidal assembly approach. They exhibit thickness-dependent near-infrared stop bands and well-defined Fabry-Perot fringes in the specular transmission and reflection spectra, which match well with the theoretical calculations using a scalar-wave approximation model and Fabry-Perot analysis. This simple yet scalable bottom-up technology can significantly improve the throughput in assembling large-area, multilayer colloidal crystals, which are of great technological importance in a variety of optical and non-optical applications ranging from all-optical integrated circuits to tissue engineering. Copyright © 2016 Elsevier Inc. All rights reserved.

Demonstrated Potential of Ion Mobility Spectrometry for Detection of Adulterated Perfumes and Plant Speciation

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

Clark, Jared Matthew; Daum, Keith Alvin; Kalival, J. H.

2003-01-01

This initial study evaluates the use of ion mobility spectrometry (IMS) as a rapid test procedure for potential detection of adulterated perfumes and speciation of plant life. Sample types measured consist of five genuine perfumes, two species of sagebrush, and four species of flowers. Each sample type is treated as a separate classification problem. It is shown that discrimination using principal component analysis with K-nearest neighbors can distinguish one class from another. Discriminatory models generated using principal component regressions are not as effective. Results from this examination are encouraging and represent an initial phase demonstrating that perfumes and plants possessmore » characteristic chemical signatures that can be used for reliable identification.« less

Real-Time Onboard Global Nonlinear Aerodynamic Modeling from Flight Data

NASA Technical Reports Server (NTRS)

Brandon, Jay M.; Morelli, Eugene A.

2014-01-01

Flight test and modeling techniques were developed to accurately identify global nonlinear aerodynamic models onboard an aircraft. The techniques were developed and demonstrated during piloted flight testing of an Aermacchi MB-326M Impala jet aircraft. Advanced piloting techniques and nonlinear modeling techniques based on fuzzy logic and multivariate orthogonal function methods were implemented with efficient onboard calculations and flight operations to achieve real-time maneuver monitoring and analysis, and near-real-time global nonlinear aerodynamic modeling and prediction validation testing in flight. Results demonstrated that global nonlinear aerodynamic models for a large portion of the flight envelope were identified rapidly and accurately using piloted flight test maneuvers during a single flight, with the final identified and validated models available before the aircraft landed.

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

Huff, Kathryn D.

Component level and system level abstraction of detailed computational geologic repository models have resulted in four rapid computational models of hydrologic radionuclide transport at varying levels of detail. Those models are described, as is their implementation in Cyder, a software library of interchangeable radionuclide transport models appropriate for representing natural and engineered barrier components of generic geology repository concepts. A proof of principle demonstration was also conducted in which these models were used to represent the natural and engineered barrier components of a repository concept in a reducing, homogenous, generic geology. This base case demonstrates integration of the Cyder openmore » source library with the Cyclus computational fuel cycle systems analysis platform to facilitate calculation of repository performance metrics with respect to fuel cycle choices. (authors)« less

Differential screening and mass mapping of proteins from premalignant and cancer cell lines using nonporous reversed-phase HPLC coupled with mass spectrometric analysis.

PubMed

Chong, B E; Hamler, R L; Lubman, D M; Ethier, S P; Rosenspire, A J; Miller, F R

2001-03-15

Nonporous (NPS) RP-HPLC has been used to rapidly separate proteins from whole cell lysates of human breast cell lines. The nonporous separation involves the use of hard-sphere silica beads of 1.5-microm diameter coated with C18, which can be used to separate proteins ranging from 5 to 90 kDa. Using only 30-40 microg of total protein, the protein molecular weights are detectable on-line using an ESI-oaTOF MS. Of hundreds of proteins detected in this mass range, approxinately 75-80 are more highly expressed. The molecular weight profiles can be displayed as a mass map analogous to a virtual "1-D gel" and differentially expressed proteins can be compared by image analysis. The separated proteins can also be detected by UV absorption and differentially expressed proteins quantified. The eluting proteins can be collected in the liquid phase and the molecular weight and peptide maps determined by MALDI-TOF MS for identification. It is demonstrated that the expressed protein profiles change during neoplastic progression and that many oncoproteins are readily detected. It is also shown that the response of premalignant cancer cells to estradiol can be rapidly screened by this method, demonstrating significant changes in response to an external agent. Ultimately, the proteins can be studied by peptide mapping to search for posttranslational modifications of the oncoproteins accompanying progression.

Core Dynamics Analysis for Reactivity Insertion and Loss of Coolant Flow Tests Using the High Temperature Engineering Test Reactor

NASA Astrophysics Data System (ADS)

Takamatsu, Kuniyoshi; Nakagawa, Shigeaki; Takeda, Tetsuaki

Safety demonstration tests using the High Temperature Engineering Test Reactor (HTTR) are in progress to verify its inherent safety features and improve the safety technology and design methodology for High-temperature Gas-cooled Reactors (HTGRs). The reactivity insertion test is one of the safety demonstration tests for the HTTR. This test simulates the rapid increase in the reactor power by withdrawing the control rod without operating the reactor power control system. In addition, the loss of coolant flow tests has been conducted to simulate the rapid decrease in the reactor power by tripping one, two or all out of three gas circulators. The experimental results have revealed the inherent safety features of HTGRs, such as the negative reactivity feedback effect. The numerical analysis code, which was named-ACCORD-, was developed to analyze the reactor dynamics including the flow behavior in the HTTR core. We have modified this code to use a model with four parallel channels and twenty temperature coefficients. Furthermore, we added another analytical model of the core for calculating the heat conduction between the fuel channels and the core in the case of the loss of coolant flow tests. This paper describes the validation results for the newly developed code using the experimental results. Moreover, the effect of the model is formulated quantitatively with our proposed equation. Finally, the pre-analytical result of the loss of coolant flow test by tripping all gas circulators is also discussed.

MALDI-TOF MS analysis of cellodextrins and xylo-oligosaccharides produced by hindgut homogenates of Reticulitermes santonensis.

PubMed

Brasseur, Catherine; Bauwens, Julien; Tarayre, Cédric; Mattéotti, Christel; Thonart, Philippe; Destain, Jacqueline; Francis, Frédéric; Haubruge, Eric; Portetelle, Daniel; Vandenbol, Micheline; Focant, Jean-François; De Pauw, Edwin

2014-04-11

Hindgut homogenates of the termite Reticulitermes santonensis were incubated with carboxymethyl cellulose (CMC), crystalline celluloses or xylan substrates. Hydrolysates were analyzed with matrix-assisted laser desorption/ionization coupled to time-of-flight mass spectrometry (MALDI-TOF MS). The method was first set up using acid hydrolysis analysis to characterize non-enzymatic profiles. Commercial enzymes of Trichoderma reesei or T. longibrachiatum were also tested to validate the enzymatic hydrolysis analysis. For CMC hydrolysis, data processing and visual display were optimized to obtain comprehensive profiles and allow rapid comparison and evaluation of enzymatic selectivity, according to the number of substituents of each hydrolysis product. Oligosaccharides with degrees of polymerization (DPs) ranging from three to 12 were measured from CMC and the enzymatic selectivity was demonstrated. Neutral and acidic xylo-oligosaccharides with DPs ranging from three to 11 were measured from xylan substrate. These results are of interest for lignocellulose biomass valorization and demonstrated the potential of termites and their symbiotic microbiota as a source of interesting enzymes for oligosaccharides production.

High Useful Yield and Isotopic Analysis of Uranium by Resonance Ionization Mass Spectrometry

DOE PAGES

Savina, Michael R.; Isselhardt, Brett H.; Kucher, Andrew; ...

2017-05-09

Useful yields from resonance ionization mass spectrometry can be extremely high compared to other mass spectrometry techniques, but uranium analysis shows strong matrix effects arising from the tendency of uranium to form strongly bound oxide molecules that do not dissociate appreciably on energetic ion bombardment. Here, we demonstrate a useful yield of 24% for metallic uranium. Modeling the laser ionization and ion transmission processes shows that the high useful yield is attributable to a high ion fraction achieved by resonance ionization. We quantify the reduction of uranium oxide surface layers by Ar + and Ga + sputtering. The useful yieldmore » for uranium atoms from a uranium dioxide matrix is 0.4% and rises to 2% when the surface is in sputter equilibrium with the ion beam. The lower useful yield from the oxide is almost entirely due to uranium oxide molecules reducing the neutral atom content of the sputtered flux. We also demonstrate rapid isotopic analysis of solid uranium oxide at a precision of <0.5% relative standard deviation using relatively broadband lasers to mitigate spectroscopic fractionation.« less

Taxonomic evaluation of putative Streptomyces scabiei strains held in the ARS Culture Collection (NRRL) using multi-locus sequence analysis.

PubMed

Labeda, David P

2016-03-01

Multi-locus sequence analysis has been demonstrated to be a useful tool for identification of Streptomyces species and was previously applied to phylogenetically differentiate the type strains of species pathogenic on potatoes (Solanum tuberosum L.). The ARS Culture Collection (NRRL) contains 43 strains identified as Streptomyces scabiei deposited at various times since the 1950s and these were subjected to multi-locus sequence analysis utilising partial sequences of the house-keeping genes atpD, gyrB, recA, rpoB and trpB. Phylogenetic analyses confirmed the identity of 17 of these strains as Streptomyces scabiei, 9 of the strains as the potato-pathogenic species Streptomyces europaeiscabiei and 6 strains as potentially new phytopathogenic species. Of the 16 other strains, 12 were identified as members of previously described non-pathogenic Streptomyces species while the remaining 4 strains may represent heretofore unrecognised non-pathogenic species. This study demonstrated the value of this technique for the relatively rapid, simple and sensitive molecular identification of Streptomyces strains held in culture collections.

High Useful Yield and Isotopic Analysis of Uranium by Resonance Ionization Mass Spectrometry

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

Savina, Michael R.; Isselhardt, Brett H.; Kucher, Andrew

Useful yields from resonance ionization mass spectrometry can be extremely high compared to other mass spectrometry techniques, but uranium analysis shows strong matrix effects arising from the tendency of uranium to form strongly bound oxide molecules that do not dissociate appreciably on energetic ion bombardment. Here, we demonstrate a useful yield of 24% for metallic uranium. Modeling the laser ionization and ion transmission processes shows that the high useful yield is attributable to a high ion fraction achieved by resonance ionization. We quantify the reduction of uranium oxide surface layers by Ar + and Ga + sputtering. The useful yieldmore » for uranium atoms from a uranium dioxide matrix is 0.4% and rises to 2% when the surface is in sputter equilibrium with the ion beam. The lower useful yield from the oxide is almost entirely due to uranium oxide molecules reducing the neutral atom content of the sputtered flux. We also demonstrate rapid isotopic analysis of solid uranium oxide at a precision of <0.5% relative standard deviation using relatively broadband lasers to mitigate spectroscopic fractionation.« less

Blinded study determination of high sensitivity and specificity microchip electrophoresis–SSCP/HA to detect mutations in the p53 gene

PubMed Central

Hestekin, Christa N.; Lin, Jennifer S.; Senderowicz, Lionel; Jakupciak, John P.; O’Connell, Catherine; Rademaker, Alfred; Barron, Annelise E.

2012-01-01

Knowledge of the genetic changes that lead to disease has grown and continues to grow at a rapid pace. However, there is a need for clinical devices that can be used routinely to translate this knowledge into the treatment of patients. Use in a clinical setting requires high sensitivity and specificity (>97%) in order to prevent misdiagnoses. Single strand conformational polymorphism (SSCP) and heteroduplex analysis (HA) are two DNA-based, complementary methods for mutation detection that are inexpensive and relatively easy to implement. However, both methods are most commonly detected by slab gel electrophoresis, which can be labor-intensive, time-consuming, and often the methods are unable to produce high sensitivity and specificity without the use of multiple analysis conditions. Here we demonstrate the first blinded study using microchip electrophoresis-SSCP/HA. We demonstrate the ability of microchip electrophoresis-SSCP/HA to detect with 98% sensitivity and specificity >100 samples from the p53 gene exons 5–9 in a blinded study in an analysis time of less than 10 minutes. PMID:22002021

Secure and robust cloud computing for high-throughput forensic microsatellite sequence analysis and databasing.

PubMed

Bailey, Sarah F; Scheible, Melissa K; Williams, Christopher; Silva, Deborah S B S; Hoggan, Marina; Eichman, Christopher; Faith, Seth A

2017-11-01

Next-generation Sequencing (NGS) is a rapidly evolving technology with demonstrated benefits for forensic genetic applications, and the strategies to analyze and manage the massive NGS datasets are currently in development. Here, the computing, data storage, connectivity, and security resources of the Cloud were evaluated as a model for forensic laboratory systems that produce NGS data. A complete front-to-end Cloud system was developed to upload, process, and interpret raw NGS data using a web browser dashboard. The system was extensible, demonstrating analysis capabilities of autosomal and Y-STRs from a variety of NGS instrumentation (Illumina MiniSeq and MiSeq, and Oxford Nanopore MinION). NGS data for STRs were concordant with standard reference materials previously characterized with capillary electrophoresis and Sanger sequencing. The computing power of the Cloud was implemented with on-demand auto-scaling to allow multiple file analysis in tandem. The system was designed to store resulting data in a relational database, amenable to downstream sample interpretations and databasing applications following the most recent guidelines in nomenclature for sequenced alleles. Lastly, a multi-layered Cloud security architecture was tested and showed that industry standards for securing data and computing resources were readily applied to the NGS system without disadvantageous effects for bioinformatic analysis, connectivity or data storage/retrieval. The results of this study demonstrate the feasibility of using Cloud-based systems for secured NGS data analysis, storage, databasing, and multi-user distributed connectivity. Copyright © 2017 Elsevier B.V. All rights reserved.

Use of an automated chromium reduction system for hydrogen isotope ratio analysis of physiological fluids applied to doubly labeled water analysis.

PubMed

Schoeller, D A; Colligan, A S; Shriver, T; Avak, H; Bartok-Olson, C

2000-09-01

The doubly labeled water method is commonly used to measure total energy expenditure in free-living subjects. The method, however, requires accurate and precise deuterium abundance determinations, which can be laborious. The aim of this study was to evaluate a fully automated, high-throughput, chromium reduction technique for the measurement of deuterium abundances in physiological fluids. The chromium technique was compared with an off-line zinc bomb reduction technique and also subjected to test-retest analysis. Analysis of international water standards demonstrated that the chromium technique was accurate and had a within-day precision of <1 per thousand. Addition of organic matter to water samples demonstrated that the technique was sensitive to interference at levels between 2 and 5 g l(-1). Physiological samples could be analyzed without this interference, plasma by 10000 Da exclusion filtration, saliva by sedimentation and urine by decolorizing with carbon black. Chromium reduction of urine specimens from doubly labeled water studies indicated no bias relative to zinc reduction with a mean difference in calculated energy expenditure of -0.2 +/- 3.9%. Blinded reanalysis of urine specimens from a second doubly labeled water study demonstrated a test-retest coefficient of variation of 4%. The chromium reduction method was found to be a rapid, accurate and precise method for the analysis of urine specimens from doubly labeled water. Copyright 2000 John Wiley & Sons, Ltd.

Rapid screening and identification of improvised explosive and hazardous precursor materials by Raman spectroscopy

NASA Astrophysics Data System (ADS)

Stokes, Robert J.; Smith, W. Ewen; Foulger, Brian; Lewis, Colin

2008-10-01

A low cost technique is reported for the rapid screening of containers for materials that potentially could be used for terrorist activities. For peroxide based samples it is demonstrated that full characterisation can be achieved in a continuous curve fitting monitoring mode acquiring up to 10 spectra per second. This clearly demonstrates the potential for a Raman based method to be incorporated into a check-point whilst retaining fast throughput. A number of precursor compounds to nerve agents and peroxide and nitrate based improvised explosive materials have been studied. The potential strengths and weaknesses of using Raman for multiple target identification are discussed with regard to the common vibrations associated with each group of agents. Within this context we also introduce the use of fast Raman line mapping into the trace analysis of multiple component targets. The method presented is suited to volatile or light sensitive samples (such as derived peroxides) and can be employed on a variety of surfaces. As speed and throughput are traded against spectral bandwidth categorising threat compounds into groups based on common functionalities allows the full potential for multiplexed targeting to be realised.

Bioinspired Cell-Derived Nanovesicles versus Exosomes as Drug Delivery Systems: a Cost-Effective Alternative.

PubMed

Goh, Wei Jiang; Zou, Shui; Ong, Wei Yi; Torta, Federico; Alexandra, Alvarez Fernandez; Schiffelers, Raymond M; Storm, Gert; Wang, Jiong-Wei; Czarny, Bertrand; Pastorin, Giorgia

2017-10-30

Cell Derived Nanovesicles (CDNs) have been developed from the rapidly expanding field of exosomes, representing a class of bioinspired Drug Delivery Systems (DDS). However, translation to clinical applications is limited by the low yield and multi-step approach in isolating naturally secreted exosomes. Here, we show the first demonstration of a simple and rapid production method of CDNs using spin cups via a cell shearing approach, which offers clear advantages in terms of yield and cost-effectiveness over both traditional exosomes isolation, and also existing CDNs fabrication techniques. The CDNs obtained were of a higher protein yield and showed similarities in terms of physical characterization, protein and lipid analysis to both exosomes and CDNs previously reported in the literature. In addition, we investigated the mechanisms of cellular uptake of CDNs in vitro and their biodistribution in an in vivo mouse tumour model. Colocalization of the CDNs at the tumour site in a cancer mouse model was demonstrated, highlighting the potential for CDNs as anti-cancer strategy. Taken together, the results suggest that CDNs could provide a cost-effective alternative to exosomes as an ideal drug nanocarrier.

Rapid methods for radionuclide contaminant transport in nuclear fuel cycle simulation

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

Huff, Kathryn

Here, nuclear fuel cycle and nuclear waste disposal decisions are technologically coupled. However, current nuclear fuel cycle simulators lack dynamic repository performance analysis due to the computational burden of high-fidelity hydrolgic contaminant transport models. The Cyder disposal environment and repository module was developed to fill this gap. It implements medium-fidelity hydrologic radionuclide transport models to support assessment appropriate for fuel cycle simulation in the Cyclus fuel cycle simulator. Rapid modeling of hundreds of discrete waste packages in a geologic environment is enabled within this module by a suite of four closed form models for advective, dispersive, coupled, and idealized con-more » taminant transport: a Degradation Rate model, a Mixed Cell model, a Lumped Parameter model, and a 1-D Permeable Porous Medium model. A summary of the Cyder module, its timestepping algorithm, and the mathematical models implemented within it are presented. Additionally, parametric demonstrations simulations performed with Cyder are presented and shown to demonstrate functional agreement with parametric simulations conducted in a standalone hydrologic transport model, the Clay Generic Disposal System Model developed by the Used Fuel Disposition Campaign Department of Energy Office of Nuclear Energy.« less

Rapid methods for radionuclide contaminant transport in nuclear fuel cycle simulation

DOE PAGES

Huff, Kathryn

2017-08-01

Here, nuclear fuel cycle and nuclear waste disposal decisions are technologically coupled. However, current nuclear fuel cycle simulators lack dynamic repository performance analysis due to the computational burden of high-fidelity hydrolgic contaminant transport models. The Cyder disposal environment and repository module was developed to fill this gap. It implements medium-fidelity hydrologic radionuclide transport models to support assessment appropriate for fuel cycle simulation in the Cyclus fuel cycle simulator. Rapid modeling of hundreds of discrete waste packages in a geologic environment is enabled within this module by a suite of four closed form models for advective, dispersive, coupled, and idealized con-more » taminant transport: a Degradation Rate model, a Mixed Cell model, a Lumped Parameter model, and a 1-D Permeable Porous Medium model. A summary of the Cyder module, its timestepping algorithm, and the mathematical models implemented within it are presented. Additionally, parametric demonstrations simulations performed with Cyder are presented and shown to demonstrate functional agreement with parametric simulations conducted in a standalone hydrologic transport model, the Clay Generic Disposal System Model developed by the Used Fuel Disposition Campaign Department of Energy Office of Nuclear Energy.« less

Rapid Analysis of Inorganic Species in Herbaceous Materials Using Laser-Induced Breakdown Spectroscopy

PubMed Central

Emerson, Rachel M.

2015-01-01

Abstract Inorganic compounds in biomass, often referred to as ash, are known to be problematic in the thermochemical conversion of biomass to bio-oil or syngas and, ultimately, hydrocarbon fuels because they negatively influence reaction pathways, contribute to fouling and corrosion, poison catalysts, and impact waste streams. The most common ash-analysis methods, such as inductively coupled plasma-optical emission spectrometry/mass spectrometry (ICP-OES/MS), require considerable time and expensive reagents. Laser-induced breakdown spectroscopy (LIBS) is emerging as a technique for rapid analysis of the inorganic constituents in a wide range of biomass materials. This study compares analytical results using LIBS data to results obtained from three separate ICP-OES/MS methods for 12 samples, including six standard reference materials. Analyzed elements include aluminum, calcium, iron, magnesium, manganese, phosphorus, potassium, sodium, and silicon, and results show that concentrations can be measured with an uncertainty of approximately 100 parts per million using univariate calibration models and relatively few calibration samples. These results indicate that the accuracy of LIBS is comparable to that of ICP-OES methods and indicate that some acid-digestion methods for ICP-OES may not be reliable for Na and Al. These results also demonstrate that germanium can be used as an internal standard to improve the reliability and accuracy of measuring many elements of interest, and that LIBS can be used for rapid determination of total ash in biomass samples. Key benefits of LIBS include little sample preparation, no reagent consumption, and the generation of meaningful analytical data instantaneously. PMID:26733765

A game-based crowdsourcing platform for rapidly training middle and high school students to perform biomedical image analysis

NASA Astrophysics Data System (ADS)

Feng, Steve; Woo, Min-jae; Kim, Hannah; Kim, Eunso; Ki, Sojung; Shao, Lei; Ozcan, Aydogan

2016-03-01

We developed an easy-to-use and widely accessible crowd-sourcing tool for rapidly training humans to perform biomedical image diagnostic tasks and demonstrated this platform's ability on middle and high school students in South Korea to diagnose malaria infected red-blood-cells (RBCs) using Giemsa-stained thin blood smears imaged under light microscopes. We previously used the same platform (i.e., BioGames) to crowd-source diagnostics of individual RBC images, marking them as malaria positive (infected), negative (uninfected), or questionable (insufficient information for a reliable diagnosis). Using a custom-developed statistical framework, we combined the diagnoses from both expert diagnosticians and the minimally trained human crowd to generate a gold standard library of malaria-infection labels for RBCs. Using this library of labels, we developed a web-based training and educational toolset that provides a quantified score for diagnosticians/users to compare their performance against their peers and view misdiagnosed cells. We have since demonstrated the ability of this platform to quickly train humans without prior training to reach high diagnostic accuracy as compared to expert diagnosticians. Our initial trial group of 55 middle and high school students has collectively played more than 170 hours, each demonstrating significant improvements after only 3 hours of training games, with diagnostic scores that match expert diagnosticians'. Next, through a national-scale educational outreach program in South Korea we recruited >1660 students who demonstrated a similar performance level after 5 hours of training. We plan to further demonstrate this tool's effectiveness for other diagnostic tasks involving image labeling and aim to provide an easily-accessible and quickly adaptable framework for online training of new diagnosticians.

Laser-ablation electrospray ionization mass spectrometry with ion mobility separation reveals metabolites in the symbiotic interactions of soybean roots and rhizobia.

PubMed

Stopka, Sylwia A; Agtuca, Beverly J; Koppenaal, David W; Paša-Tolić, Ljiljana; Stacey, Gary; Vertes, Akos; Anderton, Christopher R

2017-07-01

Technologies enabling in situ metabolic profiling of living plant systems are invaluable for understanding physiological processes and could be used for rapid phenotypic screening (e.g., to produce plants with superior biological nitrogen-fixing ability). The symbiotic interaction between legumes and nitrogen-fixing soil bacteria results in a specialized plant organ (i.e., root nodule) where the exchange of nutrients between host and endosymbiont occurs. Laser-ablation electrospray ionization mass spectrometry (LAESI-MS) is a method that can be performed under ambient conditions requiring minimal sample preparation. Here, we employed LAESI-MS to explore the well characterized symbiosis between soybean (Glycine max L. Merr.) and its compatible symbiont, Bradyrhizobium japonicum. The utilization of ion mobility separation (IMS) improved the molecular coverage, selectivity, and identification of the detected biomolecules. Specifically, incorporation of IMS resulted in an increase of 153 differentially abundant spectral features in the nodule samples. The data presented demonstrate the advantages of using LAESI-IMS-MS for the rapid analysis of intact root nodules, uninfected root segments, and free-living rhizobia. Untargeted pathway analysis revealed several metabolic processes within the nodule (e.g., zeatin, riboflavin, and purine synthesis). Compounds specific to the uninfected root and bacteria were also detected. Lastly, we performed depth profiling of intact nodules to reveal the location of metabolites to the cortex and inside the infected region, and lateral profiling of sectioned nodules confirmed these molecular distributions. Our results established the feasibility of LAESI-IMS-MS for the analysis and spatial mapping of plant tissues, with its specific demonstration to improve our understanding of the soybean-rhizobial symbiosis. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

A cost effective hydrogel test kit for pre and post blast trinitrotoluene.

PubMed

Choodum, Aree; Malathong, Khanitta; NicDaeid, Niamh; Limsakul, Wadcharawadee; Wongniramaikul, Worawit

2016-09-01

A cost effective hydrogel test kit was successfully developed for the detection of pre- and post-blast trinitrotoluene (TNT). A polyvinyl alcohol (PVA) hydrogel matrix was used to entrap the potassium hydroxide (KOH) colourimetric reagent. The easily portable test kit was fabricated in situ in a small tube to which the sample could be added directly. The test kit was used in conjunction with digital image colourimetry (DIC) to demonstrate the rapid quantitative analysis of TNT in a test soil sample. The built-in digital camera of an iPhone was used to capture digital images of the colourimetric products from the test kit. Red-Green-Blue (RGB) colour data from the digital images of TNT standard solutions were used to establish a calibration graph. The validation of the DIC method indicated excellent inter day precision (0.12-3.60%RSD) and accuracy (93-108% relative accuracy). Post-blast soil samples containing TNT were analysed using the test kit and were in good agreement with spectrophotometric analysis. The intensity of the RGB data from the TNT complex deviated by +6.3%, +5.1%, and -4.9% after storage of the test kits in a freezer for 3 months. The test kit was also reusable for up to 12 times with only -5.4%, +0.3%, and +4.0% deviations. The hydrogel test kit was applied in the detection of trace explosive residues at the scene of the recent Bangkok bombing at the Ratchaprasong intersection and produced positive results for TNT demonstrating its operational field application as a rapid and cost effective quantitative tool for explosive residue analysis. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Label-free bimodal waveguide immunosensor for rapid diagnosis of bacterial infections in cirrhotic patients.

PubMed

Maldonado, Jesús; González-Guerrero, Ana Belén; Domínguez, Carlos; Lechuga, Laura M

2016-11-15

Spontaneous bacterial peritonitis is an acute bacterial infection of ascitic fluid; it has a high incidence in cirrhotic patients and it is associated with high mortality. In such a situation, early diagnosis and treatment is crucial for the survival of the patient. However, bacterial analysis in ascitic fluid is currently based on culture methods, which are time-consuming and laborious. We report here the application of a photonic interferometer biosensor based on a bimodal waveguide (BiMW) for the rapid and label-free detection of bacteria directly in ascitic fluid. The device consists of a straight waveguide in which two modes of the same polarization interfere while interacting with the external medium through their evanescent fields. A bimolecular event occurring on the sensor area of the device (e.g. capturing bacteria) will differently affect each light mode, inducing a variation in the phase of the light exiting at the output of the waveguide. In this work, we demonstrate the quantitative detection of Bacillus cereus in buffer medium and Escherichia coli in undiluted ascitic fluid from cirrhotic patients. In the case of Bacillus cereus detection, the device was able to specifically detect bacteria at relevant concentrations in 12.5min and in the case of Escherichia coli detection, the analysis time was 25min. Extrapolation of the data demonstrated that the detection limits of the biosensor could reach few bacteria per milliliter. Based on the results obtained, we consider that the BiMW biosensor is positioned as a promising new clinical tool for user-friendly, cost-effective and real-time microbiological analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

Laser-ablation electrospray ionization mass spectrometry with ion mobility separation reveals metabolites in the symbiotic interactions of soybean roots and rhizobia

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

Stopka, Sylwia A.; Agtuca, Beverly J.; Koppenaal, David W.

Technologies enabling in situ metabolic profiling of living plant systems are invaluable for understanding physiological processes and could be used for rapid phenotypic screening (e.g., to produce plants with superior biological nitrogen fixing ability). The symbiotic interaction between legumes and nitrogen-fixing soil bacteria results in a specialized plant organ (i.e., root nodule), where the exchange of nutrients between host and endosymbiont occurs. Laser ablation electrospray ionization mass spectrometry (LAESI-MS) is a method that can be performed under ambient conditions requiring minimal sample preparation. Here, we employed LAESI-MS to explore the well-characterized symbiosis between soybean (Glycine max L. Merr.) and itsmore » compatible symbiont, Bradyrhizobium japonicum. The utilization of ion mobility separation (IMS) improved the molecular coverage, selectivity, and identification of the detected biomolecules. Specifically, incorporation of IMS resulted in an increase of 153 detected metabolites in the nodule samples. The data presented demonstrates the advantages of using LAESI-IMS-MS for the rapid analysis of intact root nodules, uninfected root segments, and free-living rhizobia. Untargeted pathway analysis revealed several metabolic processes within the nodule (e.g., zeatin, riboflavin, and purine synthesis). Compounds specific to the uninfected root and bacteria were also detected. Lastly, we performed depth-profiling of intact nodules to reveal the location of metabolites to the cortex and inside the infected region, and lateral profiling of sectioned nodules confirmed these molecular distributions. Our results established the feasibility of LAESI-IMS-MS for the analysis and spatial mapping of plant tissues, with its specific demonstration to improve our understanding of the soybean-rhizobial symbiosis.« less

Chemical tagging of chlorinated phenols for their facile detection and analysis by NMR spectroscopy

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

Valdez, Carlos A.; Leif, Roald N.

2015-03-22

A derivatization method that employs diethyl (bromodifluoromethyl) phosphonate (DBDFP) to efficiently tag the endocrine disruptor pentachlorophenol (PCP) and other chlorinated phenols (CPs) along with their reliable detection and analysis by NMR is presented. The method accomplishes the efficient alkylation of the hydroxyl group in CPs with the difluoromethyl (CF 2H) moiety in extremely rapid fashion (5 min), at room temperature and in an environmentally benign manner. The approach proved successful in difluoromethylating a panel of 18 chlorinated phenols, yielding derivatives that displayed unique 1H, 19F NMR spectra allowing for the clear discrimination between isomerically related CPs. Due to its biphasicmore » nature, the derivatization can be applied to both aqueous and organic mixtures where the analysis of CPs is required. Furthermore, the methodology demonstrates that PCP along with other CPs can be selectively derivatized in the presence of other various aliphatic alcohols, underscoring the superiority of the approach over other general derivatization methods that indiscriminately modify all analytes in a given sample. The present work demonstrates the first application of NMR on the qualitative analysis of these highly toxic and environmentally persistent species.« less

Multi-ingredients determination and fingerprint analysis of leaves from Ilex latifolia using ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry.

PubMed

Fan, Chunlin; Deng, Jiewei; Yang, Yunyun; Liu, Junshan; Wang, Ying; Zhang, Xiaoqi; Fai, Kuokchiu; Zhang, Qingwen; Ye, Wencai

2013-10-01

An ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) method integrating multi-ingredients determination and fingerprint analysis has been established for quality assessment and control of leaves from Ilex latifolia. The method possesses the advantages of speediness, efficiency, accuracy, and allows the multi-ingredients determination and fingerprint analysis in one chromatographic run within 13min. Multi-ingredients determination was performed based on the extracted ion chromatograms of the exact pseudo-molecular ions (with a 0.01Da window), and fingerprint analysis was performed based on the base peak chromatograms, obtained by negative-ion electrospray ionization QTOF-MS. The method validation results demonstrated our developed method possessing desirable specificity, linearity, precision and accuracy. The method was utilized to analyze 22 I. latifolia samples from different origins. The quality assessment was achieved by using both similarity analysis (SA) and principal component analysis (PCA), and the results from SA were consistent with those from PCA. Our experimental results demonstrate that the strategy integrated multi-ingredients determination and fingerprint analysis using UPLC-QTOF-MS technique is a useful approach for rapid pharmaceutical analysis, with promising prospects for the differentiation of origin, the determination of authenticity, and the overall quality assessment of herbal medicines. Copyright © 2013 Elsevier B.V. All rights reserved.

Frontal Cortex Activation Causes Rapid Plasticity of Auditory Cortical Processing

PubMed Central

Winkowski, Daniel E.; Bandyopadhyay, Sharba; Shamma, Shihab A.

2013-01-01

Neurons in the primary auditory cortex (A1) can show rapid changes in receptive fields when animals are engaged in sound detection and discrimination tasks. The source of a signal to A1 that triggers these changes is suspected to be in frontal cortical areas. How or whether activity in frontal areas can influence activity and sensory processing in A1 and the detailed changes occurring in A1 on the level of single neurons and in neuronal populations remain uncertain. Using electrophysiological techniques in mice, we found that pairing orbitofrontal cortex (OFC) stimulation with sound stimuli caused rapid changes in the sound-driven activity within A1 that are largely mediated by noncholinergic mechanisms. By integrating in vivo two-photon Ca2+ imaging of A1 with OFC stimulation, we found that pairing OFC activity with sounds caused dynamic and selective changes in sensory responses of neural populations in A1. Further, analysis of changes in signal and noise correlation after OFC pairing revealed improvement in neural population-based discrimination performance within A1. This improvement was frequency specific and dependent on correlation changes. These OFC-induced influences on auditory responses resemble behavior-induced influences on auditory responses and demonstrate that OFC activity could underlie the coordination of rapid, dynamic changes in A1 to dynamic sensory environments. PMID:24227723

A novel immunochromatographic electrochemical biosensor for highly sensitive and selective detection of trichloropyridinol, a biomarker of exposure to chlorpyrifos.

PubMed

Wang, Limin; Lu, Donglai; Wang, Jun; Du, Dan; Zou, Zhexiang; Wang, Hua; Smith, Jordan N; Timchalk, Charles; Liu, Fengquan; Lin, Yuehe

2011-02-15

We present a novel portable immunochromatographic electrochemical biosensor (IEB) for simple, rapid, and sensitive biomonitoring of trichloropyridinol (TCP), a metabolite biomarker of exposure to organophosphorus insecticides. Our new approach takes the advantage of immunochromatographic test strip for a rapid competitive immunoreaction and a disposable screen-printed carbon electrode for a rapid and sensitive electrochemical analysis of captured HRP labeling. Several key experimental parameters (e.g. immunoreaction time, the amount of HRP labeled TCP, concentration of the substrate for electrochemical measurements, and the blocking agents for the nitrocellulose membrane) were optimized to achieve a high sensitivity, selectivity and stability. Under optimal conditions, the IEB has demonstrated a wide linear range (0.1-100 ng/ml) with a detection limit as low as 0.1 ng/ml TCP. Furthermore, the IEB has been successfully applied for biomonitoring of TCP in the rat plasma samples with in vivo exposure to organophosphorus insecticides like Chlorpyrifos-oxon (CPF-oxon). The IEB thus opens up new pathways for designing a simple, rapid, clinically accurate, and quantitative tool for TCP detection, as well as holds a great promise for in-field screening of metabolite biomarkers, e.g., TCP, for humans exposed to organophosphorus insecticides. Copyright © 2010 Elsevier B.V. All rights reserved.

Intelligent Controls for Net-Zero Energy Buildings

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

Li, Haorong; Cho, Yong; Peng, Dongming

2011-10-30

The goal of this project is to develop and demonstrate enabling technologies that can empower homeowners to convert their homes into net-zero energy buildings in a cost-effective manner. The project objectives and expected outcomes are as follows: • To develop rapid and scalable building information collection and modeling technologies that can obtain and process “as-built” building information in an automated or semiautomated manner. • To identify low-cost measurements and develop low-cost virtual sensors that can monitor building operations in a plug-n-play and low-cost manner. • To integrate and demonstrate low-cost building information modeling (BIM) technologies. • To develop decision supportmore » tools which can empower building owners to perform energy auditing and retrofit analysis. • To develop and demonstrate low-cost automated diagnostics and optimal control technologies which can improve building energy efficiency in a continual manner.« less

How Anterior Cruciate Ligament Injury was averted during Knee Collapse in a NBA Point Guard

PubMed Central

Schilaty, Nathan D; Bates, Nathaniel A; Krych, Aaron J; Hewett, Timothy E

2017-01-01

Summary Non-contact anterior cruciate ligament (ACL) injuries occur with rapid decelerations and pivoting. A recent injury to a high-level National Basketball Association (NBA) player demonstrated neuromuscular control and injury-sparing mechanisms that resulted in only minor ligament injury to the medial collateral ligament. We analyzed biomechanical mechanisms via publically available orthogonal 2-D video to demonstrate how this potential ACL injury was averted. Analysis of the knee injury mechanism demonstrated that the NBA player experienced low ground reaction force, high sagittal plane flexion, and maintenance of frontal plane stability with neuromuscular control. The outcome of these factors inhibited dynamic valgus collapse of the knee throughout the fall, avoiding ACL injury – a potentially career-altering injury. Many athletes, professional and recreational, will be subjected to similar mechanisms of injury and will have improved outcomes if they can successfully utilize preventive strategies of neuromuscular control to limit injury mechanisms. PMID:28603786

How Anterior Cruciate Ligament Injury was averted during Knee Collapse in a NBA Point Guard.

PubMed

Schilaty, Nathan D; Bates, Nathaniel A; Krych, Aaron J; Hewett, Timothy E

2017-01-01

Non-contact anterior cruciate ligament (ACL) injuries occur with rapid decelerations and pivoting. A recent injury to a high-level National Basketball Association (NBA) player demonstrated neuromuscular control and injury-sparing mechanisms that resulted in only minor ligament injury to the medial collateral ligament. We analyzed biomechanical mechanisms via publically available orthogonal 2-D video to demonstrate how this potential ACL injury was averted. Analysis of the knee injury mechanism demonstrated that the NBA player experienced low ground reaction force, high sagittal plane flexion, and maintenance of frontal plane stability with neuromuscular control. The outcome of these factors inhibited dynamic valgus collapse of the knee throughout the fall, avoiding ACL injury - a potentially career-altering injury. Many athletes, professional and recreational, will be subjected to similar mechanisms of injury and will have improved outcomes if they can successfully utilize preventive strategies of neuromuscular control to limit injury mechanisms.

Dictionary-based image reconstruction for superresolution in integrated circuit imaging.

PubMed

Cilingiroglu, T Berkin; Uyar, Aydan; Tuysuzoglu, Ahmet; Karl, W Clem; Konrad, Janusz; Goldberg, Bennett B; Ünlü, M Selim

2015-06-01

Resolution improvement through signal processing techniques for integrated circuit imaging is becoming more crucial as the rapid decrease in integrated circuit dimensions continues. Although there is a significant effort to push the limits of optical resolution for backside fault analysis through the use of solid immersion lenses, higher order laser beams, and beam apodization, signal processing techniques are required for additional improvement. In this work, we propose a sparse image reconstruction framework which couples overcomplete dictionary-based representation with a physics-based forward model to improve resolution and localization accuracy in high numerical aperture confocal microscopy systems for backside optical integrated circuit analysis. The effectiveness of the framework is demonstrated on experimental data.

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

Greenberg, S.D.; Smith, S.; Swank, P.R.

Visual cell profiles were used to analyze the distribution of atypical bronchial cells in sputum specimens from cigarette-smoking volunteers, cigarette-smoking asbestos workers and cigarette-smoking uranium miners. The preliminary results of these sputum visual cell profile studies have demonstrated distinctive distributions of bronchial cell atypias in progressive patterns of squamous metaplasia, mild, moderate and severe atypias and carcinoma, similar to those the authors have previously reported using cell image analysis techniques to determine an atypia status index (ASI). The information gained from this study will be helpful in further validating this ASI and subsequently achieving the ultimate goal of employing cellmore » image analysis for the rapid and precise identification of premalignant atypias in sputum.« less

An improved K-means clustering algorithm in agricultural image segmentation

NASA Astrophysics Data System (ADS)

Cheng, Huifeng; Peng, Hui; Liu, Shanmei

Image segmentation is the first important step to image analysis and image processing. In this paper, according to color crops image characteristics, we firstly transform the color space of image from RGB to HIS, and then select proper initial clustering center and cluster number in application of mean-variance approach and rough set theory followed by clustering calculation in such a way as to automatically segment color component rapidly and extract target objects from background accurately, which provides a reliable basis for identification, analysis, follow-up calculation and process of crops images. Experimental results demonstrate that improved k-means clustering algorithm is able to reduce the computation amounts and enhance precision and accuracy of clustering.

An Expert Assistant for Computer Aided Parallelization

NASA Technical Reports Server (NTRS)

Jost, Gabriele; Chun, Robert; Jin, Haoqiang; Labarta, Jesus; Gimenez, Judit

2004-01-01

The prototype implementation of an expert system was developed to assist the user in the computer aided parallelization process. The system interfaces to tools for automatic parallelization and performance analysis. By fusing static program structure information and dynamic performance analysis data the expert system can help the user to filter, correlate, and interpret the data gathered by the existing tools. Sections of the code that show poor performance and require further attention are rapidly identified and suggestions for improvements are presented to the user. In this paper we describe the components of the expert system and discuss its interface to the existing tools. We present a case study to demonstrate the successful use in full scale scientific applications.

Magnetite-doped polydimethylsiloxane (PDMS) for phosphopeptide enrichment.

PubMed

Sandison, Mairi E; Jensen, K Tveen; Gesellchen, F; Cooper, J M; Pitt, A R

2014-10-07

Reversible phosphorylation plays a key role in numerous biological processes. Mass spectrometry-based approaches are commonly used to analyze protein phosphorylation, but such analysis is challenging, largely due to the low phosphorylation stoichiometry. Hence, a number of phosphopeptide enrichment strategies have been developed, including metal oxide affinity chromatography (MOAC). Here, we describe a new material for performing MOAC that employs a magnetite-doped polydimethylsiloxane (PDMS), that is suitable for the creation of microwell array and microfluidic systems to enable low volume, high throughput analysis. Incubation time and sample loading were explored and optimized and demonstrate that the embedded magnetite is able to enrich phosphopeptides. This substrate-based approach is rapid, straightforward and suitable for simultaneously performing multiple, low volume enrichments.

Patient specific ankle-foot orthoses using rapid prototyping

PubMed Central

2011-01-01

Background Prefabricated orthotic devices are currently designed to fit a range of patients and therefore they do not provide individualized comfort and function. Custom-fit orthoses are superior to prefabricated orthotic devices from both of the above-mentioned standpoints. However, creating a custom-fit orthosis is a laborious and time-intensive manual process performed by skilled orthotists. Besides, adjustments made to both prefabricated and custom-fit orthoses are carried out in a qualitative manner. So both comfort and function can potentially suffer considerably. A computerized technique for fabricating patient-specific orthotic devices has the potential to provide excellent comfort and allow for changes in the standard design to meet the specific needs of each patient. Methods In this paper, 3D laser scanning is combined with rapid prototyping to create patient-specific orthoses. A novel process was engineered to utilize patient-specific surface data of the patient anatomy as a digital input, manipulate the surface data to an optimal form using Computer Aided Design (CAD) software, and then download the digital output from the CAD software to a rapid prototyping machine for fabrication. Results Two AFOs were rapidly prototyped to demonstrate the proposed process. Gait analysis data of a subject wearing the AFOs indicated that the rapid prototyped AFOs performed comparably to the prefabricated polypropylene design. Conclusions The rapidly prototyped orthoses fabricated in this study provided good fit of the subject's anatomy compared to a prefabricated AFO while delivering comparable function (i.e. mechanical effect on the biomechanics of gait). The rapid fabrication capability is of interest because it has potential for decreasing fabrication time and cost especially when a replacement of the orthosis is required. PMID:21226898

Materials and Methods for Streamlined Laboratory Analysis of Environmental Samples, FY 2016 Report

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

Addleman, Raymond S.; Naes, Benjamin E.; McNamara, Bruce K.

The International Atomic Energy Agency (IAEA) relies upon laboratory analysis of environmental samples (typically referred to as “swipes”) collected during on-site inspections of safeguarded facilities to support the detection and deterrence of undeclared activities. Unfortunately, chemical processing and assay of the samples is slow and expensive. A rapid, effective, and simple extraction process and analysis method is needed to provide certified results with improved timeliness at reduced costs (principally in the form of reduced labor), while maintaining or improving sensitivity and efficacy. To address these safeguard needs the Pacific Northwest National Laboratory (PNNL) explored and demonstrated improved methods for environmentalmore » sample (ES) analysis. Improvements for both bulk and particle analysis were explored. To facilitate continuity and adoption, the new sampling materials and processing methods will be compatible with existing IAEA protocols for ES analysis. PNNL collaborated with Oak Ridge National Laboratory (ORNL), which performed independent validation of the new bulk analysis methods and compared performance to traditional IAEA’s Network of Analytical Laboratories (NWAL) protocol. ORNL efforts are reported separately. This report describes PNNL’s FY 2016 progress, which was focused on analytical application supporting environmental monitoring of uranium enrichment plants and nuclear fuel processing. In the future the technology could be applied to other safeguard applications and analytes related to fuel manufacturing, reprocessing, etc. PNNL’s FY 2016 efforts were broken into two tasks and a summary of progress, accomplishments and highlights are provided below. Principal progress and accomplishments on Task 1, Optimize Materials and Methods for ICP-MS Environmental Sample Analysis, are listed below. • Completed initial procedure for rapid uranium extraction from ES swipes based upon carbonate-peroxide chemistry (delivered to ORNL for evaluation). • Explored improvements to carbonate-peroxide rapid uranium extraction chemistry. • Evaluated new sampling materials and methods (in collaboration with ORNL). • Demonstrated successful ES extractions from standard and novel swipes for a wide range uranium compounds of interest including UO 2F 2 and UO 2(NO 3) 2, U 3O 8 and uranium ore concentrate. • Completed initial discussions with commercial suppliers of PTFE swipe materials. • Submitted one manuscript for publication. Two additional drafts are being prepared. Principal progress and accomplishments on Task 2, Optimize Materials and Methods for Direct SIMS Environmental Sample Analysis, are listed below. • Designed a SIMS swipe sample holder that retrofits into existing equipment and provides simple, effective, and rapid mounting of ES samples for direct assay while enabling automation and laboratory integration. • Identified preferred conductive sampling materials with better performance characteristics. • Ran samples on the new PNNL NWAL equivalent Cameca 1280 SIMS system. • Obtained excellent agreement between isotopic ratios for certified materials and direct SIMS assay of very low levels of LEU and HEU UO 2F 2 particles on carbon fiber sampling material. Sample activities range from 1 to 500 CPM (uranium mass on sample is dependent upon specific isotope ratio but is frequently in the subnanogram range). • Found that the presence of the UF molecular ions, as measured by SIMS, provides chemical information about the particle that is separate from the uranium isotopics and strongly suggests that those particles originated from an UF6 enrichment activity. • Submitted one manuscript for publication. Another manuscript is in preparation.« less

Use of application containers and workflows for genomic data analysis.

PubMed

Schulz, Wade L; Durant, Thomas J S; Siddon, Alexa J; Torres, Richard

2016-01-01

The rapid acquisition of biological data and development of computationally intensive analyses has led to a need for novel approaches to software deployment. In particular, the complexity of common analytic tools for genomics makes them difficult to deploy and decreases the reproducibility of computational experiments. Recent technologies that allow for application virtualization, such as Docker, allow developers and bioinformaticians to isolate these applications and deploy secure, scalable platforms that have the potential to dramatically increase the efficiency of big data processing. While limitations exist, this study demonstrates a successful implementation of a pipeline with several discrete software applications for the analysis of next-generation sequencing (NGS) data. With this approach, we significantly reduced the amount of time needed to perform clonal analysis from NGS data in acute myeloid leukemia.

Analysis of air-, moisture- and solvent-sensitive chemical compounds by mass spectrometry using an inert atmospheric pressure solids analysis probe.

PubMed

Mosely, Jackie A; Stokes, Peter; Parker, David; Dyer, Philip W; Messinis, Antonis M

2018-02-01

A novel method has been developed that enables chemical compounds to be transferred from an inert atmosphere glove box and into the atmospheric pressure ion source of a mass spectrometer whilst retaining a controlled chemical environment. This innovative method is simple and cheap to implement on some commercially available mass spectrometers. We have termed this approach inert atmospheric pressure solids analysis probe ( iASAP) and demonstrate the benefit of this methodology for two air-/moisture-sensitive chemical compounds whose characterisation by mass spectrometry is now possible and easily achieved. The simplicity of the design means that moving between iASAP and standard ASAP is straightforward and quick, providing a highly flexible platform with rapid sample turnaround.

Multimodal diagnosis and visualisation of oncologic pathologies

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

Zakharov, V P; Bratchenko, I A; Myakinin, O O

2014-08-31

The combined application of optical coherence tomography, Raman and autofluorescence spectroscopy of biotissues for the analysis of human malignant neoplasms is demonstrated. Rapid investigation of vast biotissue regions (at the scale of entire organs) is possible using the autofluorescence response. After selection of possible zones of pathologies one can visualise the neoplasm topology in the zone of interest with micron precision by using optical coherence tomography. In the case of suspecting the malignancy the analysis of the biotissue Raman spectrum is carried out that allows identification of the neoplasm type with the sensitivity and specificity ∼85%. An experimental scheme ismore » proposed with the combined use of the abovementioned methods, which is a prototype of the medical system for complex analysis of neoplasms. (laser biophotonics)« less

Analysis of photonic Doppler velocimetry data based on the continuous wavelet transform

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

Liu Shouxian; Wang Detian; Li Tao

2011-02-15

The short time Fourier transform (STFT) cannot resolve rapid velocity changes in most photonic Doppler velocimetry (PDV) data. A practical analysis method based on the continuous wavelet transform (CWT) was presented to overcome this difficulty. The adaptability of the wavelet family predicates that the continuous wavelet transform uses an adaptive time window to estimate the instantaneous frequency of signals. The local frequencies of signal are accurately determined by finding the ridge in the spectrogram of the CWT and then are converted to target velocity according to the Doppler effects. A performance comparison between the CWT and STFT is demonstrated bymore » a plate-impact experiment data. The results illustrate that the new method is automatic and adequate for analysis of PDV data.« less

Evaluation of Two Commercial Systems for Automated Processing, Reading, and Interpretation of Lyme Borreliosis Western Blots▿

PubMed Central

Binnicker, M. J.; Jespersen, D. J.; Harring, J. A.; Rollins, L. O.; Bryant, S. C.; Beito, E. M.

2008-01-01

The diagnosis of Lyme borreliosis (LB) is commonly made by serologic testing with Western blot (WB) analysis serving as an important supplemental assay. Although specific, the interpretation of WBs for diagnosis of LB (i.e., Lyme WBs) is subjective, with considerable variability in results. In addition, the processing, reading, and interpretation of Lyme WBs are laborious and time-consuming procedures. With the need for rapid processing and more objective interpretation of Lyme WBs, we evaluated the performances of two automated interpretive systems, TrinBlot/BLOTrix (Trinity Biotech, Carlsbad, CA) and BeeBlot/ViraScan (Viramed Biotech AG, Munich, Germany), using 518 serum specimens submitted to our laboratory for Lyme WB analysis. The results of routine testing with visual interpretation were compared to those obtained by BLOTrix analysis of MarBlot immunoglobulin M (IgM) and IgG and by ViraScan analysis of ViraBlot and ViraStripe IgM and IgG assays. BLOTrix analysis demonstrated an agreement of 84.7% for IgM and 87.3% for IgG compared to visual reading and interpretation. ViraScan analysis of the ViraBlot assays demonstrated agreements of 85.7% for IgM and 94.2% for IgG, while ViraScan analysis of the ViraStripe IgM and IgG assays showed agreements of 87.1 and 93.1%, respectively. Testing by the automated systems yielded an average time savings of 64 min/run compared to processing, reading, and interpretation by our current procedure. Our findings demonstrated that automated processing and interpretive systems yield results comparable to those of visual interpretation, while reducing the subjectivity and time required for Lyme WB analysis. PMID:18463211

Evaluation of two commercial systems for automated processing, reading, and interpretation of Lyme borreliosis Western blots.

PubMed

Binnicker, M J; Jespersen, D J; Harring, J A; Rollins, L O; Bryant, S C; Beito, E M

2008-07-01

The diagnosis of Lyme borreliosis (LB) is commonly made by serologic testing with Western blot (WB) analysis serving as an important supplemental assay. Although specific, the interpretation of WBs for diagnosis of LB (i.e., Lyme WBs) is subjective, with considerable variability in results. In addition, the processing, reading, and interpretation of Lyme WBs are laborious and time-consuming procedures. With the need for rapid processing and more objective interpretation of Lyme WBs, we evaluated the performances of two automated interpretive systems, TrinBlot/BLOTrix (Trinity Biotech, Carlsbad, CA) and BeeBlot/ViraScan (Viramed Biotech AG, Munich, Germany), using 518 serum specimens submitted to our laboratory for Lyme WB analysis. The results of routine testing with visual interpretation were compared to those obtained by BLOTrix analysis of MarBlot immunoglobulin M (IgM) and IgG and by ViraScan analysis of ViraBlot and ViraStripe IgM and IgG assays. BLOTrix analysis demonstrated an agreement of 84.7% for IgM and 87.3% for IgG compared to visual reading and interpretation. ViraScan analysis of the ViraBlot assays demonstrated agreements of 85.7% for IgM and 94.2% for IgG, while ViraScan analysis of the ViraStripe IgM and IgG assays showed agreements of 87.1 and 93.1%, respectively. Testing by the automated systems yielded an average time savings of 64 min/run compared to processing, reading, and interpretation by our current procedure. Our findings demonstrated that automated processing and interpretive systems yield results comparable to those of visual interpretation, while reducing the subjectivity and time required for Lyme WB analysis.

Optimisation and validation of a rapid and efficient microemulsion liquid chromatographic (MELC) method for the determination of paracetamol (acetaminophen) content in a suppository formulation.

PubMed

McEvoy, Eamon; Donegan, Sheila; Power, Joe; Altria, Kevin

2007-05-09

A rapid and efficient oil-in-water microemulsion liquid chromatographic method has been optimised and validated for the analysis of paracetamol in a suppository formulation. Excellent linearity, accuracy, precision and assay results were obtained. Lengthy sample pre-treatment/extraction procedures were eliminated due to the solubilising power of the microemulsion and rapid analysis times were achieved. The method was optimised to achieve rapid analysis time and relatively high peak efficiencies. A standard microemulsion composition of 33 g SDS, 66 g butan-1-ol, 8 g n-octane in 1l of 0.05% TFA modified with acetonitrile has been shown to be suitable for the rapid analysis of paracetamol in highly hydrophobic preparations under isocratic conditions. Validated assay results and overall analysis time of the optimised method was compared to British Pharmacopoeia reference methods. Sample preparation and analysis times for the MELC analysis of paracetamol in a suppository were extremely rapid compared to the reference method and similar assay results were achieved. A gradient MELC method using the same microemulsion has been optimised for the resolution of paracetamol and five of its related substances in approximately 7 min.

Monitoring cell culture media degradation using surface enhanced Raman scattering (SERS) spectroscopy.

PubMed

Calvet, Amandine; Ryder, Alan G

2014-08-20

The quality of the cell culture media used in biopharmaceutical manufacturing is a crucial factor affecting bioprocess performance and the quality of the final product. Due to their complex composition these media are inherently unstable, and significant compositional variations can occur particularly when in the prepared liquid state. For example photo-degradation of cell culture media can have adverse effects on cell viability and thus process performance. There is therefore, from quality control, quality assurance and process management view points, an urgent demand for the development of rapid and inexpensive tools for the stability monitoring of these complex mixtures. Spectroscopic methods, based on fluorescence or Raman measurements, have now become viable alternatives to more time-consuming and expensive (on a unit analysis cost) chromatographic and/or mass spectrometry based methods for routine analysis of media. Here we demonstrate the application of surface enhanced Raman scattering (SERS) spectroscopy for the simple, fast, analysis of cell culture media degradation. Once stringent reproducibility controls are implemented, chemometric data analysis methods can then be used to rapidly monitor the compositional changes in chemically defined media. SERS shows clearly that even when media are stored at low temperature (2-8°C) and in the dark, significant chemical changes occur, particularly with regard to cysteine/cystine concentration. Copyright © 2014 Elsevier B.V. All rights reserved.

Microwell Array Method for Rapid Generation of Uniform Agarose Droplets and Beads for Single Molecule Analysis.

PubMed

Li, Xingrui; Zhang, Dongfeng; Zhang, Huimin; Guan, Zhichao; Song, Yanling; Liu, Ruochen; Zhu, Zhi; Yang, Chaoyong

2018-02-20

Compartmentalization of aqueous samples in uniform emulsion droplets has proven to be a useful tool for many chemical, biological, and biomedical applications. Herein, we introduce an array-based emulsification method for rapid and easy generation of monodisperse agarose-in-oil droplets in a PDMS microwell array. The microwells are filled with agarose solution, and subsequent addition of hot oil results in immediate formation of agarose droplets due to the surface-tension of the liquid solution. Because droplet size is determined solely by the array unit dimensions, uniform droplets with preselectable diameters ranging from 20 to 100 μm can be produced with relative standard deviations less than 3.5%. The array-based droplet generation method was used to perform digital PCR for absolute DNA quantitation. The array-based droplet isolation and sol-gel switching property of agarose enable formation of stable beads by chilling the droplet array at -20 °C, thus, maintaining the monoclonality of each droplet and facilitating the selective retrieval of desired droplets. The monoclonality of droplets was demonstrated by DNA sequencing and FACS analysis, suggesting the robustness and flexibility of the approach for single molecule amplification and analysis. We believe our approach will lead to new possibilities for a great variety of applications, such as single-cell gene expression studies, aptamer selection, and oligonucleotide analysis.

Resistive MHD Stability Analysis in Near Real-time

NASA Astrophysics Data System (ADS)

Glasser, Alexander; Kolemen, Egemen

2017-10-01

We discuss the feasibility of a near real-time calculation of the tokamak Δ' matrix, which summarizes MHD stability to resistive modes, such as tearing and interchange modes. As the operational phase of ITER approaches, solutions for active feedback tokamak stability control are needed. It has been previously demonstrated that an ideal MHD stability analysis is achievable on a sub- O (1 s) timescale, as is required to control phenomena comparable with the MHD-evolution timescale of ITER. In the present work, we broaden this result to incorporate the effects of resistive MHD modes. Such modes satisfy ideal MHD equations in regions outside narrow resistive layers that form at singular surfaces. We demonstrate that the use of asymptotic expansions at the singular surfaces, as well as the application of state transition matrices, enable a fast, parallelized solution to the singular outer layer boundary value problem, and thereby rapidly compute Δ'. Sponsored by US DOE under DE-SC0015878 and DE-FC02-04ER54698.

Analysis on LID for highly urbanized areas' waterlogging control: demonstrated on the example of Caohejing in Shanghai.

PubMed

Liao, Z L; He, Y; Huang, F; Wang, S; Li, H Z

2013-01-01

Although a commonly applied measure across the United States and Europe for alleviating the negative impacts of urbanization on the hydrological cycle, low impact development (LID) has not been widely used in highly urbanized areas, especially in rapidly urbanizing cities in developing countries like China. In this paper, given five LID practices including Bio-Retention, Infiltration Trench, Porous Pavement, Rain Barrels, and Green Swale, an analysis on LID for highly urbanized areas' waterlogging control is demonstrated using the example of Caohejing in Shanghai, China. Design storm events and storm water management models are employed to simulate the total waterlogging volume reduction, peak flow rate reduction and runoff coefficient reduction of different scenarios. Cost-effectiveness is calculated for the five practices. The aftermath shows that LID practices can have significant effects on storm water management in a highly urbanized area, and the comparative results reveal that Rain Barrels and Infiltration Trench are the two most suitable cost-effective measures for the study area.

Respiratory motion correction in dynamic MRI using robust data decomposition registration - application to DCE-MRI.

PubMed

Hamy, Valentin; Dikaios, Nikolaos; Punwani, Shonit; Melbourne, Andrew; Latifoltojar, Arash; Makanyanga, Jesica; Chouhan, Manil; Helbren, Emma; Menys, Alex; Taylor, Stuart; Atkinson, David

2014-02-01

Motion correction in Dynamic Contrast Enhanced (DCE-) MRI is challenging because rapid intensity changes can compromise common (intensity based) registration algorithms. In this study we introduce a novel registration technique based on robust principal component analysis (RPCA) to decompose a given time-series into a low rank and a sparse component. This allows robust separation of motion components that can be registered, from intensity variations that are left unchanged. This Robust Data Decomposition Registration (RDDR) is demonstrated on both simulated and a wide range of clinical data. Robustness to different types of motion and breathing choices during acquisition is demonstrated for a variety of imaged organs including liver, small bowel and prostate. The analysis of clinically relevant regions of interest showed both a decrease of error (15-62% reduction following registration) in tissue time-intensity curves and improved areas under the curve (AUC60) at early enhancement. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

Direct Analysis and Quantification of Metaldehyde in Water using Reactive Paper Spray Mass Spectrometry

PubMed Central

Maher, Simon; Jjunju, Fred P. M.; Damon, Deidre E.; Gorton, Hannah; Maher, Yosef S.; Syed, Safaraz U.; Heeren, Ron M. A.; Young, Iain S.; Taylor, Stephen; Badu-Tawiah, Abraham K.

2016-01-01

Metaldehyde is extensively used worldwide as a contact and systemic molluscicide for controlling slugs and snails in a wide range of agricultural and horticultural crops. Contamination of surface waters due to run-off, coupled with its moderate solubility in water, has led to increased concentration of the pesticide in the environment. In this study, for the first time, rapid analysis (<~1 minute) of metaldehyde residues in water is demonstrated using paper spray mass spectrometry (PS-MS). The observed precursor molecular ions of metaldehyde were confirmed from tandem mass spectrometry (MS/MS) experiments by studying the fragmentation patterns produced via collision-induced dissociation. The signal intensity ratios of the most abundant MS/MS transitions for metaldehyde (177 → 149 for protonated ion) and atrazine (221 → 179) were found to be linear in the range 0.01 to 5 ng/mL. Metaldehyde residues were detectable in environmental water samples at low concentration (LOD < 0.1 ng/mL using reactive PS-MS), with a relative standard deviation <10% and an R2 value >0.99, without any pre-concentration/separation steps. This result is of particular importance for environmental monitoring and water quality analysis providing a potential means of rapid screening to ensure safe drinking water. PMID:27767044

Rapid Ecological Change in Two Contrasting Lake Ecosystems: Evidence of Threshold Responses, Altered Species Dynamics, and Perturbed Patterns of Variability

NASA Astrophysics Data System (ADS)

Simpson, G. L.

2015-12-01

Studying threshold responses to environmental change is often made difficult due to the paucity of monitoring data prior to and during change. Progress has been made via theoretical models of regime shifts or experimental manipulation but natural, real world, examples of threshold change are limited and in many cases inconclusive. Lake sediments provide the potential to examine abrupt ecological change by directly observing how species, communities, and biogeochemical proxies responded to environmental perturbation or recorded ecosystem change. These records are not problem-free; age uncertainties, uneven and variable temporal resolution, and time-consuming taxonomic work all act to limit the scope and scale of the data or complicate its analysis. Here I use two annually laminated records 1. Kassjön, a seasonally anoxic mesotrophic lake in N Sweden, and2. Baldeggersee, a nutrient rich, hardwater lake on the central Swiss Plateau to investigate lake ecosystem responses to abrupt environmental change using ideal paleoecological time series. Rapid cooling 2.2kyr ago in northern Sweden significantly perturbed the diatom community of Kassjön. Using wavelet analysis, this amelioration in climate also fundamentally altered patterns of variance in diatom abundances, suppressing cyclicity in species composition that required several hundred years to reestablish. Multivariate wavelet analysis of the record showed marked switching between synchronous and asynchronous species dynamics in response to rapid climatic cooling and subsequent warming. Baldeggersee has experienced a long history of eutrophication and the diatom record has been used as a classic illustration of a regime shift in response to nutrient loading. Time series analysis of the record identified some evidence of a threshold-like response in the diatoms. A stochastic volatility model identified increasing variance in composition prior to the threshold, as predicted from theory, and a switch from compensatory to synchronous species dynamics, concomitant with eutrophication, was observed. These results document in high resolution how two aquatic systems reacted to abrupt change and demonstrate that under ideal conditions sediments can preserve valuable evidence of rapid ecological change.

Clinical analysis of genome next-generation sequencing data using the Omicia platform

PubMed Central

Coonrod, Emily M; Margraf, Rebecca L; Russell, Archie; Voelkerding, Karl V; Reese, Martin G

2013-01-01

Aims Next-generation sequencing is being implemented in the clinical laboratory environment for the purposes of candidate causal variant discovery in patients affected with a variety of genetic disorders. The successful implementation of this technology for diagnosing genetic disorders requires a rapid, user-friendly method to annotate variants and generate short lists of clinically relevant variants of interest. This report describes Omicia’s Opal platform, a new software tool designed for variant discovery and interpretation in a clinical laboratory environment. The software allows clinical scientists to process, analyze, interpret and report on personal genome files. Materials & Methods To demonstrate the software, the authors describe the interactive use of the system for the rapid discovery of disease-causing variants using three cases. Results & Conclusion Here, the authors show the features of the Opal system and their use in uncovering variants of clinical significance. PMID:23895124

Crowdsourced 'R&D' and medical research.

PubMed

Callaghan, Christian William

2015-09-01

Crowdsourced R&D, a research methodology increasingly applied to medical research, has properties well suited to large-scale medical data collection and analysis, as well as enabling rapid research responses to crises such as disease outbreaks. Multidisciplinary literature offers diverse perspectives of crowdsourced R&D as a useful large-scale medical data collection and research problem-solving methodology. Crowdsourced R&D has demonstrated 'proof of concept' in a host of different biomedical research applications. A wide range of quality and ethical issues relate to crowdsourced R&D. The rapid growth in applications of crowdsourced R&D in medical research is predicted by an increasing body of multidisciplinary theory. Further research in areas such as artificial intelligence may allow better coordination and management of the high volumes of medical data and problem-solving inputs generated by the crowdsourced R&D process. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Northern Hemisphere Stratospheric Ozone Depletion Caused by Solar Proton Events: The Role of the Polar Vortex

NASA Astrophysics Data System (ADS)

Denton, M. H.; Kivi, R.; Ulich, T.; Clilverd, M. A.; Rodger, C. J.; von der Gathen, P.

2018-02-01

Ozonesonde data from four sites are analyzed in relation to 191 solar proton events from 1989 to 2016. Analysis shows ozone depletion ( 10-35 km altitude) commencing following the SPEs. Seasonally corrected ozone data demonstrate that depletions occur only in winter/early spring above sites where the northern hemisphere polar vortex (PV) can be present. A rapid reduction in stratospheric ozone is observed with the maximum decrease occurring 10-20 days after solar proton events. Ozone levels remain depleted in excess of 30 days. No depletion is observed above sites completely outside the PV. No depletion is observed in relation to 191 random epochs at any site at any time of year. Results point to the role of indirect ozone destruction, most likely via the rapid descent of long-lived NOx species in the PV during the polar winter.

Predicting kinetics of polymorphic transformations from structure mapping and coordination analysis

NASA Astrophysics Data System (ADS)

Stevanović, Vladan; Trottier, Ryan; Musgrave, Charles; Therrien, Félix; Holder, Aaron; Graf, Peter

2018-03-01

To extend materials design and discovery into the space of metastable polymorphs, rapid and reliable assessment of transformation kinetics to lower energy structures is essential. Herein we focus on diffusionless polymorphic transformations and investigate routes to assess their kinetics using solely crystallographic arguments. As part of this investigation we developed a general algorithm to map crystal structures onto each other, and ascertain the low-energy (fast-kinetics) transformation pathways between them. Pathways with minimal dissociation of chemical bonds, along which the number of bonds (in ionic systems the first-shell coordination) does not decrease below that in the end structures, are shown to always be the fast-kinetics pathways. These findings enable the rapid assessment of the kinetics of polymorphic transformation and the identification of long-lived metastable structures. The utility is demonstrated on a number of transformations including those between high-pressure SnO2 phases, which lack a detailed atomic-level understanding.

Pro-inflammatory Cytokine Expression of Spleen Dendritic Cells in Mouse Toxoplasmosis

PubMed Central

Nam, Ho-Woo; Ahn, Hye-Jin

2011-01-01

Dendritic cells have been known as a member of strong innate immune cells against infectious organelles. In this study, we evaluated the cytokine expression of splenic dendritic cells in chronic mouse toxoplasmosis by tissue cyst-forming Me49 strain and demonstrated the distribution of lymphoid dendritic cells by fluorescence-activated cell sorter (FACS). Pro-inflammatory cytokines, such as IL-1α, IL-1β, IL-6, and IL-10 increased rapidly at week 1 post-infection (PI) and peaked at week 3 PI. Serum IL-10 level followed the similar patterns. FACS analysis showed that the number of CD8α+/CD11c+ splenic dendritic cells increased at week 1 and peaked at week 3 PI. In conclusion, mouse splenic dendritic cells showed early and rapid cytokine changes and may have important protective roles in early phases of murine toxoplasmosis. PMID:21738265

Threshold and resilience management of coupled urbanization and water environmental system in the rapidly changing coastal region.

PubMed

Li, Yangfan; Li, Yi; Wu, Wei

2016-01-01

The concept of thresholds shows important implications for environmental and resource management. Here we derived potential landscape thresholds which indicated abrupt changes in water quality or the dividing points between exceeding and failing to meet national surface water quality standards for a rapidly urbanizing city on the Eastern Coast in China. The analysis of landscape thresholds was based on regression models linking each of the seven water quality variables to each of the six landscape metrics for this coupled land-water system. We found substantial and accelerating urban sprawl at the suburban areas between 2000 and 2008, and detected significant nonlinear relations between water quality and landscape pattern. This research demonstrated that a simple modeling technique could provide insights on environmental thresholds to support more-informed decision making in land use, water environmental and resilience management. Copyright © 2015 Elsevier Ltd. All rights reserved.

Real-Time Continuous Identification of Greenhouse Plant Pathogens Based on Recyclable Microfluidic Bioassay System.

PubMed

Qu, Xiangmeng; Li, Min; Zhang, Hongbo; Lin, Chenglie; Wang, Fei; Xiao, Mingshu; Zhou, Yi; Shi, Jiye; Aldalbahi, Ali; Pei, Hao; Chen, Hong; Li, Li

2017-09-20

The development of a real-time continuous analytical platform for the pathogen detection is of great scientific importance for achieving better disease control and prevention. In this work, we report a rapid and recyclable microfluidic bioassay system constructed from oligonucleotide arrays for selective and sensitive continuous identification of DNA targets of fungal pathogens. We employ the thermal denaturation method to effectively regenerate the oligonucleotide arrays for multiple sample detection, which could considerably reduce the screening effort and costs. The combination of thermal denaturation and laser-induced fluorescence detection technique enables real-time continuous identification of multiple samples (<10 min per sample). As a proof of concept, we have demonstrated that two DNA targets of fungal pathogens (Botrytis cinerea and Didymella bryoniae) can be sequentially analyzed using our rapid microfluidic bioassay system, which provides a new paradigm in the design of microfluidic bioassay system and will be valuable for chemical and biomedical analysis.

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.

Rapid and Accurate Identification of Animal Species in Natural Leather Goods by Liquid Chromatography/Mass Spectrometry

PubMed Central

Izuchi, Yukari; Takashima, Tsuneo; Hatano, Naoya

2016-01-01

The demand for leather goods has grown globally in recent years. Industry revenue is forecast to reach $91.2 billion by 2018. There is an ongoing labelling problem in the leather items market, in that it is currently impossible to identify the species that a given piece of leather is derived from. To address this issue, we developed a rapid and simple method for the specific identification of leather derived from cattle, horses, pigs, sheep, goats, and deer by analysing peptides produced by the trypsin-digestion of proteins contained in leather goods using liquid chromatography/mass spectrometry. We determined species-specific amino acid sequences by liquid chromatography/tandem mass spectrometry analysis using the Mascot software program and demonstrated that collagen α-1(I), collagen α-2(I), and collagen α-1(III) from the dermal layer of the skin are particularly useful in species identification. PMID:27313979

Design, optimisation and preliminary validation of a human specific loop-mediated amplification assay for the rapid detection of human DNA at forensic crime scenes.

PubMed

Hird, H J; Brown, M K

2017-11-01

The identification of samples at a crime scene which require forensic DNA typing has been the focus of recent research interest. We propose a simple, but sensitive analysis system which can be deployed at a crime scene to identify crime scene stains as human or non-human. The proposed system uses the isothermal amplification of DNA in a rapid assay format, which returns results in as little as 30min from sampling. The assay system runs on the Genie II device, a proven in-field detection system which could be deployed at a crime scene. The results presented here demonstrate that the system was sufficiently specific and sensitive and was able to detect the presence of human blood, semen and saliva on mock forensic samples. Copyright © 2017. Published by Elsevier B.V.

Molecular diagnostics for the detection and characterization of microbial pathogens.

PubMed

Procop, Gary W

2007-09-01

New and advanced methods of molecular diagnostics are changing the way we practice clinical microbiology, which affects the practice of medicine. Signal amplification and real-time nucleic acid amplification technologies offer a sensitive and specific result with a more rapid turnaround time than has ever before been possible. Numerous methods of postamplification analysis afford the simultaneous detection and differentiation of numerous microbial pathogens, their mechanisms of resistance, and the construction of disease-specific assays. The technical feasibility of these assays has already been demonstrated. How these new, often more expensive tests will be incorporated into routine practice and the impact they will have on patient care remain to be determined. One of the most attractive uses for such techniques is to achieve a more rapid characterization of the infectious agent so that a narrower-spectrum antimicrobial agent may be used, which should have an impact on resistance patterns.

Structural basis for cellobiose dehydrogenase action during oxidative cellulose degradation

NASA Astrophysics Data System (ADS)

Tan, Tien-Chye; Kracher, Daniel; Gandini, Rosaria; Sygmund, Christoph; Kittl, Roman; Haltrich, Dietmar; Hällberg, B. Martin; Ludwig, Roland; Divne, Christina

2015-07-01

A new paradigm for cellulose depolymerization by fungi focuses on an oxidative mechanism involving cellobiose dehydrogenases (CDH) and copper-dependent lytic polysaccharide monooxygenases (LPMO); however, mechanistic studies have been hampered by the lack of structural information regarding CDH. CDH contains a haem-binding cytochrome (CYT) connected via a flexible linker to a flavin-dependent dehydrogenase (DH). Electrons are generated from cellobiose oxidation catalysed by DH and shuttled via CYT to LPMO. Here we present structural analyses that provide a comprehensive picture of CDH conformers, which govern the electron transfer between redox centres. Using structure-based site-directed mutagenesis, rapid kinetics analysis and molecular docking, we demonstrate that flavin-to-haem interdomain electron transfer (IET) is enabled by a haem propionate group and that rapid IET requires a closed CDH state in which the propionate is tightly enfolded by DH. Following haem reduction, CYT reduces LPMO to initiate oxygen activation at the copper centre and subsequent cellulose depolymerization.

Microfluidic mixing for sperm activation and motility analysis of pearl Danio zebrafish

PubMed Central

Park, Daniel S.; Egnatchik, Robert A.; Bordelon, Hali; Tiersch, Terrence R.; Monroe, W. Todd

2013-01-01

Sperm viability in aquatic species is increasingly being evaluated by motility analysis via computer-assisted sperm analysis (CASA) following activation of sperm with manual dilution and mixing by hand. User variation can limit the speed and control over the activation process, preventing consistent motility analysis. This is further complicated by the short interval (i.e., less than 15 s) of burst motility in these species. The objectives of this study were to develop a staggered herringbone microfluidic mixer to: 1) activate small volumes of Danio pearl zebrafish (Danio albolineatus) sperm by rapid mixing with diluent, and 2) position sperm in a viewing chamber for motility evaluation using a standard CASA system. A herringbone micromixer was fabricated in polydimethylsiloxane (PDMS) to yield high quality smooth surfaces. Based on fluorescence microscopy, mixing efficiency exceeding 90% was achieved within 5 s for a range of flow rates (from 50 to 250 μL/h), with a correlation of mixing distances and mixing efficiency. For example, at the nominal flow rate of 100 μL/h, there was a significant difference in mixing efficiency between 3.5 mm (75 ± 4%; mean ± SD) and 7 mm (92 ± 2%; P = 0.002). The PDMS micromixer, integrated with standard volumetric slides, demonstrated activation of fresh zebrafish sperm with reduced user variation, greater control, and without morphologic damage to sperm. Analysis of zebrafish sperm viability by CASA revealed a statistically higher motility rate for activation by micromixing (56 ± 4%) than manual activation (45 ± 7%; n = 5, P = 0.011). This micromixer represented a first step in streamlining methods for consistent, rapid assessment of sperm quality for zebrafish and other aquatic species. The capability to rapidly activate sperm and consistently measure motility with CASA using the PDMS micromixer described herein will improve studies of germplasm physiology and cryopreservation. PMID:22494680

Microfluidic mixing for sperm activation and motility analysis of pearl Danio zebrafish.

PubMed

Park, Daniel S; Egnatchik, Robert A; Bordelon, Hali; Tiersch, Terrence R; Monroe, W Todd

2012-07-15

Sperm viability in aquatic species is increasingly being evaluated by motility analysis via computer-assisted sperm analysis (CASA) following activation of sperm with manual dilution and mixing by hand. User variation can limit the speed and control over the activation process, preventing consistent motility analysis. This is further complicated by the short interval (i.e., less than 15 s) of burst motility in these species. The objectives of this study were to develop a staggered herringbone microfluidic mixer to: 1) activate small volumes of Danio pearl zebrafish (Danio albolineatus) sperm by rapid mixing with diluent, and 2) position sperm in a viewing chamber for motility evaluation using a standard CASA system. A herringbone micromixer was fabricated in polydimethylsiloxane (PDMS) to yield high quality smooth surfaces. Based on fluorescence microscopy, mixing efficiency exceeding 90% was achieved within 5 s for a range of flow rates (from 50 to 250 μL/h), with a correlation of mixing distances and mixing efficiency. For example, at the nominal flow rate of 100 μL/h, there was a significant difference in mixing efficiency between 3.5 mm (75±4%; mean±SD) and 7 mm (92±2%; P=0.002). The PDMS micromixer, integrated with standard volumetric slides, demonstrated activation of fresh zebrafish sperm with reduced user variation, greater control, and without morphologic damage to sperm. Analysis of zebrafish sperm viability by CASA revealed a statistically higher motility rate for activation by micromixing (56±4%) than manual activation (45±7%; n=5, P=0.011). This micromixer represented a first step in streamlining methods for consistent, rapid assessment of sperm quality for zebrafish and other aquatic species. The capability to rapidly activate sperm and consistently measure motility with CASA using the PDMS micromixer described herein will improve studies of germplasm physiology and cryopreservation. Copyright © 2012 Elsevier Inc. All rights reserved.

Rapid Thermal Processing (RTP) of semiconductors in space

NASA Technical Reports Server (NTRS)

Anderson, T. J.; Jones, K. S.

1993-01-01

The progress achieved on the project entitled 'Rapid Thermal Processing of Semiconductors in Space' for a 12 month period of activity ending March 31, 1993 is summarized. The activity of this group is being performed under the direct auspices of the ROMPS program. The main objective of this program is to develop and demonstrate the use of advanced robotics in space with rapid thermal process (RTP) of semiconductors providing the test technology. Rapid thermal processing is an ideal processing step for demonstration purposes since it encompasses many of the characteristics of other processes used in solid state device manufacturing. Furthermore, a low thermal budget is becoming more important in existing manufacturing practice, while a low thermal budget is critical to successful processing in space. A secondary objective of this project is to determine the influence of microgravity on the rapid thermal process for a variety of operating modes. In many instances, this involves one or more fluid phases. The advancement of microgravity processing science is an important ancillary objective.

Rapid and precise scanning helium ion microscope milling of solid-state nanopores for biomolecule detection.

PubMed

Yang, Jijin; Ferranti, David C; Stern, Lewis A; Sanford, Colin A; Huang, Jason; Ren, Zheng; Qin, Lu-Chang; Hall, Adam R

2011-07-15

We report the formation of solid-state nanopores using a scanning helium ion microscope. The fabrication process offers the advantage of high sample throughput along with fine control over nanopore dimensions, producing single pores with diameters below 4 nm. Electronic noise associated with ion transport through the resultant pores is found to be comparable with levels measured on devices made with the established technique of transmission electron microscope milling. We demonstrate the utility of our nanopores for biomolecular analysis by measuring the passage of double-strand DNA.

A low power, on demand electrothermal valve for wireless drug delivery applications

PubMed Central

Li, Po-Ying; Givrad, Tina K.; Sheybani, Roya; Holschneider, Daniel P.; Maarek, Jean-Michel I.

2014-01-01

We present a low power, on demand Parylene MEMS electrothermal valve. A novel Ω-shaped thermal resistive element requires low power (~mW) and enables rapid valve opening (~ms). Using both finite element analysis and valve opening experiments, a robust resistive element design for improved valve opening performance in water was obtained. In addition, a thermistor, as an inrush current limiter, was added into the valve circuit to provide variable current ramping. Wireless activation of the valve using RF inductive power transfer was demonstrated. PMID:20024057

Extracellular proteins limit the dispersal of biogenic nanoparticles

USGS Publications Warehouse

Moreau, J.W.; Weber, P.K.; Martin, M.C.; Gilbert, B.; Hutcheon, I.D.; Banfield, J.F.

2007-01-01

High-spatial-resolution secondary ion microprobe spectrometry, synchrotron radiation-based Fourier-transform infrared spectroscopy, and polyacrylamide gel analysis demonstrated the intimate association of proteins with spheroidal aggregates of biogenic zinc sulfide nanocrystals, an example of extracellular biomineralization. Experiments involving synthetic zinc sulfide nanoparticles and representative amino acids indicated a driving role for cysteine in rapid nanoparticle aggregation. These findings suggest that microbially derived extracellular proteins can limit the dispersal of nanoparticulate metal-bearing phases, such as the mineral products of bioremediation, that may otherwise be transported away from their source by subsurface fluid flow.

Rocket nozzle thermal shock tests in an arc heater facility

NASA Technical Reports Server (NTRS)

Painter, James H.; Williamson, Ronald A.

1986-01-01

A rocket motor nozzle thermal structural test technique that utilizes arc heated nitrogen to simulate a motor burn was developed. The technique was used to test four heavily instrumented full-scale Star 48 rocket motor 2D carbon/carbon segments at conditions simulating the predicted thermal-structural environment. All four nozzles survived the tests without catastrophic or other structural failures. The test technique demonstrated promise as a low cost, controllable alternative to rocket motor firing. The technique includes the capability of rapid termination in the event of failure, allowing post-test analysis.

Rapid, in situ detection of cocaine residues based on paper spray ionization coupled with ion mobility spectrometry.

PubMed

Li, Ming; Zhang, Jingjing; Jiang, Jie; Zhang, Jing; Gao, Jing; Qiao, Xiaolin

2014-04-07

In this paper, a novel approach based on paper spray ionization coupled with ion mobility spectrometry (PSI-IMS) was developed for rapid, in situ detection of cocaine residues in liquid samples and on various surfaces (e.g. glass, marble, skin, wood, fingernails), without tedious sample pretreatment. The obvious advantages of PSI are its low cost, easy operation and simple configuration without using nebulizing gas or discharge gas. Compared with mass spectrometry, ion mobility spectrometry (IMS) takes advantage of its low cost, easy operation, and simple configuration without requiring a vacuum system. Therefore, IMS is a more congruous detection method for PSI in the case of rapid, in situ analysis. For the analysis of cocaine residues in liquid samples, dynamic responses from 5 μg mL(-1) to 200 μg mL(-1) with a linear coefficient (R(2)) of 0.992 were obtained. In this case, the limit of detection (LOD) was calculated to be 2 μg mL(-1) as signal to noise (S/N) was 3 with a relative standard deviation (RSD) of 6.5% for 11 measurements (n = 11). Cocaine residues on various surfaces such as metal, glass, marble, wood, skin, and fingernails were also directly analyzed before wiping the surfaces with a piece of paper. The LOD was calculated to be as low as 5 ng (S/N = 3, RSD = 6.3%, n = 11). This demonstrates the capability of the PSI-IMS method for direct detection of cocaine residues at scenes of cocaine administration. Our results show that PSI-IMS is a simple, sensitive, rapid and economical method for in situ detection of this illicit drug, which could help governments to combat drug abuse.

Validation of a rapid bacteria endospore enumeration system for use with spacecraft assembly

NASA Astrophysics Data System (ADS)

Chen, F.; Kuhlman, G.; Kirschner, L.; Kazarians, G.; Matsuyama, A.; Pickett, M.; Venkateswaran, K.; Kastner, J.; Kern, R.

NASA planetary protection policy sets forth strict limits on the number of bacterial endospores that can be present on a spacecraft at launch Currently the only approved method for counting the spores is a culture based assay that requires three days to produce results a timeframe that can be at odds with the rapid pace and rigorous deadlines of spacecraft assembly A possible alternative to the traditional culture based approach is the Millipore Rapid Microbiology Detection System RMDS which has previously been used for process and contamination control in the pharmaceutical and food industries The RMDS is rapid and simple shows high sensitivity 1 colony forming unit CFU sample and correlates well with traditional culture-based methods It combines membrane filtration adenosine triphosphate ATP bioluminescence chemistry and image analysis based on photon detection with a Charge Coupled Device CCD camera In this study we have optimized the assay condition and evaluated the use of the RMDS as a rapid spore detection tool for NASA applications Seven species of Bacillus nine strains that have been repeatedly isolated from clean room environments were assayed In order to select for spores the samples were subjected to a heat shock step before proceeding with the RMDS incubation protocol All strains were detected by the RMDS in sim 5 hours and these assay times were repeatedly demonstrated along with low image background noise The RMDS-based spore detection method is undergoing the final stages of validation and is

Structural evolution in the crystallization of rapid cooling silver melt

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

Tian, Z.A., E-mail: ze.tian@gmail.com; Laboratory for Simulation and Modelling of Particulate Systems School of Materials Science and Engineering, University of New South Wales, Sydney, NSW 2052; Dong, K.J.

2015-03-15

The structural evolution in a rapid cooling process of silver melt has been investigated at different scales by adopting several analysis methods. The results testify Ostwald’s rule of stages and Frank conjecture upon icosahedron with many specific details. In particular, the cluster-scale analysis by a recent developed method called LSCA (the Largest Standard Cluster Analysis) clarified the complex structural evolution occurred in crystallization: different kinds of local clusters (such as ico-like (ico is the abbreviation of icosahedron), ico-bcc like (bcc, body-centred cubic), bcc, bcc-like structures) in turn have their maximal numbers as temperature decreases. And in a rather wide temperaturemore » range the icosahedral short-range order (ISRO) demonstrates a saturated stage (where the amount of ico-like structures keeps stable) that breeds metastable bcc clusters. As the precursor of crystallization, after reaching the maximal number bcc clusters finally decrease, resulting in the final solid being a mixture mainly composed of fcc/hcp (face-centred cubic and hexagonal-closed packed) clusters and to a less degree, bcc clusters. This detailed geometric picture for crystallization of liquid metal is believed to be useful to improve the fundamental understanding of liquid–solid phase transition. - Highlights: • A comprehensive structural analysis is conducted focusing on crystallization. • The involved atoms in our analysis are more than 90% for all samples concerned. • A series of distinct intermediate states are found in crystallization of silver melt. • A novelty icosahedron-saturated state breeds the metastable bcc state.« less

A method for the automated detection phishing websites through both site characteristics and image analysis

NASA Astrophysics Data System (ADS)

White, Joshua S.; Matthews, Jeanna N.; Stacy, John L.

2012-06-01

Phishing website analysis is largely still a time-consuming manual process of discovering potential phishing sites, verifying if suspicious sites truly are malicious spoofs and if so, distributing their URLs to the appropriate blacklisting services. Attackers increasingly use sophisticated systems for bringing phishing sites up and down rapidly at new locations, making automated response essential. In this paper, we present a method for rapid, automated detection and analysis of phishing websites. Our method relies on near real-time gathering and analysis of URLs posted on social media sites. We fetch the pages pointed to by each URL and characterize each page with a set of easily computed values such as number of images and links. We also capture a screen-shot of the rendered page image, compute a hash of the image and use the Hamming distance between these image hashes as a form of visual comparison. We provide initial results demonstrate the feasibility of our techniques by comparing legitimate sites to known fraudulent versions from Phishtank.com, by actively introducing a series of minor changes to a phishing toolkit captured in a local honeypot and by performing some initial analysis on a set of over 2.8 million URLs posted to Twitter over a 4 days in August 2011. We discuss the issues encountered during our testing such as resolvability and legitimacy of URL's posted on Twitter, the data sets used, the characteristics of the phishing sites we discovered, and our plans for future work.

Towards the development of a rapid, portable, surface enhanced Raman spectroscopy based cleaning verification system for the drug nelarabine.

PubMed

Corrigan, Damion K; Salton, Neale A; Preston, Chris; Piletsky, Sergey

2010-09-01

Cleaning verification is a scientific and economic problem for the pharmaceutical industry. A large amount of potential manufacturing time is lost to the process of cleaning verification. This involves the analysis of residues on spoiled manufacturing equipment, with high-performance liquid chromatography (HPLC) being the predominantly employed analytical technique. The aim of this study was to develop a portable cleaning verification system for nelarabine using surface enhanced Raman spectroscopy (SERS). SERS was conducted using a portable Raman spectrometer and a commercially available SERS substrate to develop a rapid and portable cleaning verification system for nelarabine. Samples of standard solutions and swab extracts were deposited onto the SERS active surfaces, allowed to dry and then subjected to spectroscopic analysis. Nelarabine was amenable to analysis by SERS and the necessary levels of sensitivity were achievable. It is possible to use this technology for a semi-quantitative limits test. Replicate precision, however, was poor due to the heterogeneous drying pattern of nelarabine on the SERS active surface. Understanding and improving the drying process in order to produce a consistent SERS signal for quantitative analysis is desirable. This work shows the potential application of SERS for cleaning verification analysis. SERS may not replace HPLC as the definitive analytical technique, but it could be used in conjunction with HPLC so that swabbing is only carried out once the portable SERS equipment has demonstrated that the manufacturing equipment is below the threshold contamination level.

Monitoring Toxic Ionic Liquids in Zebrafish ( Danio rerio) with Desorption Electrospray Ionization Mass Spectrometry Imaging (DESI-MSI)

NASA Astrophysics Data System (ADS)

Perez, Consuelo J.; Tata, Alessandra; de Campos, Michel L.; Peng, Chun; Ifa, Demian R.

2017-06-01

Ambient mass spectrometry imaging has become an increasingly powerful technique for the direct analysis of biological tissues in the open environment with minimal sample preparation and fast analysis times. In this study, we introduce desorption electrospray ionization mass spectrometry imaging (DESI-MSI) as a novel, rapid, and sensitive approach to localize the accumulation of a mildly toxic ionic liquid (IL), AMMOENG 130 in zebrafish ( Danio rerio). The work demonstrates that DESI-MSI has the potential to rapidly monitor the accumulation of IL pollutants in aquatic organisms. AMMOENG 130 is a quaternary ammonium-based IL reported to be broadly used as a surfactant in commercialized detergents. It is known to exhibit acute toxicity to zebrafish causing extensive damage to gill secondary lamellae and increasing membrane permeability. Zebrafish were exposed to the IL in a static 96-h exposure study in concentrations near the LC50 of 1.25, 2.5, and 5.0 mg/L. DESI-MS analysis of zebrafish gills demonstrated the appearance of a dealkylated AMMOENG 130 metabolite in the lowest concentration of exposure identified by a high resolution hybrid LTQ-Orbitrap mass spectrometer as the trimethylstearylammonium ion, [C21H46N]+. With DESI-MSI, the accumulation of AMMOENG 130 and its dealkylated metabolite in zebrafish tissue was found in the nervous and respiratory systems. AMMOENG 130 and the metabolite were capable of penetrating the blood brain barrier of the fish with significant accumulation in the brain. Hence, we report for the first time the simultaneous characterization, distribution, and metabolism of a toxic IL in whole body zebrafish analyzed by DESI-MSI. This ambient mass spectrometry imaging technique shows great promise for the direct analysis of biological tissues to qualitatively monitor foreign, toxic, and persistent compounds in aquatic organisms from the environment. [Figure not available: see fulltext.

A Microelectromechanical High-Density Energy Storage/Rapid Release System

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

Rodgers, M. Steven; Allen, Jim J.; Meeks, Kent D.

1999-07-21

One highly desirable characteristic of electrostatically driven microelectromechanical systems (MEMS) is that they consume very little power. The corresponding drawback is that the force they produce may be inadequate for many applications. It has previously been demonstrated that gear reduction units or microtransmissions can substantially increase the torque generated by microengines. Operating speed, however, is also reduced by the transmission gear ratio. Some applications require both high speed and high force. If this output is only required for a limited period of time, then energy could be stored in a mechanical system and rapidly released upon demand. We have designed,more » fabricated, and demonstrated a high-density energy storage/rapid release system that accomplishes this task. Built using a 5-level surface micromachining technology, the assembly closely resembles a medieval crossbow. Energy releases on the order of tens of nanojoules have already been demonstrated, and significantly higher energy systems are under development.« less

The rapid terrain visualization interferometric synthetic aperture radar sensor

NASA Astrophysics Data System (ADS)

Graham, Robert H.; Bickel, Douglas L.; Hensley, William H.

2003-11-01

The Rapid Terrain Visualization interferometric synthetic aperture radar was designed and built at Sandia National Laboratories as part of an Advanced Concept Technology Demonstration (ACTD) to "demonstrate the technologies and infrastructure to meet the Army requirement for rapid generation of digital topographic data to support emerging crisis or contingencies." This sensor is currently being operated by Sandia National Laboratories for the Joint Precision Strike Demonstration (JPSD) Project Office to provide highly accurate digital elevation models (DEMs) for military and civilian customers, both inside and outside of the United States. The sensor achieves better than DTED Level IV position accuracy in near real-time. The system is being flown on a deHavilland DHC-7 Army aircraft. This paper outlines some of the technologies used in the design of the system, discusses the performance, and will discuss operational issues. In addition, we will show results from recent flight tests, including high accuracy maps taken of the San Diego area.

Microelectromechanical high-density energy storage/rapid release system

NASA Astrophysics Data System (ADS)

Rodgers, M. Steven; Allen, James J.; Meeks, Kent D.; Jensen, Brian D.; Miller, Samuel L.

1999-08-01

One highly desirable characteristic of electrostatically driven microelectromechanical systems (MEMS) is that they consume very little power. The corresponding drawback is that the force they produce may be inadequate for many applications. It has previously been demonstrated that gear reduction units or microtransmissions can substantially increase the torque generated by microengines. Operating speed, however, is also reduced by the transmission gear ratio. Some applications require both high speed and high force. If this output is only required for a limited period of time, then energy could be stored in a mechanical system and rapidly released upon demand. We have designed, fabricated, and demonstrated a high-density energy storage/rapid release system that accomplishes this task. Built using a 5-level surface micromachining technology, the assembly closely resembles a medieval crossbow. Energy releases on the order of tens of nanojoules have already been demonstrated, and significantly higher energy systems are under development.

Nick Grue | NREL

Science.gov Websites

geospatial data analysis using parallel processing High performance computing Renewable resource technical potential and supply curve analysis Spatial database utilization Rapid analysis of large geospatial datasets energy and geospatial analysis products Research Interests Rapid, web-based renewable resource analysis

Statistical Coupling Analysis-Guided Library Design for the Discovery of Mutant Luciferases.

PubMed

Liu, Mira D; Warner, Elliot A; Morrissey, Charlotte E; Fick, Caitlyn W; Wu, Taia S; Ornelas, Marya Y; Ochoa, Gabriela V; Zhang, Brendan S; Rathbun, Colin M; Porterfield, William B; Prescher, Jennifer A; Leconte, Aaron M

2018-02-06

Directed evolution has proven to be an invaluable tool for protein engineering; however, there is still a need for developing new approaches to continue to improve the efficiency and efficacy of these methods. Here, we demonstrate a new method for library design that applies a previously developed bioinformatic method, Statistical Coupling Analysis (SCA). SCA uses homologous enzymes to identify amino acid positions that are mutable and functionally important and engage in synergistic interactions between amino acids. We use SCA to guide a library of the protein luciferase and demonstrate that, in a single round of selection, we can identify luciferase mutants with several valuable properties. Specifically, we identify luciferase mutants that possess both red-shifted emission spectra and improved stability relative to those of the wild-type enzyme. We also identify luciferase mutants that possess a >50-fold change in specificity for modified luciferins. To understand the mutational origin of these improved mutants, we demonstrate the role of mutations at N229, S239, and G246 in altered function. These studies show that SCA can be used to guide library design and rapidly identify synergistic amino acid mutations from a small library.

Rapid Benefit Indicators (RBI) Spatial Analysis Tools

EPA Science Inventory

The Rapid Benefit Indicators (RBI) approach consists of five steps and is outlined in Assessing the Benefits of Wetland Restoration - A Rapid Benefits Indicators Approach for Decision Makers. This spatial analysis tool is intended to be used to analyze existing spatial informatio...

An object-oriented approach to risk and reliability analysis : methodology and aviation safety applications.

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

Dandini, Vincent John; Duran, Felicia Angelica; Wyss, Gregory Dane

2003-09-01

This article describes how features of event tree analysis and Monte Carlo-based discrete event simulation can be combined with concepts from object-oriented analysis to develop a new risk assessment methodology, with some of the best features of each. The resultant object-based event scenario tree (OBEST) methodology enables an analyst to rapidly construct realistic models for scenarios for which an a priori discovery of event ordering is either cumbersome or impossible. Each scenario produced by OBEST is automatically associated with a likelihood estimate because probabilistic branching is integral to the object model definition. The OBEST methodology is then applied to anmore » aviation safety problem that considers mechanisms by which an aircraft might become involved in a runway incursion incident. The resulting OBEST model demonstrates how a close link between human reliability analysis and probabilistic risk assessment methods can provide important insights into aviation safety phenomenology.« less

Portable XRF and principal component analysis for bill characterization in forensic science.

PubMed

Appoloni, C R; Melquiades, F L

2014-02-01

Several modern techniques have been applied to prevent counterfeiting of money bills. The objective of this study was to demonstrate the potential of Portable X-ray Fluorescence (PXRF) technique and the multivariate analysis method of Principal Component Analysis (PCA) for classification of bills in order to use it in forensic science. Bills of Dollar, Euro and Real (Brazilian currency) were measured directly at different colored regions, without any previous preparation. Spectra interpretation allowed the identification of Ca, Ti, Fe, Cu, Sr, Y, Zr and Pb. PCA analysis separated the bills in three groups and subgroups among Brazilian currency. In conclusion, the samples were classified according to its origin identifying the elements responsible for differentiation and basic pigment composition. PXRF allied to multivariate discriminate methods is a promising technique for rapid and no destructive identification of false bills in forensic science. Copyright © 2013 Elsevier Ltd. All rights reserved.

High-sensitivity ESCA instrument

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

Davies, R.D.; Herglotz, H.K.; Lee, J.D.

1973-01-01

A new electron spectroscopy for chemical analysis (ESCA) instrument has been developed to provide high sensitivity and efficient operation for laboratory analysis of composition and chemical bonding in very thin surface layers of solid samples. High sensitivity is achieved by means of the high-intensity, efficient x-ray source described by Davies and Herglotz at the 1968 Denver X-Ray Conference, in combination with the new electron energy analyzer described by Lee at the 1972 Pittsburgh Conference on Analytical Chemistry and Applied Spectroscopy. A sample chamber designed to provide for rapid introduction and replacement of samples has adequate facilities for various sample treatmentsmore » and conditiouing followed immediately by ESCA analysis of the sample. Examples of application are presented, demonstrating the sensitivity and resolution achievable with this instrument. Its usefulness in trace surface analysis is shown and some chemical shifts'' measured by the instrument are compared with those obtained by x-ray spectroscopy. (auth)« less

Rapid Benefit Indicators (RBI) Spatial Analysis Toolset - Manual

EPA Science Inventory

The Rapid Benefit Indicators (RBI) approach consists of five steps and is outlined in Assessing the Benefits of Wetland Restoration - A Rapid Benefits Indicators Approach for Decision Makers. This spatial analysis tool is intended to be used to analyze existing spatial informatio...

Demonstration of a rapidly-swept external cavity quantum cascade laser for rapid and sensitive quantification of chemical mixtures

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

Brumfield, Brian E.; Taubman, Matthew S.; Phillips, Mark C.

2016-02-13

A rapidly-swept external cavity quantum cascade laser (ECQCL) system for fast open-path quantification of multiple chemicals and mixtures is presented. The ECQCL system is swept over its entire tuning range (>100 cm-1) at frequencies up to 200 Hz. At 200 Hz the wavelength tuning rate and spectral resolution are 2x104 cm-1/sec and < 0.2 cm-1, respectively. The capability of the current system to quantify changes in chemical concentrations on millesecond timescales is demonstrated at atmospheric pressure using an open-path multi-pass cell. The detection limits for chemicals ranged from ppb to ppm levels depending on the absorption cross-section.

Nanomagnet-based removal of lead and digoxin from living rats

NASA Astrophysics Data System (ADS)

Herrmann, Inge K.; Schlegel, Andrea; Graf, Rolf; Schumacher, Christoph M.; Senn, Nico; Hasler, Melanie; Gschwind, Sabrina; Hirt, Ann-Marie; Günther, Detlef; Clavien, Pierre-Alain; Stark, Wendelin J.; Beck-Schimmer, Beatrice

2013-08-01

In a number of clinical conditions such as intoxication, bacteraemia or autoimmune diseases the removal of the disease-causing factor from blood would be the most direct cure. However, physicochemical characteristics of the target compounds limit the applicability of classical filtration and diffusion-based processes. In this work, we present a first in vivo magnetic blood purification rodent animal model and demonstrate its ability to rapidly clear toxins from blood circulation using two model toxins with stable plasma levels (lead (Pb2+) and digoxin). Ultra-strong functionalized metal nanomagnets are employed to eliminate the toxin from whole blood in an extracorporeal circuit. In the present experimental demonstration over 40% of the toxin (i.e. lead or digoxin) was removed within the first 10 minutes and over 75% within 40 minutes. After capturing the target substance, a magnetic trap prevents the toxin-loaded nanoparticles from entering the blood circulation. Elemental analysis and magnetic hysteresis measurements confirm full particle recovery by simple magnetic separation (residual particle concentration below 1 μg mL-1 (detection limit)). We demonstrate that magnetic separation-based blood purification offers rapid blood cleaning from noxious agents, germs or other deleterious materials with relevance to a number of clinical conditions. Based on this new approach, current blood purification technologies can be extended to efficiently remove disease-causing factors, e.g. overdosed drugs, bacteria or cancer cells without being limited by filter cut-offs or column surface saturation.

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

Vogel, John P.

The goal of this project was to apply high-throughput, non-destructive phenotyping (phenomics) to collections of natural variants and induced mutants of the model grass Brachypodium distachyon and characterize a small subset of that material in detail. B. distachyon is well suited to this phenomic approach because its small size and rapid generation time allow researchers to grow many plants under carefully controlled conditions. In addition, the simple diploid genetics, high quality genome sequence and existence of numerous experimental tools available for B. distachyon allow us to rapidly identify genes affecting specific phenotypes. Our phenomic analysis revealed great diversity in biofuel-relevantmore » traits like growth rate, biomass and photosynthetic rate. This clearly demonstrated the feasibility of applying a phenomic approach to the model grass B. distachyon. We also demonstrated the utility of B. distachyon for studying mature root system, something that is virtually impossible to do with biomass crops. We showed tremendous natural variation in root architecture that can potentially be used to design crops with superior nutrient and water harvesting capability. Finally, we demonstrated the speed with which we can link specific genes to specific phenotypes by studying two mutants in detail. Importantly, in both cases, the specific biological lessons learned were grass-specific and could not have been learned from a dicot model system. Furthermore, one of the genes affects cell wall integrity and thus may be a useful target in the context of biomass crop improvement. Ultimately, all this information can be used to accelerate the creation of improved biomass crops.« less

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

Harben, P E; Harris, D; Myers, S

Seismic imaging and tracking methods have intelligence and monitoring applications. Current systems, however, do not adequately calibrate or model the unknown geological heterogeneity. Current systems are also not designed for rapid data acquisition and analysis in the field. This project seeks to build the core technological capabilities coupled with innovative deployment, processing, and analysis methodologies to allow seismic methods to be effectively utilized in the applications of seismic imaging and vehicle tracking where rapid (minutes to hours) and real-time analysis is required. The goal of this project is to build capabilities in acquisition system design, utilization and in full 3Dmore » finite difference modeling as well as statistical characterization of geological heterogeneity. Such capabilities coupled with a rapid field analysis methodology based on matched field processing are applied to problems associated with surveillance, battlefield management, finding hard and deeply buried targets, and portal monitoring. This project benefits the U.S. military and intelligence community in support of LLNL's national-security mission. FY03 was the final year of this project. In the 2.5 years this project has been active, numerous and varied developments and milestones have been accomplished. A wireless communication module for seismic data was developed to facilitate rapid seismic data acquisition and analysis. The E3D code was enhanced to include topographic effects. Codes were developed to implement the Karhunen-Loeve (K-L) statistical methodology for generating geological heterogeneity that can be utilized in E3D modeling. The matched field processing methodology applied to vehicle tracking and based on a field calibration to characterize geological heterogeneity was tested and successfully demonstrated in a tank tracking experiment at the Nevada Test Site. A 3-seismic-array vehicle tracking testbed was installed on-site at LLNL for testing real-time seismic tracking methods. A field experiment was conducted over a tunnel at the Nevada Site that quantified the tunnel reflection signal and, coupled with modeling, identified key needs and requirements in experimental layout of sensors. A large field experiment was conducted at the Lake Lynn Laboratory, a mine safety research facility in Pennsylvania, over a tunnel complex in realistic, difficult conditions. This experiment gathered the necessary data for a full 3D attempt to apply the methodology. The experiment also collected data to analyze the capabilities to detect and locate in-tunnel explosions for mine safety and other applications.« less

Rapid and simultaneous analysis of five alkaloids in four parts of Coptidis Rhizoma by near-infrared spectroscopy

NASA Astrophysics Data System (ADS)

Jintao, Xue; Yufei, Liu; Liming, Ye; Chunyan, Li; Quanwei, Yang; Weiying, Wang; Yun, Jing; Minxiang, Zhang; Peng, Li

2018-01-01

Near-Infrared Spectroscopy (NIRS) was first used to develop a method for rapid and simultaneous determination of 5 active alkaloids (berberine, coptisine, palmatine, epiberberine and jatrorrhizine) in 4 parts (rhizome, fibrous root, stem and leaf) of Coptidis Rhizoma. A total of 100 samples from 4 main places of origin were collected and studied. With HPLC analysis values as calibration reference, the quantitative analysis of 5 marker components was performed by two different modeling methods, partial least-squares (PLS) regression as linear regression and artificial neural networks (ANN) as non-linear regression. The results indicated that the 2 types of models established were robust, accurate and repeatable for five active alkaloids, and the ANN models was more suitable for the determination of berberine, coptisine and palmatine while the PLS model was more suitable for the analysis of epiberberine and jatrorrhizine. The performance of the optimal models was achieved as follows: the correlation coefficient (R) for berberine, coptisine, palmatine, epiberberine and jatrorrhizine was 0.9958, 0.9956, 0.9959, 0.9963 and 0.9923, respectively; the root mean square error of validation (RMSEP) was 0.5093, 0.0578, 0.0443, 0.0563 and 0.0090, respectively. Furthermore, for the comprehensive exploitation and utilization of plant resource of Coptidis Rhizoma, the established NIR models were used to analysis the content of 5 active alkaloids in 4 parts of Coptidis Rhizoma and 4 main origin of places. This work demonstrated that NIRS may be a promising method as routine screening for off-line fast analysis or on-line quality assessment of traditional Chinese medicine (TCM).

Challenges of correlating pH change with relief of clinical symptoms in gastro esophageal reflux disease: a phase III, randomized study of Zegerid versus Losec.

PubMed

Walker, Dave; Ng Kwet Shing, Richard; Jones, Deborah; Gruss, Hans-Jurgen; Reguła, Jarosław

2015-01-01

Zegerid (on demand immediate-release omeprazole and sodium bicarbonate combination therapy) has demonstrated earlier absorption and more rapid pH change compared with Losec (standard enteric coated omeprazole), suggesting more rapid clinical relief of heartburn. This Phase III, multicenter, double-blind, double-dummy, randomized study assessed the clinical superiority of Zegerid versus Losec for rapid relief of heartburn associated with gastro-esophageal reflux disease (GERD). Patients with a history of frequent (2 3 days/week) uncomplicated GERD, were randomized to receive Zegerid (20 mg) or Losec (20 mg) with corresponding placebo. Study medication was self-administered on the first episode of heartburn, and could be taken for up to 3 days within a 14 day study period. Heartburn severity was self assessed up to 180 minutes post dose (9 point Likert scale). Primary endpoint was median time to sustained response (≥3 point reduction in heartburn severity for ≥45 minutes). Of patients randomized to Zegerid (N=122) or Losec (N=117), 228/239 had recorded ≥1 evaluable heartburn episodes and were included in the modified intent-to-treat population. No significant between-group differences were observed for median time to sustained response (60.0 vs. 52.2 minutes, Zegerid [N=117] and Losec [N=111], respectively), sustained partial response (both, 37.5 minutes) and sustained total relief (both, 105 minutes). Significantly more patients treated with Zegerid reached sustained total relief within 0-30 minutes post dose in all analysis sets (p<0.05). Both treatments were well tolerated and did not raise any safety concerns. Superiority of Zegerid over Losec for rapid heartburn relief was not demonstrated; both treatments were equally effective however the rapid onset of action of Losec was unexpected. Factors, including aspects of study design may have contributed to this. This study supports previously reported difficulty in correlating intra-gastric pH change with clinical effect in GERD therapy, highlighting the significance of several technical considerations for studies of this type. ClinicalTrials.gov NCT01493089.

Challenges of Correlating pH Change with Relief of Clinical Symptoms in Gastro Esophageal Reflux Disease: A Phase III, Randomized Study of Zegerid versus Losec

PubMed Central

Walker, Dave; Ng Kwet Shing, Richard; Jones, Deborah; Gruss, Hans-Jurgen; Reguła, Jarosław

2015-01-01

Background Zegerid (on demand immediate-release omeprazole and sodium bicarbonate combination therapy) has demonstrated earlier absorption and more rapid pH change compared with Losec (standard enteric coated omeprazole), suggesting more rapid clinical relief of heartburn. This Phase III, multicenter, double-blind, double-dummy, randomized study assessed the clinical superiority of Zegerid versus Losec for rapid relief of heartburn associated with gastro-esophageal reflux disease (GERD). Methods Patients with a history of frequent (2 3 days/week) uncomplicated GERD, were randomized to receive Zegerid (20mg) or Losec (20mg) with corresponding placebo. Study medication was self-administered on the first episode of heartburn, and could be taken for up to 3 days within a 14 day study period. Heartburn severity was self assessed up to 180 minutes post dose (9 point Likert scale). Primary endpoint was median time to sustained response (≥3 point reduction in heartburn severity for ≥45 minutes). Results Of patients randomized to Zegerid (N=122) or Losec (N=117), 228/239 had recorded ≥1 evaluable heartburn episodes and were included in the modified intent-to-treat population. No significant between-group differences were observed for median time to sustained response (60.0 vs. 52.2 minutes, Zegerid [N=117] and Losec [N=111], respectively), sustained partial response (both, 37.5 minutes) and sustained total relief (both, 105 minutes). Significantly more patients treated with Zegerid reached sustained total relief within 0–30 minutes post dose in all analysis sets (p<0.05). Both treatments were well tolerated and did not raise any safety concerns. Conclusions Superiority of Zegerid over Losec for rapid heartburn relief was not demonstrated; both treatments were equally effective however the rapid onset of action of Losec was unexpected. Factors, including aspects of study design may have contributed to this. This study supports previously reported difficulty in correlating intra-gastric pH change with clinical effect in GERD therapy, highlighting the significance of several technical considerations for studies of this type. Trial registration ClinicalTrials.gov NCT01493089 PMID:25706883

Strain-Level Metagenomic Analysis of the Fermented Dairy Beverage Nunu Highlights Potential Food Safety Risks.

PubMed

Walsh, Aaron M; Crispie, Fiona; Daari, Kareem; O'Sullivan, Orla; Martin, Jennifer C; Arthur, Cornelius T; Claesson, Marcus J; Scott, Karen P; Cotter, Paul D

2017-08-15

The rapid detection of pathogenic strains in food products is essential for the prevention of disease outbreaks. It has already been demonstrated that whole-metagenome shotgun sequencing can be used to detect pathogens in food but, until recently, strain-level detection of pathogens has relied on whole-metagenome assembly, which is a computationally demanding process. Here we demonstrated that three short-read-alignment-based methods, i.e., MetaMLST, PanPhlAn, and StrainPhlAn, could accurately and rapidly identify pathogenic strains in spinach metagenomes that had been intentionally spiked with Shiga toxin-producing Escherichia coli in a previous study. Subsequently, we employed the methods, in combination with other metagenomics approaches, to assess the safety of nunu, a traditional Ghanaian fermented milk product that is produced by the spontaneous fermentation of raw cow milk. We showed that nunu samples were frequently contaminated with bacteria associated with the bovine gut and, worryingly, we detected putatively pathogenic E. coli and Klebsiella pneumoniae strains in a subset of nunu samples. Ultimately, our work establishes that short-read-alignment-based bioinformatics approaches are suitable food safety tools, and we describe a real-life example of their utilization. IMPORTANCE Foodborne pathogens are responsible for millions of illnesses each year. Here we demonstrate that short-read-alignment-based bioinformatics tools can accurately and rapidly detect pathogenic strains in food products by using shotgun metagenomics data. The methods used here are considerably faster than both traditional culturing methods and alternative bioinformatics approaches that rely on metagenome assembly; therefore, they can potentially be used for more high-throughput food safety testing. Overall, our results suggest that whole-metagenome sequencing can be used as a practical food safety tool to prevent diseases or to link outbreaks to specific food products. Copyright © 2017 American Society for Microbiology.

Rapid climate change did not cause population collapse at the end of the European Bronze Age

PubMed Central

Armit, Ian; Swindles, Graeme T.; Becker, Katharina; Plunkett, Gill; Blaauw, Maarten

2014-01-01

The impact of rapid climate change on contemporary human populations is of global concern. To contextualize our understanding of human responses to rapid climate change it is necessary to examine the archeological record during past climate transitions. One episode of abrupt climate change has been correlated with societal collapse at the end of the northwestern European Bronze Age. We apply new methods to interrogate archeological and paleoclimate data for this transition in Ireland at a higher level of precision than has previously been possible. We analyze archeological 14C dates to demonstrate dramatic population collapse and present high-precision proxy climate data, analyzed through Bayesian methods, to provide evidence for a rapid climatic transition at ca. 750 calibrated years B.C. Our results demonstrate that this climatic downturn did not initiate population collapse and highlight the nondeterministic nature of human responses to past climate change. PMID:25404290

Rapid climate change did not cause population collapse at the end of the European Bronze Age.

PubMed

Armit, Ian; Swindles, Graeme T; Becker, Katharina; Plunkett, Gill; Blaauw, Maarten

2014-12-02

The impact of rapid climate change on contemporary human populations is of global concern. To contextualize our understanding of human responses to rapid climate change it is necessary to examine the archeological record during past climate transitions. One episode of abrupt climate change has been correlated with societal collapse at the end of the northwestern European Bronze Age. We apply new methods to interrogate archeological and paleoclimate data for this transition in Ireland at a higher level of precision than has previously been possible. We analyze archeological (14)C dates to demonstrate dramatic population collapse and present high-precision proxy climate data, analyzed through Bayesian methods, to provide evidence for a rapid climatic transition at ca. 750 calibrated years B.C. Our results demonstrate that this climatic downturn did not initiate population collapse and highlight the nondeterministic nature of human responses to past climate change.

A portfolio of products from the rapid terrain visualization interferometric SAR

NASA Astrophysics Data System (ADS)

Bickel, Douglas L.; Doerry, Armin W.

2007-04-01

The Rapid Terrain Visualization interferometric synthetic aperture radar was designed and built at Sandia National Laboratories as part of an Advanced Concept Technology Demonstration (ACTD) to "demonstrate the technologies and infrastructure to meet the Army requirement for rapid generation of digital topographic data to support emerging crisis or contingencies." This sensor was built by Sandia National Laboratories for the Joint Programs Sustainment and Development (JPSD) Project Office to provide highly accurate digital elevation models (DEMs) for military and civilian customers, both inside and outside of the United States. The sensor achieved better than HRTe Level IV position accuracy in near real-time. The system was flown on a deHavilland DHC-7 Army aircraft. This paper presents a collection of images and data products from the Rapid Terrain Visualization interferometric synthetic aperture radar. The imagery includes orthorectified images and DEMs from the RTV interferometric SAR radar.

Rapid Statistical Learning Supporting Word Extraction From Continuous Speech.

PubMed

Batterink, Laura J

2017-07-01

The identification of words in continuous speech, known as speech segmentation, is a critical early step in language acquisition. This process is partially supported by statistical learning, the ability to extract patterns from the environment. Given that speech segmentation represents a potential bottleneck for language acquisition, patterns in speech may be extracted very rapidly, without extensive exposure. This hypothesis was examined by exposing participants to continuous speech streams composed of novel repeating nonsense words. Learning was measured on-line using a reaction time task. After merely one exposure to an embedded novel word, learners demonstrated significant learning effects, as revealed by faster responses to predictable than to unpredictable syllables. These results demonstrate that learners gained sensitivity to the statistical structure of unfamiliar speech on a very rapid timescale. This ability may play an essential role in early stages of language acquisition, allowing learners to rapidly identify word candidates and "break in" to an unfamiliar language.

Coupling carbon nanotube film microextraction with desorption corona beam ionization for rapid analysis of Sudan dyes (I-IV) and Rhodamine B in chilli oil.

PubMed

Chen, Di; Huang, Yun-Qing; He, Xiao-Mei; Shi, Zhi-Guo; Feng, Yu-Qi

2015-03-07

A rapid analysis method by coupling carbon nanotube film (CNTF) microextraction with desorption corona beam ionization (DCBI) was developed for the determination of Sudan dyes (I-IV) and Rhodamine B in chilli oil samples. Typically, CNTF was immersed into the diluted solution of chilli oil for extraction, which was then placed directly under the visible plasma beam tip of the DCBI source for desorption and ionization. Under optimized conditions, five dyes were simultaneously determined using this method. Results showed that the analytes were enriched by the CNTF through the π-π interactions, and the proposed method could significantly improve the sensitivities of these compounds, compared to the direct analysis by DCBI-MS/MS. The method with a linear range of 0.08-12.8 μg g(-1) and good linear relationships (R(2) > 0.93) in a multiple reaction monitoring (MRM) mode was developed. Satisfactory reproducibility was achieved. Relative standard deviations (RSDs) were less than 20.0%. The recoveries ranged from 80.0 to 110.0%, and the limits of detection (LODs) were in the range of 1.4-21 ng g(-1). Finally, the feasibility of the method was further exhibited by the determination of five illegal dyes in chilli powder. These results demonstrate that the proposed method consumes less time and solvent than conventional HPLC-based methods and avoids the contamination of chromatographic column and ion source from non-volatile oil. With the help of a 72-well shaker, multiple samples could be treated simultaneously, which ensures high throughput for the entire pretreatment process. In conclusion, it provides a rapid and high-throughput approach for the determination of such illicit additions in chilli products.

Proteins with High Turnover Rate in Barley Leaves Estimated by Proteome Analysis Combined with in Planta Isotope Labeling1[W][OPEN

PubMed Central

Nelson, Clark J.; Alexova, Ralitza; Jacoby, Richard P.; Millar, A. Harvey

2014-01-01

Protein turnover is a key component in cellular homeostasis; however, there is little quantitative information on degradation kinetics for individual plant proteins. We have used 15N labeling of barley (Hordeum vulgare) plants and gas chromatography-mass spectrometry analysis of free amino acids and liquid chromatography-mass spectrometry analysis of proteins to track the enrichment of 15N into the amino acid pools in barley leaves and then into tryptic peptides derived from newly synthesized proteins. Using information on the rate of growth of barley leaves combined with the rate of degradation of 14N-labeled proteins, we calculate the turnover rates of 508 different proteins in barley and show that they vary by more than 100-fold. There was approximately a 9-h lag from label application until 15N incorporation could be reliably quantified in extracted peptides. Using this information and assuming constant translation rates for proteins during the time course, we were able to quantify degradation rates for several proteins that exhibit half-lives on the order of hours. Our workflow, involving a stringent series of mass spectrometry filtering steps, demonstrates that 15N labeling can be used for large-scale liquid chromatography-mass spectrometry studies of protein turnover in plants. We identify a series of abundant proteins in photosynthesis, photorespiration, and specific subunits of chlorophyll biosynthesis that turn over significantly more rapidly than the average protein involved in these processes. We also highlight a series of proteins that turn over as rapidly as the well-known D1 subunit of photosystem II. While these proteins need further verification for rapid degradation in vivo, they cluster in chlorophyll and thiamine biosynthesis. PMID:25082890

Fluorescence spectroscopy for rapid detection and classification of bacterial pathogens.

PubMed

Sohn, Miryeong; Himmelsbach, David S; Barton, Franklin E; Fedorka-Cray, Paula J

2009-11-01

This study deals with the rapid detection and differentiation of Escherichia coli, Salmonella, and Campylobacter, which are the most commonly identified commensal and pathogenic bacteria in foods, using fluorescence spectroscopy and multivariate analysis. Each bacterial sample cultured under controlled conditions was diluted in physiologic saline for analysis. Fluorescence spectra were collected over a range of 200-700 nm with 0.5 nm intervals on the PerkinElmer Fluorescence Spectrometer. The synchronous scan technique was employed to find the optimum excitation (lambda(ex)) and emission (lambda(em)) wavelengths for individual bacteria with the wavelength interval (Deltalambda) being varied from 10 to 200 nm. The synchronous spectra and two-dimensional plots showed two maximum lambda(ex) values at 225 nm and 280 nm and one maximum lambda(em) at 335-345 nm (lambda(em) = lambda(ex) + Deltalambda), which correspond to the lambda(ex) = 225 nm, Deltalambda = 110-120 nm, and lambda(ex) = 280 nm, Deltalambda = 60-65 nm. For all three bacterial genera, the same synchronous scan results were obtained. The emission spectra from the three bacteria groups were very similar, creating difficulty in classification. However, the application of principal component analysis (PCA) to the fluorescence spectra resulted in successful classification of the bacteria by their genus as well as determining their concentration. The detection limit was approximately 10(3)-10(4) cells/mL for each bacterial sample. These results demonstrated that fluorescence spectroscopy, when coupled with PCA processing, has the potential to detect and to classify bacterial pathogens in liquids. The methodology is rapid (>10 min), inexpensive, and requires minimal sample preparation compared to standard analytical methods for bacterial detection.

High-throughput differentiation of heparin from other glycosaminoglycans by pyrolysis mass spectrometry.

PubMed

Nemes, Peter; Hoover, William J; Keire, David A

2013-08-06

Sensors with high chemical specificity and enhanced sample throughput are vital to screening food products and medical devices for chemical or biochemical contaminants that may pose a threat to public health. For example, the rapid detection of oversulfated chondroitin sulfate (OSCS) in heparin could prevent reoccurrence of heparin adulteration that caused hundreds of severe adverse events including deaths worldwide in 2007-2008. Here, rapid pyrolysis is integrated with direct analysis in real time (DART) mass spectrometry to rapidly screen major glycosaminoglycans, including heparin, chondroitin sulfate A, dermatan sulfate, and OSCS. The results demonstrate that, compared to traditional liquid chromatography-based analyses, pyrolysis mass spectrometry achieved at least 250-fold higher sample throughput and was compatible with samples volume-limited to about 300 nL. Pyrolysis yielded an abundance of fragment ions (e.g., 150 different m/z species), many of which were specific to the parent compound. Using multivariate and statistical data analysis models, these data enabled facile differentiation of the glycosaminoglycans with high throughput. After method development was completed, authentically contaminated samples obtained during the heparin crisis by the FDA were analyzed in a blinded manner for OSCS contamination. The lower limit of differentiation and detection were 0.1% (w/w) OSCS in heparin and 100 ng/μL (20 ng) OSCS in water, respectively. For quantitative purposes the linear dynamic range spanned approximately 3 orders of magnitude. Moreover, this chemical readout was successfully employed to find clues in the manufacturing history of the heparin samples that can be used for surveillance purposes. The presented technology and data analysis protocols are anticipated to be readily adaptable to other chemical and biochemical agents and volume-limited samples.

Phytoscreening for chlorinated solvents using rapid in vitro SPME sampling: Application to urban plume in Verl, Germany

USGS Publications Warehouse

Limmer, M.A.; Balouet, J.-C.; Karg, F.; Vroblesky, D.A.; Burken, J.G.

2011-01-01

Rapid detection and delineation of contaminants in urban settings is critically important in protecting human health. Cores from trees growing above a plume of contaminated groundwater in Verl, Germany, were collected in 1 day, with subsequent analysis and plume mapping completed over several days. Solid-phase microextraction (SPME) analysis was applied to detect tetrachloroethene (PCE) and trichloroethene (TCE) to below nanogram/liter levels in the transpiration stream of the trees. The tree core concentrations showed a clear areal correlation to the distribution of PCE and TCE in the groundwater. Concentrations in tree cores were lower than the underlying groundwater, as anticipated; however, the tree core water retained the PCE:TCE signature of the underlying groundwater in the urban, populated area. The PCE:TCE ratio can indicate areas of differing degradation activity. Therefore, the phytoscreening analysis was capable not only of mapping the spatial distribution of groundwater contamination but also of delineating zones of potentially differing contaminant sources and degradation. The simplicity of tree coring and the ability to collect a large number of samples in a day with minimal disruption or property damage in the urban setting demonstrates that phytoscreening can be a powerful tool for gaining reconnaissance-level information on groundwater contaminated by chlorinated solvents. The use of SPME decreases the detection level considerably and increases the sensitivity of phytoscreening as an assessment, monitoring, and phytoforensic tool. With rapid, inexpensive, and noninvasive methods of detecting and delineating contaminants underlying homes, as in this case, human health can be better protected through screening of broader areas and with far faster response times. ?? 2011 American Chemical Society.

Laser and LED phototherapy on midpalatal suture after rapid maxilla expansion: Raman and histological analysis.

PubMed

Rosa, Cristiane Becher; Habib, Fernando Antonio Lima; de Araújo, Telma Martins; Dos Santos, Jean Nunes; Cangussu, Maria Cristina T; Barbosa, Artur Felipe Santos; de Castro, Isabele Cardoso Vieira; Pinheiro, Antônio Luiz Barbosa

2017-02-01

The aim of this study was to analyze the effect of laser or LED phototherapy on the acceleration of bone formation at the midpalatal suture after rapid maxilla expansion. Forty-five rats were divided into groups at 7 days (control, expansion, expansion and laser irradiation, and expansion and LED irradiation) and into 14 days (expansion, expansion and laser in the 1st week, expansion and LED in the 1st week, expansion and laser in the 1st and 2nd weeks, expansion and LED in the 1st and 2nd weeks). Laser/LED irradiation occurred every 48 h. Expansion was accomplished with a spatula and maintained with a triple helicoid of 0.020-in stainless steel orthodontic wire. A diode laser (λ780 nm, 70 mW, spot of 0.04 cm 2 , t = 257 s, SAEF of 18 J/cm 2 ) or a LED (λ850 ± 10 nm, 150 ± 10 mW, spot of 0.5 cm 2 , t = 120 s, SAEF of 18 J/cm 2 ) was applied in one point in the midpalatal suture immediately behind the upper incisors. Raman spectroscopy and histological analyses of the suture region were carried and data was submitted to statistical analyses (p ≤ 0.05). Raman spectrum analysis demonstrated that irradiation increases hydroxyapatite in the midpalatal suture after expansion. In the histological analysis of various inflammation, there was a higher production of collagen and osteoblastic activity and less osteoclastic activity. The results showed that LED irradiation associated to rapid maxillary expansion improves bone repair and could be an alternative to the use of laser in accelerating bone formation in the midpalatal suture.

Direct Analysis in Real Time-Mass Spectrometry & Kohonen Artificial Neural Networks for the Rapid Species Identification of Larvae, Pupae and Adult Life Stages of Carrion Insects.

PubMed

Beyramysoltan, Samira; Giffen, Justine E; Rosati, Jennifer Y; Musah, Rabi Ann

2018-06-20

Species determination of the various life stages of flies (order: Diptera) is challenging, particularly for the immature forms, because analogous life stages of different species are difficult to differentiate morphologically. It is demonstrated here that DART high-resolution mass spectrometry (DART-HRMS) combined with supervised Kohonen Self-Organizing Maps (SOM) enables accomplishment of species-level identification of larvae, pupae and adult life stages of carrion flies. DART-HRMS data for each life stage were acquired from analysis of ethanol suspensions representing Calliphoridae, Phoridae and Sarcophagidae families, without additional sample preparation. After preprocessing, the data were subjected to a combination of minimum Redundancy Maximal Relevance (mRMR) and Sparse Discriminant Analysis (SDA) methods to select the most significant variables for creating accurate SOM models. The resulting data were divided into training and validation sets, and then analyzed by the SOM method to define the proper discrimination models. The 5-fold venetian blind cross-validation misclassification error was below 7% for all life stages, and the validation samples were correctly identified in all cases. The multiclass SOM model also revealed which chemical components were the most significant markers for each species, with several of these being amino acids. The results show that processing of DART-HRMS data using artificial neural networks (ANNs) based on the Kohonen SOM approach enables rapid discrimination and identification of fly species even for the immature life stages. The ANNs can be continuously expanded to include a larger number of species, and can be used to screen DART-HRMS data from unknowns to rapidly determine species identity.

Evaluation of Fourier transform infrared (FT-IR) spectroscopy and chemometrics as a rapid approach for sub-typing Escherichia coli O157:H7 isolates.

PubMed

Davis, R; Paoli, G; Mauer, L J

2012-09-01

The importance of tracking outbreaks of foodborne illness and the emergence of new virulent subtypes of foodborne pathogens have created the need for rapid and reliable sub-typing methods for Escherichia coli O157:H7. Fourier transform infrared (FT-IR) spectroscopy coupled with multivariate statistical analyses was used for sub-typing 30 strains of E. coli O157:H7 that had previously been typed by multilocus variable number tandem repeat analysis (MLVA) and pulsed field gel electrophoresis (PFGE). Hierarchical cluster analysis (HCA) and canonical variate analysis (CVA) of the FT-IR spectra resulted in the clustering of the same or similar MLVA types and separation of different MLVA types of E. coli O157:H7. The developed FT-IR method showed better discriminatory power than PFGE in sub-typing E. coli O157:H7. Results also indicated the spectral relatedness between different outbreak strains. However, the grouping of some strains was not in complete agreement with the clustering based on PFGE and MLVA. Additionally, HCA of the spectra differentiated the strains into 30 sub-clusters, indicating the high specificity and suitability of the method for strain level identification. Strains were also classified (97% correct) based on the type of Shiga toxin present using CVA of the spectra. This study demonstrated that FT-IR spectroscopy is suitable for rapid (≤16 h) and economical sub-typing of E. coli O157:H7 with comparable accuracy to MLVA typing. This is the first report of using an FT-IR-based method for sub-typing E. coli O157:H7. Copyright © 2012 Elsevier Ltd. All rights reserved.

Water Quality Monitoring Using Tryptophan-like Fluorescence.

NASA Astrophysics Data System (ADS)

Hudson, N.; Urquhart, G.; Baker, A.; Ward, D.; Reynolds, D.; Carliell-Marquet, C.

2006-12-01

The Biochemical Oxygen Demand (BOD) test is recognised as being credible with over 90 years of application in water analysis. However it is easily affected by environmental constraints and requires the presence of a viable biological community. The BOD test takes 5-21 days and is laboratory based and so is unsuitable for rapid responses to potential pollution incidents. Analysis of fluorescence excitation emission matrices (EEM) of natural waters gives a rapid determination of the proportions of labile and refractory organic matter present. It facilitates a greater understanding of the oxygen depleting potential of organic matter in unfiltered samples in a shorter timescale than would be the case using BOD, the conventional water quality assessment method. The research presented assesses the relationship between 5-day BOD (BOD5) and the fluorescent amino acid tryptophan-like peak for a range of waters. The research is undertaken with a view to using fluorescence spectroscopy as an alternative to the BOD5 test for on-site monitoring or lab based, rapid indication of organic pollution in natural waters. A significant relationship is observed between the analytical parameters in line with the findings of previous research in which waste waters including synthetic sewage, and polluted surface waters were studied. This research demonstrates that for a large, variable data set tryptophan-like fluorescence is a strong indicator of BOD5 and may be used as a water quality monitoring tool particularly for high BOD5 samples.

Rapid and interference-free analysis of nine B-group vitamins in energy drinks using trilinear component modeling of liquid chromatography-mass spectrometry data.

PubMed

Hu, Yong; Wu, Hai-Long; Yin, Xiao-Li; Gu, Hui-Wen; Xiao, Rong; Xie, Li-Xia; Liu, Zhi; Fang, Huan; Wang, Li; Yu, Ru-Qin

2018-04-01

The aim of the present work was to develop a rapid and interference-free method based on liquid chromatography-mass spectrometry (LC-MS) for the simultaneous determination of nine B-group vitamins in various energy drinks. A smart and green strategy that modeled the three-way data array of LC-MS with second-order calibration methods based on alternating trilinear decomposition (ATLD) and alternating penalty trilinear decomposition (APTLD) algorithms was developed. By virtue of "mathematical separation" and "second-order advantage", the proposed strategy successfully solved the co-eluted peaks and unknown interferents in LC-MS analysis with the elution time less than 4.5min and simple sample preparation. Satisfactory quantitative results were obtained by the ATLD-LC-MS and APTLD-LC-MS methods for the spiked recovery assays, with the average spiked recoveries ranging from 87.2-113.9% to 92.0-111.7%, respectively. These results acquired from the proposed methods were confirmed by the LC-MS/MS method, which shows a quite good consistency with each other. All these results demonstrated that the developed chemometrics-assisted LC-MS strategy had advantages of being rapid, green, accurate and low-cost, and it could be an attractive alternative for the determination of multiple vitamins in complex food matrices, which required no laborious sample preparation, tedious condition optimization or more sophisticated instrumentations. Copyright © 2017 Elsevier B.V. All rights reserved.

Determining the effect of different environmental conditions on Ebola virus viability in clinically relevant specimens.

PubMed

Palyi, Bernadett; Magyar, Nora; Henczko, Judit; Szalai, Balint; Farkas, Agnes; Strecker, Thomas; Takacs, Maria; Kis, Zoltan

2018-03-29

In 2013-2016, West Africa experienced the largest and longest Ebola virus disease outbreak ever documented. The wide geographic spread and magnitude of the outbreak often limited the timely and rapid testing of diagnostic samples from patients with suspected Ebola virus disease, raising questions regarding the optimal storage and shipping conditions of clinically relevant specimens, including EDTA-whole blood, plasma, capillary blood, urine and seminal fluid (associated with sexual transmission of the Ebola virus after recovery from the disease). Therefore, the aim of our study was to identify the extent to which storage temperature and clinical specimen type influence Ebola virus viability. Virus infectivity was determined using a fluorescent focus-forming assay. In our study, we show that Ebola virus was the most stable in EDTA-whole blood and plasma samples, whereas rapid decay of infectivity was observed in simulated capillary blood, urine and semen samples, especially when these samples were stored at higher temperatures. The analysis of variance results demonstrated that both temperature and clinical specimen type have significant effects on virus viability, whereas donor differences were not observed. Repeated freeze and thaw cycles of the samples also had a notable impact on virus viability in EDTA-whole blood and urine. Due to the rapid temperature- and specimen-dependent degradation of the virus observed here, our study highlights the importance of proper clinical sample storage at low temperatures during transportation and laboratory analysis.

Rapid, generalized adaptation to asynchronous audiovisual speech

PubMed Central

Van der Burg, Erik; Goodbourn, Patrick T.

2015-01-01

The brain is adaptive. The speed of propagation through air, and of low-level sensory processing, differs markedly between auditory and visual stimuli; yet the brain can adapt to compensate for the resulting cross-modal delays. Studies investigating temporal recalibration to audiovisual speech have used prolonged adaptation procedures, suggesting that adaptation is sluggish. Here, we show that adaptation to asynchronous audiovisual speech occurs rapidly. Participants viewed a brief clip of an actor pronouncing a single syllable. The voice was either advanced or delayed relative to the corresponding lip movements, and participants were asked to make a synchrony judgement. Although we did not use an explicit adaptation procedure, we demonstrate rapid recalibration based on a single audiovisual event. We find that the point of subjective simultaneity on each trial is highly contingent upon the modality order of the preceding trial. We find compelling evidence that rapid recalibration generalizes across different stimuli, and different actors. Finally, we demonstrate that rapid recalibration occurs even when auditory and visual events clearly belong to different actors. These results suggest that rapid temporal recalibration to audiovisual speech is primarily mediated by basic temporal factors, rather than higher-order factors such as perceived simultaneity and source identity. PMID:25716790

Calculation of flow about posts and powerhead model

NASA Technical Reports Server (NTRS)

1988-01-01

A large number of computational fluid mechanics (CFD) problems were investigated. The primary studies include: the analysis of the turnaround duct/hot gas manifold/transfer tubes (fuel side) of the Space Shuttle Main Engine (SSME); the analysis of the LOX-T manifold (oxidizer side) of the SSME; the analysis of hydrogen accumulation in the Vandeburg flame trench; and modification of the Intel/VT241 systems to accommodate the EADS and PLOT 3D. Some of the analyses were exploratory in nature, using the CONTINUSYS code to provide preliminary information to enhance understanding of the problem, while in other the primary thrust was to acquire design information. In all cases the ability to predict information rapidly in these very complex analyses is seen to be an important demonstration of the power and utility of this mature predictive capability.

Use of application containers and workflows for genomic data analysis

PubMed Central

Schulz, Wade L.; Durant, Thomas J. S.; Siddon, Alexa J.; Torres, Richard

2016-01-01

Background: The rapid acquisition of biological data and development of computationally intensive analyses has led to a need for novel approaches to software deployment. In particular, the complexity of common analytic tools for genomics makes them difficult to deploy and decreases the reproducibility of computational experiments. Methods: Recent technologies that allow for application virtualization, such as Docker, allow developers and bioinformaticians to isolate these applications and deploy secure, scalable platforms that have the potential to dramatically increase the efficiency of big data processing. Results: While limitations exist, this study demonstrates a successful implementation of a pipeline with several discrete software applications for the analysis of next-generation sequencing (NGS) data. Conclusions: With this approach, we significantly reduced the amount of time needed to perform clonal analysis from NGS data in acute myeloid leukemia. PMID:28163975

Authentication of the botanical origin of honey by near-infrared spectroscopy.

PubMed

Ruoff, Kaspar; Luginbühl, Werner; Bogdanov, Stefan; Bosset, Jacques Olivier; Estermann, Barbara; Ziolko, Thomas; Amado, Renato

2006-09-06

Fourier transform near-infrared spectroscopy (FT-NIR) was evaluated for the authentication of eight unifloral and polyfloral honey types (n = 364 samples) previously classified using traditional methods such as chemical, pollen, and sensory analysis. Chemometric evaluation of the spectra was carried out by applying principal component analysis and linear discriminant analysis. The corresponding error rates were calculated according to Bayes' theorem. NIR spectroscopy enabled a reliable discrimination of acacia, chestnut, and fir honeydew honey from the other unifloral and polyfloral honey types studied. The error rates ranged from <0.1 to 6.3% depending on the honey type. NIR proved also to be useful for the classification of blossom and honeydew honeys. The results demonstrate that near-infrared spectrometry is a valuable, rapid, and nondestructive tool for the authentication of the above-mentioned honeys, but not for all varieties studied.

Practical issues of hyperspectral imaging analysis of solid dosage forms.

PubMed

Amigo, José Manuel

2010-09-01

Hyperspectral imaging techniques have widely demonstrated their usefulness in different areas of interest in pharmaceutical research during the last decade. In particular, middle infrared, near infrared, and Raman methods have gained special relevance. This rapid increase has been promoted by the capability of hyperspectral techniques to provide robust and reliable chemical and spatial information on the distribution of components in pharmaceutical solid dosage forms. Furthermore, the valuable combination of hyperspectral imaging devices with adequate data processing techniques offers the perfect landscape for developing new methods for scanning and analyzing surfaces. Nevertheless, the instrumentation and subsequent data analysis are not exempt from issues that must be thoughtfully considered. This paper describes and discusses the main advantages and drawbacks of the measurements and data analysis of hyperspectral imaging techniques in the development of solid dosage forms.

Laser Desorption Mass Spectrometry for DNA Sequencing and Analysis

NASA Astrophysics Data System (ADS)

Chen, C. H. Winston; Taranenko, N. I.; Golovlev, V. V.; Isola, N. R.; Allman, S. L.

1998-03-01

Rapid DNA sequencing and/or analysis is critically important for biomedical research. In the past, gel electrophoresis has been the primary tool to achieve DNA analysis and sequencing. However, gel electrophoresis is a time-consuming and labor-extensive process. Recently, we have developed and used laser desorption mass spectrometry (LDMS) to achieve sequencing of ss-DNA longer than 100 nucleotides. With LDMS, we succeeded in sequencing DNA in seconds instead of hours or days required by gel electrophoresis. In addition to sequencing, we also applied LDMS for the detection of DNA probes for hybridization LDMS was also used to detect short tandem repeats for forensic applications. Clinical applications for disease diagnosis such as cystic fibrosis caused by base deletion and point mutation have also been demonstrated. Experimental details will be presented in the meeting. abstract.

Raman spectroscopy enables noninvasive biochemical identification of the collagen regeneration in cutaneous wound healing of diabetic mice treated with MSCs.

PubMed

Yan, Wenxia; Liu, Hanping; Deng, Xiaoyuan; Jin, Ying; Sun, Huimin; Li, Caiyun; Wang, Ning; Chu, Jing

2017-07-01

Mesenchymal stem cells (MSCs) had been reported as a novel therapeutic strategy for non-healing diabetic cutaneous wound mainly by promoting the formation of extracellular matrix (ECM) and neovasculature. Collagen regeneration is one of the key processes of ECM remodeling in wound healing. Accordingly, rapid assessment of the collagen content in a noninvasive manner can promptly provide objective evaluation for MSC therapy of cutaneous wound healing and strength evidence to adjust therapeutic regimen. In the present study, noninvasive Raman microspectroscopy was used for tracing the regeneration status of collagen during diabetic wound healing with MSCs. Wound tissues of normal mice, diabetic mice, and MSC-treated diabetic mice were subjected to Masson trichrome staining assay and submitted to spectroscopic analysis by Raman microspectroscopy after wounding 7, 14, and 21 days. Masson trichrome staining demonstrated that there was more collagen deposition in diabetic + MSCs group relative to diabetic group. The relative intensity of Raman collagen peak positions at 937, 1004, 1321, 1452, and 1662 cm -1 increased in MSC-treated diabetic group compared to diabetic group, although normal mice group had the highest relative intensity of collagen peak bands. Correlation analysis suggested that the spectral bands had a high positive correlation with the collagen intensity detected by Masson trichrome staining in wound tissues of three groups. Our results demonstrate that Raman microspectroscopy has potential application in rapidly and quantitatively assessing diabetic wound healing with MSCs by monitoring collagen variation, which may provide a novel method for the study of skin regeneration.

Surface enhanced Raman spectroscopy (SERS) for the discrimination of Arthrobacter strains based on variations in cell surface composition.

PubMed

Stephen, Kate E; Homrighausen, Darren; DePalma, Glen; Nakatsu, Cindy H; Irudayaraj, Joseph

2012-09-21

Surface enhanced Raman spectroscopy (SERS) is a rapid and highly sensitive spectroscopic technique that has the potential to measure chemical changes in bacterial cell surface in response to environmental changes. The objective of this study was to determine whether SERS had sufficient resolution to differentiate closely related bacteria within a genus grown on solid and liquid medium, and a single Arthrobacter strain grown in multiple chromate concentrations. Fourteen closely related Arthrobacter strains, based on their 16S rRNA gene sequences, were used in this study. After performing principal component analysis in conjunction with Linear Discriminant Analysis, we used a novel, adapted cross-validation method, which more faithfully models the classification of spectra. All fourteen strains could be classified with up to 97% accuracy. The hierarchical trees comparing SERS spectra from the liquid and solid media datasets were different. Additionally, hierarchical trees created from the Raman data were different from those obtained using 16S rRNA gene sequences (a phylogenetic measure). A single bacterial strain grown on solid media culture with three different chromate levels also showed significant spectral distinction at discrete points identified by the new Elastic Net regularized regression method demonstrating the ability of SERS to detect environmentally induced changes in cell surface composition. This study demonstrates that SERS is effective in distinguishing between a large number of very closely related Arthrobacter strains and could be a valuable tool for rapid monitoring and characterization of phenotypic variations in a single population in response to environmental conditions.

Real-time full-motion color Flash lidar for target detection and identification

NASA Astrophysics Data System (ADS)

Nelson, Roy; Coppock, Eric; Craig, Rex; Craner, Jeremy; Nicks, Dennis; von Niederhausern, Kurt

2015-05-01

Greatly improved understanding of areas and objects of interest can be gained when real time, full-motion Flash LiDAR is fused with inertial navigation data and multi-spectral context imagery. On its own, full-motion Flash LiDAR provides the opportunity to exploit the z dimension for improved intelligence vs. 2-D full-motion video (FMV). The intelligence value of this data is enhanced when it is combined with inertial navigation data to produce an extended, georegistered data set suitable for a variety of analysis. Further, when fused with multispectral context imagery the typical point cloud now becomes a rich 3-D scene which is intuitively obvious to the user and allows rapid cognitive analysis with little or no training. Ball Aerospace has developed and demonstrated a real-time, full-motion LIDAR system that fuses context imagery (VIS to MWIR demonstrated) and inertial navigation data in real time, and can stream these information-rich geolocated/fused 3-D scenes from an airborne platform. In addition, since the higher-resolution context camera is boresighted and frame synchronized to the LiDAR camera and the LiDAR camera is an array sensor, techniques have been developed to rapidly interpolate the LIDAR pixel values creating a point cloud that has the same resolution as the context camera, effectively creating a high definition (HD) LiDAR image. This paper presents a design overview of the Ball TotalSight™ LIDAR system along with typical results over urban and rural areas collected from both rotary and fixed-wing aircraft. We conclude with a discussion of future work.

Molecular typing of Vibrio parahaemolyticus strains isolated from the Philippines by PCR-based methods.

PubMed

Maluping, R P; Ravelo, C; Lavilla-Pitogo, C R; Krovacek, K; Romalde, J L

2005-01-01

The main aim of the present study was to use three PCR-based techniques for the analysis of genetic variability among Vibrio parahaemolyticus strains isolated from the Philippines. Seventeen strains of V. parahaemolyticus isolated from shrimps (Penaeus monodon) and from the environments where these shrimps are being cultivated were analysed by random amplified polymorphic DNA PCR (RAPD-PCR), enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR) and repetitive extragenic palindromic PCR (REP-PCR). The results of this work have demonstrated genetic variability within the V. parahaemolyticus strains that were isolated from the Philippines. In addition, RAPD, ERIC and REP-PCR are suitable rapid typing methods for V. parahaemolyticus. All three methods have good discriminative ability and can be used as a rapid means of comparing V. parahaemolyticus strains for epidemiological investigation. Based on the results of this study, we could say that REP-PCR is inferior to RAPD and ERIC-PCR owing to the fact that it is less reproducible. Moreover, the REP-PCR analysis yielded a relatively small number of products. This may suggests that the REP sequences may not be widely distributed in the V. parahaemolyticus genome. Genetic variability within V. parahaemolyticus strains isolated in the Philippines has been demonstrated. The presence of ERIC and REP sequences in the genome of this bacterial species was confirmed. The RAPD, ERIC and REP-PCR techniques are useful methods for molecular typing of V. parahaemolyticus strains. To our knowledge this is the first study of this kind carried out on V. parahaemolyticus strains isolated from the Philippines.

Coordinated metabolic transitions during Drosophila embryogenesis and the onset of aerobic glycolysis.

PubMed

Tennessen, Jason M; Bertagnolli, Nicolas M; Evans, Janelle; Sieber, Matt H; Cox, James; Thummel, Carl S

2014-03-12

Rapidly proliferating cells such as cancer cells and embryonic stem cells rely on a specialized metabolic program known as aerobic glycolysis, which supports biomass production from carbohydrates. The fruit fly Drosophila melanogaster also utilizes aerobic glycolysis to support the rapid growth that occurs during larval development. Here we use singular value decomposition analysis of modENCODE RNA-seq data combined with GC-MS-based metabolomic analysis to analyze the changes in gene expression and metabolism that occur during Drosophila embryogenesis, spanning the onset of aerobic glycolysis. Unexpectedly, we find that the most common pattern of co-expressed genes in embryos includes the global switch to glycolytic gene expression that occurs midway through embryogenesis. In contrast to the canonical aerobic glycolytic pathway, however, which is accompanied by reduced mitochondrial oxidative metabolism, the expression of genes involved in the tricarboxylic cycle (TCA cycle) and the electron transport chain are also upregulated at this time. Mitochondrial activity, however, appears to be attenuated, as embryos exhibit a block in the TCA cycle that results in elevated levels of citrate, isocitrate, and α-ketoglutarate. We also find that genes involved in lipid breakdown and β-oxidation are upregulated prior to the transcriptional initiation of glycolysis, but are downregulated before the onset of larval development, revealing coordinated use of lipids and carbohydrates during development. These observations demonstrate the efficient use of nutrient stores to support embryonic development, define sequential metabolic transitions during this stage, and demonstrate striking similarities between the metabolic state of late-stage fly embryos and tumor cells. Copyright © 2014 Tennessen et al.

Comparative analysis of Gram's stain, PNA-FISH and Sepsityper with MALDI-TOF MS for the identification of yeast direct from positive blood cultures.

PubMed

Gorton, Rebecca L; Ramnarain, P; Barker, K; Stone, N; Rattenbury, S; McHugh, T D; Kibbler, C C

2014-10-01

Fungaemia diagnosis could be improved by reducing the time to identification of yeast from blood cultures. This study aimed to evaluate three rapid methods for the identification of yeast direct from blood cultures; Gram's stain analysis, the AdvanDX Peptide Nucleic Acid in Situ Hybridisation Yeast Traffic Light system (PNA-FISH YTL) and Bruker Sepsityper alongside matrix-assisted laser desorption ionisation time of flight mass spectrometry (MALDI-TOF MS). Fifty blood cultures spiked with a known single yeast strain were analysed by blinded operators experienced in each method. Identifications were compared with MALDI-TOF MS CHROMagar Candida culture and ITS rRNA sequence-based identifications. On first attempt, success rates of 96% (48/50) and 76% (36/50) were achieved using PNA-FISH YTL and Gram's stain respectively. MALDI-TOF MS demonstrated a success rate of 56% (28/50) when applying manufacturer's species log score thresholds and 76% (38/50) using in-house parameters, including lowering the species log score threshold to >1.5. In conclusion, PNA-FISH YTL demonstrated a high success rate successfully identifying yeast commonly encountered in fungaemia. Sepsityper(™) with MALDI-TOF MS was accurate but increased sensitivity is required. Due to the misidentification of commonly encountered yeast Gram's stain analysis demonstrated limited utility in this setting. © 2014 Blackwell Verlag GmbH.

Team Software Development for Aerothermodynamic and Aerodynamic Analysis and Design

NASA Technical Reports Server (NTRS)

Alexandrov, N.; Atkins, H. L.; Bibb, K. L.; Biedron, R. T.; Carpenter, M. H.; Gnoffo, P. A.; Hammond, D. P.; Jones, W. T.; Kleb, W. L.; Lee-Rausch, E. M.

2003-01-01

A collaborative approach to software development is described. The approach employs the agile development techniques: project retrospectives, Scrum status meetings, and elements of Extreme Programming to efficiently develop a cohesive and extensible software suite. The software product under development is a fluid dynamics simulator for performing aerodynamic and aerothermodynamic analysis and design. The functionality of the software product is achieved both through the merging, with substantial rewrite, of separate legacy codes and the authorship of new routines. Examples of rapid implementation of new functionality demonstrate the benefits obtained with this agile software development process. The appendix contains a discussion of coding issues encountered while porting legacy Fortran 77 code to Fortran 95, software design principles, and a Fortran 95 coding standard.

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

NASA Technical Reports Server (NTRS)

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

1983-01-01

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

Juvenile-onset Sporadic Amyotrophic Lateral Sclerosis with a Frameshift FUS Gene Mutation Presenting Unique Neuroradiological Findings and Cognitive Impairment.

PubMed

Hirayanagi, Kimitoshi; Sato, Masayuki; Furuta, Natsumi; Makioka, Kouki; Ikeda, Yoshio

2016-01-01

A 24-year-old Japanese woman developed anterocollis, weakness of the proximal arms, and subsequent cognitive impairment. A neurological examination revealed amyotrophic lateral sclerosis (ALS) without a family history. Systemic muscle atrophy progressed rapidly. Cerebral MRI clearly exhibited high signal intensities along the bilateral pyramidal tracts. An analysis of the FUS gene revealed a heterozygous two-base pair deletion, c.1507-1508delAG (p.G504WfsX515). A subset of juvenile-onset familial/sporadic ALS cases with FUS gene mutations reportedly demonstrates mental retardation or learning difficulty. Our study emphasizes the importance of conducting a FUS gene analysis in juvenile-onset ALS cases, even when no family occurrence is confirmed.

Facile MALDI-MS analysis of neutral glycans in NaOH-doped matrixes: microwave-assisted deglycosylation and one-step purification with diamond nanoparticles.

PubMed

Tzeng, Yan-Kai; Chang, Cheng-Chun; Huang, Chien-Ning; Wu, Chih-Che; Han, Chau-Chung; Chang, Huan-Cheng

2008-09-01

A streamlined protocol has been developed to accelerate, simplify, and enhance matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) of neutral underivatized glycans released from glycoproteins. It involved microwave-assisted enzymatic digestion and release of glycans, followed by rapid removal of proteins and peptides with carboxylated/oxidized diamond nanoparticles, and finally treating the analytes with NaOH before mixing them with acidic matrix (such as 2,5-dihydroxybenzoic acid) to suppress the formation of both peptide and potassiated oligosaccharide ions in MS analysis. The advantages of this protocol were demonstrated with MALDI-TOF-MS of N-linked glycans released from ovalbumin and ribonuclease B.

Electrophoretic variation in low molecular weight lens crystallins from inbred strains of rats.

PubMed

Donner, M E; Skow, L C; Kunz, H W; Gill, T J

1985-10-01

Analysis of rat lens soluble proteins by analytical isoelectric focusing detected two inherited electrophoretic differences in low molecular weight (LM) crystallins from inbred strains of rats (Rattus norvegicus). The polymorphic lens crystallins were shown to be similar to a genetically variant LM crystallin, LEN-1, previously described in mice (Mus musculus) and encoded on chromosome 1, at a locus linked to Pep-3 (dipeptidase). Linkage analysis demonstrated that the rat crystallin locus was loosely linked to Pep-3 at a recombination distance of 38 +/- 4.5 U. These data suggest the conservation of a large chromosomal region during the evolution of Rodentia and support the hypothesis that the gamma-crystallins are evolving more rapidly than alpha- or beta-crystallins.

NSEG: A segmented mission analysis program for low and high speed aircraft. Volume 3: Demonstration problems

NASA Technical Reports Server (NTRS)

Hague, D. S.; Rozendaal, H. L.

1977-01-01

Program NSEG is a rapid mission analysis code based on the use of approximate flight path equations of motion. Equation form varies with the segment type, for example, accelerations, climbs, cruises, descents, and decelerations. Realistic and detailed vehicle characteristics are specified in tabular form. In addition to its mission performance calculation capabilities, the code also contains extensive flight envelope performance mapping capabilities. For example, rate-of-climb, turn rates, and energy maneuverability parameter values may be mapped in the Mach-altitude plane. Approximate take off and landing analyses are also performed. At high speeds, centrifugal lift effects are accounted for. Extensive turbojet and ramjet engine scaling procedures are incorporated in the code.

Acoustic Enrichment of Extracellular Vesicles from Biological Fluids.

PubMed

Ku, Anson; Lim, Hooi Ching; Evander, Mikael; Lilja, Hans; Laurell, Thomas; Scheding, Stefan; Ceder, Yvonne

2018-06-11

Extracellular vesicles (EVs) have emerged as a rich source of biomarkers providing diagnostic and prognostic information in diseases such as cancer. Large-scale investigations into the contents of EVs in clinical cohorts are warranted, but a major obstacle is the lack of a rapid, reproducible, efficient, and low-cost methodology to enrich EVs. Here, we demonstrate the applicability of an automated acoustic-based technique to enrich EVs, termed acoustic trapping. Using this technology, we have successfully enriched EVs from cell culture conditioned media and urine and blood plasma from healthy volunteers. The acoustically trapped samples contained EVs ranging from exosomes to microvesicles in size and contained detectable levels of intravesicular microRNAs. Importantly, this method showed high reproducibility and yielded sufficient quantities of vesicles for downstream analysis. The enrichment could be obtained from a sample volume of 300 μL or less, an equivalent to 30 min of enrichment time, depending on the sensitivity of downstream analysis. Taken together, acoustic trapping provides a rapid, automated, low-volume compatible, and robust method to enrich EVs from biofluids. Thus, it may serve as a novel tool for EV enrichment from large number of samples in a clinical setting with minimum sample preparation.

Automated Microfluidic Platform for Serial Polymerase Chain Reaction and High-Resolution Melting Analysis.

PubMed

Cao, Weidong; Bean, Brian; Corey, Scott; Coursey, Johnathan S; Hasson, Kenton C; Inoue, Hiroshi; Isano, Taisuke; Kanderian, Sami; Lane, Ben; Liang, Hongye; Murphy, Brian; Owen, Greg; Shinoda, Nobuhiko; Zeng, Shulin; Knight, Ivor T

2016-06-01

We report the development of an automated genetic analyzer for human sample testing based on microfluidic rapid polymerase chain reaction (PCR) with high-resolution melting analysis (HRMA). The integrated DNA microfluidic cartridge was used on a platform designed with a robotic pipettor system that works by sequentially picking up different test solutions from a 384-well plate, mixing them in the tips, and delivering mixed fluids to the DNA cartridge. A novel image feedback flow control system based on a Canon 5D Mark II digital camera was developed for controlling fluid movement through a complex microfluidic branching network without the use of valves. The same camera was used for measuring the high-resolution melt curve of DNA amplicons that were generated in the microfluidic chip. Owing to fast heating and cooling as well as sensitive temperature measurement in the microfluidic channels, the time frame for PCR and HRMA was dramatically reduced from hours to minutes. Preliminary testing results demonstrated that rapid serial PCR and HRMA are possible while still achieving high data quality that is suitable for human sample testing. © 2015 Society for Laboratory Automation and Screening.

High-throughput quantitative biochemical characterization of algal biomass by NIR spectroscopy; multiple linear regression and multivariate linear regression analysis.

PubMed

Laurens, L M L; Wolfrum, E J

2013-12-18

One of the challenges associated with microalgal biomass characterization and the comparison of microalgal strains and conversion processes is the rapid determination of the composition of algae. We have developed and applied a high-throughput screening technology based on near-infrared (NIR) spectroscopy for the rapid and accurate determination of algal biomass composition. We show that NIR spectroscopy can accurately predict the full composition using multivariate linear regression analysis of varying lipid, protein, and carbohydrate content of algal biomass samples from three strains. We also demonstrate a high quality of predictions of an independent validation set. A high-throughput 96-well configuration for spectroscopy gives equally good prediction relative to a ring-cup configuration, and thus, spectra can be obtained from as little as 10-20 mg of material. We found that lipids exhibit a dominant, distinct, and unique fingerprint in the NIR spectrum that allows for the use of single and multiple linear regression of respective wavelengths for the prediction of the biomass lipid content. This is not the case for carbohydrate and protein content, and thus, the use of multivariate statistical modeling approaches remains necessary.

Nanobodies: site-specific labeling for super-resolution imaging, rapid epitope-mapping and native protein complex isolation

PubMed Central

Pleiner, Tino; Bates, Mark; Trakhanov, Sergei; Lee, Chung-Tien; Schliep, Jan Erik; Chug, Hema; Böhning, Marc; Stark, Holger; Urlaub, Henning; Görlich, Dirk

2015-01-01

Nanobodies are single-domain antibodies of camelid origin. We generated nanobodies against the vertebrate nuclear pore complex (NPC) and used them in STORM imaging to locate individual NPC proteins with <2 nm epitope-label displacement. For this, we introduced cysteines at specific positions in the nanobody sequence and labeled the resulting proteins with fluorophore-maleimides. As nanobodies are normally stabilized by disulfide-bonded cysteines, this appears counterintuitive. Yet, our analysis showed that this caused no folding problems. Compared to traditional NHS ester-labeling of lysines, the cysteine-maleimide strategy resulted in far less background in fluorescence imaging, it better preserved epitope recognition and it is site-specific. We also devised a rapid epitope-mapping strategy, which relies on crosslinking mass spectrometry and the introduced ectopic cysteines. Finally, we used different anti-nucleoporin nanobodies to purify the major NPC building blocks – each in a single step, with native elution and, as demonstrated, in excellent quality for structural analysis by electron microscopy. The presented strategies are applicable to any nanobody and nanobody-target. DOI: http://dx.doi.org/10.7554/eLife.11349.001 PMID:26633879

Blending protein separation and peptide analysis through real-time proteolytic digestion.

PubMed

Slysz, Gordon W; Schriemer, David C

2005-03-15

Typical liquid- or gel-based protein separations require enzymatic digestion as an important first step in generating protein identifications. Traditional protocols involve long-term proteolytic digestion of the separated protein, often leading to sample loss and reduced sensitivity. Previously, we presented a rapid method of proteolytic digestion that showed excellent digestion of resistant and low concentrations of protein without requiring reduction and alkylation. Here, we demonstrate on-line, real-time tryptic digestion in conjunction with reversed-phase protein separation. The studies were aimed at optimizing pH and ionic strength and the size of the digestion element, to produce maximal protein digestion with minimal effects on chromatographic integrity. Upon establishing optimal conditions, the digestion element was attached downstream from a capillary C4 reversed-phase column. A four-protein mixture was processed through the combined system, and the resulting peptides were analyzed on-line by electrospray mass spectrometry. Extracted ion chromatograms for protein chromatography based on peptide elution were generated. These were shown to emulate ion chromatograms produced in a subsequent run without the digestion element, based on protein elution. The methodology will enable rapid and sensitive analysis of liquid-based protein separations using the power of bottom-up proteomics methodologies.

Quantitative analysis of fatty-acid-based biofuels produced by wild-type and genetically engineered cyanobacteria by gas chromatography-mass spectrometry.

PubMed

Guan, Wenna; Zhao, Hui; Lu, Xuefeng; Wang, Cong; Yang, Menglong; Bai, Fali

2011-11-11

Simple and rapid quantitative determination of fatty-acid-based biofuels is greatly important for the study of genetic engineering progress for biofuels production by microalgae. Ideal biofuels produced from biological systems should be chemically similar to petroleum, like fatty-acid-based molecules including free fatty acids, fatty acid methyl esters, fatty acid ethyl esters, fatty alcohols and fatty alkanes. This study founded a gas chromatography-mass spectrometry (GC-MS) method for simultaneous quantification of seven free fatty acids, nine fatty acid methyl esters, five fatty acid ethyl esters, five fatty alcohols and three fatty alkanes produced by wild-type Synechocystis PCC 6803 and its genetically engineered strain. Data obtained from GC-MS analyses were quantified using internal standard peak area comparisons. The linearity, limit of detection (LOD) and precision (RSD) of the method were evaluated. The results demonstrated that fatty-acid-based biofuels can be directly determined by GC-MS without derivation. Therefore, rapid and reliable quantitative analysis of fatty-acid-based biofuels produced by wild-type and genetically engineered cyanobacteria can be achieved using the GC-MS method founded in this work. Copyright © 2011 Elsevier B.V. All rights reserved.

A differential mobility spectrometry/mass spectrometry platform for the rapid detection and quantitation of DNA adduct dG-ABP.

PubMed

Kafle, Amol; Klaene, Joshua; Hall, Adam B; Glick, James; Coy, Stephen L; Vouros, Paul

2013-07-15

There is continued interest in exploring new analytical technologies for the detection and quantitation of DNA adducts, biomarkers which provide direct evidence of exposure and genetic damage in cells. With the goal of reducing clean-up steps and improving sample throughput, a Differential Mobility Spectrometry/Mass Spectrometry (DMS/MS) platform has been introduced for adduct analysis. A DMS/MS platform has been utilized for the analysis of dG-ABP, the deoxyguanosine adduct of the bladder carcinogen 4-aminobiphenyl (4-ABP). After optimization of the DMS parameters, each sample was analyzed in just 30 s following a simple protein precipitation step of the digested DNA. A detection limit of one modification in 10^6 nucleosides has been achieved using only 2 µg of DNA. A brief comparison (quantitative and qualitative) with liquid chromatography/mass spectrometry is also presented highlighting the advantages of using the DMS/MS method as a high-throughput platform. The data presented demonstrate the successful application of a DMS/MS/MS platform for the rapid quantitation of DNA adducts using, as a model analyte, the deoxyguanosine adduct of the bladder carcinogen 4-aminobiphenyl. Copyright © 2013 John Wiley & Sons, Ltd.

Deactivation of Multilayered MFI Nanosheet Zeolite during Upgrading of Biomass Pyrolysis Vapors

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

Xu, Mengze; Mukarakate, Calvin; Iisa, Kristiina

Here, the catalytic fast pyrolysis (CFP) of biomass is a promising technology for producing renewable transportation fuels and chemicals. MFI-type catalysts have shown promise for CFP because they produce gasoline range hydrocarbons from oxygenated pyrolysis compounds; however, rapid catalyst deactivation due to coking is one of the major technical barriers inhibiting the commercialization of this technology. Coke deposited on the surface of the catalysts blocks access to active sites in the micropores leading to rapid catalyst deactivation. Our strategy is to minimize rapid catalyst deactivation by adding mesoporosity through forming MFI nanosheet materials. The synthesized MFI nanosheet catalysts were fullymore » characterized and evaluated for cellulose pyrolysis vapor upgrading to produce olefins and aromatic hydrocarbons. The data obtained from pyrolysis-GCMS (py-GCMS), showed that fresh MFI nanosheets produced similar aromatic hydrocarbon and olefin yields compared to conventional HZSM-5. However, MFI nanosheets demonstrated a longer lifetime than HZSM-5 even though coke contents were also higher than for HZSM-5 because the mesopores enabled better accessibility to active acid sites. This conclusion was supported by results from post-reaction analysis of various spent catalysts collected at different points during the deactivation experiments.« less

Computational Analysis of AMPK-Mediated Neuroprotection Suggests Acute Excitotoxic Bioenergetics and Glucose Dynamics Are Regulated by a Minimal Set of Critical Reactions.

PubMed

Connolly, Niamh M C; D'Orsi, Beatrice; Monsefi, Naser; Huber, Heinrich J; Prehn, Jochen H M

2016-01-01

Loss of ionic homeostasis during excitotoxic stress depletes ATP levels and activates the AMP-activated protein kinase (AMPK), re-establishing energy production by increased expression of glucose transporters on the plasma membrane. Here, we develop a computational model to test whether this AMPK-mediated glucose import can rapidly restore ATP levels following a transient excitotoxic insult. We demonstrate that a highly compact model, comprising a minimal set of critical reactions, can closely resemble the rapid dynamics and cell-to-cell heterogeneity of ATP levels and AMPK activity, as confirmed by single-cell fluorescence microscopy in rat primary cerebellar neurons exposed to glutamate excitotoxicity. The model further correctly predicted an excitotoxicity-induced elevation of intracellular glucose, and well resembled the delayed recovery and cell-to-cell heterogeneity of experimentally measured glucose dynamics. The model also predicted necrotic bioenergetic collapse and altered calcium dynamics following more severe excitotoxic insults. In conclusion, our data suggest that a minimal set of critical reactions may determine the acute bioenergetic response to transient excitotoxicity and that an AMPK-mediated increase in intracellular glucose may be sufficient to rapidly recover ATP levels following an excitotoxic insult.

Computational Analysis of AMPK-Mediated Neuroprotection Suggests Acute Excitotoxic Bioenergetics and Glucose Dynamics Are Regulated by a Minimal Set of Critical Reactions

PubMed Central

Connolly, Niamh M. C.; D’Orsi, Beatrice; Monsefi, Naser; Huber, Heinrich J.; Prehn, Jochen H. M.

2016-01-01

Loss of ionic homeostasis during excitotoxic stress depletes ATP levels and activates the AMP-activated protein kinase (AMPK), re-establishing energy production by increased expression of glucose transporters on the plasma membrane. Here, we develop a computational model to test whether this AMPK-mediated glucose import can rapidly restore ATP levels following a transient excitotoxic insult. We demonstrate that a highly compact model, comprising a minimal set of critical reactions, can closely resemble the rapid dynamics and cell-to-cell heterogeneity of ATP levels and AMPK activity, as confirmed by single-cell fluorescence microscopy in rat primary cerebellar neurons exposed to glutamate excitotoxicity. The model further correctly predicted an excitotoxicity-induced elevation of intracellular glucose, and well resembled the delayed recovery and cell-to-cell heterogeneity of experimentally measured glucose dynamics. The model also predicted necrotic bioenergetic collapse and altered calcium dynamics following more severe excitotoxic insults. In conclusion, our data suggest that a minimal set of critical reactions may determine the acute bioenergetic response to transient excitotoxicity and that an AMPK-mediated increase in intracellular glucose may be sufficient to rapidly recover ATP levels following an excitotoxic insult. PMID:26840769

Wounded cells drive rapid epidermal repair in the early Drosophila embryo

PubMed Central

Fernandez-Gonzalez, Rodrigo; Zallen, Jennifer A.

2013-01-01

Epithelial tissues are protective barriers that display a remarkable ability to repair wounds. Wound repair is often associated with an accumulation of actin and nonmuscle myosin II around the wound, forming a purse string. The role of actomyosin networks in generating mechanical force during wound repair is not well understood. Here we investigate the mechanisms of force generation during wound repair in the epidermis of early and late Drosophila embryos. We find that wound closure is faster in early embryos, where, in addition to a purse string around the wound, actomyosin networks at the medial cortex of the wounded cells contribute to rapid wound repair. Laser ablation demonstrates that both medial and purse-string actomyosin networks generate contractile force. Quantitative analysis of protein localization dynamics during wound closure indicates that the rapid contraction of medial actomyosin structures during wound repair in early embryos involves disassembly of the actomyosin network. By contrast, actomyosin purse strings in late embryos contract more slowly in a mechanism that involves network condensation. We propose that the combined action of two force-generating structures—a medial actomyosin network and an actomyosin purse string—contributes to the increased efficiency of wound repair in the early embryo. PMID:23985320

A novel method for rapid determination of total solid content in viscous liquids by multiple headspace extraction gas chromatography.

PubMed

Xin, Li-Ping; Chai, Xin-Sheng; Hu, Hui-Chao; Barnes, Donald G

2014-09-05

This work demonstrates a novel method for rapid determination of total solid content in viscous liquid (polymer-enriched) samples. The method is based multiple headspace extraction gas chromatography (MHE-GC) on a headspace vial at a temperature above boiling point of water. Thus, the trend of water loss from the tested liquid due to evaporation can be followed. With the limited MHE-GC testing (e.g., 5 extractions) and a one-point calibration procedure (i.e., recording the weight difference before and after analysis), the total amount of water in the sample can be determined, from which the total solid contents in the liquid can be calculated. A number of black liquors were analyzed by the new method which yielded results that closely matched those of the reference method; i.e., the results of these two methods differed by no more than 2.3%. Compared with the reference method, the MHE-GC method is much simpler and more practical. Therefore, it is suitable for the rapid determination of the solid content in many polymer-containing liquid samples. Copyright © 2014 Elsevier B.V. All rights reserved.

Glucocorticoid receptor interacts with PNRC2 in a ligand-dependent manner to recruit UPF1 for rapid mRNA degradation.

PubMed

Cho, Hana; Park, Ok Hyun; Park, Joori; Ryu, Incheol; Kim, Jeonghan; Ko, Jesang; Kim, Yoon Ki

2015-03-31

Glucocorticoid receptor (GR), which was originally known to function as a nuclear receptor, plays a role in rapid mRNA degradation by acting as an RNA-binding protein. The mechanism by which this process occurs remains unknown. Here, we demonstrate that GR, preloaded onto the 5'UTR of a target mRNA, recruits UPF1 through proline-rich nuclear receptor coregulatory protein 2 (PNRC2) in a ligand-dependent manner, so as to elicit rapid mRNA degradation. We call this process GR-mediated mRNA decay (GMD). Although GMD, nonsense-mediated mRNA decay (NMD), and staufen-mediated mRNA decay (SMD) share upstream frameshift 1 (UPF1) and PNRC2, we find that GMD is mechanistically distinct from NMD and SMD. We also identify de novo cellular GMD substrates using microarray analysis. Intriguingly, GMD functions in the chemotaxis of human monocytes by targeting chemokine (C-C motif) ligand 2 (CCL2) mRNA. Thus, our data provide molecular evidence of a posttranscriptional role of the well-studied nuclear hormone receptor, GR, which is traditionally considered a transcription factor.

Deactivation of Multilayered MFI Nanosheet Zeolite during Upgrading of Biomass Pyrolysis Vapors

DOE PAGES

Xu, Mengze; Mukarakate, Calvin; Iisa, Kristiina; ...

2017-05-02

Here, the catalytic fast pyrolysis (CFP) of biomass is a promising technology for producing renewable transportation fuels and chemicals. MFI-type catalysts have shown promise for CFP because they produce gasoline range hydrocarbons from oxygenated pyrolysis compounds; however, rapid catalyst deactivation due to coking is one of the major technical barriers inhibiting the commercialization of this technology. Coke deposited on the surface of the catalysts blocks access to active sites in the micropores leading to rapid catalyst deactivation. Our strategy is to minimize rapid catalyst deactivation by adding mesoporosity through forming MFI nanosheet materials. The synthesized MFI nanosheet catalysts were fullymore » characterized and evaluated for cellulose pyrolysis vapor upgrading to produce olefins and aromatic hydrocarbons. The data obtained from pyrolysis-GCMS (py-GCMS), showed that fresh MFI nanosheets produced similar aromatic hydrocarbon and olefin yields compared to conventional HZSM-5. However, MFI nanosheets demonstrated a longer lifetime than HZSM-5 even though coke contents were also higher than for HZSM-5 because the mesopores enabled better accessibility to active acid sites. This conclusion was supported by results from post-reaction analysis of various spent catalysts collected at different points during the deactivation experiments.« less

Design of Neural Networks for Fast Convergence and Accuracy: Dynamics and Control

NASA Technical Reports Server (NTRS)

Maghami, Peiman G.; Sparks, Dean W., Jr.

1997-01-01

A procedure for the design and training of artificial neural networks, used for rapid and efficient controls and dynamics design and analysis for flexible space systems, has been developed. Artificial neural networks are employed, such that once properly trained, they provide a means of evaluating the impact of design changes rapidly. Specifically, two-layer feedforward neural networks are designed to approximate the functional relationship between the component/spacecraft design changes and measures of its performance or nonlinear dynamics of the system/components. A training algorithm, based on statistical sampling theory, is presented, which guarantees that the trained networks provide a designer-specified degree of accuracy in mapping the functional relationship. Within each iteration of this statistical-based algorithm, a sequential design algorithm is used for the design and training of the feedforward network to provide rapid convergence to the network goals. Here, at each sequence a new network is trained to minimize the error of previous network. The proposed method should work for applications wherein an arbitrary large source of training data can be generated. Two numerical examples are performed on a spacecraft application in order to demonstrate the feasibility of the proposed approach.

A rapid identification of four medicinal chrysanthemum varieties with near infrared spectroscopy.

PubMed

Han, Bangxing; Yan, Hui; Chen, Cunwu; Yao, Houjun; Dai, Jun; Chen, Naifu

2014-07-01

For genuine medicinal material in Chinese herbs; the efficient, rapid, and precise identification is the focus and difficulty in the filed studying Chinese herbal medicines. Chrysanthemum morifolium as herbs has a long planting history in China, culturing high quality ones and different varieties. Different chrysanthemum varieties differ in quality, chemical composition, functions, and application. Therefore, chrysanthemum varieties in the market demands precise identification to provide reference for reasonable and correct application as genuine medicinal material. A total of 244 batches of chrysanthemum samples were randomly divided into calibration set (160 batches) and prediction set (84 batches). The near infrared diffuses reflectance spectra of chrysanthemum varieties were preprocessed by first order derivative (D1) and autoscaling and was built model with partial least squares (PLS). In this study of four chrysanthemum varieties identification, the accuracy rates in calibration sets of Boju, Chuju, Hangju, and Gongju are respectively 100, 100, 98.65, and 96.67%; while the accuracy rates in prediction sets are 100% except for 99.1% of Hangju. The research results demonstrate that the qualitative analysis can be conducted by machine learning combined with near infrared spectroscopy (NIR), which provides a new method for rapid and noninvasive identification of chrysanthemum varieties.

Design of neural networks for fast convergence and accuracy: dynamics and control.

PubMed

Maghami, P G; Sparks, D R

2000-01-01

A procedure for the design and training of artificial neural networks, used for rapid and efficient controls and dynamics design and analysis for flexible space systems, has been developed. Artificial neural networks are employed, such that once properly trained, they provide a means of evaluating the impact of design changes rapidly. Specifically, two-layer feedforward neural networks are designed to approximate the functional relationship between the component/spacecraft design changes and measures of its performance or nonlinear dynamics of the system/components. A training algorithm, based on statistical sampling theory, is presented, which guarantees that the trained networks provide a designer-specified degree of accuracy in mapping the functional relationship. Within each iteration of this statistical-based algorithm, a sequential design algorithm is used for the design and training of the feedforward network to provide rapid convergence to the network goals. Here, at each sequence a new network is trained to minimize the error of previous network. The proposed method should work for applications wherein an arbitrary large source of training data can be generated. Two numerical examples are performed on a spacecraft application in order to demonstrate the feasibility of the proposed approach.

Application of Solid Phase Microextraction Coupled with Gas Chromatography/Mass Spectrometry as a Rapid Method for Field Sampling and Analysis of Chemical Warfare Agents and Toxic Industrial Chemicals

DTIC Science & Technology

2003-01-01

PHASE MICROEXTRACTION COUPLED WITH GAS CHROMATOGRAPHY/MASS SPECTROMETRY AS A RAPID METHOD FOR FIELD SAMPLING AND ANALYSIS OF CHEMICAL WARFARE AGENTS...SAMPLING AND ANALYSIS OF CHEMICAL WARFARE AGENTS AND TOXIC INDUSTRIAL CHEMICALS 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6...GAS CHROMATOGRAPHY/MASS SPECTROMETRY AS A RAPID METHOD FOR FIELD SAMPLING AND ANALYSIS OF CHEMICAL WARFARE AGENTS AND TOXIC INDUSTRIAL CHEMICALS

Rapid DNA Amplification Using a Battery-Powered Thin-Film Resistive Thermocycler

PubMed Central

Herold, Keith E.; Sergeev, Nikolay; Matviyenko, Andriy; Rasooly, Avraham

2010-01-01

Summary A prototype handheld, compact, rapid thermocycler was developed for multiplex analysis of nucleic acids in an inexpensive, portable configuration. Instead of the commonly used Peltier heating/cooling element, electric thin-film resistive heater and a miniature fan enable rapid heating and cooling of glass capillaries leading to a simple, low-cost Thin-Film Resistive Thermocycler (TFRT). Computer-based pulse width modulation control yields heating rates of 6–7 K/s and cooling rates of 5 K/s. The four capillaries are closely coupled to the heater, resulting in low power consumption. The energy required by a nominal PCR cycle (20 s at each temperature) was found to be 57 ± 2 J yielding an average power of approximately 1.0 W (not including the computer and the control system). Thus the device can be powered by a standard 9 V alkaline battery (or other 9 V power supply). The prototype TFRT was demonstrated (in a benchtop configuration) for detection of three important food pathogens (E. coli ETEC, Shigella dysenteriae, and Salmonella enterica). PCR amplicons were analyzed by gel electrophoresis. The 35 cycle PCR protocol using a single channel was completed in less then 18 min. Simple and efficient heating/cooling, low cost, rapid amplification, and low power consumption make the device suitable for portable DNA amplification applications including clinical point of care diagnostics and field use. PMID:19159110

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

PubMed

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

2016-02-01

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

Nano-volume drop patterning for rapid on-chip neuronal connect-ability assays.

PubMed

Petrelli, Alessia; Marconi, Emanuele; Salerno, Marco; De Pietri Tonelli, Davide; Berdondini, Luca; Dante, Silvia

2013-11-21

The ability of neurons to extend projections and to form physical connections among them (i.e., "connect-ability") is altered in several neuropathologies. The quantification of these alterations is an important read-out to investigate pathogenic mechanisms and for research and development of neuropharmacological therapies, however current morphological analysis methods are very time-intensive. Here, we present and characterize a novel on-chip approach that we propose as a rapid assay. Our approach is based on the definition on a neuronal cell culture substrate of discrete patterns of adhesion protein spots (poly-d-lysine, 23 ± 5 μm in diameter) characterized by controlled inter-spot separations of increasing distance (from 40 μm to 100 μm), locally adsorbed in an adhesion-repulsive agarose layer. Under these conditions, the connect-ability of wild type primary neurons from rodents is shown to be strictly dependent on the inter-spot distance, and can be rapidly documented by simple optical read-outs. Moreover, we applied our approach to identify connect-ability defects in neurons from a mouse model of 22q11.2 deletion syndrome/DiGeorge syndrome, by comparative trials with wild type preparations. The presented results demonstrate the sensitivity and reliability of this novel on-chip-based connect-ability approach and validate the use of this method for the rapid assessment of neuronal connect-ability defects in neuropathologies.

The frequency modulated auditory evoked response (FMAER), a technical advance for study of childhood language disorders: cortical source localization and selected case studies

PubMed Central

2013-01-01

Background Language comprehension requires decoding of complex, rapidly changing speech streams. Detecting changes of frequency modulation (FM) within speech is hypothesized as essential for accurate phoneme detection, and thus, for spoken word comprehension. Despite past demonstration of FM auditory evoked response (FMAER) utility in language disorder investigations, it is seldom utilized clinically. This report's purpose is to facilitate clinical use by explaining analytic pitfalls, demonstrating sites of cortical origin, and illustrating potential utility. Results FMAERs collected from children with language disorders, including Developmental Dysphasia, Landau-Kleffner syndrome (LKS), and autism spectrum disorder (ASD) and also normal controls - utilizing multi-channel reference-free recordings assisted by discrete source analysis - provided demonstratrions of cortical origin and examples of clinical utility. Recordings from inpatient epileptics with indwelling cortical electrodes provided direct assessment of FMAER origin. The FMAER is shown to normally arise from bilateral posterior superior temporal gyri and immediate temporal lobe surround. Childhood language disorders associated with prominent receptive deficits demonstrate absent left or bilateral FMAER temporal lobe responses. When receptive language is spared, the FMAER may remain present bilaterally. Analyses based upon mastoid or ear reference electrodes are shown to result in erroneous conclusions. Serial FMAER studies may dynamically track status of underlying language processing in LKS. FMAERs in ASD with language impairment may be normal or abnormal. Cortical FMAERs can locate language cortex when conventional cortical stimulation does not. Conclusion The FMAER measures the processing by the superior temporal gyri and adjacent cortex of rapid frequency modulation within an auditory stream. Clinical disorders associated with receptive deficits are shown to demonstrate absent left or bilateral responses. Serial FMAERs may be useful for tracking language change in LKS. Cortical FMAERs may augment invasive cortical language testing in epilepsy surgical patients. The FMAER may be normal in ASD and other language disorders when pathology spares the superior temporal gyrus and surround but presumably involves other brain regions. Ear/mastoid reference electrodes should be avoided and multichannel, reference free recordings utilized. Source analysis may assist in better understanding of complex FMAER findings. PMID:23351174

Ultrafast triggered transient energy storage by atomic layer deposition into porous silicon for integrated transient electronics

NASA Astrophysics Data System (ADS)

Douglas, Anna; Muralidharan, Nitin; Carter, Rachel; Share, Keith; Pint, Cary L.

2016-03-01

Here we demonstrate the first on-chip silicon-integrated rechargeable transient power source based on atomic layer deposition (ALD) coating of vanadium oxide (VOx) into porous silicon. A stable specific capacitance above 20 F g-1 is achieved until the device is triggered with alkaline solutions. Due to the rational design of the active VOx coating enabled by ALD, transience occurs through a rapid disabling step that occurs within seconds, followed by full dissolution of all active materials within 30 minutes of the initial trigger. This work demonstrates how engineered materials for energy storage can provide a basis for next-generation transient systems and highlights porous silicon as a versatile scaffold to integrate transient energy storage into transient electronics.Here we demonstrate the first on-chip silicon-integrated rechargeable transient power source based on atomic layer deposition (ALD) coating of vanadium oxide (VOx) into porous silicon. A stable specific capacitance above 20 F g-1 is achieved until the device is triggered with alkaline solutions. Due to the rational design of the active VOx coating enabled by ALD, transience occurs through a rapid disabling step that occurs within seconds, followed by full dissolution of all active materials within 30 minutes of the initial trigger. This work demonstrates how engineered materials for energy storage can provide a basis for next-generation transient systems and highlights porous silicon as a versatile scaffold to integrate transient energy storage into transient electronics. Electronic supplementary information (ESI) available: (i) Experimental details for ALD and material fabrication, ellipsometry film thickness, preparation of gel electrolyte and separator, details for electrochemical measurements, HRTEM image of VOx coated porous silicon, Raman spectroscopy for VOx as-deposited as well as annealed in air for 1 hour at 450 °C, SEM and transient behavior dissolution tests of uniformly coated VOx on porous silicon, dissolution tests for 0.1 M and 0.01 M NaOH trigger solutions, EIS analysis for VOx coated devices, and EDS compositional analysis of VOx. (ii) Video showing transient behavior of integrated VOx/porous silicon scaffolds. See DOI: 10.1039/c5nr09095d

Rapid Covalent Fluorescence Labeling of Membrane Proteins on Live Cells via Coiled-Coil Templated Acyl Transfer.

PubMed

Reinhardt, Ulrike; Lotze, Jonathan; Mörl, Karin; Beck-Sickinger, Annette G; Seitz, Oliver

2015-10-21

Fluorescently labeled proteins enable the microscopic imaging of protein localization and function in live cells. In labeling reactions targeted against specific tag sequences, the size of the fluorophore-tag is of major concern. The tag should be small to prevent interference with protein function. Furthermore, rapid and covalent labeling methods are desired to enable the analysis of fast biological processes. Herein, we describe the development of a method in which the formation of a parallel coiled coil triggers the transfer of a fluorescence dye from a thioester-linked coil peptide conjugate onto a cysteine-modified coil peptide. This labeling method requires only small tag sequences (max 23 aa) and occurs with high tag specificity. We show that size matching of the coil peptides and a suitable thioester reactivity allow the acyl transfer reaction to proceed within minutes (rather than hours). We demonstrate the versatility of this method by applying it to the labeling of different G-protein coupled membrane receptors including the human neuropeptide Y receptors 1, 2, 4, 5, the neuropeptide FF receptors 1 and 2, and the dopamine receptor 1. The labeled receptors are fully functional and able to bind the respective ligand with high affinity. Activity is not impaired as demonstrated by activation, internalization, and recycling experiments.

Dynamic infrared imaging analysis of apical hook development in Arabidopsis: the case of brassinosteroids.

PubMed

Smet, Dajo; Žádníková, Petra; Vandenbussche, Filip; Benková, Eva; Van Der Straeten, Dominique

2014-06-01

Germination of Arabidopsis seeds in darkness induces apical hook development, based on a tightly regulated differential growth coordinated by a multiple hormone cross-talk. Here, we endeavoured to clarify the function of brassinosteroids (BRs) and cross-talk with ethylene in hook development. An automated infrared imaging system was developed to study the kinetics of hook development in etiolated Arabidopsis seedlings. To ascertain the photomorphogenic control of hook opening, the system was equipped with an automatic light dimmer. We demonstrate that ethylene and BRs are indispensable for hook formation and maintenance. Ethylene regulation of hook formation functions partly through BRs, with BR feedback inhibition of ethylene action. Conversely, BR-mediated extension of hook maintenance functions partly through ethylene. Furthermore, we revealed that a short light pulse is sufficient to induce rapid hook opening. Our dynamic infrared imaging system allows high-resolution, kinetic imaging of up to 112 seedlings in a single experimental run. At this high throughput, it is ideally suited to rapidly gain insight in pathway networks. We demonstrate that BRs and ethylene cooperatively regulate apical hook development in a phase-dependent manner. Furthermore, we show that light is a predominant regulator of hook opening, inhibiting ethylene- and BR-mediated postponement of hook opening. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

Modeling and Test Data Analysis of a Tank Rapid Chill and Fill System for the Advanced Shuttle Upper Stage (ASUS) Concept

NASA Technical Reports Server (NTRS)

Flachbart, Robin; Hedayat, Ali; Holt, Kimberly A.; Cruit, Wendy (Technical Monitor)

2001-01-01

The Advanced Shuttle Upper Stage (ASUS) concept addresses safety concerns associated .with cryogenic stages by launching empty, and filling on ascent. The ASUS employs a rapid chill and fill concept. A spray bar is used to completely chill the tank before fill, allowing the vent valve to be closed during the fill process. The first tests of this concept, using a flight size (not flight weight) tank. were conducted at Marshall Space Flight Center (MSFC) during the summer of 2000. The objectives of the testing were to: 1) demonstrate that a flight size tank could be filled in roughly 5 minutes to accommodate the shuttle ascent window, and 2) demonstrate a no-vent fill of the tank. A total of 12 tests were conducted. Models of the test facility fill and vent systems, as well as the tank, were constructed. The objective of achieving tank fill in 5 minutes was met during the test series. However, liquid began to accumulate in the tank before it was chilled. Since the tank was not chilled until the end of each test, vent valve closure during fill was not possible. Even though the chill and fill process did not occur as expected, reasonable model correlation with the test data was achieved.

Rapid test by liquid chromatography/tandem mass spectrometry to evaluate equine urine reactivity towards 17beta-OH steroids.

PubMed

Fidani, Marco; Casagni, Eleonora; Montana, Marco; Pasello, Emanuela; Pecoraro, Chiara; Gambaro, Veniero

2006-01-01

Bacteria frequently found in equine urine samples may cause degradation of 17beta-OH steroids. A simple liquid chromatography/tandem mass spectrometry (LC/MS/MS) method has been developed to evaluate the microbiological contamination of equine urine as a marker of poor storage conditions. Norethandrolone was used as the internal standard, and the linearity, sensitivity, precision and accuracy of the method were evaluated. 17beta-OH oxidation was demonstrated for testosterone, nandrolone, trenbolone and boldenone, but did not occur in alpha-epimers such as alpha-boldenone and epitestosterone, demonstrating the stereoselectivity of the reaction. A rapid test was performed by spiking one of the four 17beta-OH steroids in samples of diluted equine urine. The steroids were transformed into their respective ketones in the presence of bacterial activity. The test allows direct injection of diluted samples into the LC/MS system, without the need for prior extraction. Results show that the best method of storage is freezing at -18 degrees C. Urine specimens should be analyzed as soon as possible after thawing. This allows bacterial degradation of equine urine to be arrested temporarily, so that the urine can be used for qualitative or quantitative analysis of 17beta-OH steroids.

A new unsteady mixing model to predict NO(x) production during rapid mixing in a dual-stage combustor

NASA Technical Reports Server (NTRS)

Menon, Suresh

1992-01-01

An advanced gas turbine engine to power supersonic transport aircraft is currently under study. In addition to high combustion efficiency requirements, environmental concerns have placed stringent restrictions on the pollutant emissions from these engines. A combustor design with the potential for minimizing pollutants such as NO(x) emissions is undergoing experimental evaluation. A major technical issue in the design of this combustor is how to rapidly mix the hot, fuel-rich primary zone product with the secondary diluent air to obtain a fuel-lean mixture for combustion in the second stage. Numerical predictions using steady-state methods cannot account for the unsteady phenomena in the mixing region. Therefore, to evaluate the effect of unsteady mixing and combustion processes, a novel unsteady mixing model is demonstrated here. This model has been used to study multispecies mixing as well as propane-air and hydrogen-air jet nonpremixed flames, and has been used to predict NO(x) production in the mixing region. Comparison with available experimental data show good agreement, thereby providing validation of the mixing model. With this demonstration, this mixing model is ready to be implemented in conjunction with steady-state prediction methods and provide an improved engineering design analysis tool.

One step DNA assembly for combinatorial metabolic engineering.

PubMed

Coussement, Pieter; Maertens, Jo; Beauprez, Joeri; Van Bellegem, Wouter; De Mey, Marjan

2014-05-01

The rapid and efficient assembly of multi-step metabolic pathways for generating microbial strains with desirable phenotypes is a critical procedure for metabolic engineering, and remains a significant challenge in synthetic biology. Although several DNA assembly methods have been developed and applied for metabolic pathway engineering, many of them are limited by their suitability for combinatorial pathway assembly. The introduction of transcriptional (promoters), translational (ribosome binding site (RBS)) and enzyme (mutant genes) variability to modulate pathway expression levels is essential for generating balanced metabolic pathways and maximizing the productivity of a strain. We report a novel, highly reliable and rapid single strand assembly (SSA) method for pathway engineering. The method was successfully optimized and applied to create constructs containing promoter, RBS and/or mutant enzyme libraries. To demonstrate its efficiency and reliability, the method was applied to fine-tune multi-gene pathways. Two promoter libraries were simultaneously introduced in front of two target genes, enabling orthogonal expression as demonstrated by principal component analysis. This shows that SSA will increase our ability to tune multi-gene pathways at all control levels for the biotechnological production of complex metabolites, achievable through the combinatorial modulation of transcription, translation and enzyme activity. Copyright © 2014 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

The continued promise of stem cell therapy in regenerative medicine.

PubMed

Eve, David J

2011-12-01

The use of stem cells is galvanizing regenerative medicine research. An analysis of recent trends as typified by articles published between 2009 and 2010 in the journals Cell Transplantation--The Regenerative Medicine Journal and Medical Science Monitor demonstrate the increasing importance of stem cell research as being on the cutting edge of regenerative medicine research. The analysis revealed an even split between transplantation and non-transplantation studies, showing that both the applicability and general research is being pursued. New methods and tissue engineering are also highly important components of regenerative medicine as demonstrated by a number of the stem cell studies being involved with either ex vivo manipulation, or cotransplantation with other cells or biomaterials. This suggests that the best results may be achieved with adjuvant therapies. The non-transplantation studies were more focused on manipulation of transplantable agents including cells and scaffold systems, as well as the use of medicines and dietary supplements. The further elucidation of disease mechanisms was a major contribution. This analysis suggests that regenerative medicine is proceeding at a rapid pace and the next few years should be of considerable interest with the initial results of pioneering stem cell therapies being announced.

The application of neural networks to myoelectric signal analysis: a preliminary study.

PubMed

Kelly, M F; Parker, P A; Scott, R N

1990-03-01

Two neural network implementations are applied to myoelectric signal (MES) analysis tasks. The motivation behind this research is to explore more reliable methods of deriving control for multidegree of freedom arm prostheses. A discrete Hopfield network is used to calculate the time series parameters for a moving average MES model. It is demonstrated that the Hopfield network is capable of generating the same time series parameters as those produced by the conventional sequential least squares (SLS) algorithm. Furthermore, it can be extended to applications utilizing larger amounts of data, and possibly to higher order time series models, without significant degradation in computational efficiency. The second neural network implementation involves using a two-layer perceptron for classifying a single site MES based on two features, specifically the first time series parameter, and the signal power. Using these features, the perceptron is trained to distinguish between four separate arm functions. The two-dimensional decision boundaries used by the perceptron classifier are delineated. It is also demonstrated that the perceptron is able to rapidly compensate for variations when new data are incorporated into the training set. This adaptive quality suggests that perceptrons may provide a useful tool for future MES analysis.

Blinded study determination of high sensitivity and specificity microchip electrophoresis-SSCP/HA to detect mutations in the p53 gene.

PubMed

Hestekin, Christa N; Lin, Jennifer S; Senderowicz, Lionel; Jakupciak, John P; O'Connell, Catherine; Rademaker, Alfred; Barron, Annelise E

2011-11-01

Knowledge of the genetic changes that lead to disease has grown and continues to grow at a rapid pace. However, there is a need for clinical devices that can be used routinely to translate this knowledge into the treatment of patients. Use in a clinical setting requires high sensitivity and specificity (>97%) in order to prevent misdiagnoses. Single-strand conformational polymorphism (SSCP) and heteroduplex analysis (HA) are two DNA-based, complementary methods for mutation detection that are inexpensive and relatively easy to implement. However, both methods are most commonly detected by slab gel electrophoresis, which can be labor-intensive, time-consuming, and often the methods are unable to produce high sensitivity and specificity without the use of multiple analysis conditions. Here, we demonstrate the first blinded study using microchip electrophoresis (ME)-SSCP/HA. We demonstrate the ability of ME-SSCP/HA to detect with 98% sensitivity and specificity >100 samples from the p53 gene exons 5-9 in a blinded study in an analysis time of <10 min. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Identification of pulmonary edema in forensic autopsy cases of fatal anaphylactic shock using Fourier transform infrared microspectroscopy.

PubMed

Lin, Hancheng; Luo, Yiwen; Wang, Lei; Deng, Kaifei; Sun, Qiran; Fang, Ruoxi; Wei, Xin; Zha, Shuai; Wang, Zhenyuan; Huang, Ping

2018-03-01

Anaphylaxis is a rapid allergic reaction that may cause sudden death. Currently, postmortem diagnosis of anaphylactic shock is sometimes difficult and often achieved through exclusion. The aim of our study was to investigate whether Fourier transform infrared (FTIR) microspectroscopy combined with pattern recognition methods would be complementary to traditional methods and provide a more accurate postmortem diagnosis of fatal anaphylactic shock. First, the results of spectral peak area analysis showed that the pulmonary edema fluid of the fatal anaphylactic shock group was richer in protein components than the control group, which included mechanical asphyxia, brain injury, and acute cardiac death. Subsequently, principle component analysis (PCA) was performed and showed that the anaphylactic shock group contained more turn and α-helix protein structures as well as less tyrosine-rich proteins than the control group. Ultimately, a partial least-square discriminant analysis (PLS-DA) model combined with a variables selection method called the genetic algorithm (GA) was built and demonstrated good separation between these two groups. This pilot study demonstrates that FTIR microspectroscopy has the potential to be an effective aid for postmortem diagnosis of fatal anaphylactic shock.

A Semi-Automatic Method for Image Analysis of Edge Dynamics in Living Cells

PubMed Central

Huang, Lawrence; Helmke, Brian P.

2011-01-01

Spatial asymmetry of actin edge ruffling contributes to the process of cell polarization and directional migration, but mechanisms by which external cues control actin polymerization near cell edges remain unclear. We designed a quantitative image analysis strategy to measure the spatiotemporal distribution of actin edge ruffling. Time-lapse images of endothelial cells (ECs) expressing mRFP-actin were segmented using an active contour method. In intensity line profiles oriented normal to the cell edge, peak detection identified the angular distribution of polymerized actin within 1 µm of the cell edge, which was localized to lamellipodia and edge ruffles. Edge features associated with filopodia and peripheral stress fibers were removed. Circular statistical analysis enabled detection of cell polarity, indicated by a unimodal distribution of edge ruffles. To demonstrate the approach, we detected a rapid, nondirectional increase in edge ruffling in serum-stimulated ECs and a change in constitutive ruffling orientation in quiescent, nonpolarized ECs. Error analysis using simulated test images demonstrate robustness of the method to variations in image noise levels, edge ruffle arc length, and edge intensity gradient. These quantitative measurements of edge ruffling dynamics enable investigation at the cellular length scale of the underlying molecular mechanisms regulating actin assembly and cell polarization. PMID:21643526

Demonstration of rapid and sensitive module leak certification for space station freedom. Final report

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

Dietz, R.N.; Goodrich, R.W.

1991-03-01

A leak detection and quantification demonstration using perflurocarbon tracer (PFT) technology was successfully performed at the NASA Marshall Space Flight Center on January 25, 1991. The real-time Dual Trap Analyzer (DTA) at one-half hour after the start of the first run gave an estimated leak rate of 0.7 mL/min. This has since been refined to be 1.15 {plus_minus} 0.09 mL/min. The leak rates in the next three runs were determined to be 9.8 {plus_minus} 0.7, {minus}0.4 {plus_minus} 0.3, and 76 {plus_minus} 6 mL/min, respectively. The theory on leak quantification in the steady-state and time-dependent modes for a single zone testmore » facility was developed and applied to the above determinations. The laboratory PFT analysis system gave a limit-of-detection (LOD) of 0.05 fL for ocPDCH. This is the tracer of choice and is about 100-fold better than that for the DTA. Applied to leak certification, the LOD is about 0.00002 mL/s (0.000075 L/h), a 5 order-of-magnitude improvement over the original leak certification specification. Furthermore, this limit can be attained in a measurement period of 3 to 4 hours instead of days, weeks, or months. A new Leak Certification Facility is also proposed to provide for zonal (three zones) determination of leak rates. The appropriate multizone equations, their solutions, and error analysis have already been derived. A new concept of seal-integrity certification has been demonstrated for a variety of controlled leaks in the range of module leak testing. High structural integrity leaks were shown to have a linear dependence of flow on {Delta}p. The rapid determination of leak rates at different pressures is proposed and is to be determined while subjecting the module to other external force-generating parameters such as vibration, torque, solar intensity, etc. 13 refs.« less

Demonstration of rapid and sensitive module leak certification for space station freedom

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

Dietz, R.N.; Goodrich, R.W.

1991-03-01

A leak detection and quantification demonstration using perflurocarbon tracer (PFT) technology was successfully performed at the NASA Marshall Space Flight Center on January 25, 1991. The real-time Dual Trap Analyzer (DTA) at one-half hour after the start of the first run gave an estimated leak rate of 0.7 mL/min. This has since been refined to be 1.15 {plus minus} 0.09 mL/min. The leak rates in the next three runs were determined to be 9.8 {plus minus} 0.7, {minus}0.4 {plus minus} 0.3, and 76 {plus minus} 6 mL/min, respectively. The theory on leak quantification in the steady-state and time-dependent modes formore » a single zone test facility was developed and applied to the above determinations. The laboratory PFT analysis system gave a limit-of-detection (LOD) of 0.05 fL for ocPDCH. This is the tracer of choice and is about 100-fold better than that for the DTA. Applied to leak certification, the LOD is about 0.00002 mL/s (0.000075 L/h), a 5 order-of-magnitude improvement over the original leak certification specification. Furthermore, this limit can be attained in a measurement period of 3 to 4 hours instead of days, weeks, or months. A new Leak Certification Facility is also proposed to provide for zonal (three zones) determination of leak rates. The appropriate multizone equations, their solutions, and error analysis have already been derived. A new concept of seal-integrity certification has been demonstrated for a variety of controlled leaks in the range of module leak testing. High structural integrity leaks were shown to have a linear dependence of flow on {Delta}p. The rapid determination of leak rates at different pressures is proposed and is to be determined while subjecting the module to other external force-generating parameters such as vibration, torque, solar intensity, etc. 13 refs.« less

Demonstration of rapid and sensitive module leak certification for Space Station Freedom

NASA Technical Reports Server (NTRS)

Dietz, R. N.; Goodrich, R. W.

1991-01-01

A leak detection and quantification demonstration using perflurocarbon tracer (PFT) technology was successfully performed at the NASA Marshall Space Flight Center on January 25, 1991. The real-time Dual Trap Analyzer (DTA) at one-half hour after the start of the first run gave an estimated leak rate of 0.7 mL/min. This has since been refined to be 1.15 (+ or -) 0.09 mL/min. The leak rates in the next three runs were determined to be 9.8 (+ or -) 0.7, -0.4 (+ or -) 0.3, and 76 (+ or -) 6 mL/min, respectively. The theory on leak quantification in the steady-state and time-dependent modes for a single zone test facility was developed and applied to the above determinations. The laboratory PFT analysis system gave a limit-of-detection (LOD) of 0.05 fL for ocPDCH. This is the tracer of choice and is about 100-fold better than that for the DTA. Applied to leak certification, the LOD is about 0.00002 mL/s (0.000075 L/h), a 5 order-of-magnitude improvement over the original leak certification specification. Furthermore, this limit can be attained in a measurement period of 3 to 4 hours instead of days, weeks, or months. A new Leak Certification Facility is also proposed to provide for zonal (three zones) determination of leak rates. The appropriate multizone equations, their solutions, and error analysis have already been derived. A new concept of seal-integrity certification has been demonstrated for a variety of controlled leaks in the range of module leak testing. High structural integrity leaks were shown to have a linear dependence of flow on (Delta)p. The rapid determination of leak rates at different pressures is proposed and is to be determined while subjecting the module to other external force-generating parameters such as vibration, torque, solar intensity, etc.

Technology Demonstration: Acoustic Condition Assessment of Wastewater Collection Systems

EPA Science Inventory

The overall objective of this EPA-funded study was to demonstrate innovative sewer line assessment technologies that are designed for rapid deployment using portable equipment. This study focused on demonstration of technologies that are suitable for smaller diameter pipes (less ...

Demonstration of Innovative Sewer System Inspection Technology: SL-RAT

EPA Science Inventory

The overall objective of this EPA-funded study was to demonstrate innovative sewer line assessment technologies that are designed for rapid deployment using portable equipment. This study focused on demonstration of technologies that are suitable for smaller diameter pipes (less ...

Rapid stabilization of thawing soils For enhanced vehicle mobility: a field demonstration project

DOT National Transportation Integrated Search

1999-02-01

Thawing soil presents a formidable challenge for vehicle operations cross-country and on unsurfaced roads. To mitigate the problem, a variety of stabilization techniques were evaluated for their suitability for rapid employment to enhance military ve...

DEMONSTRATION BULLETIN: RAPID OPTICAL SCREEN TOOL (ROST™) - LORAL CORPORATION

EPA Science Inventory

The Loral Rapid Optical Screen Tool (ROST™) is a tunable dye laser system used for the detection of petroleum, semi-volatile, and some volatile organic compounds in soils. The technology is used in conjunction with a cone penetrometer (CP).

Air-launched GPR evaluation for rapid assessment of MoDOT bridge decks.

DOT National Transportation Integrated Search

2014-08-01

The overarching goal of this study is to demonstrate that advanced nondestructive testing/evaluation (NDT/NDE) techniques can be rapidly, effectively, and economically implemented as part of routine MoDOT bridge deck surveys to determine the general ...

Cost Analysis of Implementing Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Plus Real-Time Antimicrobial Stewardship Intervention for Bloodstream Infections

PubMed Central

Patel, Twisha S.; Kaakeh, Rola; Nagel, Jerod L.; Newton, Duane W.

2016-01-01

ABSTRACT Studies evaluating rapid diagnostic testing plus stewardship intervention have consistently demonstrated improved clinical outcomes for patients with bloodstream infections. However, the cost of implementing new rapid diagnostic testing can be significant, and such testing usually does not generate additional revenue. There are minimal data evaluating the impact of adding matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) for rapid organism identification and dedicating pharmacy stewardship personnel time on the total hospital costs. A cost analysis was performed utilizing patient data generated from the hospital cost accounting system and included additional costs of MALDI-TOF equipment, supplies and personnel, and dedicated pharmacist time for blood culture review and of making interventions to antimicrobial therapy. The cost analysis was performed from a hospital perspective for 3-month blocks before and after implementation of MALDI-TOF plus stewardship intervention. A total of 480 patients with bloodstream infections were included in the analysis: 247 in the preintervention group and 233 in the intervention group. Thirty-day mortality was significantly improved in the intervention group (12% versus 21%, P < 0.01), and the mean length of stay was reduced, although the difference was not statistically significant (13.0 ± 16.5 days versus 14.2 ± 16.7 days, P = 0.44). The total hospital cost per bloodstream infection was lower in the intervention group ($42,580 versus $45,019). Intensive care unit cost per bloodstream infection accounted for the largest share of the total costs in each group and was also lower in the intervention group ($10,833 versus $13,727). Implementing MALDI-TOF plus stewardship review and intervention decreased mortality for patients with bloodstream infections. Despite the additional costs of implementing MALDI-TOF and of dedicating pharmacy stewardship personnel time to interventions, the total hospital costs decreased by $2,439 per bloodstream infection, for an approximate annual cost savings of $2.34 million. PMID:27795335

Demonstration and Validation of a Portable Raman Sensor for In-Situ Detection and Monitoring of Perchlorate (ClO 4 -)

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

Hatzinger, Paul B.; Eres, Gyula; Gu, Baohua

Costs for environmental analysis and monitoring are increasing at a rapid rate and represent a significant percentage of the total and future remedial expenses at many U.S. Department of Defense (DoD) contaminated sites. It has been reported that about 30 to 40% of the remediation budget is usually spent on long-term monitoring (LTM), of which a large percentage represents laboratory analytical costs. Energetics such as perchlorate (ClO 4 -) are among the most frequently detected contaminants in groundwater and surface water at or near military installations due to their persistence and mobility. Currently, the standard protocol entails collecting samples inmore » the field, packaging them, and shipping them overnight to a designated laboratory for analysis. This process requires significant sample preparation and handling, and analytical results may not be available for several days to weeks. In this project, we developed and demonstrated a portable Raman sensor based on surface enhanced Raman scattering (SERS) technology to detect ClO 4 - in contaminated water. We summarize major accomplishments as follows: • A SERS sensor based on elevated gold (Au) nano-ellipse dimer architectures was designed and developed for ClO 4 - with a detection limit of ~10 -6 M (or 100 μg/L); The performance of these sensors was evaluated and optimized through variation of their geometric characteristics (i.e., dimer aspect ratio, dimer separation, etc.). • Large-scale commercial production of SERS substrate sensors via nanoimprinting by Nanova Inc. and Nanoimprint lithography (NIL) technology was successfully demonstrated. This is a substantial step forward toward the commercialization of the SERS sensors and may potentially lead to significantly reduced fabrication costs of SERS substrates. • Commercially produced SERS sensors were demonstrated to detect ClO 4 - at levels above 10 -6 M using a portable Raman analyzer. The performance of the commercial SERS sensors for ClO 4 - detection in the presence and absence of interferences was determined for a series of standard solutions. Sulfate (SO 4 2-) was found to exhibit the greatest interference for the anions tested, which included Cl-, NO 3 -, and SO 4 2-. • Field demonstration of the portable Raman sensor with commercially produced SERS substrates was completed at two Department of Defense (DoD) sites; twice at the Indian Head Naval Surface Warfare Center, Indian Head, MD, and once at Redstone Arsenal, Huntsville, AL. Multiple wells were sampled at both DoD sites, where a standard addition method was employed using the sensor to determine the ClO 4 -4 - and possibly other energetics that are both important for environmental monitoring and of interest for national security. However, we point out that SERS technology is also prone to interferences due to its sensitivity and responses to other ionic species, such as NO 3 -, SO 4 2-, and dissolved organics or co-contaminants present in the groundwater, which could potentially mask the SERS signal of the target analyte (i.e., ClO 4 -). As such, SERS analysis was subject to significant variations (e.g., ±20% or more), and its detection limit for ClO 4 --8 M) and was substantially higher than what we anticipated from laboratory studies. However, despite these complications, the portable Raman sensor developed in this project could be used as a rapid screening tool for ClO 4 - at concentrations above 10 -6 M. Future studies are warranted to further develop the technology and to optimize its performance, and eventually to bring the technology to the market. With additional development and demonstration, the sensor has the potential to reduce analytical costs by eliminating shipping and typical costs associated with laboratory analysis. A cost savings of 30–45% may be realized during a typical sampling event and, more importantly, the technology could allow rapid turn-around of information to decision makers for site characterization and remediation.« less

Multicomponent quantitative spectroscopic analysis without reference substances based on ICA modelling.

PubMed

Monakhova, Yulia B; Mushtakova, Svetlana P

2017-05-01

A fast and reliable spectroscopic method for multicomponent quantitative analysis of targeted compounds with overlapping signals in complex mixtures has been established. The innovative analytical approach is based on the preliminary chemometric extraction of qualitative and quantitative information from UV-vis and IR spectral profiles of a calibration system using independent component analysis (ICA). Using this quantitative model and ICA resolution results of spectral profiling of "unknown" model mixtures, the absolute analyte concentrations in multicomponent mixtures and authentic samples were then calculated without reference solutions. Good recoveries generally between 95% and 105% were obtained. The method can be applied to any spectroscopic data that obey the Beer-Lambert-Bouguer law. The proposed method was tested on analysis of vitamins and caffeine in energy drinks and aromatic hydrocarbons in motor fuel with 10% error. The results demonstrated that the proposed method is a promising tool for rapid simultaneous multicomponent analysis in the case of spectral overlap and the absence/inaccessibility of reference materials.

Optimal subinterval selection approach for power system transient stability simulation

DOE PAGES

Kim, Soobae; Overbye, Thomas J.

2015-10-21

Power system transient stability analysis requires an appropriate integration time step to avoid numerical instability as well as to reduce computational demands. For fast system dynamics, which vary more rapidly than what the time step covers, a fraction of the time step, called a subinterval, is used. However, the optimal value of this subinterval is not easily determined because the analysis of the system dynamics might be required. This selection is usually made from engineering experiences, and perhaps trial and error. This paper proposes an optimal subinterval selection approach for power system transient stability analysis, which is based on modalmore » analysis using a single machine infinite bus (SMIB) system. Fast system dynamics are identified with the modal analysis and the SMIB system is used focusing on fast local modes. An appropriate subinterval time step from the proposed approach can reduce computational burden and achieve accurate simulation responses as well. As a result, the performance of the proposed method is demonstrated with the GSO 37-bus system.« less

HC StratoMineR: A Web-Based Tool for the Rapid Analysis of High-Content Datasets.

PubMed

Omta, Wienand A; van Heesbeen, Roy G; Pagliero, Romina J; van der Velden, Lieke M; Lelieveld, Daphne; Nellen, Mehdi; Kramer, Maik; Yeong, Marley; Saeidi, Amir M; Medema, Rene H; Spruit, Marco; Brinkkemper, Sjaak; Klumperman, Judith; Egan, David A

2016-10-01

High-content screening (HCS) can generate large multidimensional datasets and when aligned with the appropriate data mining tools, it can yield valuable insights into the mechanism of action of bioactive molecules. However, easy-to-use data mining tools are not widely available, with the result that these datasets are frequently underutilized. Here, we present HC StratoMineR, a web-based tool for high-content data analysis. It is a decision-supportive platform that guides even non-expert users through a high-content data analysis workflow. HC StratoMineR is built by using My Structured Query Language for storage and querying, PHP: Hypertext Preprocessor as the main programming language, and jQuery for additional user interface functionality. R is used for statistical calculations, logic and data visualizations. Furthermore, C++ and graphical processor unit power is diffusely embedded in R by using the rcpp and rpud libraries for operations that are computationally highly intensive. We show that we can use HC StratoMineR for the analysis of multivariate data from a high-content siRNA knock-down screen and a small-molecule screen. It can be used to rapidly filter out undesirable data; to select relevant data; and to perform quality control, data reduction, data exploration, morphological hit picking, and data clustering. Our results demonstrate that HC StratoMineR can be used to functionally categorize HCS hits and, thus, provide valuable information for hit prioritization.

Nonlethal evaluation of the physiological health of unionid mussels: Method for biopsy and glycogen analysis

USGS Publications Warehouse

Naimo, T.J.; Damschen, E.D.; Rada, R.G.; Monroe, E.M.

1998-01-01

In long-lived unionid mussels, many short-term measures of growth are of limited value. Changes in physiological condition may be an early indication of stress, because the increased energy demand associated with stress often results in a depletion of glycogen reserves, the principal storage form of carbohydrates in unionid mussels. Our goal was to nonlethally extract tissue from freshwater mussels and then to develop a rapid and dependable method for the analysis of glycogen in the tissue extracts. A biopsy technique was developed to remove between 5 and 10 mg of food tissue in Amblema plicata plicata. The survival rate did not differ between biopsied and non-biopsied mussels during a 581-d observation period, demonstrating that the biopsy technique will allow nonlethal evaluation of the physiological condition of individual mussels through measurement of changes in contaminant, genetic, and biochemical indicators in tissue. We also modified the standard alkaline digestion and phenol-sulfuric acid analysis of glycogen for use on the small samples of biopsied tissue and to reduce analysis time and cost. We present quality control data, including method detection limits and estimates of precision and bias. The modified analytical method is rapid and accurate and has a method detection limit of 0.014 mg glycogen. Glycogen content in the biopsied samples was well above the method detection limit; it ranged from 0.09 to 0.36 mg, indicating that the method should be applicable to native mussels.

Quantitative analysis of essential oils of Thymus daenensis using laser-induced fluorescence and Raman spectroscopy.

PubMed

Khoshroo, H; Khadem, H; Bahreini, M; Tavassoli, S H; Hadian, J

2015-11-10

Laser-induced fluorescence and Raman spectroscopy are used for the investigation of different genotypes of Thymus daenensis native to the Ilam province of Iran. Different genotypes of T. daenensis essential oils, labeled T1 through T7, possess slight differences with regard to the composition of the thymol. The gas chromatography-mass spectrometry (GC-MS) method is performed to determine the concentration of each constituent as a reference method. The Raman spectra of different concentrations of pure thymol dissolved in hexane as standard samples are obtained via a laboratory prototype Raman spectroscopy setup for the calculation of the calibration curve. The regression coefficient and limit of detection are calculated. The possibility of the differentiation of different genotypes of T. daenensis is also examined by laser-induced fluorescence spectroscopy, although we do not know the exact amounts of their components. All the fluorescence spectral information is used jointly by cluster analysis to differentiate between 7 genotypes. Our results demonstrate the acceptable precision of Raman spectroscopy with GC-MS and corroborate the capacity of Raman spectroscopy in applications in the quantitative analysis field. Furthermore, the cluster analysis results show that laser-induced fluorescence spectroscopy is an acceptable technique for the rapid classification of different genotypes of T. daenensis without having any previous information of their exact amount of constituents. So, the ability to rapidly and nondestructively differentiate between genotypes makes it possible to efficiently select high-quality herbs from many samples.

The efficacy of dexamethasone reducing postoperative pain and emesis after total knee arthroplasty: A systematic review and meta-analysis.

PubMed

Fan, Zhengrui; Ma, Jianxiong; Kuang, Mingjie; Zhang, Lukai; Han, Biao; Yang, Baocheng; Wang, Ying; Ma, Xinlong

2018-04-01

Total knee arthroplasty (TKA) is gradually emerging as the treatment of choice for end-stage osteoarthritis. In the past, Perioperative dexamethasone treatment is still a controversial subject in total knee arthroplasty. Therefore, we write this systematic review and meta-analysis to evaluate the efficacy of dexamethasone on pain and recovery after Total knee Arthroplasty. Embase, Pubmed, and Cochrane Library were comprehensively searched. Randomized controlled trials, cohort studies were included in our meta-analysis. Eight studies that compared dexamethasone groups with placebo groups were included in our meta-analysis. The research was reported according to the preferred reporting items for systematic reviews and meta-analysis (PRISMA) guidelines. Randomized controlled trials were included in our meta-analysis. Our study demonstrated that the dexamethasone group was more effective than the placebo group in term of VAS score at 24 h(P < 0.00001), 48 h(P = 0.0002); Opioid consumption (P < 0.00001); postoperative nausea (P < 0.00001); and Inflammatory factors of CPR at 24 h (P = 0.003). Our meta-analysis demonstrated that dexamethasone decreased postoperative pain, the incidence of POVN, and total opioid consumption effectively which played a critical role in rapid recovery to TKA. However, we still need large sample size, high quality studies to explore the relationship between complications and dose response to give the final conclusion. Copyright © 2018. Published by Elsevier Ltd.

A nanosecond pulsed laser heating system for studying liquid and supercooled liquid films in ultrahigh vacuum

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

Xu, Yuntao; Dibble, Collin J.; Petrik, Nikolay G.

2016-04-26

A pulsed laser heating system has been developed that enables investigations of the dynamics and kinetics of nanoscale liquid films and liquid/solid interfaces on the nanosecond timescale in ultrahigh vacuum (UHV). Details of the design, implementation and characterization of a nanosecond pulsed laser system for transiently heating nanoscale films are described. Nanosecond pulses from a Nd:YAG laser are used to rapidly heat thin films of adsorbed water or other volatile materials on a clean, well-characterized Pt(111) crystal in UHV. Heating rates of ~1010 K/s for temperature increases of ~100 – 200 K are obtained. Subsequent rapid cooling (~5 × 109more » K/s) quenches the film, permitting in-situ, post-mortem analysis using a variety of surface science techniques. Lateral variations in the laser pulse energy are ~ ± 3% leading to a temperature uncertainty of ~ ± 5 K for a temperature jump of 200 K. Initial experiments with the apparatus demonstrate that crystalline ice films initially held at 90 K can be rapidly transformed into liquid water films with T > 273 K. No discernable recrystallization occurs during the rapid cooling back to cryogenic temperatures. In contrast, amorphous solid water films heated below the melting point rapidly crystallize. The nanosecond pulsed laser heating system can prepare nanoscale liquid and supercooled liquid films that persist for nanoseconds per heat pulse in an UHV environment, enabling experimental studies of a wide range of phenomena in liquids and at liquid/solid interfaces.« less

Telomere dynamics in an immortal human cell line.

PubMed Central

Murnane, J P; Sabatier, L; Marder, B A; Morgan, W F

1994-01-01

The integration of transfected plasmid DNA at the telomere of chromosome 13 in an immortalized simian virus 40-transformed human cell line provided the first opportunity to study polymorphism in the number of telomeric repeat sequences on the end of a single chromosome. Three subclones of this cell line were selected for analysis: one with a long telomere on chromosome 13, one with a short telomere, and one with such extreme polymorphism that no distinct band was discernible. Further subcloning demonstrated that telomere polymorphism resulted from both gradual changes and rapid changes that sometimes involved many kilobases. The gradual changes were due to the shortening of telomeres at a rate similar to that reported for telomeres of somatic cells without telomerase, eventually resulting in the loss of nearly all of the telomere. However, telomeres were not generally lost completely, as shown by the absence of polymorphism in the subtelomeric plasmid sequences. Instead, telomeres that were less than a few hundred base pairs in length showed a rapid, highly heterogeneous increase in size. Rapid changes in telomere length also occurred on longer telomeres. The frequency of this type of change in telomere length varied among the subclones and correlated with chromosome fusion. Therefore, the rapid changes in telomere length appeared occasionally to result in the complete loss of telomeric repeat sequences. Rapid changes in telomere length have been associated with telomere loss and chromosome instability in yeast and could be responsible for the high rate of chromosome fusion observed in many human tumor cell lines. Images PMID:7957062

A nanosecond pulsed laser heating system for studying liquid and supercooled liquid films in ultrahigh vacuum.

PubMed

Xu, Yuntao; Dibble, Collin J; Petrik, Nikolay G; Smith, R Scott; Joly, Alan G; Tonkyn, Russell G; Kay, Bruce D; Kimmel, Greg A

2016-04-28

A pulsed laser heating system has been developed that enables investigations of the dynamics and kinetics of nanoscale liquid films and liquid/solid interfaces on the nanosecond time scale in ultrahigh vacuum (UHV). Details of the design, implementation, and characterization of a nanosecond pulsed laser system for transiently heating nanoscale films are described. Nanosecond pulses from a Nd:YAG laser are used to rapidly heat thin films of adsorbed water or other volatile materials on a clean, well-characterized Pt(111) crystal in UHV. Heating rates of ∼10(10) K/s for temperature increases of ∼100-200 K are obtained. Subsequent rapid cooling (∼5 × 10(9) K/s) quenches the film, permitting in-situ, post-heating analysis using a variety of surface science techniques. Lateral variations in the laser pulse energy are ∼±2.7% leading to a temperature uncertainty of ∼±4.4 K for a temperature jump of 200 K. Initial experiments with the apparatus demonstrate that crystalline ice films initially held at 90 K can be rapidly transformed into liquid water films with T > 273 K. No discernable recrystallization occurs during the rapid cooling back to cryogenic temperatures. In contrast, amorphous solid water films heated below the melting point rapidly crystallize. The nanosecond pulsed laser heating system can prepare nanoscale liquid and supercooled liquid films that persist for nanoseconds per heat pulse in an UHV environment, enabling experimental studies of a wide range of phenomena in liquids and at liquid/solid interfaces.

Atrial Fibrillation Pacing Decreases Intravascular Shear Stress in a New Zealand White Rabbit Model: Implications in Endothelial Function

PubMed Central

Jen, Nelson; Yu, Fei; Lee, Juhyun; Wasmund, Steve; Dai, Xiaohu; Chen, Christina; Chawareeyawong, Pai; Yang, Yongmo; Li, Rongsong; Hamdan, Mohamed H.; Hsiai, Tzung

2012-01-01

Atrial fibrillation (AF) is characterized by multiple rapid and irregular atrial depolarization leading to rapid ventricular responses exceeding 100 beats per minute (bpm). We hypothesized that rapid and irregular pacing reduced intravascular shear stress (ISS) with implication to modulating endothelial responses. To simulate AF, we paced the left atrial appendage of New Zealand White (NZW) rabbits (n=4) at rapid and irregular intervals. Surface electrical cardiograms (ECG) were recorded for atrial and ventricular rhythm, and intravascular convective heat transfer was measured by micro thermal sensors, from which ISS was inferred. Rapid and irregular pacing decreased arterial systolic and diastolic pressures (baseline: 99/75 mmHg; rapid regular pacing: 92/73; rapid irregular pacing: 90/68; P < 0.001, n=4), temporal gradients (∂τ/∂t from 1275 ± 80 to 1056 ± 180 dyne/cm2·s), and reduced ISS (from baseline at 32.0 ± 2.4 to 22.7 ± 3.5 dyne/cm2). Computational fluid dynamics (CFD) code demonstrated that experimentally inferred ISS provided a close approximation to the computed wall shear stress (WSS) at a given catheter to vessel diameter ratio, shear stress range, and catheter position. In an in vitro flow system in which time-averaged shear stress was maintained at τavg=23 ±4 dyn·cm−2·s−1, we further demonstrated that rapid pulse rates at 150 bpm down-regulated endothelial nitric oxide (NO), promoted superoxide (O2·−) production, and increased monocyte binding to endothelial cells. These findings suggest that rapid pacing reduces ISS and ∂τ/∂t, and rapid pulse rates modulate endothelial responses. PMID:22983703

Circular states of atomic hydrogen

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

Lutwak, R.; Holley, J.; Chang, P.P.

1997-08-01

We describe the creation of circular states of hydrogen by adiabatic transfer of a Rydberg state in crossed electric and magnetic fields, and also by adiabatic passage in a rotating microwave field. The latter method permits rapid switching between the two circular states of a given n manifold. The two methods are demonstrated experimentally, and results are presented of an analysis of the field ionization properties of the circular states. An application for the circular states is illustrated by millimeter-wave resonance in hydrogen of the n=29{r_arrow}n=30 transition. {copyright} {ital 1997} {ital The American Physical Society}

Irregularity, volatility, risk, and financial market time series

PubMed Central

Pincus, Steve; Kalman, Rudolf E.

2004-01-01

The need to assess subtle, potentially exploitable changes in serial structure is paramount in the analysis of financial data. Herein, we demonstrate the utility of approximate entropy (ApEn), a model-independent measure of sequential irregularity, toward this goal, by several distinct applications. We consider both empirical data and models, including composite indices (Standard and Poor's 500 and Hang Seng), individual stock prices, the random-walk hypothesis, and the Black–Scholes and fractional Brownian motion models. Notably, ApEn appears to be a potentially useful marker of system stability, with rapid increases possibly foreshadowing significant changes in a financial variable. PMID:15358860

NASA advanced design program: Analysis, design, and construction of a solar powered aircraft. B.S. Thesis

NASA Technical Reports Server (NTRS)

Chan, Agnes; Conley, Kristin; Javorski, Christian T.; Cheung, Kwok-Hung; Crivelli, Paul M.; Torrey, Nancy P.; Traver, Michael L.

1992-01-01

Increase in energy demands coupled with rapid depletion of natural energy resources have deemed solar energy as the most logical alternative source of power. The major objective of this project was to build a solar powered remotely controlled aircraft to demonstrate the feasibility of solar energy as an effective, alternate source of power. The final design was optimized for minimum weight and maximum strength of the structure. These design constraints necessitated a carbon fiber composite structure. Surya is a lightweight, durable aircraft capable of achieving level flight powered entirely by solar cells.

An open data mining framework for the analysis of medical images: application on obstructive nephropathy microscopy images.

PubMed

Doukas, Charalampos; Goudas, Theodosis; Fischer, Simon; Mierswa, Ingo; Chatziioannou, Aristotle; Maglogiannis, Ilias

2010-01-01

This paper presents an open image-mining framework that provides access to tools and methods for the characterization of medical images. Several image processing and feature extraction operators have been implemented and exposed through Web Services. Rapid-Miner, an open source data mining system has been utilized for applying classification operators and creating the essential processing workflows. The proposed framework has been applied for the detection of salient objects in Obstructive Nephropathy microscopy images. Initial classification results are quite promising demonstrating the feasibility of automated characterization of kidney biopsy images.