Using an Algorithm When Solving Hardy-Weinberg Problems in Biology.

ERIC Educational Resources Information Center

Stencel, John E.

1991-01-01

A real world sample of actual data that students can use to see the application of the Hardy-Weinberg law to a real population is provided. The directions for using a six-step algorithmic procedure to determine Hardy-Weinberg percentages on the data given are described. (KR)

QUANTIFICATION OF ENTEROVIRUS AND HEPATITIS A VIRUSES IN WELLS AND SPRINGS IN EAST TENNESSEE USING REAL-TIME REVERSE TRANSCIPTION PCR

EPA Science Inventory

This project involves development, validation testing and application of a fast, efficient method of quantitatively measuring occurrence and concentration of common human viral pathogens, enterovirus and hepatitis A virus, in ground water samples using real-time reverse transcrip...

Application of quantitative real-time PCR compared to filtration methods for the enumeration of Escherichia coli in surface waters within Vietnam.

PubMed

Vital, Pierangeli G; Van Ha, Nguyen Thi; Tuyet, Le Thi Hong; Widmer, Kenneth W

2017-02-01

Surface water samples in Vietnam were collected from the Saigon River, rural and suburban canals, and urban runoff canals in Ho Chi Minh City, Vietnam, and were processed to enumerate Escherichia coli. Quantification was done through membrane filtration and quantitative real-time polymerase chain reaction (PCR). Mean log colony-forming unit (CFU)/100 ml E. coli counts in the dry season for river/suburban canals and urban canals were log 2.8 and 3.7, respectively, using a membrane filtration method, while using Taqman quantitative real-time PCR they were log 2.4 and 2.8 for river/suburban canals and urban canals, respectively. For the wet season, data determined by the membrane filtration method in river/suburban canals and urban canals samples had mean counts of log 3.7 and 4.1, respectively. While mean log CFU/100 ml counts in the wet season using quantitative PCR were log 3 and 2, respectively. Additionally, the urban canal samples were significantly lower than those determined by conventional culture methods for the wet season. These results show that while quantitative real-time PCR can be used to determine levels of fecal indicator bacteria in surface waters, there are some limitations to its application and it may be impacted by sources of runoff based on surveyed samples.

Real-time computational photon-counting LiDAR

NASA Astrophysics Data System (ADS)

Edgar, Matthew; Johnson, Steven; Phillips, David; Padgett, Miles

2018-03-01

The availability of compact, low-cost, and high-speed MEMS-based spatial light modulators has generated widespread interest in alternative sampling strategies for imaging systems utilizing single-pixel detectors. The development of compressed sensing schemes for real-time computational imaging may have promising commercial applications for high-performance detectors, where the availability of focal plane arrays is expensive or otherwise limited. We discuss the research and development of a prototype light detection and ranging (LiDAR) system via direct time of flight, which utilizes a single high-sensitivity photon-counting detector and fast-timing electronics to recover millimeter accuracy three-dimensional images in real time. The development of low-cost real time computational LiDAR systems could have importance for applications in security, defense, and autonomous vehicles.

Smart Sampling and HPC-based Probabilistic Look-ahead Contingency Analysis Implementation and its Evaluation with Real-world Data

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

Chen, Yousu; Etingov, Pavel V.; Ren, Huiying

This paper describes a probabilistic look-ahead contingency analysis application that incorporates smart sampling and high-performance computing (HPC) techniques. Smart sampling techniques are implemented to effectively represent the structure and statistical characteristics of uncertainty introduced by different sources in the power system. They can significantly reduce the data set size required for multiple look-ahead contingency analyses, and therefore reduce the time required to compute them. High-performance-computing (HPC) techniques are used to further reduce computational time. These two techniques enable a predictive capability that forecasts the impact of various uncertainties on potential transmission limit violations. The developed package has been tested withmore » real world data from the Bonneville Power Administration. Case study results are presented to demonstrate the performance of the applications developed.« less

Introducing automation to the molecular diagnosis of Trypanosoma cruzi infection: A comparative study of sample treatments, DNA extraction methods and real-time PCR assays.

PubMed

Abras, Alba; Ballart, Cristina; Llovet, Teresa; Roig, Carme; Gutiérrez, Cristina; Tebar, Silvia; Berenguer, Pere; Pinazo, María-Jesús; Posada, Elizabeth; Gascón, Joaquim; Schijman, Alejandro G; Gállego, Montserrat; Muñoz, Carmen

2018-01-01

Polymerase chain reaction (PCR) has become a useful tool for the diagnosis of Trypanosoma cruzi infection. The development of automated DNA extraction methodologies and PCR systems is an important step toward the standardization of protocols in routine diagnosis. To date, there are only two commercially available Real-Time PCR assays for the routine laboratory detection of T. cruzi DNA in clinical samples: TCRUZIDNA.CE (Diagnostic Bioprobes Srl) and RealCycler CHAG (Progenie Molecular). Our aim was to evaluate the RealCycler CHAG assay taking into account the whole process. We assessed the usefulness of an automated DNA extraction system based on magnetic particles (EZ1 Virus Mini Kit v2.0, Qiagen) combined with a commercially available Real-Time PCR assay targeting satellite DNA (SatDNA) of T. cruzi (RealCycler CHAG), a methodology used for routine diagnosis in our hospital. It was compared with a well-known strategy combining a commercial DNA isolation kit based on silica columns (High Pure PCR Template Preparation Kit, Roche Diagnostics) with an in-house Real-Time PCR targeting SatDNA. The results of the two methodologies were in almost perfect agreement, indicating they can be used interchangeably. However, when variations in protocol factors were applied (sample treatment, extraction method and Real-Time PCR), the results were less convincing. A comprehensive fine-tuning of the whole procedure is the key to successful results. Guanidine EDTA-blood (GEB) samples are not suitable for DNA extraction based on magnetic particles due to inhibition, at least when samples are not processed immediately. This is the first study to evaluate the RealCycler CHAG assay taking into account the overall process, including three variables (sample treatment, extraction method and Real-Time PCR). Our findings may contribute to the harmonization of protocols between laboratories and to a wider application of Real-Time PCR in molecular diagnostic laboratories associated with health centers.

Turbo-Satori: a neurofeedback and brain-computer interface toolbox for real-time functional near-infrared spectroscopy.

PubMed

Lührs, Michael; Goebel, Rainer

2017-10-01

Turbo-Satori is a neurofeedback and brain-computer interface (BCI) toolbox for real-time functional near-infrared spectroscopy (fNIRS). It incorporates multiple pipelines from real-time preprocessing and analysis to neurofeedback and BCI applications. The toolbox is designed with a focus in usability, enabling a fast setup and execution of real-time experiments. Turbo-Satori uses an incremental recursive least-squares procedure for real-time general linear model calculation and support vector machine classifiers for advanced BCI applications. It communicates directly with common NIRx fNIRS hardware and was tested extensively ensuring that the calculations can be performed in real time without a significant change in calculation times for all sampling intervals during ongoing experiments of up to 6 h of recording. Enabling immediate access to advanced processing features also allows the use of this toolbox for students and nonexperts in the field of fNIRS data acquisition and processing. Flexible network interfaces allow third party stimulus applications to access the processed data and calculated statistics in real time so that this information can be easily incorporated in neurofeedback or BCI presentations.

Real-time solution of linear computational problems using databases of parametric reduced-order models with arbitrary underlying meshes

NASA Astrophysics Data System (ADS)

Amsallem, David; Tezaur, Radek; Farhat, Charbel

2016-12-01

A comprehensive approach for real-time computations using a database of parametric, linear, projection-based reduced-order models (ROMs) based on arbitrary underlying meshes is proposed. In the offline phase of this approach, the parameter space is sampled and linear ROMs defined by linear reduced operators are pre-computed at the sampled parameter points and stored. Then, these operators and associated ROMs are transformed into counterparts that satisfy a certain notion of consistency. In the online phase of this approach, a linear ROM is constructed in real-time at a queried but unsampled parameter point by interpolating the pre-computed linear reduced operators on matrix manifolds and therefore computing an interpolated linear ROM. The proposed overall model reduction framework is illustrated with two applications: a parametric inverse acoustic scattering problem associated with a mockup submarine, and a parametric flutter prediction problem associated with a wing-tank system. The second application is implemented on a mobile device, illustrating the capability of the proposed computational framework to operate in real-time.

Students' Perceptions of Edmodo and Mobile Learning and Their Real Barriers towards Them

ERIC Educational Resources Information Center

Al-Said, Khaleel M.

2015-01-01

The present research aims to investigate the students' perceptions levels of Edmodo and Mobile learning and to identify the real barriers of them at Taibah University in KSA. After implemented Edmodo application as an Mlearning platform, two scales were applied on the research sample, the first scale consisted of 36 statements was constructed to…

Novel Laser-Based Technique is Ideal for Real-Time Environmental Analysis

ERIC Educational Resources Information Center

Journal of Chemical Education, 2005

2005-01-01

Ocean Optics offers laser-induced breakdown spectrometer systems (LIBS) that can be used to identify light to heavy metals in a variety of sample types and geometries in environmental analysis applications. LIBS are versatile, real-time, high-resolution analyzers for qualitative analysis, in less than one second, of every element in solids,…

Application of Ion Chromatography to the Investigation of Real-World Samples

ERIC Educational Resources Information Center

Whelan, Rebecca J.; Hannon, Theresa E.; Zare, Richard N.

2004-01-01

The use of ion chromatography (IC) as a means to teach important analytical concepts while giving the students a valuable opportunity to identify and investigate a real-world system of interest to them is described. A single IC apparatus can be tailored for different classes of analyses by the selection of different column-eluent combinations.

Extraction of trace tilmicosin in real water samples using ionic liquid-based aqueous two-phase systems.

PubMed

Pan, Ru; Shao, Dejia; Qi, Xueyong; Wu, Yun; Fu, Wenyan; Ge, Yanru; Fu, Haizhen

2013-01-01

The effective method of ionic liquid-based aqueous two-phase extraction, which involves ionic liquid (IL) (1-butyl-3-methyllimidazolium chloride, [C4mim]Cl) and inorganic salt (K2HPO4) coupled with high-performance liquid chromatography (HPLC), has been used to extract trace tilmicosin in real water samples which were passed through a 0.45 μm filter. The effects of the different types of salts, the concentration of K2HPO4 and of ILs, the pH value and temperature of the systems on the extraction efficiencies have all been investigated. Under the optimum conditions, the average extraction efficiency is up to 95.8%. This method was feasible when applied to the analysis of tilmicosin in real water samples within the range 0.5-40 μg mL(-1). The limit of detection was found to be 0.05 μg mL(-1). The recovery rate of tilmicosin was 92.0-99.0% from the real water samples by the proposed method. This process is suggested to have important applications for the extraction of tilmicosin.

Multiplex Real-Time PCR for Detection of Staphylococcus aureus, mecA and Panton-Valentine Leukocidin (PVL) Genes from Selective Enrichments from Animals and Retail Meat

PubMed Central

Velasco, Valeria; Sherwood, Julie S.; Rojas-García, Pedro P.; Logue, Catherine M.

2014-01-01

The aim of this study was to compare a real-time PCR assay, with a conventional culture/PCR method, to detect S. aureus, mecA and Panton-Valentine Leukocidin (PVL) genes in animals and retail meat, using a two-step selective enrichment protocol. A total of 234 samples were examined (77 animal nasal swabs, 112 retail raw meat, and 45 deli meat). The multiplex real-time PCR targeted the genes: nuc (identification of S. aureus), mecA (associated with methicillin resistance) and PVL (virulence factor), and the primary and secondary enrichment samples were assessed. The conventional culture/PCR method included the two-step selective enrichment, selective plating, biochemical testing, and multiplex PCR for confirmation. The conventional culture/PCR method recovered 95/234 positive S. aureus samples. Application of real-time PCR on samples following primary and secondary enrichment detected S. aureus in 111/234 and 120/234 samples respectively. For detection of S. aureus, the kappa statistic was 0.68–0.88 (from substantial to almost perfect agreement) and 0.29–0.77 (from fair to substantial agreement) for primary and secondary enrichments, using real-time PCR. For detection of mecA gene, the kappa statistic was 0–0.49 (from no agreement beyond that expected by chance to moderate agreement) for primary and secondary enrichment samples. Two pork samples were mecA gene positive by all methods. The real-time PCR assay detected the mecA gene in samples that were negative for S. aureus, but positive for Staphylococcus spp. The PVL gene was not detected in any sample by the conventional culture/PCR method or the real-time PCR assay. Among S. aureus isolated by conventional culture/PCR method, the sequence type ST398, and multi-drug resistant strains were found in animals and raw meat samples. The real-time PCR assay may be recommended as a rapid method for detection of S. aureus and the mecA gene, with further confirmation of methicillin-resistant S. aureus (MRSA) using the standard culture method. PMID:24849624

Multiplex real-time PCR for detection of Staphylococcus aureus, mecA and Panton-Valentine Leukocidin (PVL) genes from selective enrichments from animals and retail meat.

PubMed

Velasco, Valeria; Sherwood, Julie S; Rojas-García, Pedro P; Logue, Catherine M

2014-01-01

The aim of this study was to compare a real-time PCR assay, with a conventional culture/PCR method, to detect S. aureus, mecA and Panton-Valentine Leukocidin (PVL) genes in animals and retail meat, using a two-step selective enrichment protocol. A total of 234 samples were examined (77 animal nasal swabs, 112 retail raw meat, and 45 deli meat). The multiplex real-time PCR targeted the genes: nuc (identification of S. aureus), mecA (associated with methicillin resistance) and PVL (virulence factor), and the primary and secondary enrichment samples were assessed. The conventional culture/PCR method included the two-step selective enrichment, selective plating, biochemical testing, and multiplex PCR for confirmation. The conventional culture/PCR method recovered 95/234 positive S. aureus samples. Application of real-time PCR on samples following primary and secondary enrichment detected S. aureus in 111/234 and 120/234 samples respectively. For detection of S. aureus, the kappa statistic was 0.68-0.88 (from substantial to almost perfect agreement) and 0.29-0.77 (from fair to substantial agreement) for primary and secondary enrichments, using real-time PCR. For detection of mecA gene, the kappa statistic was 0-0.49 (from no agreement beyond that expected by chance to moderate agreement) for primary and secondary enrichment samples. Two pork samples were mecA gene positive by all methods. The real-time PCR assay detected the mecA gene in samples that were negative for S. aureus, but positive for Staphylococcus spp. The PVL gene was not detected in any sample by the conventional culture/PCR method or the real-time PCR assay. Among S. aureus isolated by conventional culture/PCR method, the sequence type ST398, and multi-drug resistant strains were found in animals and raw meat samples. The real-time PCR assay may be recommended as a rapid method for detection of S. aureus and the mecA gene, with further confirmation of methicillin-resistant S. aureus (MRSA) using the standard culture method.

The trace analysis of microorganisms in real samples by combination of a filtration microcartridge and capillary isoelectric focusing.

PubMed

Horká, Marie; Horký, Jaroslav; Kubesová, Anna; Zapletalová, Eva; Slais, Karel

2011-07-01

Trace analysis of microorganisms in real biological samples needs very sensitive methods for their detection. Most procedures for detecting and quantifying pathogens require a sample preparation step including concentrating microorganisms from large sample volumes with high and reproducible efficiency. Electromigration techniques have great potential to include the preconcentration, separation, and detection of whole cells and therefore they can rapidly indicate the presence of pathogens. The preconcentration and separation of microorganisms from real suspensions utilising a combination of filtration and capillary isoelectric focusing was developed and the possibility for its application to real samples was verified. For our experiments, spores of Monilinia species and of Penicillium expansum were selected as model bioparticles, as they cause major losses in agrosystems. The isoelectric points of the spores of M. laxa, M. fructigena, M. fruticola, and P. expansum were determined and the method was verified using real samples taken directly from infected apples. The coupling of a filtration cartridge with a separation capillary can improve the detection limit of isoelectric focusing with UV detection by at least 4 orders of magnitude. Spores of M. fructigena and of M. laxa in numbers of hundreds of particles per milliliter were detected on a visually noninfected apple surface which was cross-contaminated during handling and storage. The efficiency of preconcentration and a preliminary identification was verified by the phenotyping technique after cultivation of the spores sampled from the apple surface.

Iridium oxide pH sensor for biomedical applications. Case urea-urease in real urine samples.

PubMed

Prats-Alfonso, Elisabet; Abad, Llibertat; Casañ-Pastor, Nieves; Gonzalo-Ruiz, Javier; Baldrich, Eva

2013-01-15

This work demonstrates the implementation of iridium oxide films (IROF) grown on silicon-based thin-film platinum microelectrodes, their utilization as a pH sensor, and their successful formatting into a urea pH sensor. In this context, Pt electrodes were fabricated on Silicon by using standard photolithography and lift-off procedures and IROF thin films were growth by a dynamic oxidation electrodeposition method (AEIROF). The AEIROF pH sensor reported showed a super-Nerstian (72.9±0.9mV/pH) response between pH 3 and 11, with residual standard deviation of both repeatability and reproducibility below 5%, and resolution of 0.03 pH units. For their application as urea pH sensors, AEIROF electrodes were reversibly modified with urease-coated magnetic microparticles (MP) using a magnet. The urea pH sensor provided fast detection of urea between 78μM and 20mM in saline solution, in sample volumes of just 50μL. The applicability to urea determination in real urine samples is discussed. Copyright © 2012 Elsevier B.V. All rights reserved.

Evaluation of Novel Broad-Range Real-Time PCR Assay for Rapid Detection of Human Pathogenic Fungi in Various Clinical Specimens▿

PubMed Central

Vollmer, Tanja; Störmer, Melanie; Kleesiek, Knut; Dreier, Jens

2008-01-01

In the present study, a novel broad-range real-time PCR was developed for the rapid detection of human pathogenic fungi. The assay targets a part of the 28S large-subunit ribosomal RNA (rDNA) gene. We investigated its application for the most important human pathogenic fungal genera, including Aspergillus, Candida, Cryptococcus, Mucor, Penicillium, Pichia, Microsporum, Trichophyton, and Scopulariopsis. Species were identified in PCR-positive reactions by direct DNA sequencing. A noncompetitive internal control was applied to prevent false-negative results due to PCR inhibition. The minimum detection limit for the PCR was determined to be one 28S rDNA copy per PCR, and the 95% detection limit was calculated to 15 copies per PCR. To assess the clinical applicability of the PCR method, intensive-care patients with artificial respiration and patients with infective endocarditis were investigated. For this purpose, 76 tracheal secretion samples and 70 heart valve tissues were analyzed in parallel by real-time PCR and cultivation. No discrepancies in results were observed between PCR analysis and cultivation methods. Furthermore, the application of the PCR method was investigated for other clinical specimens, including cervical swabs, nail and horny skin scrapings, and serum, blood, and urine samples. The combination of a broad-range real-time PCR and direct sequencing facilitates rapid screening for fungal infection in various clinical specimens. PMID:18385440

Evaluation of novel broad-range real-time PCR assay for rapid detection of human pathogenic fungi in various clinical specimens.

PubMed

Vollmer, Tanja; Störmer, Melanie; Kleesiek, Knut; Dreier, Jens

2008-06-01

In the present study, a novel broad-range real-time PCR was developed for the rapid detection of human pathogenic fungi. The assay targets a part of the 28S large-subunit ribosomal RNA (rDNA) gene. We investigated its application for the most important human pathogenic fungal genera, including Aspergillus, Candida, Cryptococcus, Mucor, Penicillium, Pichia, Microsporum, Trichophyton, and Scopulariopsis. Species were identified in PCR-positive reactions by direct DNA sequencing. A noncompetitive internal control was applied to prevent false-negative results due to PCR inhibition. The minimum detection limit for the PCR was determined to be one 28S rDNA copy per PCR, and the 95% detection limit was calculated to 15 copies per PCR. To assess the clinical applicability of the PCR method, intensive-care patients with artificial respiration and patients with infective endocarditis were investigated. For this purpose, 76 tracheal secretion samples and 70 heart valve tissues were analyzed in parallel by real-time PCR and cultivation. No discrepancies in results were observed between PCR analysis and cultivation methods. Furthermore, the application of the PCR method was investigated for other clinical specimens, including cervical swabs, nail and horny skin scrapings, and serum, blood, and urine samples. The combination of a broad-range real-time PCR and direct sequencing facilitates rapid screening for fungal infection in various clinical specimens.

Sample-based engine noise synthesis using an enhanced pitch-synchronous overlap-and-add method.

PubMed

Jagla, Jan; Maillard, Julien; Martin, Nadine

2012-11-01

An algorithm for the real time synthesis of internal combustion engine noise is presented. Through the analysis of a recorded engine noise signal of continuously varying engine speed, a dataset of sound samples is extracted allowing the real time synthesis of the noise induced by arbitrary evolutions of engine speed. The sound samples are extracted from a recording spanning the entire engine speed range. Each sample is delimitated such as to contain the sound emitted during one cycle of the engine plus the necessary overlap to ensure smooth transitions during the synthesis. The proposed approach, an extension of the PSOLA method introduced for speech processing, takes advantage of the specific periodicity of engine noise signals to locate the extraction instants of the sound samples. During the synthesis stage, the sound samples corresponding to the target engine speed evolution are concatenated with an overlap and add algorithm. It is shown that this method produces high quality audio restitution with a low computational load. It is therefore well suited for real time applications.

Estimation of real-time N load in surface water using dynamic data driven application system

Treesearch

Y. Ouyang; S.M. Luo; L.H. Cui; Q. Wang; J.E. Zhang

2011-01-01

Agricultural, industrial, and urban activities are the major sources for eutrophication of surface water ecosystems. Currently, determination of nutrients in surface water is primarily accomplished by manually collecting samples for laboratory analysis, which requires at least 24 h. In other words, little to no effort has been devoted to monitoring real-time variations...

Demonstration of the Capabilities of the KINEROS2 – AGWA 3.0 Suite of Modeling Tools

EPA Science Inventory

This poster and computer demonstration illustrates a sampling of the wide range of applications that are possible using the KINEROS2 - AGWA suite of modeling tools. Applications include: 1) Incorporation of Low Impact Development (LID) features; 2) A real-time flash flood forecas...

Advanced Engine Health Management Applications of the SSME Real-Time Vibration Monitoring System

NASA Technical Reports Server (NTRS)

Fiorucci, Tony R.; Lakin, David R., II; Reynolds, Tracy D.; Turner, James E. (Technical Monitor)

2000-01-01

The Real Time Vibration Monitoring System (RTVMS) is a 32-channel high speed vibration data acquisition and processing system developed at Marshall Space Flight Center (MSFC). It Delivers sample rates as high as 51,200 samples/second per channel and performs Fast Fourier Transform (FFT) processing via on-board digital signal processing (DSP) chips in a real-time format. Advanced engine health assessment is achieved by utilizing the vibration spectra to provide accurate sensor validation and enhanced engine vibration redlines. Discrete spectral signatures (such as synchronous) that are indicators of imminent failure can be assessed and utilized to mitigate catastrophic engine failures- a first in rocket engine health assessment. This paper is presented in viewgraph form.

Clinical Application of Ambient Ionization Mass Spectrometry

PubMed Central

Li, Li-Hua; Hsieh, Hua-Yi; Hsu, Cheng-Chih

2017-01-01

Ambient ionization allows mass spectrometry analysis directly on the sample surface under atmospheric pressure with almost zero sample pretreatment. Since the development of desorption electrospray ionization (DESI) in 2004, many other ambient ionization techniques were developed. Due to their simplicity and low operation cost, rapid and on-site clinical mass spectrometry analysis becomes real. In this review, we will highlight some of the most widely used ambient ionization mass spectrometry approaches and their applications in clinical study. PMID:28337399

Manifold Regularized Experimental Design for Active Learning.

PubMed

Zhang, Lining; Shum, Hubert P H; Shao, Ling

2016-12-02

Various machine learning and data mining tasks in classification require abundant data samples to be labeled for training. Conventional active learning methods aim at labeling the most informative samples for alleviating the labor of the user. Many previous studies in active learning select one sample after another in a greedy manner. However, this is not very effective because the classification models has to be retrained for each newly labeled sample. Moreover, many popular active learning approaches utilize the most uncertain samples by leveraging the classification hyperplane of the classifier, which is not appropriate since the classification hyperplane is inaccurate when the training data are small-sized. The problem of insufficient training data in real-world systems limits the potential applications of these approaches. This paper presents a novel method of active learning called manifold regularized experimental design (MRED), which can label multiple informative samples at one time for training. In addition, MRED gives an explicit geometric explanation for the selected samples to be labeled by the user. Different from existing active learning methods, our method avoids the intrinsic problems caused by insufficiently labeled samples in real-world applications. Various experiments on synthetic datasets, the Yale face database and the Corel image database have been carried out to show how MRED outperforms existing methods.

Quantification of HIV-1 DNA using real-time recombinase polymerase amplification.

PubMed

Crannell, Zachary Austin; Rohrman, Brittany; Richards-Kortum, Rebecca

2014-06-17

Although recombinase polymerase amplification (RPA) has many advantages for the detection of pathogenic nucleic acids in point-of-care applications, RPA has not yet been implemented to quantify sample concentration using a standard curve. Here, we describe a real-time RPA assay with an internal positive control and an algorithm that analyzes real-time fluorescence data to quantify HIV-1 DNA. We show that DNA concentration and the onset of detectable amplification are correlated by an exponential standard curve. In a set of experiments in which the standard curve and algorithm were used to analyze and quantify additional DNA samples, the algorithm predicted an average concentration within 1 order of magnitude of the correct concentration for all HIV-1 DNA concentrations tested. These results suggest that quantitative RPA (qRPA) may serve as a powerful tool for quantifying nucleic acids and may be adapted for use in single-sample point-of-care diagnostic systems.

The detection of T-Nos, a genetic element present in GMOs, by cross-priming isothermal amplification with real-time fluorescence.

PubMed

Zhang, Fang; Wang, Liu; Fan, Kai; Wu, Jian; Ying, Yibin

2014-05-01

An isothermal cross-priming amplification (CPA) assay for Agrobacterium tumefaciens nopaline synthase terminator (T-Nos) was established and investigated in this work. A set of six specific primers, recognizing eight distinct regions on the T-Nos sequence, was designed. The CPA assay was performed at a constant temperature, 63 °C, and detected by real-time fluorescence. The results indicated that real-time fluorescent CPA had high specificity, and the limit of detection was 1.06 × 10(3) copies of rice genomic DNA, which could be detected in 40 min. Comparison of real-time fluorescent CPA and conventional polymerase chain reaction (PCR) was also performed. Results revealed that real-time fluorescent CPA had a comparable sensitivity to conventional real-time PCR and had taken a shorter time. In addition, different contents of genetically modified (GM)-contaminated rice seed powder samples were detected for practical application. The result showed real-time fluorescent CPA could detect 0.5 % GM-contaminated samples at least, and the whole reaction could be finished in 35 min. Real-time fluorescent CPA is sensitive enough to monitor labeling systems and provides an attractive method for the detection of GMO.

Application of real-time PCR and melting curve analysis in rapid Diego blood group genotyping.

PubMed

Novaretti, M C Z; Ruiz, A S; Dorlhiac-Llacer, P E; Chamone, D A F

2010-01-01

The paucity of appropriate reagents for serologic typing of the Diego blood group antigens has prompted the development of a real-time PCR and melting curve analysis for Diego blood group genotyping. In this study, we phenotyped 4326 donor blood samples for Di(a) using semiautomated equipment. All 157 Di(a+) samples were then genotyped by PCR using sequence-specific primers (PCR-SSP) for DI*02 because of anti-Di(b) scarcity. Of the 4326 samples, we simultaneously tested 160 samples for Di(a) and Di(b) serology, and DI*01 and DI*02 by PCR-SSP and by real-time PCR. We used the same primers for Diego genotyping by real-time PCR and PCR-SSP. Melting curve profiles obtained using the dissociation software of the real-time PCR apparatus enabled the discrimination of Diego alleles. Of the total samples tested, 4169 blood donors, 96.4 percent (95% confidence interval [CI], 95.8-96.9%), were homozygous for DI*02 and 157, 3.6 percent (95% CI, 3.1%-4.2%), were heterozygous DI*01/02. No blood donor was found to be homozygous for DI*01 in this study. The calculated DI*01 and DI*02 allele frequencies were 0.0181 (95% CI, 0.0173-0.0189) and 0.9819 (95% CI, 0.9791-0.9847), respectively, showing a good fit for the Hardy-Weinberg equilibrium. There was full concordance among Diego phenotype results by PCR-SSP and real-time PCR. DI*01 and DI*02 allele determination with SYBR Green I and thermal cycler technology are useful methods for Diego determination. The real-time PCR with SYBR Green I melting temperature protocol can be used as a rapid screening tool for DI*01 and DI*02 blood group genotyping.

DAQ application of PC oscilloscope for chaos fiber-optic fence system based on LabVIEW

NASA Astrophysics Data System (ADS)

Lu, Manman; Fang, Nian; Wang, Lutang; Huang, Zhaoming; Sun, Xiaofei

2011-12-01

In order to obtain simultaneously high sample rate and large buffer in data acquisition (DAQ) for a chaos fiber-optic fence system, we developed a double-channel high-speed DAQ application of a digital oscilloscope of PicoScope 5203 based on LabVIEW. We accomplished it by creating call library function (CLF) nodes to call the DAQ functions in the two dynamic link libraries (DLLs) of PS5000.dll and PS5000wrap.dll provided by Pico Technology Company. The maximum real-time sample rate of the DAQ application can reach 1GS/s. We can control the resolutions of the application at the sample time and data amplitudes by changing their units in the block diagram, and also control the start and end times of the sampling operations. The experimental results show that the application has enough high sample rate and large buffer to meet the demanding DAQ requirements of the chaos fiber-optic fence system.

Real-Time Processing Library for Open-Source Hardware Biomedical Sensors

PubMed Central

Castro-García, Juan A.; Lebrato-Vázquez, Clara

2018-01-01

Applications involving data acquisition from sensors need samples at a preset frequency rate, the filtering out of noise and/or analysis of certain frequency components. We propose a novel software architecture based on open-software hardware platforms which allows programmers to create data streams from input channels and easily implement filters and frequency analysis objects. The performances of the different classes given in the size of memory allocated and execution time (number of clock cycles) were analyzed in the low-cost platform Arduino Genuino. In addition, 11 people took part in an experiment in which they had to implement several exercises and complete a usability test. Sampling rates under 250 Hz (typical for many biomedical applications) makes it feasible to implement filters, sliding windows and Fourier analysis, operating in real time. Participants rated software usability at 70.2 out of 100 and the ease of use when implementing several signal processing applications was rated at just over 4.4 out of 5. Participants showed their intention of using this software because it was percieved as useful and very easy to use. The performances of the library showed that it may be appropriate for implementing small biomedical real-time applications or for human movement monitoring, even in a simple open-source hardware device like Arduino Genuino. The general perception about this library is that it is easy to use and intuitive. PMID:29596394

Real-Time Processing Library for Open-Source Hardware Biomedical Sensors.

PubMed

Molina-Cantero, Alberto J; Castro-García, Juan A; Lebrato-Vázquez, Clara; Gómez-González, Isabel M; Merino-Monge, Manuel

2018-03-29

Applications involving data acquisition from sensors need samples at a preset frequency rate, the filtering out of noise and/or analysis of certain frequency components. We propose a novel software architecture based on open-software hardware platforms which allows programmers to create data streams from input channels and easily implement filters and frequency analysis objects. The performances of the different classes given in the size of memory allocated and execution time (number of clock cycles) were analyzed in the low-cost platform Arduino Genuino. In addition, 11 people took part in an experiment in which they had to implement several exercises and complete a usability test. Sampling rates under 250 Hz (typical for many biomedical applications) makes it feasible to implement filters, sliding windows and Fourier analysis, operating in real time. Participants rated software usability at 70.2 out of 100 and the ease of use when implementing several signal processing applications was rated at just over 4.4 out of 5. Participants showed their intention of using this software because it was percieved as useful and very easy to use. The performances of the library showed that it may be appropriate for implementing small biomedical real-time applications or for human movement monitoring, even in a simple open-source hardware device like Arduino Genuino. The general perception about this library is that it is easy to use and intuitive.

Relative sensitivity of conventional and real-time PCR assays for detection of SFG Rickettsia in blood and tissue samples from laboratory animals.

PubMed

Zemtsova, Galina E; Montgomery, Merrill; Levin, Michael L

2015-01-01

Studies on the natural transmission cycles of zoonotic pathogens and the reservoir competence of vertebrate hosts require methods for reliable diagnosis of infection in wild and laboratory animals. Several PCR-based applications have been developed for detection of infections caused by Spotted Fever group Rickettsia spp. in a variety of animal tissues. These assays are being widely used by researchers, but they differ in their sensitivity and reliability. We compared the sensitivity of five previously published conventional PCR assays and one SYBR green-based real-time PCR assay for the detection of rickettsial DNA in blood and tissue samples from Rickettsia- infected laboratory animals (n = 87). The real-time PCR, which detected rickettsial DNA in 37.9% of samples, was the most sensitive. The next best were the semi-nested ompA assay and rpoB conventional PCR, which detected as positive 18.4% and 14.9% samples respectively. Conventional assays targeting ompB, gltA and hrtA genes have been the least sensitive. Therefore, we recommend the SYBR green-based real-time PCR as a tool for the detection of rickettsial DNA in animal samples due to its higher sensitivity when compared to more traditional assays.

Relative Sensitivity of Conventional and Real-Time PCR Assays for Detection of SFG Rickettsia in Blood and Tissue Samples from Laboratory Animals

PubMed Central

Zemtsova, Galina E.; Montgomery, Merrill; Levin, Michael L.

2015-01-01

Studies on the natural transmission cycles of zoonotic pathogens and the reservoir competence of vertebrate hosts require methods for reliable diagnosis of infection in wild and laboratory animals. Several PCR-based applications have been developed for detection of infections caused by Spotted Fever group Rickettsia spp. in a variety of animal tissues. These assays are being widely used by researchers, but they differ in their sensitivity and reliability. We compared the sensitivity of five previously published conventional PCR assays and one SYBR green-based real-time PCR assay for the detection of rickettsial DNA in blood and tissue samples from Rickettsia- infected laboratory animals (n = 87). The real-time PCR, which detected rickettsial DNA in 37.9% of samples, was the most sensitive. The next best were the semi-nested ompA assay and rpoB conventional PCR, which detected as positive 18.4% and 14.9% samples respectively. Conventional assays targeting ompB, gltA and hrtA genes have been the least sensitive. Therefore, we recommend the SYBR green-based real-time PCR as a tool for the detection of rickettsial DNA in animal samples due to its higher sensitivity when compared to more traditional assays. PMID:25607846

Original and Mirror Face Images and Minimum Squared Error Classification for Visible Light Face Recognition.

PubMed

Wang, Rong

2015-01-01

In real-world applications, the image of faces varies with illumination, facial expression, and poses. It seems that more training samples are able to reveal possible images of the faces. Though minimum squared error classification (MSEC) is a widely used method, its applications on face recognition usually suffer from the problem of a limited number of training samples. In this paper, we improve MSEC by using the mirror faces as virtual training samples. We obtained the mirror faces generated from original training samples and put these two kinds of samples into a new set. The face recognition experiments show that our method does obtain high accuracy performance in classification.

The Halpern Critical Thinking Assessment and Real-World Outcomes: Cross-National Applications

ERIC Educational Resources Information Center

Butler, Heather A.; Dwyer, Christopher P.; Hogan, Michael J.; Franco, Amanda; Rivas, Silvia F.; Saiz, Carlos; Almeida, Leandro S.

2012-01-01

The Halpern Critical Thinking Assessment (HCTA) is a reliable measure of critical thinking that has been validated with numerous qualitatively different samples and measures of academic success (Halpern, 2010a). This paper presents several cross-national applications of the assessment, and recent work to expand the validation of the HCTA with…

Rocket Flight.

ERIC Educational Resources Information Center

Van Evera, Bill; Sterling, Donna R.

2002-01-01

Describes an activity for designing, building, and launching rockets that provides students with an intrinsically motivating and real-life application of what could have been classroom-only concepts. Includes rocket design guidelines and a sample grading rubric. (KHR)

S-Band POSIX Device Drivers for RTEMS

NASA Technical Reports Server (NTRS)

Lux, James P.; Lang, Minh; Peters, Kenneth J.; Taylor, Gregory H.

2011-01-01

This is a set of POSIX device driver level abstractions in the RTEMS RTOS (Real-Time Executive for Multiprocessor Systems real-time operating system) to SBand radio hardware devices that have been instantiated in an FPGA (field-programmable gate array). These include A/D (analog-to-digital) sample capture, D/A (digital-to-analog) sample playback, PLL (phase-locked-loop) tuning, and PWM (pulse-width-modulation)-controlled gain. This software interfaces to Sband radio hardware in an attached Xilinx Virtex-2 FPGA. It uses plug-and-play device discovery to map memory to device IDs. Instead of interacting with hardware devices directly, using direct-memory mapped access at the application level, this driver provides an application programming interface (API) offering that easily uses standard POSIX function calls. This simplifies application programming, enables portability, and offers an additional level of protection to the hardware. There are three separate device drivers included in this package: sband_device (ADC capture and DAC playback), pll_device (RF front end PLL tuning), and pwm_device (RF front end AGC control).

Grain reconstruction of porous media: application to a Bentheim sandstone.

PubMed

Thovert, J-F; Adler, P M

2011-05-01

The two-point correlation measured on a thin section can be used to derive the probability density of the radii of a population of penetrable spheres. The geometrical, transport, and deformation properties of samples derived by this method compare well with the properties of the digitized real sample and of the samples generated by the standard grain reconstruction method. © 2011 American Physical Society

Data-Driven Sampling Matrix Boolean Optimization for Energy-Efficient Biomedical Signal Acquisition by Compressive Sensing.

PubMed

Wang, Yuhao; Li, Xin; Xu, Kai; Ren, Fengbo; Yu, Hao

2017-04-01

Compressive sensing is widely used in biomedical applications, and the sampling matrix plays a critical role on both quality and power consumption of signal acquisition. It projects a high-dimensional vector of data into a low-dimensional subspace by matrix-vector multiplication. An optimal sampling matrix can ensure accurate data reconstruction and/or high compression ratio. Most existing optimization methods can only produce real-valued embedding matrices that result in large energy consumption during data acquisition. In this paper, we propose an efficient method that finds an optimal Boolean sampling matrix in order to reduce the energy consumption. Compared to random Boolean embedding, our data-driven Boolean sampling matrix can improve the image recovery quality by 9 dB. Moreover, in terms of sampling hardware complexity, it reduces the energy consumption by 4.6× and the silicon area by 1.9× over the data-driven real-valued embedding.

Image Quality Assessment for Fake Biometric Detection: Application to Iris, Fingerprint, and Face Recognition.

PubMed

Galbally, Javier; Marcel, Sébastien; Fierrez, Julian

2014-02-01

To ensure the actual presence of a real legitimate trait in contrast to a fake self-manufactured synthetic or reconstructed sample is a significant problem in biometric authentication, which requires the development of new and efficient protection measures. In this paper, we present a novel software-based fake detection method that can be used in multiple biometric systems to detect different types of fraudulent access attempts. The objective of the proposed system is to enhance the security of biometric recognition frameworks, by adding liveness assessment in a fast, user-friendly, and non-intrusive manner, through the use of image quality assessment. The proposed approach presents a very low degree of complexity, which makes it suitable for real-time applications, using 25 general image quality features extracted from one image (i.e., the same acquired for authentication purposes) to distinguish between legitimate and impostor samples. The experimental results, obtained on publicly available data sets of fingerprint, iris, and 2D face, show that the proposed method is highly competitive compared with other state-of-the-art approaches and that the analysis of the general image quality of real biometric samples reveals highly valuable information that may be very efficiently used to discriminate them from fake traits.

Turbulent fluxes by "Conditional Eddy Sampling"

NASA Astrophysics Data System (ADS)

Siebicke, Lukas

2015-04-01

Turbulent flux measurements are key to understanding ecosystem scale energy and matter exchange, including atmospheric trace gases. While the eddy covariance approach has evolved as an invaluable tool to quantify fluxes of e.g. CO2 and H2O continuously, it is limited to very few atmospheric constituents for which sufficiently fast analyzers exist. High instrument cost, lack of field-readiness or high power consumption (e.g. many recent laser-based systems requiring strong vacuum) further impair application to other tracers. Alternative micrometeorological approaches such as conditional sampling might overcome major limitations. Although the idea of eddy accumulation has already been proposed by Desjardin in 1972 (Desjardin, 1977), at the time it could not be realized for trace gases. Major simplifications by Businger and Oncley (1990) lead to it's widespread application as 'Relaxed Eddy Accumulation' (REA). However, those simplifications (flux gradient similarity with constant flow rate sampling irrespective of vertical wind velocity and introduction of a deadband around zero vertical wind velocity) have degraded eddy accumulation to an indirect method, introducing issues of scalar similarity and often lack of suitable scalar flux proxies. Here we present a real implementation of a true eddy accumulation system according to the original concept. Key to our approach, which we call 'Conditional Eddy Sampling' (CES), is the mathematical formulation of conditional sampling in it's true form of a direct eddy flux measurement paired with a performant real implementation. Dedicated hardware controlled by near-real-time software allows full signal recovery at 10 or 20 Hz, very fast valve switching, instant vertical wind velocity proportional flow rate control, virtually no deadband and adaptive power management. Demonstrated system performance often exceeds requirements for flux measurements by orders of magnitude. The system's exceptionally low power consumption is ideal for the field (one to two orders of magnitude lower compared to current closed-path laser based eddy covariance systems). Potential applications include fluxes of CO2, CH4, N2O, VOCs and other tracers. Finally we assess the flux accuracy of the Conditional Eddy Sampling (CES) approach as in our real implementation relative to alternative techniques including eddy covariance (EC) and relaxed eddy accumulation (REA). We further quantify various sources of instrument and method specific measurement errors. This comparison uses real measurements of 20 Hz turbulent time series of 3D wind velocity, sonic temperature and CO2 mixing ratio over a mixed decidious forest at the 'ICOS' flux tower site 'Hainich', Germany. Results from a simulation using real wind and CO2 timeseries from the Hainich site from 30 April to 3 November 2014 and real instrument performance suggest that the maximum flux estimates error (50% and 75% error quantiles) from Conditional Eddy Sampling (CES) relative to the true flux is 1.3% and 10%, respectively for monthly net fluxes, 1.6% and 7%, respectively for daily net fluxes and 8% and 35%, respectively for 30-minute CO2 flux estimates. Those results from CES are promising and outperform our REA estimates by about a factor of 50 assuming REA with constant b value. Results include flux time series from the EC, CES and REA approaches from 30-min to annual resolution.

Fiber Optic Wing Shape Sensing on NASA's Ikhana UAV

NASA Technical Reports Server (NTRS)

Richards, Lance; Parker, Allen R.; Ko, William L.; Piazza, Anthony

2008-01-01

Fiber Optic Wing Shape Sensing on Ikhana involves five major areas 1) Algorithm development: Local-strain-to-displacement algorithms have been developed for complex wing shapes for real-time implementation (NASA TP-2007-214612, patent application submitted) 2) FBG system development: Dryden advancements to fiber optic sensing technology have increased data sampling rates to levels suitable for monitoring structures in flight (patent application submitted) 3) Instrumentation: 2880 FBG strain sensors have been successfully installed on the Ikhana wings 4) Ground Testing: Fiber optic wing shape sensing methods for high aspect ratio UAVs have been validated through extensive ground testing in Dryden s Flight Loads Laboratory 5) Flight Testing: Real time fiber Bragg strain measurements successfully acquired and validated in flight (4/28/2008) Real-time fiber optic wing shape sensing successfully demonstrated in flight

Application of rapid onsite PCR (TaqMan) for Phytophthora ramorum under U.S. conditions

Treesearch

Kelvin Hughes; Jenny Tomlinson; Neil Boonham; Kelly Ivors; Matteo Garbelotto; Ian Barker

2006-01-01

Currently, diagnosis of Phytophthora ramorum involves sending samples to a laboratory for traditional isolation and morphological characterisation, and/or PCR analysis. This can take as long as 2 weeks from sampling to final diagnosis. However, the Plant Health Group, Central Science Laboratory, has produced on-site DNA extraction and real-time PCR (...

Characterization of friction and moisture of porcine lingual tissue in vitro in response to artificial saliva and mouthwash solutions.

PubMed

Zundel, J; Ansari, S A; Trivedi, H M; Masters, J G; Mascaro, S

2018-05-07

The purpose of this research is to characterize the effects of mouthwash solutions on oral friction and moisture using a quantitative in vitro approach. The frictional coefficient of in vitro porcine tongue samples was measured using a magnetic levitation haptic device equipped with a custom tactor designed to mimic human skin. A commercially available moisture meter was used to measure moisture content of the samples. Tongue samples were first tested before treatment, then after application of saliva (either human or artificial), and again after application of 1 of 11 different mouthwash solutions. The data indicate that the samples treated with artificial saliva vs real saliva have comparable friction coefficient and moisture content. Furthermore, the moisture and friction coefficient remain relatively constant for up to 60 minutes after exposure to ambient conditions. Samples treated with artificial saliva have an average friction coefficient in the range of 0.70-0.80. Application of mouthwash solutions produced an average friction coefficient of 0.39-0.49 but retained the high moisture content of the artificial salivary layer. Several mouthwash solutions resulted in statistically significant differences in the friction coefficient relative to each other. The results of this study demonstrate that a magnetic levitation device can be an effective tool for in vitro oral tribology and that artificial saliva is an effective substitute for real saliva in extended in vitro experiments. The application of mouthwash generally reduces the coefficient of friction of the tongue samples while preserving a relatively high moisture level, and some mouthwashes reduce friction significantly more than others. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Comparison between a Direct-Flow SPR Immunosensor for Ampicillin and a Competitive Conventional Amperometric Device: Analytical Features and Possible Applications to Real Samples

PubMed Central

Tomassetti, Mauro; Merola, Giovanni; Martini, Elisabetta; Campanella, Luigi; Sanzò, Gabriella; Favero, Gabriele; Mazzei, Franco

2017-01-01

In this research, we developed a direct-flow surface plasmon resonance (SPR) immunosensor for ampicillin to perform direct, simple, and fast measurements of this important antibiotic. In order to better evaluate the performance, it was compared with a conventional amperometric immunosensor, working with a competitive format with the aim of finding out experimental real advantages and disadvantages of two respective methods. Results showed that certain analytical features of the new SPR immunodevice, such as the lower limit of detection (LOD) value and the width of the linear range, are poorer than those of a conventional amperometric immunosensor, which adversely affects the application to samples such as natural waters. On the other hand, the SPR immunosensor was more selective to ampicillin, and measurements were more easily and quickly attained compared to those performed with the conventional competitive immunosensor. PMID:28394296

Optimal sampling theory and population modelling - Application to determination of the influence of the microgravity environment on drug distribution and elimination

NASA Technical Reports Server (NTRS)

Drusano, George L.

1991-01-01

The optimal sampling theory is evaluated in applications to studies related to the distribution and elimination of several drugs (including ceftazidime, piperacillin, and ciprofloxacin), using the SAMPLE module of the ADAPT II package of programs developed by D'Argenio and Schumitzky (1979, 1988) and comparing the pharmacokinetic parameter values with results obtained by traditional ten-sample design. The impact of the use of optimal sampling was demonstrated in conjunction with NONMEM (Sheiner et al., 1977) approach, in which the population is taken as the unit of analysis, allowing even fragmentary patient data sets to contribute to population parameter estimates. It is shown that this technique is applicable in both the single-dose and the multiple-dose environments. The ability to study real patients made it possible to show that there was a bimodal distribution in ciprofloxacin nonrenal clearance.

Real-time quantitative PCR of Staphylococcus aureus and application in restaurant meals.

PubMed

Berrada, H; Soriano, J M; Mañes, J; Picó, Y

2006-01-01

Staphylococcus aureus is considered the second most common pathogen to cause outbreaks of food poisoning, exceeded only by Campylobacter. Consumption of foods containing this microorganism is often identified as the cause of illness. In this study, a rapid, reliable, and sensitive real-time quantitative PCR was developed and compared with conventional culture methods. Real-time quantitative PCR was carried out by purifying DNA extracts of S. aureus with a Staphylococcus sample preparation kit and quantifying it in the LightCycler system with hybridization probes. The assay was linear from a range of 10 to 10(6) S. aureus cells (r2 > 0.997). The PCR reaction presented an efficiency of >85%. Accuracy of the PCR-based assay, expressed as percent bias, was around 13%, and the precision, expressed as a percentage of the coefficient of variation, was 7 to 10%. Intraday and interday variability were studied at 10(2) CFU/g and was 12 and 14%, respectively. The proposed method was applied to the analysis of 77 samples of restaurant meals in Valencia (Spain). In 11.6% of samples S. aureus was detected by real-time quantitative PCR, as well as by the conventional microbiological method. An excellent correspondence between real-time quantitative PCR and microbiological numbers (CFU/g) was observed with deviations of < 28%.

Real-time estimation of BDS/GPS high-rate satellite clock offsets using sequential least squares

NASA Astrophysics Data System (ADS)

Fu, Wenju; Yang, Yuanxi; Zhang, Qin; Huang, Guanwen

2018-07-01

The real-time precise satellite clock product is one of key prerequisites for real-time Precise Point Positioning (PPP). The accuracy of the 24-hour predicted satellite clock product with 15 min sampling interval and an update of 6 h provided by the International GNSS Service (IGS) is only 3 ns, which could not meet the needs of all real-time PPP applications. The real-time estimation of high-rate satellite clock offsets is an efficient method for improving the accuracy. In this paper, the sequential least squares method to estimate real-time satellite clock offsets with high sample rate is proposed to improve the computational speed by applying an optimized sparse matrix operation to compute the normal equation and using special measures to take full advantage of modern computer power. The method is first applied to BeiDou Navigation Satellite System (BDS) and provides real-time estimation with a 1 s sample rate. The results show that the amount of time taken to process a single epoch is about 0.12 s using 28 stations. The Standard Deviation (STD) and Root Mean Square (RMS) of the real-time estimated BDS satellite clock offsets are 0.17 ns and 0.44 ns respectively when compared to German Research Center for Geosciences (GFZ) final clock products. The positioning performance of the real-time estimated satellite clock offsets is evaluated. The RMSs of the real-time BDS kinematic PPP in east, north, and vertical components are 7.6 cm, 6.4 cm and 19.6 cm respectively. The method is also applied to Global Positioning System (GPS) with a 10 s sample rate and the computational time of most epochs is less than 1.5 s with 75 stations. The STD and RMS of the real-time estimated GPS satellite clocks are 0.11 ns and 0.27 ns, respectively. The accuracies of 5.6 cm, 2.6 cm and 7.9 cm in east, north, and vertical components are achieved for the real-time GPS kinematic PPP.

Neuromorphic learning of continuous-valued mappings in the presence of noise: Application to real-time adaptive control

NASA Technical Reports Server (NTRS)

Troudet, Terry; Merrill, Walter C.

1989-01-01

The ability of feed-forward neural net architectures to learn continuous-valued mappings in the presence of noise is demonstrated in relation to parameter identification and real-time adaptive control applications. Factors and parameters influencing the learning performance of such nets in the presence of noise are identified. Their effects are discussed through a computer simulation of the Back-Error-Propagation algorithm by taking the example of the cart-pole system controlled by a nonlinear control law. Adequate sampling of the state space is found to be essential for canceling the effect of the statistical fluctuations and allowing learning to take place.

Paper-based SERS swab for rapid trace detection on real-world surfaces.

PubMed

Lee, Chang H; Tian, Limei; Singamaneni, Srikanth

2010-12-01

One of the important but often overlooked considerations in the design of surface-enhanced Raman scattering (SERS) substrates for trace detection is the efficiency of sample collection. Conventional designs based on rigid substrates such as silicon, alumina, and glass resist conformal contact with the surface under investigation, making the sample collection inefficient. We demonstrate a novel SERS substrate based on common filter paper adsorbed with gold nanorods, which allows conformal contact with real-world surfaces, thus dramatically enhancing the sample collection efficiency compared to conventional rigid substrates. We demonstrate the detection of trace amounts of analyte (140 pg spread over 4 cm2) by simply swabbing the surface under investigation with the novel SERS substrate. The hierarchical fibrous structure of paper serves as a 3D vasculature for easy uptake and transport of the analytes to the electromagnetic hot spots in the paper. Simple yet highly efficient and cost-effective SERS substrate demonstrated here brings SERS-based trace detection closer to real-world applications.

Real-time Series Resistance Monitoring in PV Systems; NREL (National Renewable Energy Laboratory)

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

Deceglie, M. G.; Silverman, T. J.; Marion, B.

We apply the physical principles of a familiar method, suns-Voc, to a new application: the real-time detection of series resistance changes in modules and systems operating outside. The real-time series resistance (RTSR) method that we describe avoids the need for collecting IV curves or constructing full series-resistance-free IV curves. RTSR is most readily deployable at the module level on apply the physical principles of a familiar method, suns-Voc, to a new application: the real-time detection of series resistance changes in modules and systems operating outside. The real-time series resistance (RTSR) method that we describe avoids the need for collecting IVmore » curves or constructing full series-resistance-free IV curves. RTSR is most readily deployable at the module level on micro-inverters or module-integrated electronics, but it can also be extended to full strings. Automated detection of series resistance increases can provide early warnings of some of the most common reliability issues, which also pose fire risks, including broken ribbons, broken solder bonds, and contact problems in the junction or combiner box. We describe the method in detail and describe a sample application to data collected from modules operating in the field.« less

GMO detection using a bioluminescent real time reporter (BART) of loop mediated isothermal amplification (LAMP) suitable for field use.

PubMed

Kiddle, Guy; Hardinge, Patrick; Buttigieg, Neil; Gandelman, Olga; Pereira, Clint; McElgunn, Cathal J; Rizzoli, Manuela; Jackson, Rebecca; Appleton, Nigel; Moore, Cathy; Tisi, Laurence C; Murray, James A H

2012-04-30

There is an increasing need for quantitative technologies suitable for molecular detection in a variety of settings for applications including food traceability and monitoring of genetically modified (GM) crops and their products through the food processing chain. Conventional molecular diagnostics utilising real-time polymerase chain reaction (RT-PCR) and fluorescence-based determination of amplification require temperature cycling and relatively complex optics. In contrast, isothermal amplification coupled to a bioluminescent output produced in real-time (BART) occurs at a constant temperature and only requires a simple light detection and integration device. Loop mediated isothermal amplification (LAMP) shows robustness to sample-derived inhibitors. Here we show the applicability of coupled LAMP and BART reactions (LAMP-BART) for determination of genetically modified (GM) maize target DNA at low levels of contamination (0.1-5.0% GM) using certified reference material, and compare this to RT-PCR. Results show that conventional DNA extraction methods developed for PCR may not be optimal for LAMP-BART quantification. Additionally, we demonstrate that LAMP is more tolerant to plant sample-derived inhibitors, and show this can be exploited to develop rapid extraction techniques suitable for simple field-based qualitative tests for GM status determination. We also assess the effect of total DNA assay load on LAMP-BART quantitation. LAMP-BART is an effective and sensitive technique for GM detection with significant potential for quantification even at low levels of contamination and in samples derived from crops such as maize with a large genome size. The resilience of LAMP-BART to acidic polysaccharides makes it well suited to rapid sample preparation techniques and hence to both high throughput laboratory settings and to portable GM detection applications. The impact of the plant sample matrix and genome loading within a reaction must be controlled to ensure quantification at low target concentrations.

TaqMan real-time RT-PCR detection of infectious salmon anaemia virus (ISAV) from formalin-fixed paraffin-embedded Atlantic salmon Salmo salar tissues.

PubMed

Godoy, M G; Kibenge, F S; Kibenge, M J; Olmos, P; Ovalle, L; Yañez, A J; Avendaño-Herrera, R

2010-05-18

The objective of this study was to evaluate the application of a TaqMan real-time reverse transcriptase PCR (RT-PCR) assay for the detection of infectious salmon anaemia virus (ISAV) in formalin-fixed paraffin-embedded (FFPE) fish tissues from Atlantic salmon Salmo salar with and without clinical signs of infection, and to compare it with histological and immunohistochemical (IHC) techniques. Sixteen fish samples obtained in 2007 and 2008 from 4 different farms in Chile were examined. The real-time RT-PCR allowed the detection of ISAV in FFPE samples from 9 of 16 fish, regardless of the organs analyzed, whereas 4 of the real-time RT-PCR negative fish were positive as indicated by histological examination and 3 of the real-time RT-PCR positive fish were negative as indicated by immunohistochemistry evaluation. The presence of ISAV in RT-PCR positive samples was confirmed by amplicon sequencing. This work constitutes the first report on the use of real-time RT-PCR for the detection of ISAV in FFPE sections. The assay is very useful for the examination of archival wax-embedded tissues, and allows for both prospective and retrospective evaluation of tissue samples for the presence of ISAV. However, the method only confirms the presence of the pathogen and should be used in combination with histopathology, which is a more precise tool. The combination of both techniques would be invaluable for confirmatory diagnosis of infectious salmon anaemia (ISA), which is essential for solving salmon farm problems.

Applications of QCL mid-IR imaging to the advancement of pathology

NASA Astrophysics Data System (ADS)

Sreedhar, Hari; Varma, Vishal K.; Bird, Benjamin; Guzman, Grace; Walsh, Michael J.

2017-03-01

Quantum Cascade Laser (QCL) spectroscopic imaging is a novel technique with many potential applications to histopathology. Like traditional Fourier Transform Infrared (FT-IR) imaging, QCL spectroscopic imaging derives biochemical data coupled to the spatial information of a tissue sample, and can be used to improve the diagnostic and prognostic value of assessment of a tissue biopsy. This technique also offers advantages over traditional FT-IR imaging, specifically the capacity for discrete frequency and real-time imaging. In this work we present applications of QCL spectroscopic imaging to tissue samples, including discrete frequency imaging, to compare with FT-IR and its potential value to pathology.

Real time quantitative phase microscopy based on single-shot transport of intensity equation (ssTIE) method

NASA Astrophysics Data System (ADS)

Yu, Wei; Tian, Xiaolin; He, Xiaoliang; Song, Xiaojun; Xue, Liang; Liu, Cheng; Wang, Shouyu

2016-08-01

Microscopy based on transport of intensity equation provides quantitative phase distributions which opens another perspective for cellular observations. However, it requires multi-focal image capturing while mechanical and electrical scanning limits its real time capacity in sample detections. Here, in order to break through this restriction, real time quantitative phase microscopy based on single-shot transport of the intensity equation method is proposed. A programmed phase mask is designed to realize simultaneous multi-focal image recording without any scanning; thus, phase distributions can be quantitatively retrieved in real time. It is believed the proposed method can be potentially applied in various biological and medical applications, especially for live cell imaging.

Ratiometric, visual, dual-signal fluorescent sensing and imaging of pH/copper ions in real samples based on carbon dots-fluorescein isothiocyanate composites.

PubMed

Zhu, Xinxin; Jin, Hui; Gao, Cuili; Gui, Rijun; Wang, Zonghua

2017-01-01

In this article, a facile aqueous synthesis of carbon dots (CDs) was developed by using natural kelp as a new carbon source. Through hydrothermal carbonization of kelp juice, fluorescent CDs were prepared and the CDs' surface was modified with polyethylenimine (PEI). The PEI-modified CDs were conjugated with fluorescein isothiocyanate (FITC) to fabricate CDs-FITC composites. To exploit broad applications, the CDs-FITC composites were developed as fluorescent sensing or imaging platforms of pH and Cu 2+ . Analytical performances of the composites-based fluorescence (FL) sensors were evaluated, including visual FL imaging of pH in glass bottle, ratiometric FL sensing of pH in yogurt samples, visual FL latent fingerprint and leaf imaging detection of [Cu 2+ ], dual-signal FL sensing of [Cu 2+ ] in yogurt and human serum samples. Experimental results from ratiometric, visual, dual-signal FL sensing and imaging applications confirmed the high feasibility, accuracy, stabilization and simplicity of CDs-FITC composites-based FL sensors for the detection of pH and Cu 2+ ions in real samples. Copyright © 2016 Elsevier B.V. All rights reserved.

Recent Development in Optical Fiber Biosensors

PubMed Central

Bosch, María Espinosa; Sánchez, Antonio Jesús Ruiz; Rojas, Fuensanta Sánchez; Ojeda, Catalina Bosch

2007-01-01

Remarkable developments can be seen in the field of optical fibre biosensors in the last decade. More sensors for specific analytes have been reported, novel sensing chemistries or transduction principles have been introduced, and applications in various analytical fields have been realised. This review consists of papers mainly reported in the last decade and presents about applications of optical fiber biosensors. Discussions on the trends in optical fiber biosensor applications in real samples are enumerated.

Culturally Specific Youth Substance Abuse Resistance Skills: Applicability across the U.S.-Mexico Border

PubMed Central

Marsiglia, Flavio F.; Kulis, Stephen; Rodriguez, Gregorio Martinez; Becerra, David; Castillo, Jason

2009-01-01

This study tests the applicability among adolescents in Mexico of the keepin' it REAL (refuse, explain, avoid, and leave) strategies that are common and effective ways that U.S. youth resist substance use. Following a social learning, communication competence and ecological theory integrated approach, the study draws on self-reported questionnaire data from a non-probability sample of 327 adolescents attending two public high schools in Monterrey, Nuevo León. Multivariate regressions were used to test whether the respondents' use of the REAL strategies by the participants could be predicted by key demographic variables. Separate models were estimated for the frequency of use of each strategy and for different substances. Findings indicate that most adolescents in this sample utilized each of the REAL strategies as well as other strategies to respond to offers of alcohol, cigarettes, or marijuana. Mexican and U.S. youth residing close to the US border appear to use similar drug resistance strategies. Use of the strategies varied considerably by the level of exposure to offers, but only minimally by gender and age. There were no notable differences by socioeconomic status or academic performance. Implications for prevention science, social work practice and social work research are discussed in the context of the bi-national border region and the applicability and prospect for dissemination of U.S. evidence based youth substance use prevention interventions. PMID:19924268

Culturally Specific Youth Substance Abuse Resistance Skills: Applicability across the U.S.-Mexico Border.

PubMed

Marsiglia, Flavio F; Kulis, Stephen; Rodriguez, Gregorio Martinez; Becerra, David; Castillo, Jason

2009-03-01

This study tests the applicability among adolescents in Mexico of the keepin' it REAL (refuse, explain, avoid, and leave) strategies that are common and effective ways that U.S. youth resist substance use. Following a social learning, communication competence and ecological theory integrated approach, the study draws on self-reported questionnaire data from a non-probability sample of 327 adolescents attending two public high schools in Monterrey, Nuevo León. Multivariate regressions were used to test whether the respondents' use of the REAL strategies by the participants could be predicted by key demographic variables. Separate models were estimated for the frequency of use of each strategy and for different substances. Findings indicate that most adolescents in this sample utilized each of the REAL strategies as well as other strategies to respond to offers of alcohol, cigarettes, or marijuana. Mexican and U.S. youth residing close to the US border appear to use similar drug resistance strategies. Use of the strategies varied considerably by the level of exposure to offers, but only minimally by gender and age. There were no notable differences by socioeconomic status or academic performance. Implications for prevention science, social work practice and social work research are discussed in the context of the bi-national border region and the applicability and prospect for dissemination of U.S. evidence based youth substance use prevention interventions.

Detecting spatial patterns of rivermouth processes using a geostatistical framework for near-real-time analysis

USGS Publications Warehouse

Xu, Wenzhao; Collingsworth, Paris D.; Bailey, Barbara; Carlson Mazur, Martha L.; Schaeffer, Jeff; Minsker, Barbara

2017-01-01

This paper proposes a geospatial analysis framework and software to interpret water-quality sampling data from towed undulating vehicles in near-real time. The framework includes data quality assurance and quality control processes, automated kriging interpolation along undulating paths, and local hotspot and cluster analyses. These methods are implemented in an interactive Web application developed using the Shiny package in the R programming environment to support near-real time analysis along with 2- and 3-D visualizations. The approach is demonstrated using historical sampling data from an undulating vehicle deployed at three rivermouth sites in Lake Michigan during 2011. The normalized root-mean-square error (NRMSE) of the interpolation averages approximately 10% in 3-fold cross validation. The results show that the framework can be used to track river plume dynamics and provide insights on mixing, which could be related to wind and seiche events.

Efficient Imaging and Real-Time Display of Scanning Ion Conductance Microscopy Based on Block Compressive Sensing

NASA Astrophysics Data System (ADS)

Li, Gongxin; Li, Peng; Wang, Yuechao; Wang, Wenxue; Xi, Ning; Liu, Lianqing

2014-07-01

Scanning Ion Conductance Microscopy (SICM) is one kind of Scanning Probe Microscopies (SPMs), and it is widely used in imaging soft samples for many distinctive advantages. However, the scanning speed of SICM is much slower than other SPMs. Compressive sensing (CS) could improve scanning speed tremendously by breaking through the Shannon sampling theorem, but it still requires too much time in image reconstruction. Block compressive sensing can be applied to SICM imaging to further reduce the reconstruction time of sparse signals, and it has another unique application that it can achieve the function of image real-time display in SICM imaging. In this article, a new method of dividing blocks and a new matrix arithmetic operation were proposed to build the block compressive sensing model, and several experiments were carried out to verify the superiority of block compressive sensing in reducing imaging time and real-time display in SICM imaging.

Development of a multiplex real time PCR to detect thermophilic lactic acid bacteria in natural whey starters.

PubMed

Bottari, Benedetta; Agrimonti, Caterina; Gatti, Monica; Neviani, Erasmo; Marmiroli, Nelson

2013-01-01

A multiplex real time PCR (mRealT-PCR) useful to rapidly screen microbial composition of thermophilic starter cultures for hard cooked cheeses and to compare samples with potentially different technological properties was developed. Novel primers directed toward pheS gene were designed and optimized for multiple detection of Lactobacillus helveticus, Lactobacillus delbrueckii, Streptococcus thermophilus and Lactobacillus fermentum. The assay was based on SYBR Green chemistry followed by melting curves analysis. The method was then evaluated for applications in the specific detection of the 4 lactic acid bacteria (LAB) in 29 different natural whey starters for Parmigiano Reggiano cheese production. The results obtained by mRealT-PCR were also compared with those obtained on the same samples by Fluorescence in Situ Hybridization (FISH) and Length-Heterogeneity PCR (LH-PCR). The mRealT-PCR developed in this study, was found to be effective for analyzing species present in the samples with an average sensitivity down to less than 600 copies of DNA and therefore sensitive enough to detect even minor LAB community members of thermophilic starter cultures. The assay was able to describe the microbial population of all the different natural whey starter samples analyzed, despite their natural variability. A higher number of whey starter samples with S. thermophilus and L. fermentum present in their microbial community were revealed, suggesting that these species could be more frequent in Parmigiano Reggiano natural whey starter samples than previously shown. The method was more effective than LH-PCR and FISH and, considering that these two techniques have to be used in combination to detect the less abundant species, the mRealT-PCR was also faster. Providing a single step sensitive detection of L. helveticus, L. delbrueckii, S. thermophilus and L. fermentum, the developed mRealT-PCR could be used for screening thermophilic starter cultures and to follow the presence of those species during ripening of derived dairy products. A major increase in understanding the starter culture contribution to cheese ecosystem could be harnessed to control cheese ripening and flavor formation. Copyright © 2012 Elsevier B.V. All rights reserved.

Real-Time Series Resistance Monitoring in PV Systems Without the Need for I-V Curves

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

Deceglie, Michael G.; Silverman, Timothy J.; Marion, Bill

We apply the physical principles of a familiar method, suns-V oc, to a new application: the real-time detection of series resistance changes in modules and systems operating outside. The real-time series resistance (RTSR) method that we describe avoids the need for collecting I-V curves or constructing full series resistance-free I-V curves. RTSR is most readily deployable at the module level on microinverters or module-integrated electronics, but it can also be extended to full strings. We found that automated detection of series resistance increases can provide early warnings of some of the most common reliability issues, which also pose fire risks,more » including broken ribbons, broken solder bonds, and contact problems in the junction or combiner box. We also describe the method in detail and describe a sample application to data collected from modules operating in the field.« less

Real-Time Series Resistance Monitoring in PV Systems Without the Need for IV Curves

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

Deceglie, Michael G.; Silverman, Timothy J.; Marion, Bill

We apply the physical principles of a familiar method, suns-Voc, to a new application: the real-time detection of series resistance changes in modules and systems operating outside. The real-time series resistance (RTSR) method that we describe avoids the need for collecting IV curves or constructing full series-resistance-free IV curves. RTSR is most readily deployable at the module level on micro-inverters or module-integrated electronics, but it can also be extended to full strings. Automated detection of series resistance increases can provide early warnings of some of the most common reliability issues, which also pose fire risks, including broken ribbons, broken soldermore » bonds, and contact problems in the junction or combiner box. We describe the method in detail and describe a sample application to data collected from modules operating in the field.« less

A multiplex real-time PCR assay for identification of Pneumocystis jirovecii, Histoplasma capsulatum, and Cryptococcus neoformans/Cryptococcus gattii in samples from AIDS patients with opportunistic pneumonia.

PubMed

Gago, Sara; Esteban, Cristina; Valero, Clara; Zaragoza, Oscar; Puig de la Bellacasa, Jorge; Buitrago, María José

2014-04-01

A molecular diagnostic technique based on real-time PCR was developed for the simultaneous detection of three of the most frequent causative agents of fungal opportunistic pneumonia in AIDS patients: Pneumocystis jirovecii, Histoplasma capsulatum, and Cryptococcus neoformans/Cryptococcus gattii. This technique was tested in cultured strains and in clinical samples from HIV-positive patients. The methodology used involved species-specific molecular beacon probes targeted to the internal transcribed spacer regions of the rDNA. An internal control was also included in each assay. The multiplex real-time PCR assay was tested in 24 clinical strains and 43 clinical samples from AIDS patients with proven fungal infection. The technique developed showed high reproducibility (r(2) of >0.98) and specificity (100%). For H. capsulatum and Cryptococcus spp., the detection limits of the method were 20 and 2 fg of genomic DNA/20 μl reaction mixture, respectively, while for P. jirovecii the detection limit was 2.92 log10 copies/20 μl reaction mixture. The sensitivity in vitro was 100% for clinical strains and 90.7% for clinical samples. The assay was positive for 92.5% of the patients. For one of the patients with proven histoplasmosis, P. jirovecii was also detected in a bronchoalveolar lavage sample. No PCR inhibition was detected. This multiplex real-time PCR technique is fast, sensitive, and specific and may have clinical applications.

Development and validation of a SYBR Green I-based real-time polymerase chain reaction method for detection of haptoglobin gene deletion in clinical materials.

PubMed

Soejima, Mikiko; Tsuchiya, Yuji; Egashira, Kouichi; Kawano, Hiroyuki; Sagawa, Kimitaka; Koda, Yoshiro

2010-06-01

Anhaptoglobinemic patients run the risk of severe anaphylactic transfusion reaction because they produce serum haptoglobin (Hp) antibodies. Being homozygous for the Hp gene deletion (HP(del)) is the only known cause of congenital anhaptoglobinemia, and clinical diagnosis of HP(del) before transfusion is important to prevent anaphylactic shock. We recently developed a 5'-nuclease (TaqMan) real-time polymerase chain reaction (PCR) method. A SYBR Green I-based duplex real-time PCR assay using two forward primers and a common reverse primer followed by melting curve analysis was developed to determine HP(del) zygosity in a single tube. In addition, to obviate initial DNA extraction, we examined serially diluted blood samples as PCR templates. Allelic discrimination of HP(del) yielded optimal results at blood sample dilutions of 1:64 to 1:1024. The results from 2231 blood samples were fully concordant with those obtained by the TaqMan-based real-time PCR method. The detection rate of the HP(del) allele by the SYBR Green I-based method is comparable with that using the TaqMan-based method. This method is readily applicable due to its low initial cost and analyzability using economical real-time PCR machines and is suitable for high-throughput analysis as an alternative method for allelic discrimination of HP(del).

Vector Doppler: spatial sampling analysis and presentation techniques for real-time systems

NASA Astrophysics Data System (ADS)

Capineri, Lorenzo; Scabia, Marco; Masotti, Leonardo F.

2001-05-01

The aim of the vector Doppler (VD) technique is the quantitative reconstruction of a velocity field independently of the ultrasonic probe axis to flow angle. In particular vector Doppler is interesting for studying vascular pathologies related to complex blood flow conditions. Clinical applications require a real-time operating mode and the capability to perform Doppler measurements over a defined volume. The combination of these two characteristics produces a real-time vector velocity map. In previous works the authors investigated the theory of pulsed wave (PW) vector Doppler and developed an experimental system capable of producing off-line 3D vector velocity maps. Afterwards, for producing dynamic velocity vector maps, we realized a new 2D vector Doppler system based on a modified commercial echograph. The measurement and presentation of a vector velocity field requires a correct spatial sampling that must satisfy the Shannon criterion. In this work we tackled this problem, establishing a relationship between sampling steps and scanning system characteristics. Another problem posed by the vector Doppler technique is the data representation in real-time that should be easy to interpret for the physician. With this in mine we attempted a multimedia solution that uses both interpolated images and sound to represent the information of the measured vector velocity map. These presentation techniques were experimented for real-time scanning on flow phantoms and preliminary measurements in vivo on a human carotid artery.

The use of newly developed real-time PCR for the rapid identification of bacteria in culture-negative osteomyelitis.

PubMed

Kobayashi, Naomi; Bauer, Thomas W; Sakai, Hiroshige; Togawa, Daisuke; Lieberman, Isador H; Fujishiro, Takaaki; Procop, Gary W

2006-12-01

We report a case of a culture-negative osteomyelitis in which our newly developed real-time polymerase chain reaction (PCR) could differentiate Staphylococcus aureus from Staphylococcus epidermidis. This is the first report that described the application of this novel assay to an orthopedics clinical sample. This assay may be useful for other clinical culture-negative cases in a combination with a broad-spectrum assay as a rapid microorganism identification method.

Inclusivity, exclusivity and limit of detection of commercially available real-time PCR assays for the detection of Salmonella.

PubMed

Margot, H; Stephan, R; Guarino, S; Jagadeesan, B; Chilton, D; O'Mahony, E; Iversen, C

2013-08-01

The traditional cultural detection of Salmonella spp. is both time- and labour-intensive. Salmonella is often a release criterion for the food industry and time to result is therefore an important factor. Storage of finished products and raw materials can be costly and may adversely impact available shelf-life. The application of real-time PCR for the detection of Salmonella spp. in food samples enables a potential time-saving of up to four days. The advancement of real-time PCR coupled with the development of commercially available systems in different formats has made this technology accessible for laboratories in an industrial environment. Ideally these systems are reliable and rapid as well as easy to use. The current study represents a comparative evaluation of seven commercial real-time PCR systems for the detection of Salmonella. Forty-nine target and twenty-nine non-target strains were included in the study to assess inclusivity and exclusivity. The limit of detection for each of the method was determined in four different food products. All systems evaluated were able to correctly identify the 49 Salmonella strains. Nevertheless, false positive results (Citrobacter spp.) were obtained with four of the seven systems. In milk powder and bouillon powder, the limit of detection was similar for all systems, suggesting a minimal matrix effect with these samples. Conversely, for black tea and cocoa powder some systems were prone to inhibition from matrix components. Up to 100% of the samples were inhibited using the proprietary extracts but inhibition could be reduced considerably by application of a DNA clean-up kit. Copyright © 2013 Elsevier B.V. All rights reserved.

Floor Covering and Surface Identification for Assistive Mobile Robotic Real-Time Room Localization Application

PubMed Central

Gillham, Michael; Howells, Gareth; Spurgeon, Sarah; McElroy, Ben

2013-01-01

Assistive robotic applications require systems capable of interaction in the human world, a workspace which is highly dynamic and not always predictable. Mobile assistive devices face the additional and complex problem of when and if intervention should occur; therefore before any trajectory assistance is given, the robotic device must know where it is in real-time, without unnecessary disruption or delay to the user requirements. In this paper, we demonstrate a novel robust method for determining room identification from floor features in a real-time computational frame for autonomous and assistive robotics in the human environment. We utilize two inexpensive sensors: an optical mouse sensor for straightforward and rapid, texture or pattern sampling, and a four color photodiode light sensor for fast color determination. We show how data relating floor texture and color obtained from typical dynamic human environments, using these two sensors, compares favorably with data obtained from a standard webcam. We show that suitable data can be extracted from these two sensors at a rate 16 times faster than a standard webcam, and that these data are in a form which can be rapidly processed using readily available classification techniques, suitable for real-time system application. We achieved a 95% correct classification accuracy identifying 133 rooms' flooring from 35 classes, suitable for fast coarse global room localization application, boundary crossing detection, and additionally some degree of surface type identification. PMID:24351647

Floor covering and surface identification for assistive mobile robotic real-time room localization application.

PubMed

Gillham, Michael; Howells, Gareth; Spurgeon, Sarah; McElroy, Ben

2013-12-17

Assistive robotic applications require systems capable of interaction in the human world, a workspace which is highly dynamic and not always predictable. Mobile assistive devices face the additional and complex problem of when and if intervention should occur; therefore before any trajectory assistance is given, the robotic device must know where it is in real-time, without unnecessary disruption or delay to the user requirements. In this paper, we demonstrate a novel robust method for determining room identification from floor features in a real-time computational frame for autonomous and assistive robotics in the human environment. We utilize two inexpensive sensors: an optical mouse sensor for straightforward and rapid, texture or pattern sampling, and a four color photodiode light sensor for fast color determination. We show how data relating floor texture and color obtained from typical dynamic human environments, using these two sensors, compares favorably with data obtained from a standard webcam. We show that suitable data can be extracted from these two sensors at a rate 16 times faster than a standard webcam, and that these data are in a form which can be rapidly processed using readily available classification techniques, suitable for real-time system application. We achieved a 95% correct classification accuracy identifying 133 rooms' flooring from 35 classes, suitable for fast coarse global room localization application, boundary crossing detection, and additionally some degree of surface type identification.

Rule Based Expert System for Monitoring Real Time Drug Supply in Hospital Using Radio Frequency Identification Technology

NASA Astrophysics Data System (ADS)

Driandanu, Galih; Surarso, Bayu; Suryono

2018-02-01

A radio frequency identification (RFID) has obtained increasing attention with the emergence of various applications. This study aims to examine the implementation of rule based expert system supported by RFID technology into a monitoring information system of drug supply in a hospital. This research facilitates in monitoring the real time drug supply by using data sample from the hospital pharmacy. This system able to identify and count the number of drug and provide warning and report in real time. the conclusion is the rule based expert system and RFID technology can facilitate the performance in monitoring the drug supply quickly and precisely.

Solid-state dewetting of thin Au films studied with real-time, in situ spectroscopic ellipsometry

NASA Astrophysics Data System (ADS)

Magnozzi, M.; Bisio, F.; Canepa, M.

2017-11-01

We report the design and testing of a small, high vacuum chamber that allows real-time, in situ spectroscopic ellipsometry (SE) measurements; the chamber was designed to be easily inserted within the arms of a commercial ellipsometer. As a test application, we investigated the temperature-induced solid-state dewetting of thin (20 to 8 nm) Au layers on Si wafers. In situ SE measurements acquired in real time during the heating of the samples reveal features that can be related to the birth of a localized surface plasmon resonance (LSPR), and demonstrate the presence of a temperature threshold for the solid-state dewetting.

Number-Density Measurements of CO2 in Real Time with an Optical Frequency Comb for High Accuracy and Precision

NASA Astrophysics Data System (ADS)

Scholten, Sarah K.; Perrella, Christopher; Anstie, James D.; White, Richard T.; Al-Ashwal, Waddah; Hébert, Nicolas Bourbeau; Genest, Jérôme; Luiten, Andre N.

2018-05-01

Real-time and accurate measurements of gas properties are highly desirable for numerous real-world applications. Here, we use an optical-frequency comb to demonstrate absolute number-density and temperature measurements of a sample gas with state-of-the-art precision and accuracy. The technique is demonstrated by measuring the number density of 12C16O2 with an accuracy of better than 1% and a precision of 0.04% in a measurement and analysis cycle of less than 1 s. This technique is transferable to numerous molecular species, thus offering an avenue for near-universal gas concentration measurements.

TRMM Precipitation Application Examples Using Data Services at NASA GES DISC

NASA Technical Reports Server (NTRS)

Liu, Zhong; Ostrenga, D.; Teng, W.; Kempler, S.; Greene, M.

2012-01-01

Data services to support precipitation applications are important for maximizing the NASA TRMM (Tropical Rainfall Measuring Mission) and the future GPM (Global Precipitation Mission) mission's societal benefits. TRMM Application examples using data services at the NASA GES DISC, including samples from users around the world will be presented in this poster. Precipitation applications often require near-real-time support. The GES DISC provides such support through: 1) Providing near-real-time precipitation products through TOVAS; 2) Maps of current conditions for monitoring precipitation and its anomaly around the world; 3) A user friendly tool (TOVAS) to analyze and visualize near-real-time and historical precipitation products; and 4) The GES DISC Hurricane Portal that provides near-real-time monitoring services for the Atlantic basin. Since the launch of TRMM, the GES DISC has developed data services to support precipitation applications around the world. In addition to the near-real-time services, other services include: 1) User friendly TRMM Online Visualization and Analysis System (TOVAS; URL: http://disc2.nascom.nasa.gov/Giovanni/tovas/); 2) Mirador (http://mirador.gsfc.nasa.gov/), a simplified interface for searching, browsing, and ordering Earth science data at GES DISC. Mirador is designed to be fast and easy to learn; 3) Data via OPeNDAP (http://disc.sci.gsfc.nasa.gov/services/opendap/). The OPeNDAP provides remote access to individual variables within datasets in a form usable by many tools, such as IDV, McIDAS-V, Panoply, Ferret and GrADS; and 4) The Open Geospatial Consortium (OGC) Web Map Service (WMS) (http://disc.sci.gsfc.nasa.gov/services/wxs_ogc.shtml). The WMS is an interface that allows the use of data and enables clients to build customized maps with data coming from a different network.

Real-Time Cellular Exometabolome Analysis with a Microfluidic-Mass Spectrometry Platform

PubMed Central

Marasco, Christina C.; Enders, Jeffrey R.; Seale, Kevin T.; McLean, John A.; Wikswo, John P.

2015-01-01

To address the challenges of tracking the multitude of signaling molecules and metabolites that is the basis of biological complexity, we describe a strategy to expand the analytical techniques for dynamic systems biology. Using microfluidics, online desalting, and mass spectrometry technologies, we constructed and validated a platform well suited for sampling the cellular microenvironment with high temporal resolution. Our platform achieves success in: automated cellular stimulation and microenvironment control; reduced non-specific adsorption to polydimethylsiloxane due to surface passivation; real-time online sample collection; near real-time sample preparation for salt removal; and real-time online mass spectrometry. When compared against the benchmark of “in-culture” experiments combined with ultraperformance liquid chromatography-electrospray ionization-ion mobility-mass spectrometry (UPLC-ESI-IM-MS), our platform alleviates the volume challenge issues caused by dilution of autocrine and paracrine signaling and dramatically reduces sample preparation and data collection time, while reducing undesirable external influence from various manual methods of manipulating cells and media (e.g., cell centrifugation). To validate this system biologically, we focused on cellular responses of Jurkat T cells to microenvironmental stimuli. Application of these stimuli, in conjunction with the cell’s metabolic processes, results in changes in consumption of nutrients and secretion of biomolecules (collectively, the exometabolome), which enable communication with other cells or tissues and elimination of waste. Naïve and experienced T-cell metabolism of cocaine is used as an exemplary system to confirm the platform’s capability, highlight its potential for metabolite discovery applications, and explore immunological memory of T-cell drug exposure. Our platform proved capable of detecting metabolomic variations between naïve and experienced Jurkat T cells and highlights the dynamics of the exometabolome over time. Upregulation of the cocaine metabolite, benzoylecgonine, was noted in experienced T cells, indicating potential cellular memory of cocaine exposure. These metabolomics distinctions were absent from the analogous, traditional “in-culture” UPLC-ESI-IM-MS experiment, further demonstrating this platform’s capabilities. PMID:25723555

Electronic Tongue—A Tool for All Tastes?

PubMed Central

Podrażka, Marta; Bączyńska, Ewa; Kundys, Magdalena; Jeleń, Paulina S.; Witkowska Nery, Emilia

2017-01-01

Electronic tongue systems are traditionally used to analyse: food products, water samples and taste masking technologies for pharmaceuticals. In principle, their applications are almost limitless, as they are able to almost completely reduce the impact of interferents and can be applied to distinguish samples of extreme complexity as for example broths from different stages of fermentation. Nevertheless, their applications outside the three principal sample types are, in comparison, rather scarce. In this review, we would like to take a closer look on what are real capabilities of electronic tongue systems, what can be achieved using mixed sensor arrays and by introduction of biosensors or molecularly imprinted polymers in the matrix. We will discuss future directions both in the sense of applications as well as system development in the ever-growing trend of low cost analysis. PMID:29301230

Applications of DART-MS for food quality and safety assurance in food supply chain.

PubMed

Guo, Tianyang; Yong, Wei; Jin, Yong; Zhang, Liya; Liu, Jiahui; Wang, Sai; Chen, Qilong; Dong, Yiyang; Su, Haijia; Tan, Tianwei

2017-03-01

Direct analysis in real time (DART) represents a new generation of ion source which is used for rapid ionization of small molecules under ambient conditions. The combination of DART and various mass spectrometers allows analyzing multiple food samples with simple or no sample treatment, or in conjunction with prevailing protocolized sample preparation methods. Abundant applications by DART-MS have been reviewed in this paper. The DART-MS strategy applied to food supply chain (FSC), including production, processing, and storage and transportation, provides a comprehensive solution to various food components, contaminants, authenticity, and traceability. Additionally, typical applications available in food analysis by other ambient ionization mass spectrometers were summarized, and fundamentals mainly including mechanisms, devices, and parameters were discussed as well. © 2015 Wiley Periodicals, Inc. Mass Spec Rev. 36:161-187, 2017. © 2015 Wiley Periodicals, Inc.

A Real-Time PCR Assay for Bat SARS-Like Coronavirus Detection and Its Application to Italian Greater Horseshoe Bat Faecal Sample Surveys

PubMed Central

Balboni, Andrea; Gallina, Laura; Palladini, Alessandra; Prosperi, Santino; Battilani, Mara

2012-01-01

Bats are source of coronaviruses closely related to the severe acute respiratory syndrome (SARS) virus. Numerous studies have been carried out to identify new bat viruses related to SARS-coronavirus (bat-SARS-like CoVs) using a reverse-transcribed-polymerase chain reaction assay. However, a qualitative PCR could underestimate the prevalence of infection, affecting the epidemiological evaluation of bats in viral ecology. In this work an SYBR Green-real time PCR assay was developed for diagnosing infection with SARS-related coronaviruses from bat guano and was applied as screening tool in a survey carried out on 45 greater horseshoe bats (Rhinolophus ferrumequinum) sampled in Italy in 2009. The assay showed high sensitivity and reproducibility. Its application on bats screening resulted in a prevalence of 42%. This method could be suitable as screening tool in epidemiological surveys about the presence of bat-SARS-like CoVs, consequently to obtain a more realistic scenario of the viral prevalence in the population. PMID:22654650

Application of graphene oxide/lanthanum-modified carbon paste electrode for the selective determination of dopamine

NASA Astrophysics Data System (ADS)

Ye, Fengying; Feng, Chenqi; Fu, Ning; Wu, Huihui; Jiang, Jibo; Han, Sheng

2015-12-01

A home-made carbon paste electrode (CPE) was reformed by graphene oxide (GO)/lanthanum (La) complexes, and a modified electrode, called GO-La/CPE, was fabricated for the selective determination of dopamine (DA) by cyclic voltammetry (CV) and differential pulse voltammetry (DPV). Several factors affecting the electrocatalytic performance of the modified sensor were investigated. Owning to the combination of GO and La ions, the GO-La/CPE sensor exhibited large surface area, well selectivity, good repeatability and stability in the oxidation reaction of DA. At optimal conditions, the response of the GO-La/CPE electrode for determining DA was linear in the region of 0.01-0.1 μM and 0.1-400.0 μM. The limit of detection was down to 0.32 nM (S/N = 3). In addition, this modified electrode was successfully applied to the detection of DA in real urine and serum samples by using standard adding method, showing its promising application in the electroanalysis of real samples.

Paper based Flexible and Conformal SERS Substrate for Rapid Trace Detection on Real-world Surfaces

NASA Astrophysics Data System (ADS)

Singamaneni, Srikanth; Lee, Chang; Tian, Limei

2011-03-01

One of the important but often overlooked considerations in the design of surface enhanced Raman scattering (SERS) substrates for trace detection is the efficiency of sample collection. Conventional designs based on rigid substrates such as silicon, alumina, and glass resist conformal contact with the surface under investigation, making the sample collection inefficient. We demonstrate a novel SERS substrate based on common filter paper adsorbed with gold nanorods, which allows conformal contact with real-world surfaces, thus dramatically enhancing the sample collection efficiency compared to conventional rigid substrates. We demonstrate the detection of trace amounts of analyte (140 pg spread over 4 cm2) by simply swabbing the surface under investigation with the novel SERS substrate. The hierarchical fibrous structure of paper serves as a 3D vasculature for easy uptake and transport of the analytes to the electromagnetic hot spots in the paper. Simple yet highly efficient and cost effective SERS substrate demonstrated here brings SERS based trace detection closer to real-world applications. We acknowledge the financial support from Center for Materials Innovation at Washington University.

Using Real-Time PCR as a tool for monitoring the authenticity of commercial coffees.

PubMed

Ferreira, Thiago; Farah, Adriana; Oliveira, Tatiane C; Lima, Ivanilda S; Vitório, Felipe; Oliveira, Edna M M

2016-05-15

Coffee is one of the main food products commercialized in the world. Its considerable market value among food products makes it susceptible to adulteration, especially with cereals. Therefore, the objective of this study was to develop a method based on Real-Time Polymerase Chain Reaction (PCR) for detection of cereals in commercial ground roast and soluble coffees. After comparison with standard curves obtained by serial dilution of DNA extracted from barley, corn and rice, the method was sensitive and specific to quantify down to 0.6 pg, 14 pg and 16 pg of barley, corn and rice DNA, respectively. To verify the applicability of the method, 30 commercial samples obtained in different countries were evaluated and those classified as gourmets or superior did not present the tested cereals DNA. However, barley was detected in various traditional (cheaper) samples from South America. In addition, corn and rice were also detected in different samples. Real-Time PCR showed to be suitable for detection of food adulterants in commercial ground roast and soluble coffees. Copyright © 2015 Elsevier Ltd. All rights reserved.

Analyzing machine noise for real time maintenance

NASA Astrophysics Data System (ADS)

Yamato, Yoji; Fukumoto, Yoshifumi; Kumazaki, Hiroki

2017-02-01

Recently, IoT technologies have been progressed and applications of maintenance area are expected. However, IoT maintenance applications are not spread in Japan yet because of one-off solution of sensing and analyzing for each case, high cost to collect sensing data and insufficient maintenance automation. This paper proposes a maintenance platform which analyzes sound data in edges, analyzes only anomaly data in cloud and orders maintenance automatically to resolve existing technology problems. We also implement a sample application and compare related work.

Friction coefficient of skin in real-time.

PubMed

Sivamani, Raja K; Goodman, Jack; Gitis, Norm V; Maibach, Howard I

2003-08-01

Friction studies are useful in quantitatively investigating the skin surface. Previous studies utilized different apparatuses and materials for these investigations but there was no real-time test parameter control or monitoring. Our studies incorporated the commercially available UMT Series Micro-Tribometer, a tribology instrument that permits real-time monitoring and calculation of the important parameters in friction studies, increasing the accuracy over previous tribology and friction measurement devices used on skin. Our friction tests were performed on four healthy volunteers and on abdominal skin samples. A stainless steel ball was pressed on to the skin with at a pre-set load and then moved across the skin at a constant velocity of 5 mm/min. The UMT continuously monitored the friction force of the skin and the normal force of the ball to calculate the friction coefficient in real-time. Tests investigated the applicability of Amonton's law, the impact of increased and decreased hydration, and the effect of the application of moisturizers. The friction coefficient depends on the normal load applied, and Amonton's law does not provide an accurate description for the skin surface. Application of water to the skin increased the friction coefficient and application of isopropyl alcohol decreased it. Fast acting moisturizers immediately increased the friction coefficient, but did not have the prolonged effect of the slow, long lasting moisturizers. The UMT is capable of making real-time measurements on the skin and can be used as an effective tool to study friction properties. Results from the UMT measurements agree closely with theory regarding the skin surface.

Real-time label-free quantitative fluorescence microscopy-based detection of ATP using a tunable fluorescent nano-aptasensor platform

NASA Astrophysics Data System (ADS)

Shrivastava, Sajal; Sohn, Il-Yung; Son, Young-Min; Lee, Won-Il; Lee, Nae-Eung

2015-11-01

Although real-time label-free fluorescent aptasensors based on nanomaterials are increasingly recognized as a useful strategy for the detection of target biomolecules with high fidelity, the lack of an imaging-based quantitative measurement platform limits their implementation with biological samples. Here we introduce an ensemble strategy for a real-time label-free fluorescent graphene (Gr) aptasensor platform. This platform employs aptamer length-dependent tunability, thus enabling the reagentless quantitative detection of biomolecules through computational processing coupled with real-time fluorescence imaging data. We demonstrate that this strategy effectively delivers dose-dependent quantitative readouts of adenosine triphosphate (ATP) concentration on chemical vapor deposited (CVD) Gr and reduced graphene oxide (rGO) surfaces, thereby providing cytotoxicity assessment. Compared with conventional fluorescence spectrometry methods, our highly efficient, universally applicable, and rational approach will facilitate broader implementation of imaging-based biosensing platforms for the quantitative evaluation of a range of target molecules.Although real-time label-free fluorescent aptasensors based on nanomaterials are increasingly recognized as a useful strategy for the detection of target biomolecules with high fidelity, the lack of an imaging-based quantitative measurement platform limits their implementation with biological samples. Here we introduce an ensemble strategy for a real-time label-free fluorescent graphene (Gr) aptasensor platform. This platform employs aptamer length-dependent tunability, thus enabling the reagentless quantitative detection of biomolecules through computational processing coupled with real-time fluorescence imaging data. We demonstrate that this strategy effectively delivers dose-dependent quantitative readouts of adenosine triphosphate (ATP) concentration on chemical vapor deposited (CVD) Gr and reduced graphene oxide (rGO) surfaces, thereby providing cytotoxicity assessment. Compared with conventional fluorescence spectrometry methods, our highly efficient, universally applicable, and rational approach will facilitate broader implementation of imaging-based biosensing platforms for the quantitative evaluation of a range of target molecules. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr05839b

ALMA Correlator Real-Time Data Processor

NASA Astrophysics Data System (ADS)

Pisano, J.; Amestica, R.; Perez, J.

2005-10-01

The design of a real-time Linux application utilizing Real-Time Application Interface (RTAI) to process real-time data from the radio astronomy correlator for the Atacama Large Millimeter Array (ALMA) is described. The correlator is a custom-built digital signal processor which computes the cross-correlation function of two digitized signal streams. ALMA will have 64 antennas with 2080 signal streams each with a sample rate of 4 giga-samples per second. The correlator's aggregate data output will be 1 gigabyte per second. The software is defined by hard deadlines with high input and processing data rates, while requiring interfaces to non real-time external computers. The designed computer system - the Correlator Data Processor or CDP, consists of a cluster of 17 SMP computers, 16 of which are compute nodes plus a master controller node all running real-time Linux kernels. Each compute node uses an RTAI kernel module to interface to a 32-bit parallel interface which accepts raw data at 64 megabytes per second in 1 megabyte chunks every 16 milliseconds. These data are transferred to tasks running on multiple CPUs in hard real-time using RTAI's LXRT facility to perform quantization corrections, data windowing, FFTs, and phase corrections for a processing rate of approximately 1 GFLOPS. Highly accurate timing signals are distributed to all seventeen computer nodes in order to synchronize them to other time-dependent devices in the observatory array. RTAI kernel tasks interface to the timing signals providing sub-millisecond timing resolution. The CDP interfaces, via the master node, to other computer systems on an external intra-net for command and control, data storage, and further data (image) processing. The master node accesses these external systems utilizing ALMA Common Software (ACS), a CORBA-based client-server software infrastructure providing logging, monitoring, data delivery, and intra-computer function invocation. The software is being developed in tandem with the correlator hardware which presents software engineering challenges as the hardware evolves. The current status of this project and future goals are also presented.

Microbial Monitoring of Common Opportunistic Pathogens by Comparing Multiple Real-time PCR Platforms for Potential Space Applications

NASA Technical Reports Server (NTRS)

Roman, Monserrate C.; Jones, Kathy U.; Oubre, Cherie M.; Castro, Victoria; Ott, Mark C.; Birmele, Michele; Venkateswaran, Kasthuri J.; Vaishampayan, Parag A.

2013-01-01

Current methods for microbial detection: a) Labor & time intensive cultivation-based approaches that can fail to detect or characterize all cells present. b) Requires collection of samples on orbit and transportation back to ground for analysis. Disadvantages to current detection methods: a) Unable to perform quick and reliable detection on orbit. b) Lengthy sampling intervals. c) No microbe identification.

Introduction of a dermatophyte polymerase chain reaction assay to the diagnostic mycology service in Scotland.

PubMed

Alexander, C L; Shankland, G S; Carman, W; Williams, C

2011-05-01

Dermatophytes are the major cause of superficial mycoses in samples submitted to Clinical Mycology, Glasgow. The most prevalent species is Trichophyton rubrum as identified classically by microscopy and culture. Recent advances in polymerase chain reaction (PCR) technology were examined for the feasibility of introducing a T. rubrum real-time PCR assay into a routine diagnostic service. To improve the diagnostic mycology service by the introduction of a real-time PCR test for T. rubrum. The DNA from 4972 nail and skin samples was obtained using the Qiagen QIAsymphony automated extractor. This DNA was subjected to real-time PCR using T. rubrum-specific primers and a probe. During phase 1 of the study, 862 samples were analysed; 446 of 470 specimens that grew T. rubrum were detected by PCR. Out of 4110 samples analysed during phase 2, 753 T. rubrum infections were diagnosed and reported within 72 h. A total of 3357 samples were negative for a fungal infection by PCR and microscopy; these were also reported within 72 h. A vast reduction in the turnaround times can be achieved using this technique as opposed to classical methods. Samples which are PCR negative but microscopy positive are still subjected to culture. Screening samples for their suitability for PCR prior to processing eliminates the application of PCR for T. rubrum on inappropriate samples such those from the scalp or pityriasis versicolor. © 2011 The Authors. BJD © 2011 British Association of Dermatologists.

Energy-filtered real- and k-space secondary and energy-loss electron imaging with Dual Emission Electron spectro-Microscope: Cs/Mo(110).

PubMed

Grzelakowski, Krzysztof P

2016-05-01

Since its introduction the importance of complementary k||-space (LEED) and real space (LEEM) information in the investigation of surface science phenomena has been widely demonstrated over the last five decades. In this paper we report the application of a novel kind of electron spectromicroscope Dual Emission Electron spectroMicroscope (DEEM) with two independent electron optical channels for reciprocal and real space quasi-simultaneous imaging in investigation of a Cs covered Mo(110) single crystal by using the 800eV electron beam from an "in-lens" electron gun system developed for the sample illumination. With the DEEM spectromicroscope it is possible to observe dynamic, irreversible processes at surfaces in the energy-filtered real space and in the corresponding energy-filtered kǁ-space quasi-simultaneously in two independent imaging columns. The novel concept of the high energy electron beam sample illumination in the cathode lens based microscopes allows chemically selective imaging and analysis under laboratory conditions. Copyright © 2015 Elsevier B.V. All rights reserved.

Application of Fiber Optic ATR-FTIR Methods for In Situ Characterization of Protein Delivery Systems in Real Time

PubMed Central

McFearin, Cathryn L.; Sankaranarayanan, Jagadis; Almutairi, Adah

2011-01-01

Real Time Characterization of Protein Delivery Systems A fiber optic coupled ATR-FTIR spectroscopy technique was applied to the study of two different therapeutic delivery systems, acid degradable hydrogels and nanoparticles. Real time exponential release of a model protein, human serum albumin (HSA), was observed from two different polymeric hydrogels formulated with a pH sensitive crosslinker. Spectroscopic examination of nanoparticles formulated with an acid degradable polymer shell and encapsulated HSA exhibited vibrational signatures characteristic of both particle and payload when exposed to lowered pH conditions demonstrating the ability of this methodology to simultaneously measure phenomena arising from a system with a mixture of components. In addition, thorough characterization of these pH sensitive delivery vehicles without encapsulated protein was also accomplished in order to separate the effects of the payload during degradation. By providing in situ, real time detection in combination with the ability to specifically identify different components in a mixture without involved sample preparation and minimal sample disturbance, the versatility and suitability of this type of experiment for research in the pharmaceutical field is demonstrated. PMID:21476582

Investigation of Low Cost Sensor-Based Leak Detection System for Fence Line Applications

EPA Science Inventory

With recent technological advances, low-cost time-resolved sensors may become effective tools to support time-integrated passive sampling strategies by helping to decipher origin of emissions in real-time. As part of the Petroleum Refinery Risk and Technology Review, New Source ...

A 'smart' tube holder enables real-time sample monitoring in a standard lab centrifuge.

PubMed

Hoang, Tony; Moskwa, Nicholas; Halvorsen, Ken

2018-01-01

The centrifuge is among the oldest and most widely used pieces of laboratory equipment, with significant applications that include clinical diagnostics and biomedical research. A major limitation of laboratory centrifuges is their "black box" nature, limiting sample observation to before and after centrifugation. Thus, optimized protocols require significant trial and error, while unoptimized protocols waste time by centrifuging longer than necessary or material due to incomplete sedimentation. Here, we developed an instrumented centrifuge tube receptacle compatible with several commercial benchtop centrifuges that can provide real-time sample analysis during centrifugation. We demonstrated the system by monitoring cell separations during centrifugation for different spin speeds, concentrations, buffers, cell types, and temperatures. We show that the collected data are valuable for analytical purposes (e.g. quality control), or as feedback to the user or the instrument. For the latter, we verified an adaptation where complete sedimentation turned off the centrifuge and notified the user by a text message. Our system adds new functionality to existing laboratory centrifuges, saving users time and providing useful feedback. This add-on potentially enables new analytical applications for an instrument that has remained largely unchanged for decades.

A ‘smart’ tube holder enables real-time sample monitoring in a standard lab centrifuge

PubMed Central

Hoang, Tony; Moskwa, Nicholas

2018-01-01

The centrifuge is among the oldest and most widely used pieces of laboratory equipment, with significant applications that include clinical diagnostics and biomedical research. A major limitation of laboratory centrifuges is their “black box” nature, limiting sample observation to before and after centrifugation. Thus, optimized protocols require significant trial and error, while unoptimized protocols waste time by centrifuging longer than necessary or material due to incomplete sedimentation. Here, we developed an instrumented centrifuge tube receptacle compatible with several commercial benchtop centrifuges that can provide real-time sample analysis during centrifugation. We demonstrated the system by monitoring cell separations during centrifugation for different spin speeds, concentrations, buffers, cell types, and temperatures. We show that the collected data are valuable for analytical purposes (e.g. quality control), or as feedback to the user or the instrument. For the latter, we verified an adaptation where complete sedimentation turned off the centrifuge and notified the user by a text message. Our system adds new functionality to existing laboratory centrifuges, saving users time and providing useful feedback. This add-on potentially enables new analytical applications for an instrument that has remained largely unchanged for decades. PMID:29659624

Superhydrophobic Analyte Concentration Utilizing Colloid-Pillar Array SERS Substrates

DOE PAGES

Wallace, Ryan A.; Charlton, Jennifer J.; Kirchner, Teresa B.; ...

2014-11-04

In order to detect a few molecules present in a large sample it is important to know the trace components in the medicinal and environmental sample. Surface enhanced Raman spectroscopy (SERS) is a technique that can be utilized to detect molecules at very low absolute numbers. However, detection at trace concentration levels in real samples requires properly designed delivery and detection systems. Moreover, the following work involves superhydrophobic surfaces that includes silicon pillar arrays formed by lithographic and dewetting protocols. In order to generate the necessary plasmonic substrate for SERS detection, simple and flow stable Ag colloid was added tomore » the functionalized pillar array system via soaking. The pillars are used native and with hydrophobic modification. The pillars provide a means to concentrate analyte via superhydrophobic droplet evaporation effects. A 100-fold concentration of analyte was estimated, with a limit of detection of 2.9 10-12 M for mitoxantrone dihydrochloride. Additionally, analytes were delivered to the surface via a multiplex approach in order to demonstrate an ability to control droplet size and placement for scaled-up applications in real world applications. Finally, a concentration process involving transport and sequestration based on surface treatment selective wicking is demonstrated.« less

Trends and advances in food analysis by real-time polymerase chain reaction.

PubMed

Salihah, Nur Thaqifah; Hossain, Mohammad Mosharraf; Lubis, Hamadah; Ahmed, Minhaz Uddin

2016-05-01

Analyses to ensure food safety and quality are more relevant now because of rapid changes in the quantity, diversity and mobility of food. Food-contamination must be determined to maintain health and up-hold laws, as well as for ethical and cultural concerns. Real-time polymerase chain reaction (RT-PCR), a rapid and inexpensive quantitative method to detect the presence of targeted DNA-segments in samples, helps in determining both accidental and intentional adulterations of foods by biological contaminants. This review presents recent developments in theory, techniques, and applications of RT-PCR in food analyses, RT-PCR addresses the limitations of traditional food analyses in terms of sensitivity, range of analytes, multiplexing ability, cost, time, and point-of-care applications. A range of targets, including species of plants or animals which are used as food ingredients, food-borne bacteria or viruses, genetically modified organisms, and allergens, even in highly processed foods can be identified by RT-PCR, even at very low concentrations. Microfluidic RT-PCR eliminates the separate sample-processing step to create opportunities for point-of-care analyses. We also cover the challenges related to using RT-PCR for food analyses, such as the need to further improve sample handling.

Superhydrophobic Analyte Concentration Utilizing Colloid-Pillar Array SERS Substrates

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

Wallace, Ryan A.; Charlton, Jennifer J.; Kirchner, Teresa B.

In order to detect a few molecules present in a large sample it is important to know the trace components in the medicinal and environmental sample. Surface enhanced Raman spectroscopy (SERS) is a technique that can be utilized to detect molecules at very low absolute numbers. However, detection at trace concentration levels in real samples requires properly designed delivery and detection systems. Moreover, the following work involves superhydrophobic surfaces that includes silicon pillar arrays formed by lithographic and dewetting protocols. In order to generate the necessary plasmonic substrate for SERS detection, simple and flow stable Ag colloid was added tomore » the functionalized pillar array system via soaking. The pillars are used native and with hydrophobic modification. The pillars provide a means to concentrate analyte via superhydrophobic droplet evaporation effects. A 100-fold concentration of analyte was estimated, with a limit of detection of 2.9 10-12 M for mitoxantrone dihydrochloride. Additionally, analytes were delivered to the surface via a multiplex approach in order to demonstrate an ability to control droplet size and placement for scaled-up applications in real world applications. Finally, a concentration process involving transport and sequestration based on surface treatment selective wicking is demonstrated.« less

Drivers’ Visual Behavior-Guided RRT Motion Planner for Autonomous On-Road Driving

PubMed Central

Du, Mingbo; Mei, Tao; Liang, Huawei; Chen, Jiajia; Huang, Rulin; Zhao, Pan

2016-01-01

This paper describes a real-time motion planner based on the drivers’ visual behavior-guided rapidly exploring random tree (RRT) approach, which is applicable to on-road driving of autonomous vehicles. The primary novelty is in the use of the guidance of drivers’ visual search behavior in the framework of RRT motion planner. RRT is an incremental sampling-based method that is widely used to solve the robotic motion planning problems. However, RRT is often unreliable in a number of practical applications such as autonomous vehicles used for on-road driving because of the unnatural trajectory, useless sampling, and slow exploration. To address these problems, we present an interesting RRT algorithm that introduces an effective guided sampling strategy based on the drivers’ visual search behavior on road and a continuous-curvature smooth method based on B-spline. The proposed algorithm is implemented on a real autonomous vehicle and verified against several different traffic scenarios. A large number of the experimental results demonstrate that our algorithm is feasible and efficient for on-road autonomous driving. Furthermore, the comparative test and statistical analyses illustrate that its excellent performance is superior to other previous algorithms. PMID:26784203

Drivers' Visual Behavior-Guided RRT Motion Planner for Autonomous On-Road Driving.

PubMed

Du, Mingbo; Mei, Tao; Liang, Huawei; Chen, Jiajia; Huang, Rulin; Zhao, Pan

2016-01-15

This paper describes a real-time motion planner based on the drivers' visual behavior-guided rapidly exploring random tree (RRT) approach, which is applicable to on-road driving of autonomous vehicles. The primary novelty is in the use of the guidance of drivers' visual search behavior in the framework of RRT motion planner. RRT is an incremental sampling-based method that is widely used to solve the robotic motion planning problems. However, RRT is often unreliable in a number of practical applications such as autonomous vehicles used for on-road driving because of the unnatural trajectory, useless sampling, and slow exploration. To address these problems, we present an interesting RRT algorithm that introduces an effective guided sampling strategy based on the drivers' visual search behavior on road and a continuous-curvature smooth method based on B-spline. The proposed algorithm is implemented on a real autonomous vehicle and verified against several different traffic scenarios. A large number of the experimental results demonstrate that our algorithm is feasible and efficient for on-road autonomous driving. Furthermore, the comparative test and statistical analyses illustrate that its excellent performance is superior to other previous algorithms.

The Maia Spectroscopy Detector System: Engineering for Integrated Pulse Capture, Low-Latency Scanning and Real-Time Processing

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

Kirkham, R.; Siddons, D.; Dunn, P.A.

2010-06-23

The Maia detector system is engineered for energy dispersive x-ray fluorescence spectroscopy and elemental imaging at photon rates exceeding 10{sup 7}/s, integrated scanning of samples for pixel transit times as small as 50 {micro}s and high definition images of 10{sup 8} pixels and real-time processing of detected events for spectral deconvolution and online display of pure elemental images. The system developed by CSIRO and BNL combines a planar silicon 384 detector array, application-specific integrated circuits for pulse shaping and peak detection and sampling and optical data transmission to an FPGA-based pipelined, parallel processor. This paper describes the system and themore » underpinning engineering solutions.« less

In-Situ Real-Time Focus Detection during Laser Processing Using Double-Hole Masks and Advanced Image Sensor Software

PubMed Central

Hoang, Phuong Le; Ahn, Sanghoon; Kim, Jeng-o; Kang, Heeshin; Noh, Jiwhan

2017-01-01

In modern high-intensity ultrafast laser processing, detecting the focal position of the working laser beam, at which the intensity is the highest and the beam diameter is the lowest, and immediately locating the target sample at that point are challenging tasks. A system that allows in-situ real-time focus determination and fabrication using a high-power laser has been in high demand among both engineers and scientists. Conventional techniques require the complicated mathematical theory of wave optics, employing interference as well as diffraction phenomena to detect the focal position; however, these methods are ineffective and expensive for industrial application. Moreover, these techniques could not perform detection and fabrication simultaneously. In this paper, we propose an optical design capable of detecting the focal point and fabricating complex patterns on a planar sample surface simultaneously. In-situ real-time focus detection is performed using a bandpass filter, which only allows for the detection of laser transmission. The technique enables rapid, non-destructive, and precise detection of the focal point. Furthermore, it is sufficiently simple for application in both science and industry for mass production, and it is expected to contribute to the next generation of laser equipment, which can be used to fabricate micro-patterns with high complexity. PMID:28671566

Characterization of controlled bone defects using 2D and 3D ultrasound imaging techniques.

PubMed

Parmar, Biren J; Longsine, Whitney; Sabonghy, Eric P; Han, Arum; Tasciotti, Ennio; Weiner, Bradley K; Ferrari, Mauro; Righetti, Raffaella

2010-08-21

Ultrasound is emerging as an attractive alternative modality to standard x-ray and CT methods for bone assessment applications. As of today, however, there is a lack of systematic studies that investigate the performance of diagnostic ultrasound techniques in bone imaging applications. This study aims at understanding the performance limitations of new ultrasound techniques for imaging bones in controlled experiments in vitro. Experiments are performed on samples of mammalian and non-mammalian bones with controlled defects with size ranging from 400 microm to 5 mm. Ultrasound findings are statistically compared with those obtained from the same samples using standard x-ray imaging modalities and optical microscopy. The results of this study demonstrate that it is feasible to use diagnostic ultrasound imaging techniques to assess sub-millimeter bone defects in real time and with high accuracy and precision. These results also demonstrate that ultrasound imaging techniques perform comparably better than x-ray imaging and optical imaging methods, in the assessment of a wide range of controlled defects both in mammalian and non-mammalian bones. In the future, ultrasound imaging techniques might provide a cost-effective, real-time, safe and portable diagnostic tool for bone imaging applications.

A data acquisition protocol for a reactive wireless sensor network monitoring application.

PubMed

Aderohunmu, Femi A; Brunelli, Davide; Deng, Jeremiah D; Purvis, Martin K

2015-04-30

Limiting energy consumption is one of the primary aims for most real-world deployments of wireless sensor networks. Unfortunately, attempts to optimize energy efficiency are often in conflict with the demand for network reactiveness to transmit urgent messages. In this article, we propose SWIFTNET: a reactive data acquisition scheme. It is built on the synergies arising from a combination of the data reduction methods and energy-efficient data compression schemes. Particularly, it combines compressed sensing, data prediction and adaptive sampling strategies. We show how this approach dramatically reduces the amount of unnecessary data transmission in the deployment for environmental monitoring and surveillance networks. SWIFTNET targets any monitoring applications that require high reactiveness with aggressive data collection and transmission. To test the performance of this method, we present a real-world testbed for a wildfire monitoring as a use-case. The results from our in-house deployment testbed of 15 nodes have proven to be favorable. On average, over 50% communication reduction when compared with a default adaptive prediction method is achieved without any loss in accuracy. In addition, SWIFTNET is able to guarantee reactiveness by adjusting the sampling interval from 5 min up to 15 s in our application domain.

A Data Acquisition Protocol for a Reactive Wireless Sensor Network Monitoring Application

PubMed Central

Aderohunmu, Femi A.; Brunelli, Davide; Deng, Jeremiah D.; Purvis, Martin K.

2015-01-01

Limiting energy consumption is one of the primary aims for most real-world deployments of wireless sensor networks. Unfortunately, attempts to optimize energy efficiency are often in conflict with the demand for network reactiveness to transmit urgent messages. In this article, we propose SWIFTNET: a reactive data acquisition scheme. It is built on the synergies arising from a combination of the data reduction methods and energy-efficient data compression schemes. Particularly, it combines compressed sensing, data prediction and adaptive sampling strategies. We show how this approach dramatically reduces the amount of unnecessary data transmission in the deployment for environmental monitoring and surveillance networks. SWIFTNET targets any monitoring applications that require high reactiveness with aggressive data collection and transmission. To test the performance of this method, we present a real-world testbed for a wildfire monitoring as a use-case. The results from our in-house deployment testbed of 15 nodes have proven to be favorable. On average, over 50% communication reduction when compared with a default adaptive prediction method is achieved without any loss in accuracy. In addition, SWIFTNET is able to guarantee reactiveness by adjusting the sampling interval from 5 min up to 15 s in our application domain. PMID:25942642

A novel time-domain signal processing algorithm for real time ventricular fibrillation detection

NASA Astrophysics Data System (ADS)

Monte, G. E.; Scarone, N. C.; Liscovsky, P. O.; Rotter S/N, P.

2011-12-01

This paper presents an application of a novel algorithm for real time detection of ECG pathologies, especially ventricular fibrillation. It is based on segmentation and labeling process of an oversampled signal. After this treatment, analyzing sequence of segments, global signal behaviours are obtained in the same way like a human being does. The entire process can be seen as a morphological filtering after a smart data sampling. The algorithm does not require any ECG digital signal pre-processing, and the computational cost is low, so it can be embedded into the sensors for wearable and permanent applications. The proposed algorithms could be the input signal description to expert systems or to artificial intelligence software in order to detect other pathologies.

Static, Mixed-Array Total Evaporation for Improved Quantitation of Plutonium Minor Isotopes in Small Samples

NASA Astrophysics Data System (ADS)

Stanley, F. E.; Byerly, Benjamin L.; Thomas, Mariam R.; Spencer, Khalil J.

2016-06-01

Actinide isotope measurements are a critical signature capability in the modern nuclear forensics "toolbox", especially when interrogating anthropogenic constituents in real-world scenarios. Unfortunately, established methodologies, such as traditional total evaporation via thermal ionization mass spectrometry, struggle to confidently measure low abundance isotope ratios (<10-6) within already limited quantities of sample. Herein, we investigate the application of static, mixed array total evaporation techniques as a straightforward means of improving plutonium minor isotope measurements, which have been resistant to enhancement in recent years because of elevated radiologic concerns. Results are presented for small sample (~20 ng) applications involving a well-known plutonium isotope reference material, CRM-126a, and compared with traditional total evaporation methods.

Static, Mixed-Array Total Evaporation for Improved Quantitation of Plutonium Minor Isotopes in Small Samples.

PubMed

Stanley, F E; Byerly, Benjamin L; Thomas, Mariam R; Spencer, Khalil J

2016-06-01

Actinide isotope measurements are a critical signature capability in the modern nuclear forensics "toolbox", especially when interrogating anthropogenic constituents in real-world scenarios. Unfortunately, established methodologies, such as traditional total evaporation via thermal ionization mass spectrometry, struggle to confidently measure low abundance isotope ratios (<10(-6)) within already limited quantities of sample. Herein, we investigate the application of static, mixed array total evaporation techniques as a straightforward means of improving plutonium minor isotope measurements, which have been resistant to enhancement in recent years because of elevated radiologic concerns. Results are presented for small sample (~20 ng) applications involving a well-known plutonium isotope reference material, CRM-126a, and compared with traditional total evaporation methods. Graphical Abstract ᅟ.

In vivo Real-Time Mass Spectrometry for Guided Surgery Application

NASA Astrophysics Data System (ADS)

Fatou, Benoit; Saudemont, Philippe; Leblanc, Eric; Vinatier, Denis; Mesdag, Violette; Wisztorski, Maxence; Focsa, Cristian; Salzet, Michel; Ziskind, Michael; Fournier, Isabelle

2016-05-01

Here we describe a new instrument (SpiderMass) designed for in vivo and real-time analysis. In this instrument ion production is performed remotely from the MS instrument and the generated ions are transported in real-time to the MS analyzer. Ion production is promoted by Resonant Infrared Laser Ablation (RIR-LA) based on the highly effective excitation of O-H bonds in water molecules naturally present in most biological samples. The retrieved molecular patterns are specific to the cell phenotypes and benign versus cancer regions of patient biopsies can be easily differentiated. We also demonstrate by analysis of human skin that SpiderMass can be used under in vivo conditions with minimal damage and pain. Furthermore SpiderMass can also be used for real-time drug metabolism and pharmacokinetic (DMPK) analysis or food safety topics. SpiderMass is thus the first MS based system designed for in vivo real-time analysis under minimally invasive conditions.

Vision-Based Real-Time Traversable Region Detection for Mobile Robot in the Outdoors.

PubMed

Deng, Fucheng; Zhu, Xiaorui; He, Chao

2017-09-13

Environment perception is essential for autonomous mobile robots in human-robot coexisting outdoor environments. One of the important tasks for such intelligent robots is to autonomously detect the traversable region in an unstructured 3D real world. The main drawback of most existing methods is that of high computational complexity. Hence, this paper proposes a binocular vision-based, real-time solution for detecting traversable region in the outdoors. In the proposed method, an appearance model based on multivariate Gaussian is quickly constructed from a sample region in the left image adaptively determined by the vanishing point and dominant borders. Then, a fast, self-supervised segmentation scheme is proposed to classify the traversable and non-traversable regions. The proposed method is evaluated on public datasets as well as a real mobile robot. Implementation on the mobile robot has shown its ability in the real-time navigation applications.

Real time groove characterization combining partial least squares and SVR strategies: application to eddy current testing

NASA Astrophysics Data System (ADS)

Ahmed, S.; Salucci, M.; Miorelli, R.; Anselmi, N.; Oliveri, G.; Calmon, P.; Reboud, C.; Massa, A.

2017-10-01

A quasi real-time inversion strategy is presented for groove characterization of a conductive non-ferromagnetic tube structure by exploiting eddy current testing (ECT) signal. Inversion problem has been formulated by non-iterative Learning-by-Examples (LBE) strategy. Within the framework of LBE, an efficient training strategy has been adopted with the combination of feature extraction and a customized version of output space filling (OSF) adaptive sampling in order to get optimal training set during offline phase. Partial Least Squares (PLS) and Support Vector Regression (SVR) have been exploited for feature extraction and prediction technique respectively to have robust and accurate real time inversion during online phase.

Investigation of a Low Cost Sensor-Based Leak Detection System for Fence Line Applications

EPA Science Inventory

With recent technological advances, low-cost time-resolved sensors may become effective tools to support time-integrated passive sampling strategies by helping to decipher origin of emissions in real-time. As part of the Petroleum Refinery Risk and Technology Review, New Source P...

Determining water sensitive card spread factors for real world tank mixes

USDA-ARS?s Scientific Manuscript database

The use of water sensitive cards provides a quick and easy method to sample the coverage and deposition from spray applications. Typically, this measure is limited to percent coverage as measures of droplet size, and thus deposition rate, are highly influenced by the stain diameter resulting from t...

Protein Detection with Aptamer Biosensors

PubMed Central

Strehlitz, Beate; Nikolaus, Nadia; Stoltenburg, Regina

2008-01-01

Aptamers have been developed for different applications. Their use as new biological recognition elements in biosensors promises progress for fast and easy detection of proteins. This new generation of biosensor (aptasensors) will be more stable and well adapted to the conditions of real samples because of the specific properties of aptamers. PMID:27879936

Non-invasive light-weight integration engine for building EHR from autonomous distributed systems.

PubMed

Crespo Molina, Pere; Angulo Fernández, Carlos; Maldonado Segura, José A; Moner Cano, David; Robles Viejo, Montserrat

2006-01-01

Pangea-LE is a message oriented light-weight integration engine, allowing concurrent access to clinical information from disperse and heterogeneous data sources. The engine extracts the information and serves it to the requester client applications in a flexible XML format. This XML response message can be formatted on demand by the appropriate XSL (Extensible Stylesheet Language) transformation in order to fit client application needs. In this article we present a real use case sample where Pangea-LE collects and generates "on the fly" a structured view of all the patient clinical information available in a healthcare organisation. This information is presented to healthcare professionals in an EHR (Electronic Health Record) viewer Web application with patient search and EHR browsing capabilities. Implantation in a real environment has been a notable success due to the non-invasive method which extremely respects the existing information systems.

Design of a portable electronic nose for real-fake detection of liquors

NASA Astrophysics Data System (ADS)

Qi, Pei-Feng; Zeng, Ming; Li, Zhi-Hua; Sun, Biao; Meng, Qing-Hao

2017-09-01

Portability is a major issue that influences the practical application of electronic noses (e-noses). For liquors detection, an e-nose must preprocess the liquid samples (e.g., using evaporation and thermal desorption), which makes the portable design even more difficult. To realize convenient and rapid detection of liquors, we designed a portable e-nose platform that consists of hardware and software systems. The hardware system contains an evaporation/sampling module, a reaction module, a control/data acquisition and analysis module, and a power module. The software system provides a user-friendly interface and can achieve automatic sampling and data processing. This e-nose platform has been applied to the real-fake recognition of Chinese liquors. Through parameter optimization of a one-class support vector machine classifier, the error rate of the negative samples is greatly reduced, and the overall recognition accuracy is improved. The results validated the feasibility of the designed portable e-nose platform.

Evaluation of a Traffic Sign Detector by Synthetic Image Data for Advanced Driver Assistance Systems

NASA Astrophysics Data System (ADS)

Hanel, A.; Kreuzpaintner, D.; Stilla, U.

2018-05-01

Recently, several synthetic image datasets of street scenes have been published. These datasets contain various traffic signs and can therefore be used to train and test machine learning-based traffic sign detectors. In this contribution, selected datasets are compared regarding ther applicability for traffic sign detection. The comparison covers the process to produce the synthetic images and addresses the virtual worlds, needed to produce the synthetic images, and their environmental conditions. The comparison covers variations in the appearance of traffic signs and the labeling strategies used for the datasets, as well. A deep learning traffic sign detector is trained with multiple training datasets with different ratios between synthetic and real training samples to evaluate the synthetic SYNTHIA dataset. A test of the detector on real samples only has shown that an overall accuracy and ROC AUC of more than 95 % can be achieved for both a small rate of synthetic samples and a large rate of synthetic samples in the training dataset.

Detection of airborne genetically modified maize pollen by real-time PCR.

PubMed

Folloni, Silvia; Kagkli, Dafni-Maria; Rajcevic, Bojan; Guimarães, Nilson C C; Van Droogenbroeck, Bart; Valicente, Fernando H; Van den Eede, Guy; Van den Bulcke, Marc

2012-09-01

The cultivation of genetically modified (GM) crops has raised numerous concerns in the European Union and other parts of the world about their environmental and economic impact. Especially outcrossing of genetically modified organisms (GMO) was from the beginning a critical issue as airborne pollen has been considered an important way of GMO dispersal. Here, we investigate the use of airborne pollen sampling combined with microscopic analysis and molecular PCR analysis as an approach to monitor GM maize cultivations in a specific area. Field trial experiments in the European Union and South America demonstrated the applicability of the approach under different climate conditions, in rural and semi-urban environment, even at very low levels of airborne pollen. The study documents in detail the sampling of GM pollen, sample DNA extraction and real-time PCR analysis. Our results suggest that this 'GM pollen monitoring by bioaerosol sampling and PCR screening' approach might represent an useful aid in the surveillance of GM-free areas, centres of origin and natural reserves. © 2012 Blackwell Publishing Ltd.

First steps towards real-time radiography at the NECTAR facility

NASA Astrophysics Data System (ADS)

Bücherl, T.; Wagner, F. M.; v. Gostomski, Ch. Lierse

2009-06-01

The beam tube SR10 at Forschungsneutronenquelle Heinz Maier-Leibnitz (FRM II) provides an intense beam of fission neutrons for medical application (MEDAPP) and for radiography and tomography of technical and other objects (NECTAR). The high neutron flux of up to 9.8E+07 cm -2 s -1 (depending on filters and collimation) with a mean energy of about 1.9 MeV at the sample position at the NECTAR facility prompted an experimental feasibility study to investigate the potential for real-time (RT) radiography.

Real-time geomagnetic monitoring for space weather-related applications: Opportunities and challenges

USGS Publications Warehouse

Love, Jeffrey J.; Finn, Carol

2017-01-01

An examination is made of opportunities and challenges for enhancing global, real-time geomagnetic monitoring that would be beneficial for a variety of operational projects. This enhancement in geomagnetic monitoring can be attained by expanding the geographic distribution of magnetometer stations, improving the quality of magnetometer data, increasing acquisition sampling rates, increasing the promptness of data transmission, and facilitating access to and use of the data. Progress will benefit from new partnerships to leverage existing capacities and harness multisector, cross-disciplinary, and international interests.

Do placebo based validation standards mimic real batch products behaviour? Case studies.

PubMed

Bouabidi, A; Talbi, M; Bouklouze, A; El Karbane, M; Bourichi, H; El Guezzar, M; Ziemons, E; Hubert, Ph; Rozet, E

2011-06-01

Analytical methods validation is a mandatory step to evaluate the ability of developed methods to provide accurate results for their routine application. Validation usually involves validation standards or quality control samples that are prepared in placebo or reconstituted matrix made of a mixture of all the ingredients composing the drug product except the active substance or the analyte under investigation. However, one of the main concerns that can be made with this approach is that it may lack an important source of variability that come from the manufacturing process. The question that remains at the end of the validation step is about the transferability of the quantitative performance from validation standards to real authentic drug product samples. In this work, this topic is investigated through three case studies. Three analytical methods were validated using the commonly spiked placebo validation standards at several concentration levels as well as using samples coming from authentic batch samples (tablets and syrups). The results showed that, depending on the type of response function used as calibration curve, there were various degrees of differences in the results accuracy obtained with the two types of samples. Nonetheless the use of spiked placebo validation standards was showed to mimic relatively well the quantitative behaviour of the analytical methods with authentic batch samples. Adding these authentic batch samples into the validation design may help the analyst to select and confirm the most fit for purpose calibration curve and thus increase the accuracy and reliability of the results generated by the method in routine application. Copyright © 2011 Elsevier B.V. All rights reserved.

Real-time fMRI processing with physiological noise correction - Comparison with off-line analysis.

PubMed

Misaki, Masaya; Barzigar, Nafise; Zotev, Vadim; Phillips, Raquel; Cheng, Samuel; Bodurka, Jerzy

2015-12-30

While applications of real-time functional magnetic resonance imaging (rtfMRI) are growing rapidly, there are still limitations in real-time data processing compared to off-line analysis. We developed a proof-of-concept real-time fMRI processing (rtfMRIp) system utilizing a personal computer (PC) with a dedicated graphic processing unit (GPU) to demonstrate that it is now possible to perform intensive whole-brain fMRI data processing in real-time. The rtfMRIp performs slice-timing correction, motion correction, spatial smoothing, signal scaling, and general linear model (GLM) analysis with multiple noise regressors including physiological noise modeled with cardiac (RETROICOR) and respiration volume per time (RVT). The whole-brain data analysis with more than 100,000voxels and more than 250volumes is completed in less than 300ms, much faster than the time required to acquire the fMRI volume. Real-time processing implementation cannot be identical to off-line analysis when time-course information is used, such as in slice-timing correction, signal scaling, and GLM. We verified that reduced slice-timing correction for real-time analysis had comparable output with off-line analysis. The real-time GLM analysis, however, showed over-fitting when the number of sampled volumes was small. Our system implemented real-time RETROICOR and RVT physiological noise corrections for the first time and it is capable of processing these steps on all available data at a given time, without need for recursive algorithms. Comprehensive data processing in rtfMRI is possible with a PC, while the number of samples should be considered in real-time GLM. Copyright © 2015 Elsevier B.V. All rights reserved.

Development and validation of an UHPLC-MS/MS method for β2-agonists quantification in human urine and application to clinical samples.

PubMed

Bozzolino, Cristina; Leporati, Marta; Gani, Federica; Ferrero, Cinzia; Vincenti, Marco

2018-02-20

A fast analytical method for the simultaneous detection of 24 β 2 -agonists in human urine was developed and validated. The method covers the therapeutic drugs most commonly administered, but also potentially abused β 2 -agonists. The procedure is based on enzymatic deconjugation with β-glucuronidase followed by SPE clean up using mixed-phase cartridges with both ion-exchange and lipophilic properties. Instrumental analysis conducted by UHPLC-MS/MS allowed high peak resolution and rapid chromatographic separation, with reduced time and costs. The method was fully validated according ISO 17025:2005 principles. The following parameters were determined for each analyte: specificity, selectivity, linearity, limit of detection, limit of quantification, precision, accuracy, matrix effect, recovery and carry-over. The method was tested on real samples obtained from patients subjected to clinical treatment under chronic or acute therapy with either formoterol, indacaterol, salbutamol, or salmeterol. The drugs were administered using pressurized metered dose inhalers. All β 2 -agonists administered to the patients were detected in the real samples. The method proved adequate to accurately measure the concentration of these analytes in the real samples. The observed analytical data are discussed with reference to the administered dose and the duration of the therapy. Copyright © 2017 Elsevier B.V. All rights reserved.

Surface Plasmon Resonance imaging-based sensing for anti-bovine immunoglobulins detection in human milk and serum.

PubMed

Scarano, S; Scuffi, C; Mascini, M; Minunni, M

2011-11-30

Only few papers deal with Surface Plasmon Resonance imaging (SPRi) direct detection on complex matrices, limiting the biosensor application to real analytical problems. In this work a SPRi biosensor for anti-bovine IgG detection in untreated human bodily fluids, i.e. diluted human serum and milk, was developed. Enhanced levels of cow's milk antibodies in children's serum are suspected for their possible correlation with Type 1 diabetes during childhood and their detection in real samples was up to now performed by classical immunoassays based on indirect detection. The biosensor was optimised in standard samples and then in untreated human milk for anti-bovine IgG direct detection. The key novelty of the work is the evaluation of matrix effect by applying to real samples an experimental and ex ante method previously developed for SPRi signal sampling in standard solutions, called "Data Analyzer"; it punctually visualises and analyses the behaviour of receptor spots of the array, to select only spot areas with the best specific vs. unspecific signal values. In this way, benefits provide by SPRi image analysis are exploited here to quantify and minimise drawbacks due to the matrix effect, allowing to by-pass every matrix pre-treatment except dilution. Copyright © 2011 Elsevier B.V. All rights reserved.

Development of a micropulverized extraction method for rapid toxicological analysis of methamphetamine in hair.

PubMed

Miyaguchi, Hajime; Kakuta, Masaya; Iwata, Yuko T; Matsuda, Hideaki; Tazawa, Hidekatsu; Kimura, Hiroko; Inoue, Hiroyuki

2007-09-07

We developed a rapid sample preparation method for the toxicological analysis of methamphetamine and amphetamine (the major metabolite of methamphetamine) in human hair by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS), to facilitate fast screening and quantitation. Two milligrams of hair were mechanically micropulverized for 5 min in a 2-ml plastic tube together with 100 microl of an aqueous solvent containing 10% acetonitrile, 100 mM trifluoroacetic acid and the corresponding deuterium analogues as internal standards. The pulverizing highly disintegrated the hair components, simultaneously allowing the extraction of any drugs present in the hair. After filtering the suspension with a membrane-filter unit, the clear filtrate was directly analyzed by HPLC-MS/MS. No evaporation processes were required for sample preparation. Method optimization and validation study were carried out using real-case specimens and fortified samples in which the drugs had been artificially absorbed, respectively. Concentration ranges for quantitation were 0.040-125 and 0.040-25 ng/mg for methamphetamine and amphetamine, respectively. Real-case specimens were analyzed by the method presented here and by conventional ones to verify the applicability of our method to real-world analysis. Our method took less than 30 min for a set of chromatograms to be obtained from a washed hair sample.

Standardization and application of real-time polymerase chain reaction for rapid detection of bluetongue virus.

PubMed

Lakshmi, I Karthika; Putty, Kalyani; Raut, Satya Samparna; Patil, Sunil R; Rao, P P; Bhagyalakshmi, B; Jyothi, Y Krishna; Susmitha, B; Reddy, Y Vishnuvardhan; Kasulanati, Sowmya; Jyothi, J Shiva; Reddy, Y N

2018-04-01

The present study was designed to standardize real-time polymerase chain reaction (PCR) for detecting the bluetongue virus from blood samples of sheep collected during outbreaks of bluetongue disease in the year 2014 in Andhra Pradesh and Telangana states of India. A 10-fold serial dilution of Plasmid PUC59 with bluetongue virus (BTV) NS3 insert was used to plot the standard curve. BHK-21 and KC cells were used for in vitro propagation of virus BTV-9 at a TCID50/ml of 10 5 ml and RNA was isolated by the Trizol method. Both reverse transcription-PCR and real-time PCR using TaqMan probe were carried out with RNA extracted from virus-spiked culture medium and blood to compare the sensitivity by means of finding out the limit of detection (LoD). The results were verified by inoculating the detected and undetected dilutions onto cell cultures with further cytological (cytopathic effect) and molecular confirmation (by BTV-NS1 group-specific PCR). The standardized technique was then applied to field samples (blood) for detecting BTV. The slope of the standard curve obtained was -3.23, and the efficiency was 103%. The LoD with RT-PCR was 8.269E×10 3 number of copies of plasmid, whereas it was 13 with real-time PCR for plasmid dilutions. Similarly, LoD was determined for virus-spiked culture medium, and blood with both the types of PCR and the values were 10 3 TCID 50/ml and 10 4 TCID 50/ml with RT-PCR and 10° TCID 50/ml and 10 2 TCID 50/ml with real-time PCR, respectively. The standardized technique was applied to blood samples collected from BTV suspected animals; 10 among 20 samples were found positive with Cq values ranging from 27 to 39. The Cq value exhibiting samples were further processed in cell cultures and were confirmed to be BT positive. Likewise, Cq undetected samples on processing in cell cultures turned out to be BTV negative. Real-time PCR was found to be a very sensitive as well as reliable method to detect BTV present in different types of samples, including blood samples collected from BTV-infected sheep, compared to RT-PCR. The LoD of BTV is likely influenced by sample type, possibly by the interference by the other components present in the sample.

High resolution DNA melting analysis: an application for prenatal control of alpha-thalassemia.

PubMed

Sirichotiyakul, Supatra; Wanapirak, Chanane; Saetung, Rattika; Sanguansermsri, Torpong

2010-04-01

To report the use of real-time gap-PCR using SYTO9 with high-resolution melting analysis (HRMA) in prenatal diagnosis of alpha-thalassemia 1. Real-time gap-PCR using SYTO9 with HRMA was performed in 33 DNA samples from chorionic villi sampling (8 normal, 16 heterozygous, and 9 homozygous) to determine the alpha-thalassemia 1 gene [normal and Southeast Asia (-SEA) allele]. The dissociation curve analysis in normal and - SEA allele gave a peak of T(m) at 91.80 +/- 0.14 degrees C and 88.67 +/- 0.08 degrees C, respectively. Normal genotype and homozygous alpha-thalassemia 1 showed a single peak of T(m) that corresponded to their alleles. The heterozygotes gave both peaks with higher normal peak and smaller - SEA peak. Thirty one samples showed consistent results with the conventional gap-PCR. Two samples with ambiguous results were confirmed to be maternal DNA contamination on real-time quantitative PCR and microsatellite assay. HRMA from both samples showed similar pattern to that of heterozygotes. However, they showed much smaller normal peak compared with the - SEA peak, which is in contrast to those of heterozygotes and can readily be distinguished. HRMA with SYTO9 is feasible for prenatal diagnosis of alpha-thalassemia. It had potential advantage of prompt detection maternal DNA contamination. Copyright (c) 2010 John Wiley & Sons, Ltd.

Algorithm-based arterial blood sampling recognition increasing safety in point-of-care diagnostics.

PubMed

Peter, Jörg; Klingert, Wilfried; Klingert, Kathrin; Thiel, Karolin; Wulff, Daniel; Königsrainer, Alfred; Rosenstiel, Wolfgang; Schenk, Martin

2017-08-04

To detect blood withdrawal for patients with arterial blood pressure monitoring to increase patient safety and provide better sample dating. Blood pressure information obtained from a patient monitor was fed as a real-time data stream to an experimental medical framework. This framework was connected to an analytical application which observes changes in systolic, diastolic and mean pressure to determine anomalies in the continuous data stream. Detection was based on an increased mean blood pressure caused by the closing of the withdrawal three-way tap and an absence of systolic and diastolic measurements during this manipulation. For evaluation of the proposed algorithm, measured data from animal studies in healthy pigs were used. Using this novel approach for processing real-time measurement data of arterial pressure monitoring, the exact time of blood withdrawal could be successfully detected retrospectively and in real-time. The algorithm was able to detect 422 of 434 (97%) blood withdrawals for blood gas analysis in the retrospective analysis of 7 study trials. Additionally, 64 sampling events for other procedures like laboratory and activated clotting time analyses were detected. The proposed algorithm achieved a sensitivity of 0.97, a precision of 0.96 and an F1 score of 0.97. Arterial blood pressure monitoring data can be used to perform an accurate identification of individual blood samplings in order to reduce sample mix-ups and thereby increase patient safety.

The application of a novel optical SPM in biomedicine

NASA Astrophysics Data System (ADS)

Li, Yinli; Chen, Haibo; Wu, Shifa; Song, Linfeng; Zhang, Jian

2005-01-01

As an analysis tool, SPM has been broadly used in biomedicine in recent years, such as AFM and SNOM; they are effective instruments in detecting life nanostructures at atomic level. Atomic force and photon scanning tunneling microscope (AF/PSTM) is one of member of SPM, it can be used to obtain sample" optical and atomic fore images at once scanning, these images include the transmissivity image, reflection index image and topography image. This report mainly introduces the application of AF/PSTM in red blood membrane and the effect of different sample dealt with processes on the experiment result. The materials for preparing red cells membrane samples are anticoagulant blood, isotonic phosphatic buffer solution (PBS) and new two times distilled water. The images of AF/PSTM give real expression to the biology samples" fact despite of different sample dealt with processes, which prove that AF/PSTM suits to biology sample imaging. At the same time, the optical images and the topography image of AF/PSTM of the same sample are complementary with each other; this will make AF/PSTM a facile tool to analysis biologic samples" nanostructure. As another sample, this paper gives the application of AF/PSTM in immunoassay, the result shows that AF/PSTM is suit to analysis biologic sample, and it will become a new tool for biomedicine test.

UV254 absorbance as real-time monitoring and control parameter for micropollutant removal in advanced wastewater treatment with powdered activated carbon.

PubMed

Altmann, Johannes; Massa, Lukas; Sperlich, Alexander; Gnirss, Regina; Jekel, Martin

2016-05-01

This study investigates the applicability of UV absorbance measurements at 254 nm (UVA254) to serve as a simple and reliable surrogate parameter to monitor and control the removal of organic micropollutants (OMPs) in advanced wastewater treatment applying powdered activated carbon (PAC). Correlations between OMP removal and corresponding UVA254 reduction were determined in lab-scale adsorption batch tests and successfully applied to a pilot-scale PAC treatment stage to predict OMP removals in aggregate samples with good accuracy. Real-time UVA254 measurements were utilized to evaluate adapted PAC dosing strategies and proved to be effective for online monitoring of OMP removal. Furthermore, active PAC dosing control according to differential UVA254 measurements was implemented and tested. While precise removal predictions based on real-time measurements were not accurate for all OMPs, UVA254-controlled dynamic PAC dosing was capable of achieving stable OMP removals. UVA254 can serve as an effective surrogate parameter for OMP removal in technical PAC applications. Even though the applicability as control parameter to adjust PAC dosing to water quality changes might be limited to applications with fast response between PAC adjustment and adsorptive removal (e.g. direct filtration), UVA254 measurements can also be used to monitor the adsorption efficiency in more complex PAC applications. Copyright © 2016 Elsevier Ltd. All rights reserved.

Laser Induced Breakdown Spectroscopy of Glass and Crystal Samples

NASA Astrophysics Data System (ADS)

Sharma, Prakash; Sandoval, Alejandra; Carter, Michael; Kumar, Akshaya

2015-03-01

Different types of quartz crystals and rare earth ions doped glasses have been identified using the laser induced breakdown spectroscopy (LIBS) technique. LIBS is a real time technique, can be used to identify samples in solid, liquid and gas phases. The advantage of LIBS technique is that no sample preparation is required and laser causes extremely minimal damage to the sample surface. The LIBS spectrum of silicate glasses, prepared by sol-gel method and doped with different concentration of rare earth ions, has been recorded. The limit of detection of rare earth ions in glass samples has been calculated. Total 10 spectrums of each sample were recorded and then averaged to get a final spectrum. The ocean optics LIBS2500 plus spectrometer along with a Q- switched Nd: YAG laser (Quantel, Big Sky) were used to record the LIBS spectrum. This spectrometer can analyze the sample in the spectral range of 200 nm to 980 nm. The spectrum was processed by OOILIBS-plus (v1.0) software. This study has application in the industry where different crystals can be easily identified before they go for shaping and polishing. Also, concentration of rare earth ions in glass can be monitored in real time for quality control.

Multi-Wavelength Based Optical Density Sensor for Autonomous Monitoring of Microalgae

PubMed Central

Jia, Fei; Kacira, Murat; Ogden, Kimberly L.

2015-01-01

A multi-wavelength based optical density sensor unit was designed, developed, and evaluated to monitor microalgae growth in real time. The system consisted of five main components including: (1) laser diode modules as light sources; (2) photodiodes as detectors; (3) driver circuit; (4) flow cell; and (5) sensor housing temperature controller. The sensor unit was designed to be integrated into any microalgae culture system for both real time and non-real time optical density measurements and algae growth monitoring applications. It was shown that the sensor unit was capable of monitoring the dynamics and physiological changes of the microalgae culture in real-time. Algae biomass concentration was accurately estimated with optical density measurements at 650, 685 and 780 nm wavelengths used by the sensor unit. The sensor unit was able to monitor cell concentration as high as 1.05 g·L−1 (1.51 × 108 cells·mL−1) during the culture growth without any sample preparation for the measurements. Since high cell concentrations do not need to be diluted using the sensor unit, the system has the potential to be used in industrial microalgae cultivation systems for real time monitoring and control applications that can lead to improved resource use efficiency. PMID:26364640

Rapid detection method for Bacillus anthracis using a combination of multiplexed real-time PCR and pyrosequencing and its application for food biodefense.

PubMed

Janzen, Timothy W; Thomas, Matthew C; Goji, Noriko; Shields, Michael J; Hahn, Kristen R; Amoako, Kingsley K

2015-02-01

Bacillus anthracis, the causative agent of anthrax, has the capacity to form highly resilient spores as part of its life cycle. The potential for the dissemination of these spores using food as a vehicle is a huge public health concern and, hence, requires the development of a foodborne bioterrorism response approach. In this work, we address a critical gap in food biodefense by presenting a novel, combined, sequential method involving the use of real-time PCR and pyrosequencing for the rapid, specific detection of B. anthracis spores in three food matrices: milk, apple juice, and bottled water. The food samples were experimentally inoculated with 40 CFU ml(-1), and DNA was extracted from the spores and analyzed after immunomagnetic separation. Applying the combination of multiplex real-time PCR and pyrosequencing, we successfully detected the presence of targets on both of the virulence plasmids and the chromosome. The results showed that DNA amplicons generated from a five-target multiplexed real-time PCR detection using biotin-labeled primers can be used for single-plex pyrosequencing detection. The combined use of multiplexed real-time PCR and pyrosequencing is a novel, rapid detection method for B. anthracis from food and provides a tool for accurate, quantitative identification with potential biodefense applications.

Validated method for quantification of genetically modified organisms in samples of maize flour.

PubMed

Kunert, Renate; Gach, Johannes S; Vorauer-Uhl, Karola; Engel, Edwin; Katinger, Hermann

2006-02-08

Sensitive and accurate testing for trace amounts of biotechnology-derived DNA from plant material is the prerequisite for detection of 1% or 0.5% genetically modified ingredients in food products or raw materials thereof. Compared to ELISA detection of expressed proteins, real-time PCR (RT-PCR) amplification has easier sample preparation and detection limits are lower. Of the different methods of DNA preparation CTAB method with high flexibility in starting material and generation of sufficient DNA with relevant quality was chosen. Previous RT-PCR data generated with the SYBR green detection method showed that the method is highly sensitive to sample matrices and genomic DNA content influencing the interpretation of results. Therefore, this paper describes a real-time DNA quantification based on the TaqMan probe method, indicating high accuracy and sensitivity with detection limits of lower than 18 copies per sample applicable and comparable to highly purified plasmid standards as well as complex matrices of genomic DNA samples. The results were evaluated with ValiData for homology of variance, linearity, accuracy of the standard curve, and standard deviation.

Real-time polymerase chain reaction in transfusion medicine: applications for detection of bacterial contamination in blood products.

PubMed

Dreier, Jens; Störmer, Melanie; Kleesiek, Knut

2007-07-01

Bacterial contamination of blood components, particularly of platelet concentrates (PCs), represents the greatest infectious risk in blood transfusion. Although the incidence of platelet bacterial contamination is approximately 1 per 2,000 U, the urgent need for a method for the routine screening of PCs to improve safety for patients had not been considered for a long time. Besides the culturing systems, which will remain the criterion standard, rapid methods for sterility screening will play a more important role in transfusion medicine in the future. In particular, nucleic acid amplification techniques (NATs) are powerful potential tools for bacterial screening assays. The combination of excellent sensitivity and specificity, reduced contamination risk, ease of performance, and speed has made real-time polymerase chain reaction (PCR) technology an appealing alternative to conventional culture-based testing methods. When using real-time PCR for the detection of bacterial contamination, several points have to be considered. The main focus is the choice of the target gene; the assay format; the nucleic acid extraction method, depending on the sample type; and the evaluation of an ideal sampling strategy. However, several factors such as the availability of bacterial-derived nucleic acid amplification reagents, the impracticability, and the cost have limited the use of NATs until now. Attempts to reduce the presence of contaminating nucleic acids from reagents in real-time PCR have been described, but none of these approaches have proven to be very effective or to lower the sensitivity of the assay. Recently, a number of broad-range NAT assays targeting the 16S ribosomal DNA or 23S ribosomal RNA for the detection of bacteria based on real-time technology have been reported. This review will give a short survey of current approaches to and the limitations of the application of real-time PCR for bacterial detection in blood components, with emphasis on the bacterial contamination of PCs.

Detection of chronic wasting disease prion seeding activity in deer and elk feces by real-time quaking-induced conversion

PubMed Central

Tennant, Joanne M.; Haley, Nicholas J.; Denkers, Nathaniel D.; Mathiason, Candace K.; Hoover, Edward A.

2017-01-01

Chronic wasting disease (CWD) is an emergent prion disease affecting cervid species in North America, Canada, South Korea, and recently, Norway. Detection of CWD has been advanced by techniques that rely on amplification of low levels of prion amyloid to a detectable level. However, the increased sensitivity of amplification assays is often compromised by inhibitors and/or activators in complex biologic samples including body fluids, excreta, or the environment. Here, we adapt real-time quaking-induced conversion conditions to specifically detect CWD prions in fecal samples from both experimentally infected deer and naturally infected elk and estimate environmental contamination. The results have application to detection, surveillance and management of CWD, and potentially to other protein-misfolding diseases. PMID:28703697

[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.

Real-Time PCR Identification of Six Malassezia Species.

PubMed

Ilahi, Amin; Hadrich, Inès; Neji, Sourour; Trabelsi, Houaida; Makni, Fattouma; Ayadi, Ali

2017-06-01

Lipophilic yeast Malassezia species is widely found on the skin surface of humans and other animals. This fungus can cause pityriasis versicolor, Malassezia folliculitis, and seborrheic dermatitis. Still now, there is a problem with species identification of Malassezia with conventional methods. We developed a real-time polymerase chain reaction (PCR) assay with multiple hybridization probes for detecting M. globosa, M. furfur, M. restricta, M. sympodialis, M. slooffiae, and M. pachydermatis. The amplification curves and specific melting peaks of the probes hybridized with real-time PCR product were used for species identifications. The assay was further evaluated on 120 samples which were performed by swabbing from 60 domestic animals (23 goats, 10 dogs, 15 cows, 3 cats, 8 rabbits, and 1 donkey) and in 70 human samples (28 patients with pityriasis versicolor, 17 breeders, and 25 control group). Fifteen M. pachydermatis were identified from animals. From human, 61 isolates were identified as M. globosa (28), M. furfur (15), M. restricta (6), M. sympodialis (8), M. slooffiae (2), and M. pachydermatis (2). Eight cases of co-detection from 6 patients and 2 breeders were revealed. Our findings show that the assay was highly effective in identifying Malassezia species. The application of multiplex real-time PCR provides a sensitive and rapid identification system for Malassezia species, which may be applied in further epidemiological surveys from clinical samples.

IGBT Switching Characteristic Curve Embedded Half-Bridge MMC Modelling and Real Time Simulation Realization

NASA Astrophysics Data System (ADS)

Zhengang, Lu; Hongyang, Yu; Xi, Yang

2017-05-01

The Modular Multilevel Converter (MMC) is one of the most attractive topologies in recent years for medium or high voltage industrial applications, such as high voltage dc transmission (HVDC) and medium voltage varying speed motor drive. The wide adoption of MMCs in industry is mainly due to its flexible expandability, transformer-less configuration, common dc bus, high reliability from redundancy, and so on. But, when the sub module number of MMC is more, the test of MMC controller will cost more time and effort. Hardware in the loop test based on real time simulator will save a lot of time and money caused by the MMC test. And due to the flexible of HIL, it becomes more and more popular in the industry area. The MMC modelling method remains an important issue for the MMC HIL test. Specifically, the VSC model should realistically reflect the nonlinear device switching characteristics, switching and conduction losses, tailing current, and diode reverse recovery behaviour of a realistic converter. In this paper, an IGBT switching characteristic curve embedded half-bridge MMC modelling method is proposed. This method is based on the switching curve referring and sample circuit calculation, and it is sample for implementation. Based on the proposed method, a FPGA real time simulation is carried out with 200ns sample time. The real time simulation results show the proposed method is correct.

An optimal sampling approach to modelling whole-body vibration exposure in all-terrain vehicle driving.

PubMed

Lü, Xiaoshu; Takala, Esa-Pekka; Toppila, Esko; Marjanen, Ykä; Kaila-Kangas, Leena; Lu, Tao

2017-08-01

Exposure to whole-body vibration (WBV) presents an occupational health risk and several safety standards obligate to measure WBV. The high cost of direct measurements in large epidemiological studies raises the question of the optimal sampling for estimating WBV exposures given by a large variation in exposure levels in real worksites. This paper presents a new approach to addressing this problem. A daily exposure to WBV was recorded for 9-24 days among 48 all-terrain vehicle drivers. Four data-sets based on root mean squared recordings were obtained from the measurement. The data were modelled using semi-variogram with spectrum analysis and the optimal sampling scheme was derived. The optimum sampling period was 140 min apart. The result was verified and validated in terms of its accuracy and statistical power. Recordings of two to three hours are probably needed to get a sufficiently unbiased daily WBV exposure estimate in real worksites. The developed model is general enough that is applicable to other cumulative exposures or biosignals. Practitioner Summary: Exposure to whole-body vibration (WBV) presents an occupational health risk and safety standards obligate to measure WBV. However, direct measurements can be expensive. This paper presents a new approach to addressing this problem. The developed model is general enough that is applicable to other cumulative exposures or biosignals.

Static, mixed-array total evaporation for improved quantitation of plutonium minor isotopes in small samples

DOE PAGES

Stanley, F. E.; Byerly, Benjamin L.; Thomas, Mariam R.; ...

2016-03-31

Actinide isotope measurements are a critical signature capability in the modern nuclear forensics “toolbox”, especially when interrogating anthropogenic constituents in real-world scenarios. Unfortunately, established methodologies, such as traditional total evaporation via thermal ionization mass spectrometry, struggle to confidently measure low abundance isotope ratios (<10 -6) within already limited quantities of sample. Herein, we investigate the application of static, mixed array total evaporation techniques as a straightforward means of improving plutonium minor isotope measurements, which have been resistant to enhancement in recent years because of elevated radiologic concerns. Furthermore, results are presented for small sample (~20 ng) applications involving a well-knownmore » plutonium isotope reference material, CRM-126a, and compared with traditional total evaporation methods.« less

The relationship between the FFM and personality disorders in a personnel selection sample.

PubMed

Nederström, Mikael; Furnham, Adrian

2012-10-01

The relationships between the Five Factor Model (FFM) personality and personality disorders were investigated. A sample of real-life job applicants completed two personality questionnaires with different theoretical backgrounds in a psychological assessment center. The job applicants provided self-descriptions both on the FFM inventory and on a personality disorder trait inventory. A subsample of these candidates was interviewed by expert psychologists upon entrance to the assessment center. The psychologists assessed the same disorder traits of each target in job interviews. Both self-descriptions were used to predict the expert assessments. The results demonstrated considerable overlap between the FFM measures of normal and measures of abnormal personality in both samples and regardless of assessment method. © 2012 The Authors. Scandinavian Journal of Psychology © 2012 The Scandinavian Psychological Associations.

45 CFR 12.7 - Applications for surplus real property.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 45 Public Welfare 1 2011-10-01 2011-10-01 false Applications for surplus real property. 12.7... UTILIZATION OF SURPLUS REAL PROPERTY FOR PUBLIC HEALTH PURPOSES § 12.7 Applications for surplus real property. Applications for surplus real property for public health purposes shall be made to the Department through the...

45 CFR 12.7 - Applications for surplus real property.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 45 Public Welfare 1 2012-10-01 2012-10-01 false Applications for surplus real property. 12.7... UTILIZATION OF SURPLUS REAL PROPERTY FOR PUBLIC HEALTH PURPOSES § 12.7 Applications for surplus real property. Applications for surplus real property for public health purposes shall be made to the Department through the...

Advanced classical thermodynamics

NASA Astrophysics Data System (ADS)

Emanuel, George

The theoretical and mathematical foundations of thermodynamics are presented in an advanced text intended for graduate engineering students. Chapters are devoted to definitions and postulates, the fundamental equation, equilibrium, the application of Jacobian theory to thermodynamics, the Maxwell equations, stability, the theory of real gases, critical-point theory, and chemical thermodynamics. Diagrams, graphs, tables, and sample problems are provided.

The Cocoa Shop: A Database Management Case

ERIC Educational Resources Information Center

Pratt, Renée M. E.; Smatt, Cindi T.

2015-01-01

This is an example of a real-world applicable case study, which includes background information on a small local business (i.e., TCS), description of functional business requirements, and sample data. Students are asked to design and develop a database to improve the management of the company's customers, products, and purchases by emphasizing…

A bayesian hierarchical model for classification with selection of functional predictors.

PubMed

Zhu, Hongxiao; Vannucci, Marina; Cox, Dennis D

2010-06-01

In functional data classification, functional observations are often contaminated by various systematic effects, such as random batch effects caused by device artifacts, or fixed effects caused by sample-related factors. These effects may lead to classification bias and thus should not be neglected. Another issue of concern is the selection of functions when predictors consist of multiple functions, some of which may be redundant. The above issues arise in a real data application where we use fluorescence spectroscopy to detect cervical precancer. In this article, we propose a Bayesian hierarchical model that takes into account random batch effects and selects effective functions among multiple functional predictors. Fixed effects or predictors in nonfunctional form are also included in the model. The dimension of the functional data is reduced through orthonormal basis expansion or functional principal components. For posterior sampling, we use a hybrid Metropolis-Hastings/Gibbs sampler, which suffers slow mixing. An evolutionary Monte Carlo algorithm is applied to improve the mixing. Simulation and real data application show that the proposed model provides accurate selection of functional predictors as well as good classification.

Large-scale machine learning and evaluation platform for real-time traffic surveillance

NASA Astrophysics Data System (ADS)

Eichel, Justin A.; Mishra, Akshaya; Miller, Nicholas; Jankovic, Nicholas; Thomas, Mohan A.; Abbott, Tyler; Swanson, Douglas; Keller, Joel

2016-09-01

In traffic engineering, vehicle detectors are trained on limited datasets, resulting in poor accuracy when deployed in real-world surveillance applications. Annotating large-scale high-quality datasets is challenging. Typically, these datasets have limited diversity; they do not reflect the real-world operating environment. There is a need for a large-scale, cloud-based positive and negative mining process and a large-scale learning and evaluation system for the application of automatic traffic measurements and classification. The proposed positive and negative mining process addresses the quality of crowd sourced ground truth data through machine learning review and human feedback mechanisms. The proposed learning and evaluation system uses a distributed cloud computing framework to handle data-scaling issues associated with large numbers of samples and a high-dimensional feature space. The system is trained using AdaBoost on 1,000,000 Haar-like features extracted from 70,000 annotated video frames. The trained real-time vehicle detector achieves an accuracy of at least 95% for 1/2 and about 78% for 19/20 of the time when tested on ˜7,500,000 video frames. At the end of 2016, the dataset is expected to have over 1 billion annotated video frames.

Multiplex PCR detection of Cryptosporidium sp, Giardia lamblia and Entamoeba histolytica directly from dried stool samples from Guinea-Bissauan children with diarrhoea.

PubMed

Mero, Sointu; Kirveskari, Juha; Antikainen, Jenni; Ursing, Johan; Rombo, Lars; Kofoed, Poul-Erik; Kantele, Anu

2017-09-01

In developing countries, diarrhoea is the most common cause of death for children under five years of age, with Giardia lamblia, Cryptosporidium and Entamoeba histolytica as the most frequent pathogenic parasites. Traditional microscopy for stool parasites has poor sensitivity and specificity, while new molecular methods may provide more accurate diagnostics. In poor regions with sample storage hampered by uncertain electricity supply, research would benefit from a method capable of analysing dried stools. A real-time multiplex PCR method with internal inhibition control was developed for detecting Giardia lamblia, Cryptosporidium hominis/parvum and Entamoeba histolytica directly from stool specimens. Applicability to dried samples was checked by comparing with fresh ones in a small test material. Finally, the assay was applied to dried specimens collected from Guinea-Bissauan children with diarrhoea. The PCR's analytical sensitivity limit was 0.1 ng/ml for G. lamblia DNA, 0.01 ng/ml for E. histolytica DNA and 0.1 ng/ml for Cryptosporidium sp. In the test material, the assay performed similarly with fresh and dried stools. Of the 52 Guinea-Bissauan samples, local microscopy revealed a parasite in 15%, while PCR detected 62% positive for at least one parasite: 44% of the dried samples had Giardia, 23% Cryptosporidium and 0% E. histolytica. Our new multiplex real-time PCR for protozoa presents a sensitive method applicable to dried samples. As proof of concept, it worked well on stools collected from Guinea-Bissauan children with diarrhoea. It provides an epidemiological tool for analysing dried specimens from regions poor in resources.

Diffraction-limited real-time terahertz imaging by optical frequency up-conversion in a DAST crystal.

PubMed

Fan, Shuzhen; Qi, Feng; Notake, Takashi; Nawata, Kouji; Takida, Yuma; Matsukawa, Takeshi; Minamide, Hiroaki

2015-03-23

Real-time terahertz (THz) wave imaging has wide applications in areas such as security, industry, biology, medicine, pharmacy, and the arts. This report describes real-time room-temperature THz imaging by nonlinear optical frequency up-conversion in an organic 4-dimethylamino-N'-methyl-4'-stilbazolium tosylate (DAST) crystal, with high resolution reaching the diffraction limit. THz-wave images were converted to the near infrared region and then captured using an InGaAs camera in a tandem imaging system. The resolution of the imaging system was analyzed. Diffraction and interference of THz wave were observed in the experiments. Videos are supplied to show the interference pattern variation that occurs with sample moving and tilting.

Optical Processing Techniques For Pseudorandom Sequence Prediction

NASA Astrophysics Data System (ADS)

Gustafson, Steven C.

1983-11-01

Pseudorandom sequences are series of apparently random numbers generated, for example, by linear or nonlinear feedback shift registers. An important application of these sequences is in spread spectrum communication systems, in which, for example, the transmitted carrier phase is digitally modulated rapidly and pseudorandomly and in which the information to be transmitted is incorporated as a slow modulation in the pseudorandom sequence. In this case the transmitted information can be extracted only by a receiver that uses for demodulation the same pseudorandom sequence used by the transmitter, and thus this type of communication system has a very high immunity to third-party interference. However, if a third party can predict in real time the probable future course of the transmitted pseudorandom sequence given past samples of this sequence, then interference immunity can be significantly reduced.. In this application effective pseudorandom sequence prediction techniques should be (1) applicable in real time to rapid (e.g., megahertz) sequence generation rates, (2) applicable to both linear and nonlinear pseudorandom sequence generation processes, and (3) applicable to error-prone past sequence samples of limited number and continuity. Certain optical processing techniques that may meet these requirements are discussed in this paper. In particular, techniques based on incoherent optical processors that perform general linear transforms or (more specifically) matrix-vector multiplications are considered. Computer simulation examples are presented which indicate that significant prediction accuracy can be obtained using these transforms for simple pseudorandom sequences. However, the useful prediction of more complex pseudorandom sequences will probably require the application of more sophisticated optical processing techniques.

Determination of ten pyrethroids in various fruit juices: comparison of dispersive liquid-liquid microextraction sample preparation and QuEChERS method combined with dispersive liquid-liquid microextraction.

PubMed

Zhang, Yaohai; Zhang, Xuelian; Jiao, Bining

2014-09-15

Dispersive liquid-liquid microextraction (DLLME) sample preparation and the quick, easy, cheap, effective, rugged and safe (QuEChERS) method combined with DLLME were developed and compared for the analysis of ten pyrethroids in various fruit juices using gas chromatography-electron capture detection (GC-ECD). QuEChERS-DLLME method has found its widespread applications to all the fruit juices including those samples with more complex matrices (orange, lemon, kiwi and mango) while DLLME was confined to the fruit juices with simpler matrices (apple, pear, grape and peach). The two methods provided acceptable recoveries and repeatability. In addition, the applicabilities of two methods were demonstrated with the real samples and further confirmed by gas chromatography-mass spectrometry (GC-MS). Copyright © 2014. Published by Elsevier Ltd.

Wireless, battery-operated data acquisition system for mobile spectrometry applications and (potentially) for the Internet of things

NASA Astrophysics Data System (ADS)

Fitzgerald, Ryan; Karanassios, Vassili

2017-05-01

There are many applications requiring chemical analysis in the field and analytical results in (near) real-time. For example, when accidental spills occur. In others, collecting samples in the field followed by analysis in a lab increases costs and introduces time-delays. In such cases, "bring part of the lab to the sample" would be ideal. Toward this ideal (and to further reduce size and weight), we developed a relatively inexpensive, battery-operated, wireless data acquisition hardware system around an Arduino nano micro-controller and a 16-bit ADC (Analog-to- Digital Converter) with a max sampling rate of 860 samples/s. The hardware communicates the acquired data using low-power Bluetooth. Software for data acquisition and data display was written in Python. Potential ways of making the hardware-software approach described here a part of the Internet-of-Things (IoT) are presented.

An investigation of potential applications of OP-SAPS: Operational sampled analog processors

NASA Technical Reports Server (NTRS)

Parrish, E. A.; Mcvey, E. S.

1976-01-01

The impact of charge-coupled device (CCD) processors on future instrumentation was investigated. The CCD devices studied process sampled analog data and are referred to as OP-SAPS - operational sampled analog processors. Preliminary studies into various architectural configurations for systems composed of OP-SAPS show that they have potential in such diverse applications as pattern recognition and automatic control. It appears probable that OP-SAPS may be used to construct computing structures which can serve as special peripherals to large-scale computer complexes used in real time flight simulation. The research was limited to the following benchmark programs: (1) face recognition, (2) voice command and control, (3) terrain classification, and (4) terrain identification. A small amount of effort was spent on examining a method by which OP-SAPS may be used to decrease the limiting ground sampling distance encountered in remote sensing from satellites.

Maia Mapper: high definition XRF imaging in the lab

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

Ryan, Chris G.; Kirkham, R.; Moorhead, G. F.

Here, Maia Mapper is a laboratory μXRF mapping system for efficient elemental imaging of drill core sections serving minerals research and industrial applications. It targets intermediate spatial scales, with imaging of up to ~80 M pixels over a 500×150 mm 2 sample area. It brings together (i) the Maia detector and imaging system, with its large solid-angle, event-mode operation, millisecond pixel transit times in fly-scan mode and real-time spectral deconvolution and imaging, (ii) the high brightness MetalJet D2 liquid metal micro-focus X-ray source from Excillum, and (iii) an efficient XOS polycapillary lens with a flux gain ~15,900 at 21 keVmore » into a ~32 μm focus, and (iv) a sample scanning stage engineered for standard drill-core sections. Count-rates up to ~3 M/s are observed on drill core samples with low dead-time up to ~1.5%. Automated scans are executed in sequence with display of deconvoluted element component images accumulated in real-time in the Maia detector. Application images on drill core and polished rock slabs illustrate Maia Mapper capabilities as part of the analytical workflow of the Advanced Resource Characterisation Facility, which spans spatial dimensions from ore deposit to atomic scales.« less

Maia Mapper: high definition XRF imaging in the lab

DOE PAGES

Ryan, Chris G.; Kirkham, R.; Moorhead, G. F.; ...

2018-03-13

Here, Maia Mapper is a laboratory μXRF mapping system for efficient elemental imaging of drill core sections serving minerals research and industrial applications. It targets intermediate spatial scales, with imaging of up to ~80 M pixels over a 500×150 mm 2 sample area. It brings together (i) the Maia detector and imaging system, with its large solid-angle, event-mode operation, millisecond pixel transit times in fly-scan mode and real-time spectral deconvolution and imaging, (ii) the high brightness MetalJet D2 liquid metal micro-focus X-ray source from Excillum, and (iii) an efficient XOS polycapillary lens with a flux gain ~15,900 at 21 keVmore » into a ~32 μm focus, and (iv) a sample scanning stage engineered for standard drill-core sections. Count-rates up to ~3 M/s are observed on drill core samples with low dead-time up to ~1.5%. Automated scans are executed in sequence with display of deconvoluted element component images accumulated in real-time in the Maia detector. Application images on drill core and polished rock slabs illustrate Maia Mapper capabilities as part of the analytical workflow of the Advanced Resource Characterisation Facility, which spans spatial dimensions from ore deposit to atomic scales.« less

Maia Mapper: high definition XRF imaging in the lab

NASA Astrophysics Data System (ADS)

Ryan, C. G.; Kirkham, R.; Moorhead, G. F.; Parry, D.; Jensen, M.; Faulks, A.; Hogan, S.; Dunn, P. A.; Dodanwela, R.; Fisher, L. A.; Pearce, M.; Siddons, D. P.; Kuczewski, A.; Lundström, U.; Trolliet, A.; Gao, N.

2018-03-01

Maia Mapper is a laboratory μXRF mapping system for efficient elemental imaging of drill core sections serving minerals research and industrial applications. It targets intermediate spatial scales, with imaging of up to ~80 M pixels over a 500×150 mm2 sample area. It brings together (i) the Maia detector and imaging system, with its large solid-angle, event-mode operation, millisecond pixel transit times in fly-scan mode and real-time spectral deconvolution and imaging, (ii) the high brightness MetalJet D2 liquid metal micro-focus X-ray source from Excillum, and (iii) an efficient XOS polycapillary lens with a flux gain ~15,900 at 21 keV into a ~32 μm focus, and (iv) a sample scanning stage engineered for standard drill-core sections. Count-rates up to ~3 M/s are observed on drill core samples with low dead-time up to ~1.5%. Automated scans are executed in sequence with display of deconvoluted element component images accumulated in real-time in the Maia detector. Application images on drill core and polished rock slabs illustrate Maia Mapper capabilities as part of the analytical workflow of the Advanced Resource Characterisation Facility, which spans spatial dimensions from ore deposit to atomic scales.

Recombinant plasmid-based quantitative Real-Time PCR analysis of Salmonella enterica serotypes and its application to milk samples.

PubMed

Gokduman, Kurtulus; Avsaroglu, M Dilek; Cakiris, Aris; Ustek, Duran; Gurakan, G Candan

2016-03-01

The aim of the current study was to develop, a new, rapid, sensitive and quantitative Salmonella detection method using a Real-Time PCR technique based on an inexpensive, easy to produce, convenient and standardized recombinant plasmid positive control. To achieve this, two recombinant plasmids were constructed as reference molecules by cloning the two most commonly used Salmonella-specific target gene regions, invA and ttrRSBC. The more rapid detection enabled by the developed method (21 h) compared to the traditional culture method (90 h) allows the quantitative evaluation of Salmonella (quantification limits of 10(1)CFU/ml and 10(0)CFU/ml for the invA target and the ttrRSBC target, respectively), as illustrated using milk samples. Three advantages illustrated by the current study demonstrate the potential of the newly developed method to be used in routine analyses in the medical, veterinary, food and water/environmental sectors: I--The method provides fast analyses including the simultaneous detection and determination of correct pathogen counts; II--The method is applicable to challenging samples, such as milk; III--The method's positive controls (recombinant plasmids) are reproducible in large quantities without the need to construct new calibration curves. Copyright © 2016 Elsevier B.V. All rights reserved.

Comprehensive two-dimensional liquid chromatography for polyphenol analysis in foodstuffs.

PubMed

Cacciola, Francesco; Farnetti, Sara; Dugo, Paola; Marriott, Philip John; Mondello, Luigi

2017-01-01

Polyphenols are a class of plant secondary metabolites that are recently drawing a special interest because of their broad spectrum of pharmacological effects. As they are characterized by an enormous structural variability, the identification of these molecules in food samples is a difficult task, and sometimes having only a limited number of commercially available reference materials is not of great help. One-dimensional liquid chromatography is the most widely applied analytical approach for their analysis. In particular, the hyphenation of liquid chromatography to mass spectrometry has come to play an influential role by allowing relatively fast tentative identification and accurate quantification of polyphenolic compounds at trace levels in vegetable media. However, when dealing with very complex real-world food samples, a single separation system often does not provide sufficient resolving power for attaining rewarding results. Comprehensive two-dimensional liquid chromatography is a technique of great analytical impact, since it offers much higher peak capacities than separations in a single dimension. In the present review, we describe applications in the field of comprehensive two-dimensional liquid chromatography for polyphenol analysis in real-world food samples. Comprehensive two-dimensional liquid chromatography applications to nonfood matrices fall outside the scope of the current report and will not be discussed. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evaluation of DNA extraction methods for PCR-based detection of Listeria monocytogenes from vegetables.

PubMed

Vojkovska, H; Kubikova, I; Kralik, P

2015-03-01

Epidemiological data indicate that raw vegetables are associated with outbreaks of Listeria monocytogenes. Therefore, there is a demand for the availability of rapid and sensitive methods, such as PCR assays, for the detection and accurate discrimination of L. monocytogenes. However, the efficiency of PCR methods can be negatively affected by inhibitory compounds commonly found in vegetable matrices that may cause false-negative results. Therefore, the sample processing and DNA isolation steps must be carefully evaluated prior to the introduction of such methods into routine practice. In this study, we compared the ability of three column-based and four magnetic bead-based commercial DNA isolation kits to extract DNA of the model micro-organism L. monocytogenes from raw vegetables. The DNA isolation efficiency of all isolation kits was determined using a triplex real-time qPCR assay designed to specifically detect L. monocytogenes. The kit with best performance, the PowerSoil(™) Microbial DNA Isolation Kit, is suitable for the extraction of amplifiable DNA from L. monocytogenes cells in vegetable with efficiencies ranging between 29.6 and 70.3%. Coupled with the triplex real-time qPCR assay, this DNA isolation kit is applicable to the samples with bacterial loads of 10(3) bacterial cells per gram of L. monocytogenes. Several recent outbreaks of Listeria monocytogenes have been associated with the consumption of fruits and vegetables. Real-time PCR assays allow fast detection and accurate quantification of microbes. However, the success of real-time PCR is dependent on the success with which template DNA can be extracted. The results of this study suggest that the PowerSoil(™) Microbial DNA Isolation Kit can be used for the extraction of amplifiable DNA from L. monocytogenes cells in vegetable with efficiencies ranging between 29.6 and 70.3%. This method is applicable to samples with bacterial loads of 10(3) bacterial cells per gram of L. monocytogenes. © 2014 The Society for Applied Microbiology.

Near Real-time Operational Use of eMODIS Expedited NDVI for Monitoring Applications and Famine Early Warning

NASA Astrophysics Data System (ADS)

Rowland, J.; Budde, M. E.

2010-12-01

The Famine Early Warning Systems Network (FEWS NET) has requirements for near real-time monitoring of vegetation conditions for food security applications. Accurate and timely assessments of crop conditions are an important element of food security decision making. FEWS NET scientists at the U.S. Geological Survey (USGS) Earth Resources Observation and Science (EROS) Center are utilizing a new Moderate Resolution Imaging Spectroradiometer (MODIS) Normalized Difference Vegetation Index (NDVI) dataset for operational monitoring of crop and pasture conditions in parts of the world where food availability is highly dependent on subsistence agriculture and animal husbandry. The expedited MODIS, or eMODIS, production system processes NDVI data using MODIS surface reflectance provided by the Land Atmosphere Near-real-time Capability for EOS (LANCE). Benefits of this production system include customized compositing schedules, near real-time data availability, and minimized re-sampling. FEWS NET has implemented a 10-day compositing scheme every five days to accommodate the need for timely information on vegetation conditions. The data are currently being processed at 250-meter spatial resolution for Central America, Hispaniola, and Africa. Data are further enhanced by the application of a temporal smoothing filter which helps remove contamination due to clouds and other atmospheric effects. The results of this near real-time monitoring capability have been the timely provision of NDVI and NDVI anomaly maps for each of the FEWS NET monitoring regions and the availability of a consistently processed dataset to aid crop assessment missions and to facilitate customized analyses of crop production, drought, and agro-pastoral conditions.

Detection of drugs and explosives using neutron computerized tomography and artificial intelligence techniques.

PubMed

Ferreira, F J O; Crispim, V R; Silva, A X

2010-06-01

In this study the development of a methodology to detect illicit drugs and plastic explosives is described with the objective of being applied in the realm of public security. For this end, non-destructive assay with neutrons was used and the technique applied was the real time neutron radiography together with computerized tomography. The system is endowed with automatic responses based upon the application of an artificial intelligence technique. In previous tests using real samples, the system proved capable of identifying 97% of the inspected materials. Copyright 2010 Elsevier Ltd. All rights reserved.

Milling strategies evaluation when simulating the forming dies' functional surfaces production

NASA Astrophysics Data System (ADS)

Ižol, Peter; Tomáš, Miroslav; Beňo, Jozef

2016-05-01

The paper deals with selection and evaluation of milling strategies, available in CAM systems and applicable when complicated shape parts are produced, such as forming dies. A method to obtain samples is proposed and this stems from real forming die surface machined by proper strategies. The strategy applicability for the whole part - forming die - is reviewed by the particular specimen evaluation. The presented methodology has been verified by machining model die and comparing it to the production procedure proposed in other CAM systems.

Real-time label-free quantitative fluorescence microscopy-based detection of ATP using a tunable fluorescent nano-aptasensor platform.

PubMed

Shrivastava, Sajal; Sohn, Il-Yung; Son, Young-Min; Lee, Won-Il; Lee, Nae-Eung

2015-12-14

Although real-time label-free fluorescent aptasensors based on nanomaterials are increasingly recognized as a useful strategy for the detection of target biomolecules with high fidelity, the lack of an imaging-based quantitative measurement platform limits their implementation with biological samples. Here we introduce an ensemble strategy for a real-time label-free fluorescent graphene (Gr) aptasensor platform. This platform employs aptamer length-dependent tunability, thus enabling the reagentless quantitative detection of biomolecules through computational processing coupled with real-time fluorescence imaging data. We demonstrate that this strategy effectively delivers dose-dependent quantitative readouts of adenosine triphosphate (ATP) concentration on chemical vapor deposited (CVD) Gr and reduced graphene oxide (rGO) surfaces, thereby providing cytotoxicity assessment. Compared with conventional fluorescence spectrometry methods, our highly efficient, universally applicable, and rational approach will facilitate broader implementation of imaging-based biosensing platforms for the quantitative evaluation of a range of target molecules.

Simultaneous detection of papaya ringspot virus, papaya leaf distortion mosaic virus, and papaya mosaic virus by multiplex real-time reverse transcription PCR.

PubMed

Huo, P; Shen, W T; Yan, P; Tuo, D C; Li, X Y; Zhou, P

2015-12-01

Both the single infection of papaya ringspot virus (PRSV), papaya leaf distortion mosaic virus (PLDMV) or papaya mosaic virus (PapMV) and double infection of PRSV and PLDMV or PapMV which cause indistinguishable symptoms, threaten the papaya industry in Hainan Island, China. In this study, a multiplex real-time reverse transcription PCR (RT-PCR) was developed to detect simultaneously the three viruses based on their distinctive melting temperatures (Tms): 81.0±0.8°C for PRSV, 84.7±0.6°C for PLDMV, and 88.7±0.4°C for PapMV. The multiplex real-time RT-PCR method was specific and sensitive in detecting the three viruses, with a detection limit of 1.0×10(1), 1.0×10(2), and 1.0×10(2) copies for PRSV, PLDMV, and PapMV, respectively. Indeed, the reaction was 100 times more sensitive than the multiplex RT-PCR for PRSV, and 10 times more sensitive than multiplex RT-PCR for PLDMV. Field application of the multiplex real-time RT-PCR demonstrated that some non-symptomatic samples were positive for PLDMV by multiplex real-time RT-PCR but negative by multiplex RT-PCR, whereas some samples were positive for both PRSV and PLDMV by multiplex real-time RT-PCR assay but only positive for PLDMV by multiplex RT-PCR. Therefore, this multiplex real-time RT-PCR assay provides a more rapid, sensitive and reliable method for simultaneous detection of PRSV, PLDMV, PapMV and their mixed infections in papaya.

A probe-based quantitative PCR assay for detecting Tetracapsuloides bryosalmonae in fish tissue and environmental DNA water samples

USGS Publications Warehouse

Hutchins, Patrick; Sepulveda, Adam; Martin, Renee; Hopper, Lacey

2017-01-01

A probe-based quantitative real-time PCR assay was developed to detect Tetracapsuloides bryosalmonae, which causes proliferative kidney disease in salmonid fish, in kidney tissue and environmental DNA (eDNA) water samples. The limits of detection and quantification were 7 and 100 DNA copies for calibration standards and T. bryosalmonae was reliably detected down to 100 copies in tissue and eDNA samples. The assay presented here is a highly sensitive and quantitative tool for detecting T. bryosalmonae with potential applications for tissue diagnostics and environmental detection.

Novel ion imprinted magnetic mesoporous silica for selective magnetic solid phase extraction of trace Cd followed by graphite furnace atomic absorption spectrometry detection

NASA Astrophysics Data System (ADS)

Zhao, Bingshan; He, Man; Chen, Beibei; Hu, Bin

2015-05-01

Determination of trace Cd in environmental, biological and food samples is of great significance to toxicological research and environmental pollution monitoring. While the direct determination of Cd in real-world samples is difficult due to its low concentration and the complex matrix. Herein, a novel Cd(II)-ion imprinted magnetic mesoporous silica (Cd(II)-II-MMS) was prepared and was employed as a selective magnetic solid-phase extraction (MSPE) material for extraction of trace Cd in real-world samples followed by graphite furnace atomic absorption spectrometry (GFAAS) detection. Under the optimized conditions, the detection limit of the proposed method was 6.1 ng L- 1 for Cd with the relative standard deviation (RSD) of 4.0% (c = 50 ng L- 1, n = 7), and the enrichment factor was 50-fold. To validate the proposed method, Certified Reference Materials of GSBZ 50009-88 environmental water, ZK018-1 lyophilized human urine and NIES10-b rice flour were analyzed and the determined values were in a good agreement with the certified values. The proposed method exhibited a robust anti-interference ability due to the good selectivity of Cd(II)-II-MMS toward Cd(II). It was successfully employed for the determination of trace Cd(II) in environmental water, human urine and rice samples with recoveries of 89.3-116%, demonstrating that the proposed method has good application potential in real world samples with complex matrix.

A Modular Pipelined Processor for High Resolution Gamma-Ray Spectroscopy

NASA Astrophysics Data System (ADS)

Veiga, Alejandro; Grunfeld, Christian

2016-02-01

The design of a digital signal processor for gamma-ray applications is presented in which a single ADC input can simultaneously provide temporal and energy characterization of gamma radiation for a wide range of applications. Applying pipelining techniques, the processor is able to manage and synchronize very large volumes of streamed real-time data. Its modular user interface provides a flexible environment for experimental design. The processor can fit in a medium-sized FPGA device operating at ADC sampling frequency, providing an efficient solution for multi-channel applications. Two experiments are presented in order to characterize its temporal and energy resolution.

A Class of Population Covariance Matrices in the Bootstrap Approach to Covariance Structure Analysis

ERIC Educational Resources Information Center

Yuan, Ke-Hai; Hayashi, Kentaro; Yanagihara, Hirokazu

2007-01-01

Model evaluation in covariance structure analysis is critical before the results can be trusted. Due to finite sample sizes and unknown distributions of real data, existing conclusions regarding a particular statistic may not be applicable in practice. The bootstrap procedure automatically takes care of the unknown distribution and, for a given…

HYDRA: High Speed Simulation Architecture for Precision Spacecraft Formation Flying

NASA Technical Reports Server (NTRS)

Martin, Bryan J.; Sohl, Garett A.

2003-01-01

This viewgraph presentation describes HYDRA, which is architecture to facilitate high-fidelity and real-time simulation of formation flying missions. The contents include: 1) Motivation; 2) Objective; 3) HYDRA-Description and Overview; 4) HYDRA-Hierarchy; 5) Communication in HYDRA; 6) Simulation Specific Concerns in HYDRA; 7) Example application (Formation Acquisition); and 8) Sample Problem Results.

Real-time determination of fringe pattern frequencies: An application to pressure measurement

NASA Astrophysics Data System (ADS)

Sciammarella, Cesar A.; Piroozan, Parham

2007-05-01

Retrieving information in real time from fringe patterns is a topic of a great deal of interest in scientific and engineering applications of optical methods. This paper presents a method for fringe frequency determination based on the capability of neural networks to recognize signals that are similar but not identical to signals used to train the neural network. Sampled patterns are generated by calibration and stored in memory. Incoming patterns are analyzed by a back-propagation neural network at the speed of the recording device, a CCD camera. This method of information retrieval is utilized to measure pressures on a boundary layer flow. The sensor combines optics and electronics to analyze dynamic pressure distributions and to feed information to a control system that is capable to preserve the stability of the flow.

Sources of uncertainty in the quantification of genetically modified oilseed rape contamination in seed lots.

PubMed

Begg, Graham S; Cullen, Danny W; Iannetta, Pietro P M; Squire, Geoff R

2007-02-01

Testing of seed and grain lots is essential in the enforcement of GM labelling legislation and needs reliable procedures for which associated errors have been identified and minimised. In this paper we consider the testing of oilseed rape seed lots obtained from the harvest of a non-GM crop known to be contaminated by volunteer plants from a GM herbicide tolerant variety. The objective was to identify and quantify the error associated with the testing of these lots from the initial sampling to completion of the real-time PCR assay with which the level of GM contamination was quantified. The results showed that, under the controlled conditions of a single laboratory, the error associated with the real-time PCR assay to be negligible in comparison with sampling error, which was exacerbated by heterogeneity in the distribution of GM seeds, most notably at a small scale, i.e. 25 cm3. Sampling error was reduced by one to two thirds on the application of appropriate homogenisation procedures.

Real-time terahertz wave imaging by nonlinear optical frequency up-conversion in a 4-dimethylamino-N'-methyl-4'-stilbazolium tosylate crystal

NASA Astrophysics Data System (ADS)

Fan, Shuzhen; Qi, Feng; Notake, Takashi; Nawata, Kouji; Matsukawa, Takeshi; Takida, Yuma; Minamide, Hiroaki

2014-03-01

Real-time terahertz (THz) wave imaging has wide applications in areas such as security, industry, biology, medicine, pharmacy, and arts. In this letter, we report on real-time room-temperature THz imaging by nonlinear optical frequency up-conversion in organic 4-dimethylamino-N'-methyl-4'-stilbazolium tosylate crystal. The active projection-imaging system consisted of (1) THz wave generation, (2) THz-near-infrared hybrid optics, (3) THz wave up-conversion, and (4) an InGaAs camera working at 60 frames per second. The pumping laser system consisted of two optical parametric oscillators pumped by a nano-second frequency-doubled Nd:YAG laser. THz-wave images of handmade samples at 19.3 THz were taken, and videos of a sample moving and a ruler stuck with a black polyethylene film moving were supplied online to show real-time ability. Thanks to the high speed and high responsivity of this technology, real-time THz imaging with a higher signal-to-noise ratio than a commercially available THz micro-bolometer camera was proven to be feasible. By changing the phase-matching condition, i.e., by changing the wavelength of the pumping laser, we suggest THz imaging with a narrow THz frequency band of interest in a wide range from approximately 2 to 30 THz is possible.

Application of real-time PCR for total airborne bacterial assessment: Comparison with epifluorescence microscopy and culture-dependent methods

NASA Astrophysics Data System (ADS)

Rinsoz, Thomas; Duquenne, Philippe; Greff-Mirguet, Guylaine; Oppliger, Anne

Traditional culture-dependent methods to quantify and identify airborne microorganisms are limited by factors such as short-duration sampling times and inability to count non-culturable or non-viable bacteria. Consequently, the quantitative assessment of bioaerosols is often underestimated. Use of the real-time quantitative polymerase chain reaction (Q-PCR) to quantify bacteria in environmental samples presents an alternative method, which should overcome this problem. The aim of this study was to evaluate the performance of a real-time Q-PCR assay as a simple and reliable way to quantify the airborne bacterial load within poultry houses and sewage treatment plants, in comparison with epifluorescence microscopy and culture-dependent methods. The estimates of bacterial load that we obtained from real-time PCR and epifluorescence methods, are comparable, however, our analysis of sewage treatment plants indicate these methods give values 270-290 fold greater than those obtained by the "impaction on nutrient agar" method. The culture-dependent method of air impaction on nutrient agar was also inadequate in poultry houses, as was the impinger-culture method, which gave a bacterial load estimate 32-fold lower than obtained by Q-PCR. Real-time quantitative PCR thus proves to be a reliable, discerning, and simple method that could be used to estimate airborne bacterial load in a broad variety of other environments expected to carry high numbers of airborne bacteria.

MS-BWME: A Wireless Real-Time Monitoring System for Brine Well Mining Equipment

PubMed Central

Xiao, Xinqing; Zhu, Tianyu; Qi, Lin; Moga, Liliana Mihaela; Zhang, Xiaoshuan

2014-01-01

This paper describes a wireless real-time monitoring system (MS-BWME) to monitor the running state of pumps equipment in brine well mining and prevent potential failures that may produce unexpected interruptions with severe consequences. MS-BWME consists of two units: the ZigBee Wireless Sensors Network (WSN) unit and the real-time remote monitoring unit. MS-BWME was implemented and tested in sampled brine wells mining in Qinghai Province and four kinds of indicators were selected to evaluate the performance of the MS-BWME, i.e., sensor calibration, the system's real-time data reception, Received Signal Strength Indicator (RSSI) and sensor node lifetime. The results show that MS-BWME can accurately judge the running state of the pump equipment by acquiring and transmitting the real-time voltage and electric current data of the equipment from the spot and provide real-time decision support aid to help workers overhaul the equipment in a timely manner and resolve failures that might produce unexpected production down-time. The MS-BWME can also be extended to a wide range of equipment monitoring applications. PMID:25340455

Feasibility of real-time geochemical analysis using LIBS (Laser-Induced Breakdown Spectroscopy) in oil wells

NASA Astrophysics Data System (ADS)

Shahin, Mohamed

2014-05-01

The oil and gas industry has attempted for many years to find new ways to analyze and determine the type of rocks drilled on a real time basis. Mud analysis logging is a direct method of detecting oil and gas in formations drilled, it depends on the "feel" of the bit to decide formation type, as well as, geochemical analysis which was introduced 30 years ago, starting with a pulsed-neutron generator (PNG) based wireline tool upon which LWD technology was based. In this paper, we are studying the feasibility of introducing a new technology for real-time geochemical analysis. Laser-induced breakdown spectroscopy (LIBS) is a type of atomic emission spectroscopy, It is a cutting-edge technology that is used for many applications such as determination of alloy composition, origin of manufacture (by monitoring trace components), and molecular analysis (unknown identification). LIBS can analyze any material regardless of its state (solid, liquid or gas), based upon that fact, we can analyze rocks, formation fluids' types and contacts between them. In cooperation with the National Institute of Laser Enhanced Science, Cairo University in Egypt, we've done tests on sandstone, limestone and coal samples acquired from different places using Nd: YAG Laser with in addition to other components that are explained in details through this paper to understand the ability of Laser to analyze rock samples and provide their elemental composition using LIBS technique. We've got promising results from the sample analysis via LIBS and discussed the possibility of deploying this technology in oilfields suggesting many applications and giving a base for achieving a quantitative elemental analysis method in view of its shortcomings and solutions.

Real-time Graphics Processing Unit Based Fourier Domain Optical Coherence Tomography and Surgical Applications

NASA Astrophysics Data System (ADS)

Zhang, Kang

2011-12-01

In this dissertation, real-time Fourier domain optical coherence tomography (FD-OCT) capable of multi-dimensional micrometer-resolution imaging targeted specifically for microsurgical intervention applications was developed and studied. As a part of this work several ultra-high speed real-time FD-OCT imaging and sensing systems were proposed and developed. A real-time 4D (3D+time) OCT system platform using the graphics processing unit (GPU) to accelerate OCT signal processing, the imaging reconstruction, visualization, and volume rendering was developed. Several GPU based algorithms such as non-uniform fast Fourier transform (NUFFT), numerical dispersion compensation, and multi-GPU implementation were developed to improve the impulse response, SNR roll-off and stability of the system. Full-range complex-conjugate-free FD-OCT was also implemented on the GPU architecture to achieve doubled image range and improved SNR. These technologies overcome the imaging reconstruction and visualization bottlenecks widely exist in current ultra-high speed FD-OCT systems and open the way to interventional OCT imaging for applications in guided microsurgery. A hand-held common-path optical coherence tomography (CP-OCT) distance-sensor based microsurgical tool was developed and validated. Through real-time signal processing, edge detection and feed-back control, the tool was shown to be capable of track target surface and compensate motion. The micro-incision test using a phantom was performed using a CP-OCT-sensor integrated hand-held tool, which showed an incision error less than +/-5 microns, comparing to >100 microns error by free-hand incision. The CP-OCT distance sensor has also been utilized to enhance the accuracy and safety of optical nerve stimulation. Finally, several experiments were conducted to validate the system for surgical applications. One of them involved 4D OCT guided micro-manipulation using a phantom. Multiple volume renderings of one 3D data set were performed with different view angles to allow accurate monitoring of the micro-manipulation, and the user to clearly monitor tool-to-target spatial relation in real-time. The system was also validated by imaging multiple biological samples, such as human fingerprint, human cadaver head and small animals. Compared to conventional surgical microscopes, GPU-based real-time FD-OCT can provide the surgeons with a real-time comprehensive spatial view of the microsurgical region and accurate depth perception.

Comparison of droplet digital PCR with quantitative real-time PCR for determination of zygosity in transgenic maize.

PubMed

Xu, Xiaoli; Peng, Cheng; Wang, Xiaofu; Chen, Xiaoyun; Wang, Qiang; Xu, Junfeng

2016-12-01

This study evaluated the applicability of droplet digital PCR (ddPCR) as a tool for maize zygosity determination using quantitative real-time PCR (qPCR) as a reference technology. Quantitative real-time PCR is commonly used to determine transgene copy number or GMO zygosity characterization. However, its effectiveness is based on identical reaction efficiencies for the transgene and the endogenous reference gene. Additionally, a calibrator sample should be utilized for accuracy. Droplet digital PCR is a DNA molecule counting technique that directly counts the absolute number of target and reference DNA molecules in a sample, independent of assay efficiency or external calibrators. The zygosity of the transgene can be easily determined using the ratio of the quantity of the target gene to the reference single copy endogenous gene. In this study, both the qPCR and ddPCR methods were used to determine insect-resistant transgenic maize IE034 zygosity. Both methods performed well, but the ddPCR method was more convenient because of its absolute quantification property.

A Real-Time Image Acquisition And Processing System For A RISC-Based Microcomputer

NASA Astrophysics Data System (ADS)

Luckman, Adrian J.; Allinson, Nigel M.

1989-03-01

A low cost image acquisition and processing system has been developed for the Acorn Archimedes microcomputer. Using a Reduced Instruction Set Computer (RISC) architecture, the ARM (Acorn Risc Machine) processor provides instruction speeds suitable for image processing applications. The associated improvement in data transfer rate has allowed real-time video image acquisition without the need for frame-store memory external to the microcomputer. The system is comprised of real-time video digitising hardware which interfaces directly to the Archimedes memory, and software to provide an integrated image acquisition and processing environment. The hardware can digitise a video signal at up to 640 samples per video line with programmable parameters such as sampling rate and gain. Software support includes a work environment for image capture and processing with pixel, neighbourhood and global operators. A friendly user interface is provided with the help of the Archimedes Operating System WIMP (Windows, Icons, Mouse and Pointer) Manager. Windows provide a convenient way of handling images on the screen and program control is directed mostly by pop-up menus.

[Development and application of real-time PCR for identification and detection of horse meat in animal-origin products].

PubMed

Li, Nan; Wang, Jiahui; Shen, Qing; Han, Chunhui; Zhang, Jing; Li, Fengqin; Xu, Jin; Jiang, Tao

2013-11-01

To develop a real-time PCR method for identification and detection of domestic horse meat (Equus caballus) in animal-origin products. The primer and TaqMan-probe was designed and synthesized according to the EU reference laboratory and 87 bp fragments was amplified for horse ingredients. The specificity and sensitivity was tested by artificially spiked horse meat into other domestic meat, such as cattle, sheep, pork, chicken, duck and rabbit. 122 samples of cattle and sheep products were random collected in Beijing market and the detection of horse meat was carried out. The real-time PCR in this study has high specificity and sensitivity for horse meat. No cross-reaction was observed between the horse and sheep, pork, chicken, duck and rabbit meat. There was little cross reaction between horse and cattle when the CT value reach 33. 81. The method can detect 0.1% of horse meat mixed with other domestic animal-origin products. No horse meat ingredients were detected in 122 samples in this survey. There was no horse meat mixed into cattle and sheep products in Beijing marked.

Novel approach to quantitative polymerase chain reaction using real-time detection: application to the detection of gene amplification in breast cancer.

PubMed

Bièche, I; Olivi, M; Champème, M H; Vidaud, D; Lidereau, R; Vidaud, M

1998-11-23

Gene amplification is a common event in the progression of human cancers, and amplified oncogenes have been shown to have diagnostic, prognostic and therapeutic relevance. A kinetic quantitative polymerase-chain-reaction (PCR) method, based on fluorescent TaqMan methodology and a new instrument (ABI Prism 7700 Sequence Detection System) capable of measuring fluorescence in real-time, was used to quantify gene amplification in tumor DNA. Reactions are characterized by the point during cycling when PCR amplification is still in the exponential phase, rather than the amount of PCR product accumulated after a fixed number of cycles. None of the reaction components is limited during the exponential phase, meaning that values are highly reproducible in reactions starting with the same copy number. This greatly improves the precision of DNA quantification. Moreover, real-time PCR does not require post-PCR sample handling, thereby preventing potential PCR-product carry-over contamination; it possesses a wide dynamic range of quantification and results in much faster and higher sample throughput. The real-time PCR method, was used to develop and validate a simple and rapid assay for the detection and quantification of the 3 most frequently amplified genes (myc, ccndl and erbB2) in breast tumors. Extra copies of myc, ccndl and erbB2 were observed in 10, 23 and 15%, respectively, of 108 breast-tumor DNA; the largest observed numbers of gene copies were 4.6, 18.6 and 15.1, respectively. These results correlated well with those of Southern blotting. The use of this new semi-automated technique will make molecular analysis of human cancers simpler and more reliable, and should find broad applications in clinical and research settings.

A Case Study of Upper-Room UVGI in Densely-Occupied Elementary Classrooms by Real-Time Fluorescent Bioaerosol Measurements.

PubMed

Su, Chunxiao; Lau, Josephine; Yu, Fang

2017-01-08

Recently, the requirement to continuously collect bioaerosol samples using shorter response times has called for the use of real-time detection. The decreased cost of this technology makes it available for a wider application than military use, and makes it accessible to pharmaceutical and academic research. In this case study, real-time bioaerosol monitors (RBMs) were applied in elementary school classrooms-a densely occupied environment-along with upper-room ultraviolet germicidal irradiation (UVGI) devices. The classrooms were separated into a UVGI group and a non-UVGI control group. Fluorescent bioaerosol counts (FBCs) were monitored on 20 visiting days over a four-month period. The classroom with upper-room UVGI showed significantly lower concentrations of fine size (<3 μm) and total FBCs than the control classroom during 13 of the 20 visiting days. The results of the study indicate that the upper-room UVGI could be effective in reducing FBCs in the school environment, and RBMs may be applicable in reflecting the transient conditions of the classrooms due to the dynamic activity levels of the students and teachers.

A noninvasive technique for real-time detection of bruises in apple surface based on machine vision

NASA Astrophysics Data System (ADS)

Zhao, Juan; Peng, Yankun; Dhakal, Sagar; Zhang, Leilei; Sasao, Akira

2013-05-01

Apple is one of the highly consumed fruit item in daily life. However, due to its high damage potential and massive influence on taste and export, the quality of apple has to be detected before it reaches the consumer's hand. This study was aimed to develop a hardware and software unit for real-time detection of apple bruises based on machine vision technology. The hardware unit consisted of a light shield installed two monochrome cameras at different angles, LED light source to illuminate the sample, and sensors at the entrance of box to signal the positioning of sample. Graphical Users Interface (GUI) was developed in VS2010 platform to control the overall hardware and display the image processing result. The hardware-software system was developed to acquire the images of 3 samples from each camera and display the image processing result in real time basis. An image processing algorithm was developed in Opencv and C++ platform. The software is able to control the hardware system to classify the apple into two grades based on presence/absence of surface bruises with the size of 5mm. The experimental result is promising and the system with further modification can be applicable for industrial production in near future.

7 CFR 1951.11 - Application of payments on real estate accounts.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 14 2011-01-01 2011-01-01 false Application of payments on real estate accounts. 1951... Servicing Policies § 1951.11 Application of payments on real estate accounts. (a) Regular payments. If a borrower owes more than one type of real estate loan, or has received initial and subsequent real estate...

7 CFR 1951.11 - Application of payments on real estate accounts.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 14 2010-01-01 2009-01-01 true Application of payments on real estate accounts. 1951... Servicing Policies § 1951.11 Application of payments on real estate accounts. (a) Regular payments. If a borrower owes more than one type of real estate loan, or has received initial and subsequent real estate...

7 CFR 1951.11 - Application of payments on real estate accounts.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 14 2012-01-01 2012-01-01 false Application of payments on real estate accounts. 1951... Servicing Policies § 1951.11 Application of payments on real estate accounts. (a) Regular payments. If a borrower owes more than one type of real estate loan, or has received initial and subsequent real estate...

7 CFR 1951.11 - Application of payments on real estate accounts.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 14 2013-01-01 2013-01-01 false Application of payments on real estate accounts. 1951... Servicing Policies § 1951.11 Application of payments on real estate accounts. (a) Regular payments. If a borrower owes more than one type of real estate loan, or has received initial and subsequent real estate...

7 CFR 1951.11 - Application of payments on real estate accounts.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 14 2014-01-01 2014-01-01 false Application of payments on real estate accounts. 1951... Servicing Policies § 1951.11 Application of payments on real estate accounts. (a) Regular payments. If a borrower owes more than one type of real estate loan, or has received initial and subsequent real estate...

Mass spectrometry of atmospheric aerosols--recent developments and applications. Part II: On-line mass spectrometry techniques.

PubMed

Pratt, Kerri A; Prather, Kimberly A

2012-01-01

Many of the significant advances in our understanding of atmospheric particles can be attributed to the application of mass spectrometry. Mass spectrometry provides high sensitivity with fast response time to probe chemically complex particles. This review focuses on recent developments and applications in the field of mass spectrometry of atmospheric aerosols. In Part II of this two-part review, we concentrate on real-time mass spectrometry techniques, which provide high time resolution for insight into brief events and diurnal changes while eliminating the potential artifacts acquired during long-term filter sampling. In particular, real-time mass spectrometry has been shown recently to provide the ability to probe the chemical composition of ambient individual particles <30 nm in diameter to further our understanding of how particles are formed through nucleation in the atmosphere. Further, transportable real-time mass spectrometry techniques are now used frequently on ground-, ship-, and aircraft-based studies around the globe to further our understanding of the spatial distribution of atmospheric aerosols. In addition, coupling aerosol mass spectrometry techniques with other measurements in series has allowed the in situ determination of chemically resolved particle effective density, refractive index, volatility, and cloud activation properties. Copyright © 2011 Wiley Periodicals, Inc.

Real-time monitoring system for improving corona electrostatic separation in the process of recovering waste printed circuit boards.

PubMed

Li, Jia; Zhou, Quan; Xu, Zhenming

2014-12-01

Although corona electrostatic separation is successfully used in recycling waste printed circuit boards in industrial applications, there are problems that cannot be resolved completely, such as nonmetal particle aggregation and spark discharge. Both of these problems damage the process of separation and are not easy to identify during the process of separation in industrial applications. This paper provides a systematic study on a real-time monitoring system. Weight monitoring systems were established to continuously monitor the separation process. A Virtual Instrumentation program written by LabVIEW was utilized to sample and analyse the mass increment of the middling product. It includes four modules: historical data storage, steady-state analysis, data computing and alarm. Three kinds of operating conditions were used to verify the applicability of the monitoring system. It was found that the system achieved the goal of monitoring during the separation process and realized the function of real-time analysis of the received data. The system also gave comprehensible feedback on the accidents of material blockages in the feed inlet and high-voltage spark discharge. With the warning function of the alarm system, the whole monitoring system could save the human cost and help the new technology to be more easily applied in industry. © The Author(s) 2014.

Ultrasonic Surface Measurements for the investigation of superficial alteration of natural stones

NASA Astrophysics Data System (ADS)

Meier, Thomas; Auras, Michael; Bilgili, Filiz; Christen, Sandra; Cristiano, Luigia; Krompholz, Rolf; Mosca, Ilaria; Rose, David

2013-04-01

Seismic waveform analysis is applicable also to the centimeter and decimeter scale for non-destructive testing of pavement, facades, plaster, sculptures, or load-bearing structures like pillars. Mostly transmission measurements are performed and travel-times of first arriving P-waves are considered that have limited resolution for the upper centimeters of an object. In contrast, surface measurements are well suited to quantify superficial alterations of material properties e.g. due to weathering. A number of surface measurements have been carried out in the laboratory as well as on real structures in order to study systematically the information content of ultrasonic waveforms and their variability under real conditions. As a preposition for ultrasonic waveform analysis, reproducible, broad-band measurements have to be carried out with a definite radiation pattern and an about 1 mm accuracy of the measurement geometry. We used special coupling devices for effective ultrasonic surface measurements in the laboratory as well as at real objects. Samples of concrete with varying composition and samples of natural stone - marble, tuff, and sandstone - were repeatedly weathered and tested by ultrasonic measurements. The resistance of the samples to weathering and the penetration depth of the weathering are analyzed. Furthermore, material specific calibration curves for changes in velocities of elastic waves due to weathering can be obtained by these tests. Tests on real structures have been carried out for marble (Schlossbrücke, Berlin) and sandstone (Porta Nigra, Trier). Altogether, these test measurements show clearly that despite of the internal inhomogeneity of many real objects, their surface roughness and topography especially ultrasonic Rayleigh waves are well suited to study material alterations in the upper centimeters. Dispersion of Rayleigh waves may be inverted for shear-wave velocity as a function of depth.

Real-time PCR assays for detection of Brucella spp. and the identification of genotype ST27 in bottlenose dolphins (Tursiops truncatus).

PubMed

Wu, Qingzhong; McFee, Wayne E; Goldstein, Tracey; Tiller, Rebekah V; Schwacke, Lori

2014-05-01

Rapid detection of Brucella spp. in marine mammals is challenging. Microbiologic culture is used for definitive diagnosis of brucellosis, but is time consuming, has low sensitivity and can be hazardous to laboratory personnel. Serological methods can aid in diagnosis, but may not differentiate prior exposure versus current active infection and may cross-react with unrelated Gram-negative bacteria. This study reports a real-time PCR assay for the detection of Brucella spp. and application to screen clinical samples from bottlenose dolphins stranded along the coast of South Carolina, USA. The assay was found to be 100% sensitive for the Brucella strains tested, and the limit of detection was 0.27fg of genomic DNA from Brucella ceti B1/94 per PCR volume. No amplification was detected for the non-Brucella pathogens tested. Brucella DNA was detected in 31% (55/178) of clinical samples tested. These studies indicate that the real-time PCR assay is highly sensitive and specific for the detection of Brucella spp. in bottlenose dolphins. We also developed a second real-time PCR assay for rapid identification of Brucella ST27, a genotype that is associated with human zoonotic infection. Positive results were obtained for Brucella strains which had been identified as ST27 by multilocus sequence typing. No amplification was found for other Brucella strains included in this study. ST27 was identified in 33% (18/54) of Brucella spp. DNA-positive clinical samples. To our knowledge, this is the first report on the use of a real-time PCR assay for identification of Brucella genotype ST27 in marine mammals. Copyright © 2014 Elsevier B.V. All rights reserved.

Instrument for Real-Time Digital Nucleic Acid Amplification on Custom Microfluidic Devices

PubMed Central

Selck, David A.

2016-01-01

Nucleic acid amplification tests that are coupled with a digital readout enable the absolute quantification of single molecules, even at ultralow concentrations. Digital methods are robust, versatile and compatible with many amplification chemistries including isothermal amplification, making them particularly invaluable to assays that require sensitive detection, such as the quantification of viral load in occult infections or detection of sparse amounts of DNA from forensic samples. A number of microfluidic platforms are being developed for carrying out digital amplification. However, the mechanistic investigation and optimization of digital assays has been limited by the lack of real-time kinetic information about which factors affect the digital efficiency and analytical sensitivity of a reaction. Commercially available instruments that are capable of tracking digital reactions in real-time are restricted to only a small number of device types and sample-preparation strategies. Thus, most researchers who wish to develop, study, or optimize digital assays rely on the rate of the amplification reaction when performed in a bulk experiment, which is now recognized as an unreliable predictor of digital efficiency. To expand our ability to study how digital reactions proceed in real-time and enable us to optimize both the digital efficiency and analytical sensitivity of digital assays, we built a custom large-format digital real-time amplification instrument that can accommodate a wide variety of devices, amplification chemistries and sample-handling conditions. Herein, we validate this instrument, we provide detailed schematics that will enable others to build their own custom instruments, and we include a complete custom software suite to collect and analyze the data retrieved from the instrument. We believe assay optimizations enabled by this instrument will improve the current limits of nucleic acid detection and quantification, improving our fundamental understanding of single-molecule reactions and providing advancements in practical applications such as medical diagnostics, forensics and environmental sampling. PMID:27760148

Validation of virtual reality as a tool to understand and prevent child pedestrian injury.

PubMed

Schwebel, David C; Gaines, Joanna; Severson, Joan

2008-07-01

In recent years, virtual reality has emerged as an innovative tool for health-related education and training. Among the many benefits of virtual reality is the opportunity for novice users to engage unsupervised in a safe environment when the real environment might be dangerous. Virtual environments are only useful for health-related research, however, if behavior in the virtual world validly matches behavior in the real world. This study was designed to test the validity of an immersive, interactive virtual pedestrian environment. A sample of 102 children and 74 adults was recruited to complete simulated road-crossings in both the virtual environment and the identical real environment. In both the child and adult samples, construct validity was demonstrated via significant correlations between behavior in the virtual and real worlds. Results also indicate construct validity through developmental differences in behavior; convergent validity by showing correlations between parent-reported child temperament and behavior in the virtual world; internal reliability of various measures of pedestrian safety in the virtual world; and face validity, as measured by users' self-reported perception of realism in the virtual world. We discuss issues of generalizability to other virtual environments, and the implications for application of virtual reality to understanding and preventing pediatric pedestrian injuries.

Quantitative detection of Lactarius deliciosus extraradical soil mycelium by real-time PCR and its application in the study of fungal persistence and interspecific competition.

PubMed

Parladé, J; Hortal, S; Pera, J; Galipienso, L

2007-01-30

Real-Time PCR has been applied to quantify extraradical soil mycelium of the edible ectomycorrhizal fungus Lactarius deliciosus in an interspecific competition experiment under greenhouse conditions. Couples of Pinus pinea seedlings inoculated with either L. deliciosus, Rhizopogon roseolus, or non-inoculated (control) were transplanted into pots filled with two types of soil in all the possible combinations. Total DNA was extracted from soil samples at 3 and 6 months after transplantation to perform real-time PCR analysis. DNA extractions from soil mixed with known amounts of mycelium of L. deliciosus were used as standards. Six months after transplantation, the percentage of mycorrhizas of L. deliciosus and seedling growth were significantly affected by the soil type. Extraradical soil mycelium of L. deliciosus was positively correlated with the final percentage of mycorrhizas and significantly affected by the sampling time and soil depth. The competition effect of R. roseolus was not significant for any of the measured parameters, probably due to the sharp decrease of the mycorrhizal colonization by this fungus. We conclude that real-time PCR is a powerful technique for extraradical mycelium quantification in studies aimed at evaluating the persistence of introduced strains of L. deliciosus in field plantations.

DBS-LC-MS/MS assay for caffeine: validation and neonatal application.

PubMed

Bruschettini, Matteo; Barco, Sebastiano; Romantsik, Olga; Risso, Francesco; Gennai, Iulian; Chinea, Benito; Ramenghi, Luca A; Tripodi, Gino; Cangemi, Giuliana

2016-09-01

DBS might be an appropriate microsampling technique for therapeutic drug monitoring of caffeine in infants. Nevertheless, its application presents several issues that still limit its use. This paper describes a validated DBS-LC-MS/MS method for caffeine. The results of the method validation showed an hematocrit dependence. In the analysis of 96 paired plasma and DBS clinical samples, caffeine levels measured in DBS were statistically significantly lower than in plasma but the observed differences were independent from hematocrit. These results clearly showed the need for extensive validation with real-life samples for DBS-based methods. DBS-LC-MS/MS can be considered to be a good alternative to traditional methods for therapeutic drug monitoring or PK studies in preterm infants.

Got a Match? Ion Extraction GC-MS Characterization of Accelerants Adsorbed in Charcoal Using Negative Pressure Dynamic Headspace Concentration

ERIC Educational Resources Information Center

Anzivino, Barbara; Tilley, Leon J.; Ingalls, Laura R.; Hall, Adam B.; Drugan, John E.

2009-01-01

An undergraduate organic chemistry experiment demonstrating real-life application of GC-MS to arson accelerant identification is described. Students are given the task of comparing a sample recovered from a "crime scene" to that from a "suspect's clothing". Accelerants subjected to different conditions are recovered using a quick and simple…

Culturally Specific Youth Substance Abuse Resistance Skills: Applicability across the U.S.-Mexico Border

ERIC Educational Resources Information Center

Marsiglia, Flavio F.; Kulis, Stephen; Rodriguez, Gregorio Martinez; Becerra, David; Castillo, Jason

2009-01-01

This article reports on the prevalence and frequency of use of a set of drug-resistance strategies among a sample of Mexican adolescents. The keepin' it REAL (refuse, explain, avoid, and leave) strategies are part of a model drug-prevention intervention program originally developed by and for youth in the United States. The present study tests the…

The Use of Handheld X-Ray Fluorescence (XRF) Technology in Unraveling the Eruptive History of the San Francisco Volcanic Field, Arizona

NASA Technical Reports Server (NTRS)

Young, Kelsey E.; Evans, C. A.; Hodges, K. V.

2012-01-01

While traditional geologic mapping includes the examination of structural relationships between rock units in the field, more advanced technology now enables us to simultaneously collect and combine analytical datasets with field observations. Information about tectonomagmatic processes can be gleaned from these combined data products. Historically, construction of multi-layered field maps that include sample data has been accomplished serially (first map and collect samples, analyze samples, combine data, and finally, readjust maps and conclusions about geologic history based on combined data sets). New instruments that can be used in the field, such as a handheld xray fluorescence (XRF) unit, are now available. Targeted use of such instruments enables geologists to collect preliminary geochemical data while in the field so that they can optimize scientific data return from each field traverse. Our study tests the application of this technology and projects the benefits gained by real-time geochemical data in the field. The integrated data set produces a richer geologic map and facilitates a stronger contextual picture for field geologists when collecting field observations and samples for future laboratory work. Real-time geochemical data on samples also provide valuable insight regarding sampling decisions by the field geologist

An operational method for the real-time monitoring of E. coli numbers in bathing waters.

PubMed

Lebaron, Philippe; Henry, A; Lepeuple, A-S; Pena, G; Servais, P

2005-06-01

The aim of this study was to investigate the potential application of the beta-d-glucuronidase (GLUase) activity measurement for the routine detection and quantification of E. coli in marine bathing waters. GLUase activity was measured as the rate of hydrolysis of 4-methylumbelliferyl-beta-d-glucuronide. Culturable E. coli were quantified by the most probable number (MPN) microplate method. Both methods were applied to a large set of seawater samples. Significant correlation was found between the log of GLUase activity and the log of culturable E. coli. The mean coefficient of variation (CV) of the GLUase activity was less than 15% at concentrations around the current standards of International regulations whereas the CV of the microplate method was around 30%. When samples were stored at 4 degrees C and 20 degrees C, the mean CV of the GLUase activity remained below 15% up to 6 hours after sample collection whereas the range of variation of the microplate method varied between 10 and 50%. We concluded that the GLUase activity is an operational, reproducible, simple, very rapid and low cost method for the real-time enumeration of E. coli in bathing waters and should be preferred to the microplate method. The GLUase activity method should be routinely applied to the rapid enumeration of E. coli in recreational waters and recommendations for its application were suggested to water quality managers.

Enantioselective column coupled electrophoresis employing large bore capillaries hyphenated with tandem mass spectrometry for ultra-trace determination of chiral compounds in complex real samples.

PubMed

Piešťanský, Juraj; Maráková, Katarína; Kovaľ, Marián; Havránek, Emil; Mikuš, Peter

2015-12-01

A new multidimensional analytical approach for the ultra-trace determination of target chiral compounds in unpretreated complex real samples was developed in this work. The proposed analytical system provided high orthogonality due to on-line combination of three different methods (separation mechanisms), i.e. (1) isotachophoresis (ITP), (2) chiral capillary zone electrophoresis (chiral CZE), and (3) triple quadrupole mass spectrometry (QqQ MS). The ITP step, performed in a large bore capillary (800 μm), was utilized for the effective sample pretreatment (preconcentration and matrix clean-up) in a large injection volume (1-10 μL) enabling to obtain as low as ca. 80 pg/mL limits of detection for the target enantiomers in urine matrices. In the chiral CZE step, the different chiral selectors (neutral, ionizable, and permanently charged cyclodextrins) and buffer systems were tested in terms of enantioselectivity and influence on the MS detection response. The performance parameters of the optimized ITP - chiral CZE-QqQ MS method were evaluated according to the FDA guidance for bioanalytical method validation. Successful validation and application (enantioselective monitoring of renally eliminated pheniramine and its metabolite in human urine) highlighted great potential of this chiral approach in advanced enantioselective biomedical applications. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A real-time KLT implementation for radio-SETI applications

NASA Astrophysics Data System (ADS)

Melis, Andrea; Concu, Raimondo; Pari, Pierpaolo; Maccone, Claudio; Montebugnoli, Stelio; Possenti, Andrea; Valente, Giuseppe; Antonietti, Nicoló; Perrodin, Delphine; Migoni, Carlo; Murgia, Matteo; Trois, Alessio; Barbaro, Massimo; Bocchinu, Alessandro; Casu, Silvia; Lunesu, Maria Ilaria; Monari, Jader; Navarrini, Alessandro; Pisanu, Tonino; Schilliró, Francesco; Vacca, Valentina

2016-07-01

SETI, the Search for ExtraTerrestrial Intelligence, is the search for radio signals emitted by alien civilizations living in the Galaxy. Narrow-band FFT-based approaches have been preferred in SETI, since their computation time only grows like N*lnN, where N is the number of time samples. On the contrary, a wide-band approach based on the Kahrunen-Lo`eve Transform (KLT) algorithm would be preferable, but it would scale like N*N. In this paper, we describe a hardware-software infrastructure based on FPGA boards and GPU-based PCs that circumvents this computation-time problem allowing for a real-time KLT.

Detection of Yersinia Enterocolitica Species in Pig Tonsils and Raw Pork Meat by the Real-Time Pcr and Culture Methods.

PubMed

Stachelska, M A

2017-09-26

The aim of the present study was to establish a rapid and accurate real-time PCR method to detect pathogenic Yersinia enterocolitica in pork. Yersinia enterocolitica is considered to be a crucial zoonosis, which can provoke diseases both in humans and animals. The classical culture methods designated to detect Y. enterocolitica species in food matrices are often very time-consuming. The chromosomal locus _tag CH49_3099 gene, that appears in pathogenic Y. enterocolitica strains, was applied as DNA target for the 5' nuclease PCR protocol. The probe was labelled at the 5' end with the fluorescent reporter dye (FAM) and at the 3' end with the quencher dye (TAMRA). The real-time PCR cycling parameters included 41 cycles. A Ct value which reached a value higher than 40 constituted a negative result. The developed for the needs of this study qualitative real-time PCR method appeared to give very specific and reliable results. The detection rate of locus _tag CH49_3099 - positive Y. enterocolitica in 150 pig tonsils was 85 % and 32 % with PCR and culture methods, respectively. Both the Real-time PCR results and culture method results were obtained from material that was enriched during overnight incubation. The subject of the study were also raw pork meat samples. Among 80 samples examined, 7 ones were positive when real-time PCR was applied, and 6 ones were positive when classical culture method was applied. The application of molecular techniques based on the analysis of DNA sequences such as the Real-time PCR enables to detect this pathogenic bacteria very rapidly and with higher specificity, sensitivity and reliability in comparison to classical culture methods.

A novel rapid genotyping technique for Collie eye anomaly: SYBR Green-based real-time polymerase chain reaction method applicable to blood and saliva specimens on Flinders Technology Associates filter paper.

PubMed

Chang, Hye-Sook; Mizukami, Keijiro; Yabuki, Akira; Hossain, Mohammad A; Rahman, Mohammad M; Uddin, Mohammad M; Arai, Toshiro; Yamato, Osamu

2010-09-01

Collie eye anomaly (CEA) is a canine inherited ocular disease that shows a wide variety of manifestations and severity of clinical lesions. Recently, a CEA-associated mutation was reported, and a DNA test that uses conventional polymerase chain reaction (PCR) has now become available. The objective of the current study was to develop a novel rapid genotyping technique by using SYBR Green-based real-time PCR for future large-scale surveys as a key part in the strategy to eradicate CEA by selective breeding. First, a SYBR Green-based real-time PCR assay for genotyping of CEA was developed and evaluated by using purified DNA samples from normal, carrier, and affected Border Collies in which genotypes had previously been determined by conventional PCR. This real-time PCR assay demonstrated appropriate amplifications in all genotypes, and the results were consistent with those of conventional PCR. Second, the availability of Flinders Technology Associates filter paper (FTA card) as DNA templates for the real-time PCR assay was evaluated by using blood and saliva specimens to determine suitability for CEA screening. DNA-containing solution prepared from a disc of blood- or saliva-spotted FTA cards was available directly as templates for the real-time PCR assay when the volume of solution was 2.5% of the PCR mixture. In conclusion, SYBR Green-based real-time PCR combined with FTA cards is a rapid genotyping technique for CEA that can markedly shorten the overall time required for genotyping as well as simplify the sample preparation. Therefore, this newly developed technique suits large-scale screening in breeding populations of Collie-related breeds.

Recommender system based on scarce information mining.

PubMed

Lu, Wei; Chung, Fu-Lai; Lai, Kunfeng; Zhang, Liang

2017-09-01

Guessing what user may like is now a typical interface for video recommendation. Nowadays, the highly popular user generated content sites provide various sources of information such as tags for recommendation tasks. Motivated by a real world online video recommendation problem, this work targets at the long tail phenomena of user behavior and the sparsity of item features. A personalized compound recommendation framework for online video recommendation called Dirichlet mixture probit model for information scarcity (DPIS) is hence proposed. Assuming that each clicking sample is generated from a representation of user preferences, DPIS models the sample level topic proportions as a multinomial item vector, and utilizes topical clustering on the user part for recommendation through a probit classifier. As demonstrated by the real-world application, the proposed DPIS achieves better performance in accuracy, perplexity as well as diversity in coverage than traditional methods. Copyright © 2017 Elsevier Ltd. All rights reserved.

Three-dimensional, automated, real-time video system for tracking limb motion in brain-machine interface studies.

PubMed

Peikon, Ian D; Fitzsimmons, Nathan A; Lebedev, Mikhail A; Nicolelis, Miguel A L

2009-06-15

Collection and analysis of limb kinematic data are essential components of the study of biological motion, including research into biomechanics, kinesiology, neurophysiology and brain-machine interfaces (BMIs). In particular, BMI research requires advanced, real-time systems capable of sampling limb kinematics with minimal contact to the subject's body. To answer this demand, we have developed an automated video tracking system for real-time tracking of multiple body parts in freely behaving primates. The system employs high-contrast markers painted on the animal's joints to continuously track the three-dimensional positions of their limbs during activity. Two-dimensional coordinates captured by each video camera are combined and converted to three-dimensional coordinates using a quadratic fitting algorithm. Real-time operation of the system is accomplished using direct memory access (DMA). The system tracks the markers at a rate of 52 frames per second (fps) in real-time and up to 100fps if video recordings are captured to be later analyzed off-line. The system has been tested in several BMI primate experiments, in which limb position was sampled simultaneously with chronic recordings of the extracellular activity of hundreds of cortical cells. During these recordings, multiple computational models were employed to extract a series of kinematic parameters from neuronal ensemble activity in real-time. The system operated reliably under these experimental conditions and was able to compensate for marker occlusions that occurred during natural movements. We propose that this system could also be extended to applications that include other classes of biological motion.

Continuous-wave terahertz digital holography by use of a pyroelectric array camera.

PubMed

Ding, Sheng-Hui; Li, Qi; Li, Yun-Da; Wang, Qi

2011-06-01

Terahertz (THz) digital holography is realized based on a 2.52 THz far-IR gas laser and a commercial 124 × 124 pyroelectric array camera. Off-axis THz holograms are obtained by recording interference patterns between light passing through the sample and the reference wave. A numerical reconstruction process is performed to obtain the field distribution at the object surface. Different targets were imaged to test the system's imaging capability. Compared with THz focal plane images, the image quality of the reconstructed images are improved a lot. The results show that the system's imaging resolution can reach at least 0.4 mm. The system also has the potential for real-time imaging application. This study confirms that digital holography is a promising technique for real-time, high-resolution THz imaging, which has extensive application prospects. © 2011 Optical Society of America

Zinc metal complex as a sensor for simultaneous detection of fluoride and HSO4(-) ions.

PubMed

Singh, Jasminder; Yadav, Manisha; Singh, Ajnesh; Singh, Narinder

2015-07-28

A Schiff base based tripodal receptor was synthesized and complexed with a zinc metal ion (n17) using a very easy single step process. The resulting complex was fully characterized by CHN and single crystal XRD. The real time application of the complex in aqueous media was devised by preparing its organic nanoparticles (ONPs) and their sensor activity was tested with various anions by observing changes in the fluorescence profile of n17. It was observed that ONPs of n17 responded excellently for fluoride and sulfate, producing two different signals, with detection limits of 4.84 × 10(-12) M and 5.67 × 10(-9) M respectively, without having any interference from each other. The real time application of the sensor was also tested using various samples collected from various daily utility items and found to respond exceptionally well.

A new framework for comprehensive, robust, and efficient global sensitivity analysis: 2. Application

NASA Astrophysics Data System (ADS)

Razavi, Saman; Gupta, Hoshin V.

2016-01-01

Based on the theoretical framework for sensitivity analysis called "Variogram Analysis of Response Surfaces" (VARS), developed in the companion paper, we develop and implement a practical "star-based" sampling strategy (called STAR-VARS), for the application of VARS to real-world problems. We also develop a bootstrap approach to provide confidence level estimates for the VARS sensitivity metrics and to evaluate the reliability of inferred factor rankings. The effectiveness, efficiency, and robustness of STAR-VARS are demonstrated via two real-data hydrological case studies (a 5-parameter conceptual rainfall-runoff model and a 45-parameter land surface scheme hydrology model), and a comparison with the "derivative-based" Morris and "variance-based" Sobol approaches are provided. Our results show that STAR-VARS provides reliable and stable assessments of "global" sensitivity across the full range of scales in the factor space, while being 1-2 orders of magnitude more efficient than the Morris or Sobol approaches.

Direct analysis in real time-Mass spectrometry (DART-MS) in forensic and security applications.

PubMed

Pavlovich, Matthew J; Musselman, Brian; Hall, Adam B

2018-03-01

Over the last decade, direct analysis in real time (DART) has emerged as a viable method for fast, easy, and reliable "ambient ionization" for forensic analysis. The ability of DART to generate ions from chemicals that might be present at the scene of a criminal activity, whether they are in the gas, liquid, or solid phase, with limited sample preparation has made the technology a useful analytical tool in numerous forensic applications. This review paper summarizes many of those applications, ranging from the analysis of trace evidence to security applications, with a focus on providing the forensic scientist with a resource for developing their own applications. The most common uses for DART in forensics are in studying seized drugs, drugs of abuse and their metabolites, bulk and detonated explosives, toxic chemicals, chemical warfare agents, inks and dyes, and commercial plant and animal products that have been adulterated for economic gain. This review is meant to complement recent reviews that have described the fundamentals of the ionization mechanism and the general use of DART. We describe a wide range of forensic applications beyond the field of analyzing drugs of abuse, which dominates the literature, including common experimental and data analysis methods. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 37:171-187, 2018. © 2016 Wiley Periodicals, Inc.

Liquid-liquid extraction assisted by a carbon nanoparticles interface. Electrophoretic determination of atrazine in environmental samples.

PubMed

Caballero-Díaz, Encarnación; Simonet, Bartolomé; Valcárcel, Miguel

2013-10-21

A novel method for the determination of atrazine, using liquid-liquid extraction assisted by a nanoparticles film formed in situ and composed of organic solvent stabilized-carbon nanoparticles, is described. The presence of nanoparticles located at the liquid-liquid interface reinforced the extraction of analyte from matrix prior to capillary electrophoresis (CE) analysis. Some influential experimental variables were optimized in order to enhance the extraction efficiency. The developed procedure confirmed that carbon nanoparticles, especially multi-walled carbon nanotubes, are suitable to be used in sample treatment processes introducing new mechanisms of interaction with the analyte. The application of the proposed preconcentration method followed by CE detection enabled the determination of atrazine in spiked river water providing acceptable RSD values (11.6%) and good recoveries (about 87.0-92.0%). Additionally, a similar extraction scheme was tested in soil matrices with a view to further applications in real soil samples.

Capacitive deionization on-chip as a method for microfluidic sample preparation.

PubMed

Roelofs, Susan H; Kim, Bumjoo; Eijkel, Jan C T; Han, Jongyoon; van den Berg, Albert; Odijk, Mathieu

2015-03-21

Desalination as a sample preparation step is essential for noise reduction and reproducibility of mass spectrometry measurements. A specific example is the analysis of proteins for medical research and clinical applications. Salts and buffers that are present in samples need to be removed before analysis to improve the signal-to-noise ratio. Capacitive deionization is an electrostatic desalination (CDI) technique which uses two porous electrodes facing each other to remove ions from a solution. Upon the application of a potential of 0.5 V ions migrate to the electrodes and are stored in the electrical double layer. In this article we demonstrate CDI on a chip, and desalinate a solution by the removal of 23% of Na(+) and Cl(-) ions, while the concentration of a larger molecule (FITC-dextran) remains unchanged. For the first time impedance spectroscopy is introduced to monitor the salt concentration in situ in real-time in between the two desalination electrodes.

Application of a Nanostructured Enzymatic Biosensor Based on Fullerene and Gold Nanoparticles to Polyphenol Detection.

PubMed

Tortolini, Cristina; Sanzò, Gabriella; Antiochia, Riccarda; Mazzei, Franco; Favero, Gabriele

2017-01-01

Electrochemical biosensors provide an attractive means of analyzing the content of a biological sample due to the direct conversion of a biological event to an electronic signal. The signal transduction and the general performance of electrochemical biosensors are often determined by the surface architectures that connect the sensing element to the biological sample at the nanometer scale. The most common surface modification techniques, the various electrochemical transduction mechanisms, and the choice of the recognition receptor molecules all influence the ultimate sensitivity of the sensor. We show herein a novel electrochemical biosensing platform based on the coupling of two different nanostructured materials (gold nanoparticles and fullerenols) displaying interesting electrochemical features. The use of these nanomaterials improved the electrochemical performance of the proposed biosensor.An application of the nanostructured enzyme-based biosensor has been developed for evaluating the detection of polyphenols either in buffer solution or in real wine samples.

L-statistics for Repeated Measurements Data With Application to Trimmed Means, Quantiles and Tolerance Intervals.

PubMed

Assaad, Houssein I; Choudhary, Pankaj K

2013-01-01

The L -statistics form an important class of estimators in nonparametric statistics. Its members include trimmed means and sample quantiles and functions thereof. This article is devoted to theory and applications of L -statistics for repeated measurements data, wherein the measurements on the same subject are dependent and the measurements from different subjects are independent. This article has three main goals: (a) Show that the L -statistics are asymptotically normal for repeated measurements data. (b) Present three statistical applications of this result, namely, location estimation using trimmed means, quantile estimation and construction of tolerance intervals. (c) Obtain a Bahadur representation for sample quantiles. These results are generalizations of similar results for independently and identically distributed data. The practical usefulness of these results is illustrated by analyzing a real data set involving measurement of systolic blood pressure. The properties of the proposed point and interval estimators are examined via simulation.

Piezoelectric sensors based on molecular imprinted polymers for detection of low molecular mass analytes.

PubMed

Uludağ, Yildiz; Piletsky, Sergey A; Turner, Anthony P F; Cooper, Matthew A

2007-11-01

Biomimetic recognition elements employed for the detection of analytes are commonly based on proteinaceous affibodies, immunoglobulins, single-chain and single-domain antibody fragments or aptamers. The alternative supra-molecular approach using a molecularly imprinted polymer now has proven utility in numerous applications ranging from liquid chromatography to bioassays. Despite inherent advantages compared with biochemical/biological recognition (which include robustness, storage endurance and lower costs) there are few contributions that describe quantitative analytical applications of molecularly imprinted polymers for relevant small molecular mass compounds in real-world samples. There is, however, significant literature describing the use of low-power, portable piezoelectric transducers to detect analytes in environmental monitoring and other application areas. Here we review the combination of molecularly imprinted polymers as recognition elements with piezoelectric biosensors for quantitative detection of small molecules. Analytes are classified by type and sample matrix presentation and various molecularly imprinted polymer synthetic fabrication strategies are also reviewed.

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.

Technical Report: Benchmarking for Quasispecies Abundance Inference with Confidence Intervals from Metagenomic Sequence Data

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

McLoughlin, K.

2016-01-22

The software application “MetaQuant” was developed by our group at Lawrence Livermore National Laboratory (LLNL). It is designed to profile microbial populations in a sample using data from whole-genome shotgun (WGS) metagenomic DNA sequencing. Several other metagenomic profiling applications have been described in the literature. We ran a series of benchmark tests to compare the performance of MetaQuant against that of a few existing profiling tools, using real and simulated sequence datasets. This report describes our benchmarking procedure and results.

A TaqMan real-time PCR method based on alternative oxidase genes for detection of plant species in animal feed samples.

PubMed

Campos, Maria Doroteia; Valadas, Vera; Campos, Catarina; Morello, Laura; Braglia, Luca; Breviario, Diego; Cardoso, Hélia G

2018-01-01

Traceability of processed food and feed products has been gaining importance due to the impact that those products can have on human/animal health and to the associated economic and legal concerns, often related to adulterations and frauds as it can be the case for meat and milk. Despite mandatory traceability requirements for the analysis of feed composition, few reliable and accurate methods are presently available to enforce the legislative frame and allow the authentication of animal feeds. In this study, nine sensitive and species-specific real-time PCR TaqMan MGB assays are described for plant species detection in animal feed samples. The method is based on selective real-time qPCR (RT-qPCR) amplification of target genes belonging to the alternative oxidase (AOX) gene family. The plant species selected for detection in feed samples were wheat, maize, barley, soybean, rice and sunflower as common components of feeds, and cotton, flax and peanut as possible undesirable contaminants. The obtained results were compared with end-point PCR methodology. The applicability of the AOX TaqMan assays was evaluated through the screening of commercial feed samples, and by the analysis of plant mixtures with known composition. The RT-qPCR methodology allowed the detection of the most abundant species in feeds but also the identification of contaminant species present in lower amounts, down to 1% w/w. AOX-based methodology provides a suitable molecular marker approach to ascertain plant species composition of animal feed samples, thus supporting feed control and enforcement of the feed sector and animal production.

Efficient screening method for determination of polycyclic aromatic hydrocarbons (PAHs) in airborne particles. Application in real samples of Santiago-Chile metropolitan urban area

NASA Astrophysics Data System (ADS)

Romero, Rodrigo; Sienra, Rosario; Richter, Pablo

A rapid analytical approach for determination of polycyclic aromatic hydrocarbons (PAHs) present in real samples of particulate matter (PM10 filters) was investigated, based on the use of water under sub critical conditions, and the subsequent determination by GC-MS (SIM). The method avoids the use of large volumes of organic solvents as dichloromethane, toluene or other unhealthy liquid organic mixtures which are normally used in time-consuming conventional sample preparation methods. By using leaching times <1 h, the method allows determination of PAHs in the range of ng/m 3 (detection limits between 0.05 and 0.2 ng/m 3 for 1458 m 3 of sampled air) with a precision expressed as RSD between 5.6% and 11.2%. The main idea behind this approach is to raise the temperature and pressure of water inside a miniaturized laboratory-made extraction unit and to decrease its dielectric constant from 80 to nearly 20. This effect allows an increase in the solubility of low polarity hydrocarbons such as PAHs. In this way, an extraction step of a few minutes can be sufficient for a quantitative extraction of airborne particles collected in high volume PM10 samplers. Parameters such as: extraction flow, static or dynamic extraction times and water volume were optimized by using a standard reference material. Technical details are given and a comparison using real samples is made between the conventional Soxhlet extraction method and the proposed approach. The proposed approach can be used as a quantitative method to characterize low molecular PAHs and simultaneously as a screening method for high molecular weight PAHs, because the recoveries are not quantitative for molecular weights over 202. In the specific case of the Santiago metropolitan area, due to the frequent occurrence of particulate matter during high pollution episodes, this approach was applied as an efficient short-time screening method for urban PAHs. Application of this screening method is recommended especially during the winter, when periods of clear detriment of the atmospheric and meteorological conditions occur in the area.

A novel real time PCR assay using melt curve analysis for ivory identification.

PubMed

Kitpipit, Thitika; Penchart, Kitichaya; Ouithavon, Kanita; Satasook, Chutamas; Linacre, Adrian; Thanakiatkrai, Phuvadol

2016-10-01

Demand for ivory and expansion of human settlements have resulted in a rapid decline in the number of elephants. Enforcement of local and international laws and regulations requires identification of the species from which any ivory, or ivory products, originated. Further geographical assignment of the dead elephant from which the ivory was taken can assist in forensic investigations. In this study, a real-time PCR assay using melt curve analysis was developed and fully validated for forensic use. The presence or absence of three Elephantidae-specific and elephant species-specific melting peaks was used to identify the elephant species. Using 141 blood and ivory samples from the three extant elephant species, the assay demonstrated very high reproducibility and accuracy. The limit of detection was as low as 0.031ng of input DNA for conventional amplification and 0.002ng for nested amplification. Both DNA concentrations are typically encountered in forensic casework, especially for degraded samples. No cross-reactivity was observed for non-target species. Evaluation of direct amplification and nested amplification demonstrated the assay's flexibility and capability of analyzing low-template DNA samples and aged samples. Additionally, blind trial testing showed the assay's suitability application in real casework. In conclusion, wildlife forensic laboratories could use this novel, quick, and low-cost assay to help combat the continuing poaching crises leading to the collapse of elephant numbers in the wild. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Revealing the microbiota of marketed edible insects through PCR-DGGE, metagenomic sequencing and real-time PCR.

PubMed

Osimani, Andrea; Milanović, Vesna; Garofalo, Cristiana; Cardinali, Federica; Roncolini, Andrea; Sabbatini, Riccardo; De Filippis, Francesca; Ercolini, Danilo; Gabucci, Claudia; Petruzzelli, Annalisa; Tonucci, Franco; Clementi, Francesca; Aquilanti, Lucia

2018-07-02

The present study aimed to identify the microbiota present in six species of processed edible insects produced in Thailand and marketed worldwide via the internet, namely, giant water bugs (Belostoma lutarium), black ants (Polyrhachis), winged termites (alates, Termitoidae), rhino beetles (Hyboschema contractum), mole crickets (Gryllotalpidae), and silkworm pupae (Bombyx mori). For each species, two samples of boiled, dried and salted insects were purchased. The microbial DNA was extracted from the insect samples and subjected to polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), high-throughput sequencing and qualitative real-time PCR assays. The microbiota of the analyzed samples were widely characterized by the presence of spore-forming bacteria mainly represented by the genera Bacillus and Clostridium. Moreover, the genera Anaerobacillus, Paenibacillus, Geobacillus, Pseudomonas, Stenotrophomonas, Massilia, Delftia, Lactobacillus, Staphylococcus, Streptococcus, Vagococcus, and Vibrio were also detected. Real-time PCR allowed for ascertainment of the absence of Coxiella burnetii, Shiga toxin-producing E. coli (STEC), and Pseudomonas aeruginosa in all samples. The results of this study confirm the importance of combining different molecular techniques to characterize the biodiversity of complex ecosystems such as edible insects. The presence of potential human pathogens suggests the need for a careful application of good manufacturing practices during insect processing. This study provides further data that will be useful in risk analyses of edible insects as a novel food source. Copyright © 2018 Elsevier B.V. All rights reserved.

PROBABILITY SAMPLING AND POPULATION INFERENCE IN MONITORING PROGRAMS

EPA Science Inventory

A fundamental difference between probability sampling and conventional statistics is that "sampling" deals with real, tangible populations, whereas "conventional statistics" usually deals with hypothetical populations that have no real-world realization. he focus here is on real ...

Development of a 5'-nuclease real-time PCR assay targeting fliP for the rapid identification of Burkholderia mallei in clinical samples.

PubMed

Tomaso, Herbert; Scholz, Holger C; Al Dahouk, Sascha; Eickhoff, Meike; Treu, Thomas M; Wernery, Renate; Wernery, Ulrich; Neubauer, Heinrich

2006-02-01

Burkholderia mallei is a potential biological agent that causes glanders or farcy in solipeds, a disease notifiable to the Office International des Epizooties (OIE). The number of reported outbreaks has increased steadily during the last decade, but diagnosis is hampered by the low bacterial load in infected tissues and excretions. We developed a B. mallei-specific 5'-nuclease real-time PCR assay that targets the fliP gene of B. mallei and includes an internal amplification control. Specificity was assessed with 19 B. mallei strains, 27 Burkholderia pseudomallei strains, other Burkholderia strains of 29 species, and clinically relevant non-Burkholderia organisms. Amplification products were observed in all B. mallei strains but in no other bacteria. The linear range of the B. mallei real-time PCR covered concentrations from 240 pg to 70 fg of bacterial DNA/reaction. The detection limit was 60 fg of B. mallei DNA. The clinical applicability of the assay was demonstrated by use of organ samples from diseased horses of a recent outbreak that was reported to the OIE by the United Arab Emirates in 2004. Compared with conventional PCR, our rapid 5'-nuclease real-time PCR assay for the specific identification of B. mallei has a lower risk of carryover contamination and eliminates the need for post-PCR manipulations. This real-time PCR assay also shortens the turnaround time for results and has the potential for automation.

Non-interferometric quantitative phase imaging of yeast cells

NASA Astrophysics Data System (ADS)

Poola, Praveen K.; Pandiyan, Vimal Prabhu; John, Renu

2015-12-01

Real-time imaging of live cells is quite difficult without the addition of external contrast agents. Various methods for quantitative phase imaging of living cells have been proposed like digital holographic microscopy and diffraction phase microscopy. In this paper, we report theoretical and experimental results of quantitative phase imaging of live yeast cells with nanometric precision using transport of intensity equations (TIE). We demonstrate nanometric depth sensitivity in imaging live yeast cells using this technique. This technique being noninterferometric, does not need any coherent light sources and images can be captured through a regular bright-field microscope. This real-time imaging technique would deliver the depth or 3-D volume information of cells and is highly promising in real-time digital pathology applications, screening of pathogens and staging of diseases like malaria as it does not need any preprocessing of samples.

Development of a real time magnetic island identification system for HL-2A tokamak.

PubMed

Chen, Chao; Sun, Shan; Ji, Xiaoquan; Yin, Zejie

2017-08-01

A novel real time magnetic island identification system for HL-2A is introduced. The identification method is based on the measurement of Mirnov probes and the equilibrium flux constructed by the equilibrium fit (EFIT) code. The system consists of an analog front board and a digital processing board connected by a shield cable. Four octal-channel analog-to-digital convertors are utilized for 100 KHz simultaneous sampling of all the probes, and the applications of PCI extensions for Instrumentation platform and reflective memory allow the system to receive EFIT results simultaneously. A high performance field programmable gate array (FPGA) is used to realize the real time identification algorithm. Based on the parallel and pipeline processing of the FPGA, the magnetic island structure can be identified with a cycle time of 3 ms during experiments.

Development of a real time magnetic island identification system for HL-2A tokamak

NASA Astrophysics Data System (ADS)

Chen, Chao; Sun, Shan; Ji, Xiaoquan; Yin, Zejie

2017-08-01

A novel real time magnetic island identification system for HL-2A is introduced. The identification method is based on the measurement of Mirnov probes and the equilibrium flux constructed by the equilibrium fit (EFIT) code. The system consists of an analog front board and a digital processing board connected by a shield cable. Four octal-channel analog-to-digital convertors are utilized for 100 KHz simultaneous sampling of all the probes, and the applications of PCI extensions for Instrumentation platform and reflective memory allow the system to receive EFIT results simultaneously. A high performance field programmable gate array (FPGA) is used to realize the real time identification algorithm. Based on the parallel and pipeline processing of the FPGA, the magnetic island structure can be identified with a cycle time of 3 ms during experiments.

Multiresource allocation and scheduling for periodic soft real-time applications

NASA Astrophysics Data System (ADS)

Gopalan, Kartik; Chiueh, Tzi-cker

2001-12-01

Real-time applications that utilize multiple system resources, such as CPU, disks, and network links, require coordinated scheduling of these resources in order to meet their end-to-end performance requirements. Most state-of-the-art operating systems support independent resource allocation and deadline-driven scheduling but lack coordination among multiple heterogeneous resources. This paper describes the design and implementation of an Integrated Real-time Resource Scheduler (IRS) that performs coordinated allocation and scheduling of multiple heterogeneous resources on the same machine for periodic soft real-time application. The principal feature of IRS is a heuristic multi-resource allocation algorithm that reserves multiple resources for real-time applications in a manner that can maximize the number of applications admitted into the system in the long run. At run-time, a global scheduler dispatches the tasks of the soft real-time application to individual resource schedulers according to the precedence constraints between tasks. The individual resource schedulers, which could be any deadline based schedulers, can make scheduling decisions locally and yet collectively satisfy a real-time application's performance requirements. The tightness of overall timing guarantees is ultimately determined by the properties of individual resource schedulers. However, IRS maximizes overall system resource utilization efficiency by coordinating deadline assignment across multiple tasks in a soft real-time application.

Real-time oil-saturation monitoring in rock cores with low-field NMR.

PubMed

Mitchell, J; Howe, A M; Clarke, A

2015-07-01

Nuclear magnetic resonance (NMR) provides a powerful suite of tools for studying oil in reservoir core plugs at the laboratory scale. Low-field magnets are preferred for well-log calibration and to minimize magnetic-susceptibility-induced internal gradients in the porous medium. We demonstrate that careful data processing, combined with prior knowledge of the sample properties, enables real-time acquisition and interpretation of saturation state (relative amount of oil and water in the pores of a rock). Robust discrimination of oil and brine is achieved with diffusion weighting. We use this real-time analysis to monitor the forced displacement of oil from porous materials (sintered glass beads and sandstones) and to generate capillary desaturation curves. The real-time output enables in situ modification of the flood protocol and accurate control of the saturation state prior to the acquisition of standard NMR core analysis data, such as diffusion-relaxation correlations. Although applications to oil recovery and core analysis are demonstrated, the implementation highlights the general practicality of low-field NMR as an inline sensor for real-time industrial process control. Copyright © 2015 Elsevier Inc. All rights reserved.

Rapid and reliable diagnostic method to detect Zika virus by real-time fluorescence reverse transcription loop-mediated isothermal amplification.

PubMed

Guo, Xu-Guang; Zhou, Yong-Zhuo; Li, Qin; Wang, Wei; Wen, Jin-Zhou; Zheng, Lei; Wang, Qian

2018-04-18

To detect Zika virus more rapidly and accurately, we developed a novel method that utilized a real-time fluorescence reverse transcription loop-mediated isothermal amplification (LAMP) technique. The NS5 gene was amplified by a set of six specific primers that recognized six distinct sequences. The amplification process, including 60 min of thermostatic reaction with Bst DNA polymerase following real-time fluorescence reverse transcriptase using genomic Zika virus standard strain (MR766), was conducted through fluorescent signaling. Among the six pairs of primers that we designate here, NS5 was the most efficient with a high sensitivity of up to 3.3 ng/μl and reproducible specificity on eight pathogen samples that were used as negative controls. The real-time fluorescence reverse transcription LAMP detection process can be completed within 35 min. Our study demonstrated that real-time fluorescence reverse transcription LAMP could be highly beneficial and convenient clinical application to detect Zika virus due to its high specificity and stability.

Nonuniform sampling theorems for random signals in the linear canonical transform domain

NASA Astrophysics Data System (ADS)

Shuiqing, Xu; Congmei, Jiang; Yi, Chai; Youqiang, Hu; Lei, Huang

2018-06-01

Nonuniform sampling can be encountered in various practical processes because of random events or poor timebase. The analysis and applications of the nonuniform sampling for deterministic signals related to the linear canonical transform (LCT) have been well considered and researched, but up to now no papers have been published regarding the various nonuniform sampling theorems for random signals related to the LCT. The aim of this article is to explore the nonuniform sampling and reconstruction of random signals associated with the LCT. First, some special nonuniform sampling models are briefly introduced. Second, based on these models, some reconstruction theorems for random signals from various nonuniform samples associated with the LCT have been derived. Finally, the simulation results are made to prove the accuracy of the sampling theorems. In addition, the latent real practices of the nonuniform sampling for random signals have been also discussed.

Development of a simple fluorescence-based microplate method for the high-throughput analysis of proline in wine samples.

PubMed

Robert-Peillard, Fabien; Boudenne, Jean-Luc; Coulomb, Bruno

2014-05-01

This paper presents a simple, accurate and multi-sample method for the determination of proline in wines thanks to a 96-well microplate technique. Proline is the most abundant amino acid in wine and is an important parameter related to wine characteristics or maturation processes of grape. In the current study, an improved application of the general method based on sodium hypochlorite oxidation and o-phthaldialdehyde (OPA)-thiol spectrofluorometric detection is described. The main interfering compounds for specific proline detection in wines are strongly reduced by selective reaction with OPA in a preliminary step under well-defined pH conditions. Application of the protocol after a 500-fold dilution of wine samples provides a working range between 0.02 and 2.90gL(-1), with a limit of detection of 7.50mgL(-1). Comparison and validation on real wine samples by ion-exchange chromatography prove that this procedure yields accurate results. Simplicity of the protocol used, with no need for centrifugation or filtration, organic solvents or high temperature enables its full implementation in plastic microplates and efficient application for routine analysis of proline in wines. Copyright © 2013 Elsevier Ltd. All rights reserved.

Modulated Raman spectroscopy for enhanced identification of bladder tumor cells in urine samples.

PubMed

Canetta, Elisabetta; Mazilu, Michael; De Luca, Anna Chiara; Carruthers, Antonia E; Dholakia, Kishan; Neilson, Sam; Sargeant, Harry; Briscoe, Tina; Herrington, C Simon; Riches, Andrew C

2011-03-01

Standard Raman spectroscopy (SRS) is a noninvasive technique that is used in the biomedical field to discriminate between normal and cancer cells. However, the presence of a strong fluorescence background detracts from the use of SRS in real-time clinical applications. Recently, we have reported a novel modulated Raman spectroscopy (MRS) technique to extract the Raman spectra from the background. In this paper, we present the first application of MRS to the identification of human urothelial cells (SV-HUC-1) and bladder cancer cells (MGH) in urine samples. These results are compared to those obtained by SRS. Classification using the principal component analysis clearly shows that MRS allows discrimination between Raman spectra of SV-HUC-1 and MGH cells with high sensitivity (98%) and specificity (95%). MRS is also used to distinguish between SV-HUC-1 and MGH cells after exposure to urine for up to 6 h. We observe a marked change in the MRS of SV-HUC-1 and MGH cells with time in urine, indicating that the conditions of sample collection will be important for the application of this methodology to clinical urine samples.

Evaluation of a new single-tube multiprobe real-time PCR for diagnosis of Entamoeba histolytica and Entamoeba dispar.

PubMed

Liang, Shih-Yu; Hsia, Kan-Tai; Chan, Yun-Hsien; Fan, Chia-Kwung; Jiang, Donald Dah-Shyong; Landt, Olfert; Ji, Dar-Der

2010-08-01

A single-tube multiprobe real-time PCR assay for simultaneous detection of Entamoeba histolytica and Entamoeba dispar was developed. One primer pair with 2 species-specific probes was designed based on new SSU RNA regions of the ribosomal DNA-containing episome. The sensitivity is 1 parasite per milliliter of feces and thus superior to the conventional nested PCR and comparable to other published real-time PCR protocols. The applicability for clinical diagnosis was validated with 218 stool specimens from patients. A total of 51 E. histolytica and 39 E. dispar positive samples was detected by the multiprobe real-time PCR compared to 39 and 22 by routine nested PCR diagnosis. The detection rate of Entamoeba species for the multiprobe real-time PCR assays was significantly higher than the nested PCR (40.8% vs. 28.0%, P < 0.01). The test did not show cross reactivity with DNA from Entamoeba moshkovskii, Giardia lamblia , Cryptosporidium sp., Escherichia coli , or other nonpathogenic enteric parasites. The multiprobe real-time PCR assay is simple and rapid and has high specificity and sensitivity. The assay could streamline the laboratory diagnosis procedure and facilitate epidemiological investigation.

Avian-specific real-time PCR assay for authenticity control in farm animal feeds and pet foods.

PubMed

Pegels, Nicolette; González, Isabel; García, Teresa; Martín, Rosario

2014-01-01

A highly sensitive TaqMan real-time PCR assay targeting the mitochondrial 12S rRNA gene was developed for detection of an avian-specific DNA fragment (68bp) in farm animal and pet feeds. The specificity of the assay was verified against a wide representation of animal and plant species. Applicability assessment of the avian real-time PCR was conducted through representative analysis of two types of compound feeds: industrial farm animal feeds (n=60) subjected to extreme temperatures, and commercial dog and cat feeds (n=210). Results obtained demonstrated the suitability of the real-time PCR assay to detect the presence of low percentages of highly processed avian material in the feed samples analysed. Although quantification results were well reproducible under the experimental conditions tested, an accurate estimation of the target content in feeds is impossible in practice. Nevertheless, the method may be useful as an alternative tool for traceability purposes within the framework of feed control. Copyright © 2013 Elsevier Ltd. All rights reserved.

Dosimetry characteristics of HDPE-SWCNT nanocomposite for real time application

NASA Astrophysics Data System (ADS)

Malekie, Shahryar; Ziaie, Farhood; Feizi, Shahzad; Esmaeli, Abdolreza

2016-10-01

In this experimental work, different dosimetric characteristics of high density polyethylene-single wall carbon nanotube nanocomposite were investigated. The nanocomposite samples were prepared with different nanotube contents of 0.22, 0.25, and 0.39 weight percentages which were before, exactly in, and after percolation region of the nanocomposite, respectively. The samples were exposed to 60Co gamma radiation source over the dose rate of 65-214 mGy/min, while the applied bias was 100 V. A linear response achieved for the sample contained 0.25 nanotube wt% verified that the percolation threshold is the optimum point for dosimetric purposes. The current-voltage characteristics curve measured for 0.25 CNT wt% nanocomposite showed that the behavior of this sample was bias polarity independent. Also, the results showed that the response of this nanocomposite was energy-independent. The maximum discrepancy of photocurrent due to angular variation within 0-90° with respect to beam incidence and the reproducibility of the response were measured as 5.4% and 0.8%, respectively. The stability study showed that this material may be suitable for protection dose level control. Therefore, this kind of nanocomposite requiring calibration can be used as a real-time dosimeter.

Capabilities needed for the next generation of thermo-hydraulic codes for use in real time applications

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

Arndt, S.A.

1997-07-01

The real-time reactor simulation field is currently at a crossroads in terms of the capability to perform real-time analysis using the most sophisticated computer codes. Current generation safety analysis codes are being modified to replace simplified codes that were specifically designed to meet the competing requirement for real-time applications. The next generation of thermo-hydraulic codes will need to have included in their specifications the specific requirement for use in a real-time environment. Use of the codes in real-time applications imposes much stricter requirements on robustness, reliability and repeatability than do design and analysis applications. In addition, the need for codemore » use by a variety of users is a critical issue for real-time users, trainers and emergency planners who currently use real-time simulation, and PRA practitioners who will increasingly use real-time simulation for evaluating PRA success criteria in near real-time to validate PRA results for specific configurations and plant system unavailabilities.« less

Anomaly Detection Based on Sensor Data in Petroleum Industry Applications

PubMed Central

Martí, Luis; Sanchez-Pi, Nayat; Molina, José Manuel; Garcia, Ana Cristina Bicharra

2015-01-01

Anomaly detection is the problem of finding patterns in data that do not conform to an a priori expected behavior. This is related to the problem in which some samples are distant, in terms of a given metric, from the rest of the dataset, where these anomalous samples are indicated as outliers. Anomaly detection has recently attracted the attention of the research community, because of its relevance in real-world applications, like intrusion detection, fraud detection, fault detection and system health monitoring, among many others. Anomalies themselves can have a positive or negative nature, depending on their context and interpretation. However, in either case, it is important for decision makers to be able to detect them in order to take appropriate actions. The petroleum industry is one of the application contexts where these problems are present. The correct detection of such types of unusual information empowers the decision maker with the capacity to act on the system in order to correctly avoid, correct or react to the situations associated with them. In that application context, heavy extraction machines for pumping and generation operations, like turbomachines, are intensively monitored by hundreds of sensors each that send measurements with a high frequency for damage prevention. In this paper, we propose a combination of yet another segmentation algorithm (YASA), a novel fast and high quality segmentation algorithm, with a one-class support vector machine approach for efficient anomaly detection in turbomachines. The proposal is meant for dealing with the aforementioned task and to cope with the lack of labeled training data. As a result, we perform a series of empirical studies comparing our approach to other methods applied to benchmark problems and a real-life application related to oil platform turbomachinery anomaly detection. PMID:25633599

Clinical evaluation of β-tubulin real-time PCR for rapid diagnosis of dermatophytosis, a comparison with mycological methods.

PubMed

Motamedi, Marjan; Mirhendi, Hossein; Zomorodian, Kamiar; Khodadadi, Hossein; Kharazi, Mahboobeh; Ghasemi, Zeinab; Shidfar, Mohammad Reza; Makimura, Koichi

2017-10-01

Following our previous report on evaluation of the beta tubulin real-time PCR for detection of dermatophytosis, this study aimed to compare the real-time PCR assay with conventional methods for the clinical assessment of its diagnostic performance. Samples from a total of 853 patients with suspected dermatophyte lesions were subjected to direct examination (all samples), culture (499 samples) and real-time PCR (all samples). Fungal DNA was extracted directly from clinical samples using a conical steel bullet, followed by purification with a commercial kit and subjected to the Taq-Man probe-based real-time PCR. The study showed that among the 499 specimens for which all three methods were used, 156 (31.2%), 128 (25.6%) and 205 (41.0%) were found to be positive by direct microscopy, culture and real-time PCR respectively. Real-time PCR significantly increased the detection rate of dermatophytes compared with microscopy (288 vs 229) with 87% concordance between the two methods. The sensitivity, specificity, positive predictive value, and negative predictive value of the real-time PCR was 87.5%, 85%, 66.5% and 95.2% respectively. Although real-time PCR performed better on skin than on nail samples, it should not yet fully replace conventional diagnosis. © 2017 Blackwell Verlag GmbH.

Construction of a Virtual Scanning Electron Microscope (VSEM)

NASA Technical Reports Server (NTRS)

Fried, Glenn; Grosser, Benjamin

2004-01-01

The Imaging Technology Group (ITG) proposed to develop a Virtual SEM (VSEM) application and supporting materials as the first installed instrument in NASA s Virtual Laboratory Project. The instrument was to be a simulator modeled after an existing SEM, and was to mimic that real instrument as closely as possible. Virtual samples would be developed and provided along with the instrument, which would be written in Java.

Designing a dynamic data driven application system for estimating real-time load of dissolved organic carbon in a river

Treesearch

Ying Ouyang

2012-01-01

Understanding the dynamics of naturally occurring dissolved organic carbon (DOC) in a river is central to estimating surface water quality, aquatic carbon cycling, and global climate change. Currently, determination of the DOC in surface water is primarily accomplished by manually collecting samples for laboratory analysis, which requires at least 24 h. In other words...

Improved detection of chemical substances from colorimetric sensor data using probabilistic machine learning

NASA Astrophysics Data System (ADS)

Mølgaard, Lasse L.; Buus, Ole T.; Larsen, Jan; Babamoradi, Hamid; Thygesen, Ida L.; Laustsen, Milan; Munk, Jens Kristian; Dossi, Eleftheria; O'Keeffe, Caroline; Lässig, Lina; Tatlow, Sol; Sandström, Lars; Jakobsen, Mogens H.

2017-05-01

We present a data-driven machine learning approach to detect drug- and explosives-precursors using colorimetric sensor technology for air-sampling. The sensing technology has been developed in the context of the CRIM-TRACK project. At present a fully- integrated portable prototype for air sampling with disposable sensing chips and automated data acquisition has been developed. The prototype allows for fast, user-friendly sampling, which has made it possible to produce large datasets of colorimetric data for different target analytes in laboratory and simulated real-world application scenarios. To make use of the highly multi-variate data produced from the colorimetric chip a number of machine learning techniques are employed to provide reliable classification of target analytes from confounders found in the air streams. We demonstrate that a data-driven machine learning method using dimensionality reduction in combination with a probabilistic classifier makes it possible to produce informative features and a high detection rate of analytes. Furthermore, the probabilistic machine learning approach provides a means of automatically identifying unreliable measurements that could produce false predictions. The robustness of the colorimetric sensor has been evaluated in a series of experiments focusing on the amphetamine pre-cursor phenylacetone as well as the improvised explosives pre-cursor hydrogen peroxide. The analysis demonstrates that the system is able to detect analytes in clean air and mixed with substances that occur naturally in real-world sampling scenarios. The technology under development in CRIM-TRACK has the potential as an effective tool to control trafficking of illegal drugs, explosive detection, or in other law enforcement applications.

Investigation of sulphur isotope variation due to different processes applied during uranium ore concentrate production.

PubMed

Krajkó, Judit; Varga, Zsolt; Wallenius, Maria; Mayer, Klaus; Konings, Rudy

The applicability and limitations of sulphur isotope ratio as a nuclear forensic signature have been studied. The typically applied leaching methods in uranium mining processes were simulated for five uranium ore samples and the n ( 34 S)/ n ( 32 S) ratios were measured. The sulphur isotope ratio variation during uranium ore concentrate (UOC) production was also followed using two real-life sample sets obtained from industrial UOC production facilities. Once the major source of sulphur is revealed, its appropriate application for origin assessment can be established. Our results confirm the previous assumption that process reagents have a significant effect on the n ( 34 S)/ n ( 32 S) ratio, thus the sulphur isotope ratio is in most cases a process-related signature.

Efficient Computation of Anharmonic Force Constants via q-space, with Application to Graphene

NASA Astrophysics Data System (ADS)

Kornbluth, Mordechai; Marianetti, Chris

We present a new approach for extracting anharmonic force constants from a sparse sampling of the anharmonic dynamical tensor. We calculate the derivative of the energy with respect to q-space displacements (phonons) and strain, which guarantees the absence of supercell image errors. Central finite differences provide a well-converged quadratic error tail for each derivative, separating the contribution of each anharmonic order. These derivatives populate the anharmonic dynamical tensor in a sparse mesh that bounds the Brillouin Zone, which ensures comprehensive sampling of q-space while exploiting small-cell calculations for efficient, high-throughput computation. This produces a well-converged and precisely-defined dataset, suitable for big-data approaches. We transform this sparsely-sampled anharmonic dynamical tensor to real-space anharmonic force constants that obey full space-group symmetries by construction. Machine-learning techniques identify the range of real-space interactions. We show the entire process executed for graphene, up to and including the fifth-order anharmonic force constants. This method successfully calculates strain-based phonon renormalization in graphene, even under large strains, which solves a major shortcoming of previous potentials.

Photoacoustic study of percutaneous absorption of Carbopol and transdermic gels for topic use in skin

NASA Astrophysics Data System (ADS)

Rossi, R. C. P.; de Paiva, R. F.; da Silva, M. D.; Barja, P. R.

2008-01-01

Topical medicine application has been used to treat a good number of pathological processes. Its efficacy is associated to an efficient penetration of the drug in the internal skin layers, promoting systemic effects and excluding the possibility of drug degradation by the digestive tract and hepatic elimination. This work analyzes the penetration kinetics of two soluble bases employed as vehicles for topic application: superficial gel (Carbopol 940) and transdermic (transdermal) gel. Analysis was performed with the photoacoustic technique, based upon the absorption of modulated light by a sample with subsequent conversion of the absorbed energy in heat, generating acoustic waves in the air layer adjacent to the sample. Each of the two vehicles was evaluated through in vivo (human skin) and in vitro application. Measurements in vitro employed samples of VitroSkin (synthetic material with properties similar to those of real skin, employed in the pharmaceutical industry research). Results show that the permeation was faster for the transdermal gel, both for in vivo and in vitro measurements, indicating that in vitro measurements may be utilized in qualitative, comparative permeation studies.

Grain reconstruction of porous media: application to a low-porosity Fontainebleau sandstone.

PubMed

Thovert, J F; Yousefian, F; Spanne, P; Jacquin, C G; Adler, P M

2001-06-01

The fundamental issue of reconstructing a porous medium is examined anew in this paper, thanks to a sample of low-porosity Fontainebleau sandstone that has been analyzed by computed microtomography. Various geometric properties are determined on the experimental sample. A statistical property, namely, the probability density of the covering radius, is determined. This is used in order to reconstruct a porous medium by means of a Poissonian generation of polydisperse spheres. In a second part, the properties of the real experimental sample and of the reconstructed one are compared. The most important success of the present reconstruction technique is the fact that the numerical sample percolates despite its low porosity. Moreover, other geometrical features and conductivity are found to be in good agreement.

34 CFR 12.6 - What must an application for surplus Federal real property contain?

Code of Federal Regulations, 2011 CFR

2011-07-01

... 34 Education 1 2011-07-01 2011-07-01 false What must an application for surplus Federal real... Property § 12.6 What must an application for surplus Federal real property contain? An application for... educational purposes at the time of application and that it is so needed for the duration of the period of...

Microfluidics and Raman microscopy: current applications and future challenges.

PubMed

Chrimes, Adam F; Khoshmanesh, Khashayar; Stoddart, Paul R; Mitchell, Arnan; Kalantar-Zadeh, Kourosh

2013-07-07

Raman microscopy systems are becoming increasingly widespread and accessible for characterising chemical species. Microfluidic systems are also progressively finding their way into real world applications. Therefore, it is anticipated that the integration of Raman systems with microfluidics will become increasingly attractive and practical. This review aims to provide an overview of Raman microscopy-microfluidics integrated systems for researchers who are actively interested in utilising these tools. The fundamental principles and application strengths of Raman microscopy are discussed in the context of microfluidics. Various configurations of microfluidics that incorporate Raman microscopy methods are presented, with applications highlighted. Data analysis methods are discussed, with a focus on assisting the interpretation of Raman-microfluidics data from complex samples. Finally, possible future directions of Raman-microfluidic systems are presented.

Development and application of two independent real-time PCR assays to detect clinically relevant Mucorales species.

PubMed

Springer, Jan; Goldenberger, Daniel; Schmidt, Friderike; Weisser, Maja; Wehrle-Wieland, Elisabeth; Einsele, Hermann; Frei, Reno; Löffler, Jürgen

2016-03-01

PCR-based detection of Mucorales species could improve diagnosis of suspected invasive fungal infection, leading to a better patient outcome. This study describes two independent probe-based real-time PCR tests for detection of clinically relevant Mucorales, targeting specific fragments of the 18S and the 28S rRNA genes. Both assays have a short turnaround time, allow fast, specific and very sensitive detection of clinically relevant Mucorales and have the potential to be used as quantitative tests. They were validated on various clinical samples (fresh and formalin-fixed paraffin-embedded specimens, mainly biopsies, n = 17). The assays should be used as add-on tools to complement standard techniques; a combined approach of both real-time PCR assays has 100 % sensitivity. Genus identification by subsequent sequencing is possible for amplicons of the 18S PCR assay. In conclusion, combination of the two independent Mucorales assays described in this study, 18S and 28S, detected all clinical samples associated with proven Mucorales infection (n = 10). Reliable and specific identification of Mucorales is a prerequisite for successful antifungal therapy as these fungi show intrinsic resistance to voriconazole and caspofungin.

Fabrication of graphene/Fe3O4@polythiophene nanocomposite and its application in the magnetic solid-phase extraction of polycyclic aromatic hydrocarbons from environmental water samples.

PubMed

Mehdinia, Ali; Khodaee, Nader; Jabbari, Ali

2015-04-08

Polythiophene (PT) was used as a surface modifier of graphene/Fe3O4 (G/Fe3O4) composite to increase merit of it, and also overcome some limitations and disadvantages of using G/Fe3O4 alone as solid phase extraction (SPE) sorbent. An in-situ chemical polymerization method was employed to prepare G/Fe3O4@PT nanocomposites. Application of this newly designed material in the magnetic SPE (MSPE) of polycyclic aromatic hydrocarbons (PAHs), as model analytes, in the environmental water samples was investigated. The characterization of the hybrid material was performed using transmission electron microscopy, scanning electron microscopy, energy-dispersive X-ray analysis, Fourier transform-infrared (FT-IR) spectroscopy and vibrating sample magnetometry. Seven important parameters, affecting the extraction efficiency of PAHs, including: amount of adsorbent, adsorption and desorption times, type and volume of the eluent solvent, initial sample volume and salt content of the sample were evaluated. The optimum extraction conditions were obtained as: 4 min for extraction time, 20 mg for sorbent amount, 100mL for initial sample volume, toluene as desorption solvent, 0.6 mL for desorption solvent volume, 6 min for desorption time and 30% (w/v) for NaCl concentration. Good performance data were obtained at the optimized conditions. Detection limits were in the range of 0.009-0.020 μg L(-1) in the real matrix. The calibration curves were linear over the concentration ranges from 0.03 to 80 μg L(-1) with correlation coefficients (R(2)) between 0.995 and 0.998 for all the analytes. Relative standard deviations were ranged from 4.3 to 6.3%. Appropriate recovery values, in the range of 83-107%, were also obtained for the real sample analysis. Copyright © 2014 Elsevier B.V. All rights reserved.

A fast algorithm to compute precise type-2 centroids for real-time control applications.

PubMed

Chakraborty, Sumantra; Konar, Amit; Ralescu, Anca; Pal, Nikhil R

2015-02-01

An interval type-2 fuzzy set (IT2 FS) is characterized by its upper and lower membership functions containing all possible embedded fuzzy sets, which together is referred to as the footprint of uncertainty (FOU). The FOU results in a span of uncertainty measured in the defuzzified space and is determined by the positional difference of the centroids of all the embedded fuzzy sets taken together. This paper provides a closed-form formula to evaluate the span of uncertainty of an IT2 FS. The closed-form formula offers a precise measurement of the degree of uncertainty in an IT2 FS with a runtime complexity less than that of the classical iterative Karnik-Mendel algorithm and other formulations employing the iterative Newton-Raphson algorithm. This paper also demonstrates a real-time control application using the proposed closed-form formula of centroids with reduced root mean square error and computational overhead than those of the existing methods. Computer simulations for this real-time control application indicate that parallel realization of the IT2 defuzzification outperforms its competitors with respect to maximum overshoot even at high sampling rates. Furthermore, in the presence of measurement noise in system (plant) states, the proposed IT2 FS based scheme outperforms its type-1 counterpart with respect to peak overshoot and root mean square error in plant response.

A Control Chart Approach for Representing and Mining Data Streams with Shape Based Similarity

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

Omitaomu, Olufemi A

The mining of data streams for online condition monitoring is a challenging task in several domains including (electric) power grid system, intelligent manufacturing, and consumer science. Considering a power grid application in which thousands of sensors, called the phasor measurement units, are deployed on the power grid network to continuously collect streams of digital data for real-time situational awareness and system management. Depending on design, each sensor could stream between ten and sixty data samples per second. The myriad of sensory data captured could convey deeper insights about sequence of events in real-time and before major damages are done. However,more » the timely processing and analysis of these high-velocity and high-volume data streams is a challenge. Hence, a new data processing and transformation approach, based on the concept of control charts, for representing sequence of data streams from sensors is proposed. In addition, an application of the proposed approach for enhancing data mining tasks such as clustering using real-world power grid data streams is presented. The results indicate that the proposed approach is very efficient for data streams storage and manipulation.« less

Real-time microstructure imaging by Laue microdiffraction: A sample application in laser 3D printed Ni-based superalloys

PubMed Central

Zhou, Guangni; Zhu, Wenxin; Shen, Hao; Li, Yao; Zhang, Anfeng; Tamura, Nobumichi; Chen, Kai

2016-01-01

Synchrotron-based Laue microdiffraction has been widely applied to characterize the local crystal structure, orientation, and defects of inhomogeneous polycrystalline solids by raster scanning them under a micro/nano focused polychromatic X-ray probe. In a typical experiment, a large number of Laue diffraction patterns are collected, requiring novel data reduction and analysis approaches, especially for researchers who do not have access to fast parallel computing capabilities. In this article, a novel approach is developed by plotting the distributions of the average recorded intensity and the average filtered intensity of the Laue patterns. Visualization of the characteristic microstructural features is realized in real time during data collection. As an example, this method is applied to image key features such as microcracks, carbides, heat affected zone, and dendrites in a laser assisted 3D printed Ni-based superalloy, at a speed much faster than data collection. Such analytical approach remains valid for a wide range of crystalline solids, and therefore extends the application range of the Laue microdiffraction technique to problems where real-time decision-making during experiment is crucial (for instance time-resolved non-reversible experiments). PMID:27302087

Sensitive detection of porcine DNA in processed animal proteins using a TaqMan real-time PCR assay.

PubMed

Pegels, N; González, I; Fernández, S; García, T; Martín, R

2012-01-01

A TaqMan real-time PCR method was developed for specific detection of porcine-prohibited material in industrial feeds. The assay combines the use of a porcine-specific primer pair, which amplifies a 79 bp fragment of the mitochondrial (mt) 12 S rRNA gene, and a locked nucleic acid (LNA) TaqMan probe complementary to a target sequence lying between the porcine-specific primers. The nuclear 18 S rRNA gene system, yielding a 77 bp amplicon, was employed as a positive amplification control to monitor the total content of amplifiable DNA in the samples. The specificity of the porcine primers-probe system was verified against different animal and plant species, including mammals, birds and fish. The applicability of the real-time PCR protocol to detect the presence of porcine mt DNA in feeds was determined through the analysis of 190 industrial feeds (19 known reference and 171 blind samples) subjected to stringent processing treatments. The performance of the method allows qualitative and highly sensitive detection of short fragments from porcine DNA in all the industrial feeds declared to contain porcine material. Although the method has quantitative potential, the real quantitative capability of the assay is limited by the existing variability in terms of composition and processing conditions of the feeds, which affect the amount and quality of amplifiable DNA.

Critical points of DNA quantification by real-time PCR – effects of DNA extraction method and sample matrix on quantification of genetically modified organisms

PubMed Central

Cankar, Katarina; Štebih, Dejan; Dreo, Tanja; Žel, Jana; Gruden, Kristina

2006-01-01

Background Real-time PCR is the technique of choice for nucleic acid quantification. In the field of detection of genetically modified organisms (GMOs) quantification of biotech products may be required to fulfil legislative requirements. However, successful quantification depends crucially on the quality of the sample DNA analyzed. Methods for GMO detection are generally validated on certified reference materials that are in the form of powdered grain material, while detection in routine laboratories must be performed on a wide variety of sample matrixes. Due to food processing, the DNA in sample matrixes can be present in low amounts and also degraded. In addition, molecules of plant origin or from other sources that affect PCR amplification of samples will influence the reliability of the quantification. Further, the wide variety of sample matrixes presents a challenge for detection laboratories. The extraction method must ensure high yield and quality of the DNA obtained and must be carefully selected, since even components of DNA extraction solutions can influence PCR reactions. GMO quantification is based on a standard curve, therefore similarity of PCR efficiency for the sample and standard reference material is a prerequisite for exact quantification. Little information on the performance of real-time PCR on samples of different matrixes is available. Results Five commonly used DNA extraction techniques were compared and their suitability for quantitative analysis was assessed. The effect of sample matrix on nucleic acid quantification was assessed by comparing 4 maize and 4 soybean matrixes. In addition 205 maize and soybean samples from routine analysis were analyzed for PCR efficiency to assess variability of PCR performance within each sample matrix. Together with the amount of DNA needed for reliable quantification, PCR efficiency is the crucial parameter determining the reliability of quantitative results, therefore it was chosen as the primary criterion by which to evaluate the quality and performance on different matrixes and extraction techniques. The effect of PCR efficiency on the resulting GMO content is demonstrated. Conclusion The crucial influence of extraction technique and sample matrix properties on the results of GMO quantification is demonstrated. Appropriate extraction techniques for each matrix need to be determined to achieve accurate DNA quantification. Nevertheless, as it is shown that in the area of food and feed testing matrix with certain specificities is impossible to define strict quality controls need to be introduced to monitor PCR. The results of our study are also applicable to other fields of quantitative testing by real-time PCR. PMID:16907967

Objects Architecture: A Comprehensive Design Approach for Real-Time, Distributed, Fault-Tolerant, Reactive Operating Systems.

DTIC Science & Technology

1987-09-01

real - time operating system should be efficient from the real-time point...5,8]) system naming scheme. 3.2 Protecting Objects Real-time embedded systems usually neglect protection mechanisms. However, a real - time operating system cannot...allocation mechanism should adhere to application constraints. This strong relationship between a real - time operating system and the application

Real time flaw detection and characterization in tube through partial least squares and SVR: Application to eddy current testing

NASA Astrophysics Data System (ADS)

Ahmed, Shamim; Miorelli, Roberto; Calmon, Pierre; Anselmi, Nicola; Salucci, Marco

2018-04-01

This paper describes Learning-By-Examples (LBE) technique for performing quasi real time flaw localization and characterization within a conductive tube based on Eddy Current Testing (ECT) signals. Within the framework of LBE, the combination of full-factorial (i.e., GRID) sampling and Partial Least Squares (PLS) feature extraction (i.e., GRID-PLS) techniques are applied for generating a suitable training set in offine phase. Support Vector Regression (SVR) is utilized for model development and inversion during offine and online phases, respectively. The performance and robustness of the proposed GIRD-PLS/SVR strategy on noisy test set is evaluated and compared with standard GRID/SVR approach.

A High-Resolution Minimicroscope System for Wireless Real-Time Monitoring.

PubMed

Wang, Zongjie; Boddeda, Akash; Parker, Benjamin; Samanipour, Roya; Ghosh, Sanjoy; Menard, Frederic; Kim, Keekyoung

2018-07-01

Compact, cost-effective, and high-performance microscope that enables the real-time imaging of cells and lab-on-a-chip devices is highly demanded for cell biology and biomedical engineering. This paper aims to present the design and application of an inexpensive wireless minimicroscope with resolution up to 2592 × 1944 pixels and speed up to 90 f/s. The minimicroscope system was built on a commercial embedded system (Raspberry Pi). We modified a camera module and adopted an inverse dual lens system to obtain the clear field of view and appropriate magnification for tens of micrometer objects. The system was capable of capturing time-lapse images and transferring image data wirelessly. The entire system can be operated wirelessly and cordlessly in a conventional cell culturing incubator. The developed minimicroscope was used to monitor the attachment and proliferation of NIH-3T3 and HEK 293 cells inside an incubator for 50 h. In addition, the minimicroscope was used to monitor a droplet generation process in a microfluidic device. The high-quality images captured by the minimicroscope enabled us an automated analysis of experimental parameters. The successful applications prove the great potential of the developed minimicroscope for monitoring various biological samples and microfluidic devices. This paper presents the design of a high-resolution minimicroscope system that enables the wireless real-time imaging of cells inside the incubator. This system has been verified to be a useful tool to obtain high-quality images and videos for the automated quantitative analysis of biological samples and lab-on-a-chip devices in the long term.

Sample normalization methods in quantitative metabolomics.

PubMed

Wu, Yiman; Li, Liang

2016-01-22

To reveal metabolomic changes caused by a biological event in quantitative metabolomics, it is critical to use an analytical tool that can perform accurate and precise quantification to examine the true concentration differences of individual metabolites found in different samples. A number of steps are involved in metabolomic analysis including pre-analytical work (e.g., sample collection and storage), analytical work (e.g., sample analysis) and data analysis (e.g., feature extraction and quantification). Each one of them can influence the quantitative results significantly and thus should be performed with great care. Among them, the total sample amount or concentration of metabolites can be significantly different from one sample to another. Thus, it is critical to reduce or eliminate the effect of total sample amount variation on quantification of individual metabolites. In this review, we describe the importance of sample normalization in the analytical workflow with a focus on mass spectrometry (MS)-based platforms, discuss a number of methods recently reported in the literature and comment on their applicability in real world metabolomics applications. Sample normalization has been sometimes ignored in metabolomics, partially due to the lack of a convenient means of performing sample normalization. We show that several methods are now available and sample normalization should be performed in quantitative metabolomics where the analyzed samples have significant variations in total sample amounts. Copyright © 2015 Elsevier B.V. All rights reserved.

Comparison of three-way and four-way calibration for the real-time quantitative analysis of drug hydrolysis in complex dynamic samples by excitation-emission matrix fluorescence.

PubMed

Yin, Xiao-Li; Gu, Hui-Wen; Liu, Xiao-Lu; Zhang, Shan-Hui; Wu, Hai-Long

2018-03-05

Multiway calibration in combination with spectroscopic technique is an attractive tool for online or real-time monitoring of target analyte(s) in complex samples. However, how to choose a suitable multiway calibration method for the resolution of spectroscopic-kinetic data is a troubling problem in practical application. In this work, for the first time, three-way and four-way fluorescence-kinetic data arrays were generated during the real-time monitoring of the hydrolysis of irinotecan (CPT-11) in human plasma by excitation-emission matrix fluorescence. Alternating normalization-weighted error (ANWE) and alternating penalty trilinear decomposition (APTLD) were used as three-way calibration for the decomposition of the three-way kinetic data array, whereas alternating weighted residual constraint quadrilinear decomposition (AWRCQLD) and alternating penalty quadrilinear decomposition (APQLD) were applied as four-way calibration to the four-way kinetic data array. The quantitative results of the two kinds of calibration models were fully compared from the perspective of predicted real-time concentrations, spiked recoveries of initial concentration, and analytical figures of merit. The comparison study demonstrated that both three-way and four-way calibration models could achieve real-time quantitative analysis of the hydrolysis of CPT-11 in human plasma under certain conditions. However, it was also found that both of them possess some critical advantages and shortcomings during the process of dynamic analysis. The conclusions obtained in this paper can provide some helpful guidance for the reasonable selection of multiway calibration models to achieve the real-time quantitative analysis of target analyte(s) in complex dynamic systems. Copyright © 2017 Elsevier B.V. All rights reserved.

The Role of Presented Objects in Deriving Color Preference Criteria from Psychophysical Studies

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

Royer, Michael P.; Wei, Minchen

Of the many “components” of a color rendering measure, one is perhaps the most important: the set of color samples (spectral reflectance functions) that are employed as a standardized means of evaluating and rating a light source. At the same time, a standardized set of color samples can never apply perfectly to a real space or a real set of observed objects, meaning there will always be some level of mismatch between the predicted and observed color shifts. This mismatch is important for lighting specifiers to consider, but even more critical for experiments that seek to evaluate the relationship betweenmore » color rendering measures and human perception. This article explores how the color distortions of three possible experimental object sets compare to the color distortions predicted using the color evaluation samples of IES TM-30-15 (TM-30). The experimental object sets include those from Royer and colleagues [2016], a set of produce (10 fruits and vegetables), and the X-rite Color Checker Classic. The differences are traced back to properties of the samples sets, such as the coverage of color space, average chroma level, and specific spectral features. The consequence of the differences, that the visual evaluation is based on color distortions that are substantially different from what is predicted, can lead to inaccurate criteria or models of a given perception, such as preference. To minimize the error in using criteria or models when specifying color rendering attributes for a given application, the criteria or models should be developed using a set of experimental objects that matches the typical objects of the application as closely as possible. Alternatively, if typical objects of an application cannot be reasonably determined, an object set that matches the distortions predicted by TM-30 as close as possible is likely to provide the most meaningful results.« less

Expert systems for real-time monitoring and fault diagnosis

NASA Technical Reports Server (NTRS)

Edwards, S. J.; Caglayan, A. K.

1989-01-01

Methods for building real-time onboard expert systems were investigated, and the use of expert systems technology was demonstrated in improving the performance of current real-time onboard monitoring and fault diagnosis applications. The potential applications of the proposed research include an expert system environment allowing the integration of expert systems into conventional time-critical application solutions, a grammar for describing the discrete event behavior of monitoring and fault diagnosis systems, and their applications to new real-time hardware fault diagnosis and monitoring systems for aircraft.

LIBS: a potential tool for industrial/agricultural waste water analysis

NASA Astrophysics Data System (ADS)

Karpate, Tanvi; K. M., Muhammed Shameem; Nayak, Rajesh; V. K., Unnikrishnan; Santhosh, C.

2016-04-01

Laser Induced Breakdown Spectroscopy (LIBS) is a multi-elemental analysis technique with various advantages and has the ability to detect any element in real time. This technique holds a potential for environmental monitoring and various such analysis has been done in soil, glass, paint, water, plastic etc confirms the robustness of this technique for such applications. Compared to the currently available water quality monitoring methods and techniques, LIBS has several advantages, viz. no need for sample preparation, fast and easy operation, and chemical free during the process. In LIBS, powerful pulsed laser generates plasma which is then analyzed to get quantitative and qualitative details of the elements present in the sample. Another main advantage of LIBS technique is that it can perform in standoff mode for real time analysis. Water samples from industries and agricultural strata tend to have a lot of pollutants making it harmful for consumption. The emphasis of this project is to determine such harmful pollutants present in trace amounts in industrial and agricultural wastewater. When high intensity laser is made incident on the sample, a plasma is generated which gives a multielemental emission spectra. LIBS analysis has shown outstanding success for solids samples. For liquid samples, the analysis is challenging as the liquid sample has the chances of splashing due to the high energy of laser and thus making it difficult to generate plasma. This project also deals with determining the most efficient method for testing of water sample for qualitative as well as quantitative analysis using LIBS.

Quantitative capillary electrophoresis and its application in analysis of alkaloids in tea, coffee, coca cola, and theophylline tablets.

PubMed

Li, Mengjia; Zhou, Junyi; Gu, Xue; Wang, Yan; Huang, Xiaojing; Yan, Chao

2009-01-01

A quantitative CE (qCE) system with high precision has been developed, in which a 4-port nano-valve was isolated from the electric field and served as sample injector. The accurate amount of sample was introduced into the CE system with high reproducibility. Based on this system, consecutive injections and separations were performed without voltage interruption. Reproducibilities in terms of RSD lower than 0.8% for retention time and 1.7% for peak area were achieved. The effectiveness of the system was demonstrated by the quantitative analysis of caffeine, theobromine, and theophylline in real samples, such as tea leaf, roasted coffee, coca cola, and theophylline tablets.

Molecular methods (digital PCR and real-time PCR) for the quantification of low copy DNA of Phytophthora nicotianae in environmental samples.

PubMed

Blaya, Josefa; Lloret, Eva; Santísima-Trinidad, Ana B; Ros, Margarita; Pascual, Jose A

2016-04-01

Currently, real-time polymerase chain reaction (qPCR) is the technique most often used to quantify pathogen presence. Digital PCR (dPCR) is a new technique with the potential to have a substantial impact on plant pathology research owing to its reproducibility, sensitivity and low susceptibility to inhibitors. In this study, we evaluated the feasibility of using dPCR and qPCR to quantify Phytophthora nicotianae in several background matrices, including host tissues (stems and roots) and soil samples. In spite of the low dynamic range of dPCR (3 logs compared with 7 logs for qPCR), this technique proved to have very high precision applicable at very low copy numbers. The dPCR was able to detect accurately the pathogen in all type of samples in a broad concentration range. Moreover, dPCR seems to be less susceptible to inhibitors than qPCR in plant samples. Linear regression analysis showed a high correlation between the results obtained with the two techniques in soil, stem and root samples, with R(2) = 0.873, 0.999 and 0.995 respectively. These results suggest that dPCR is a promising alternative for quantifying soil-borne pathogens in environmental samples, even in early stages of the disease. © 2015 Society of Chemical Industry.

Image analysis of representative food structures: application of the bootstrap method.

PubMed

Ramírez, Cristian; Germain, Juan C; Aguilera, José M

2009-08-01

Images (for example, photomicrographs) are routinely used as qualitative evidence of the microstructure of foods. In quantitative image analysis it is important to estimate the area (or volume) to be sampled, the field of view, and the resolution. The bootstrap method is proposed to estimate the size of the sampling area as a function of the coefficient of variation (CV(Bn)) and standard error (SE(Bn)) of the bootstrap taking sub-areas of different sizes. The bootstrap method was applied to simulated and real structures (apple tissue). For simulated structures, 10 computer-generated images were constructed containing 225 black circles (elements) and different coefficient of variation (CV(image)). For apple tissue, 8 images of apple tissue containing cellular cavities with different CV(image) were analyzed. Results confirmed that for simulated and real structures, increasing the size of the sampling area decreased the CV(Bn) and SE(Bn). Furthermore, there was a linear relationship between the CV(image) and CV(Bn) (.) For example, to obtain a CV(Bn) = 0.10 in an image with CV(image) = 0.60, a sampling area of 400 x 400 pixels (11% of whole image) was required, whereas if CV(image) = 1.46, a sampling area of 1000 x 100 pixels (69% of whole image) became necessary. This suggests that a large-size dispersion of element sizes in an image requires increasingly larger sampling areas or a larger number of images.

A neural algorithm for the non-uniform and adaptive sampling of biomedical data.

PubMed

Mesin, Luca

2016-04-01

Body sensors are finding increasing applications in the self-monitoring for health-care and in the remote surveillance of sensitive people. The physiological data to be sampled can be non-stationary, with bursts of high amplitude and frequency content providing most information. Such data could be sampled efficiently with a non-uniform schedule that increases the sampling rate only during activity bursts. A real time and adaptive algorithm is proposed to select the sampling rate, in order to reduce the number of measured samples, but still recording the main information. The algorithm is based on a neural network which predicts the subsequent samples and their uncertainties, requiring a measurement only when the risk of the prediction is larger than a selectable threshold. Four examples of application to biomedical data are discussed: electromyogram, electrocardiogram, electroencephalogram, and body acceleration. Sampling rates are reduced under the Nyquist limit, still preserving an accurate representation of the data and of their power spectral densities (PSD). For example, sampling at 60% of the Nyquist frequency, the percentage average rectified errors in estimating the signals are on the order of 10% and the PSD is fairly represented, until the highest frequencies. The method outperforms both uniform sampling and compressive sensing applied to the same data. The discussed method allows to go beyond Nyquist limit, still preserving the information content of non-stationary biomedical signals. It could find applications in body sensor networks to lower the number of wireless communications (saving sensor power) and to reduce the occupation of memory. Copyright © 2016 Elsevier Ltd. All rights reserved.

Enantioselective determination by capillary electrophoresis with cyclodextrins as chiral selectors.

PubMed

Fanali, S

2000-04-14

This review surveys the separation of enantiomers by capillary electrophoresis using cyclodextrins as chiral selector. Cyclodextrins or their derivatives have been widely employed for the direct chiral resolution of a wide number of enantiomers, mainly of pharmaceutical interest, selected examples are reported in the tables. For method optimisation, several parameters influencing the enantioresolution, e.g., cyclodextrin type and concentration, buffer pH and composition, presence of organic solvents or complexing additives in the buffer were considered and discussed. Finally, selected applications to real samples such as pharmaceutical formulations, biological and medical samples are also discussed.

Application of micro-Fourier transform infrared spectroscopy to the examination of paint samples

NASA Astrophysics Data System (ADS)

Zięba-Palus, J.

1999-11-01

The examination and identification of automobile paints is an important problem in road accidents investigations. Since the real sample available is very small, only sensitive microtechniques can be applied. The methods of optical microscopy and micro-Fourier transform infrared spectroscopy (MK-FTIR) supported by scanning electron microscopy together with X-ray microanalysis (SEM-EDX) allow one to carry out the examination of each paint layer without any separation procedure. In this paper an attempt is made to discriminate between different automobile paints of the same colour by the use of these methods for criminalistic investigations.

Automated force controller for amplitude modulation atomic force microscopy

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

Miyagi, Atsushi, E-mail: atsushi.miyagi@inserm.fr, E-mail: simon.scheuring@inserm.fr; Scheuring, Simon, E-mail: atsushi.miyagi@inserm.fr, E-mail: simon.scheuring@inserm.fr

Atomic Force Microscopy (AFM) is widely used in physics, chemistry, and biology to analyze the topography of a sample at nanometer resolution. Controlling precisely the force applied by the AFM tip to the sample is a prerequisite for faithful and reproducible imaging. In amplitude modulation (oscillating) mode AFM, the applied force depends on the free and the setpoint amplitudes of the cantilever oscillation. Therefore, for keeping the applied force constant, not only the setpoint amplitude but also the free amplitude must be kept constant. While the AFM user defines the setpoint amplitude, the free amplitude is typically subject to uncontrollablemore » drift, and hence, unfortunately, the real applied force is permanently drifting during an experiment. This is particularly harmful in biological sciences where increased force destroys the soft biological matter. Here, we have developed a strategy and an electronic circuit that analyzes permanently the free amplitude of oscillation and readjusts the excitation to maintain the free amplitude constant. As a consequence, the real applied force is permanently and automatically controlled with picoNewton precision. With this circuit associated to a high-speed AFM, we illustrate the power of the development through imaging over long-duration and at various forces. The development is applicable for all AFMs and will widen the applicability of AFM to a larger range of samples and to a larger range of (non-specialist) users. Furthermore, from controlled force imaging experiments, the interaction strength between biomolecules can be analyzed.« less

Rapid and simultaneous detection of Salmonella spp., Escherichia coli O157, and Listeria monocytogenes by magnetic capture hybridization and multiplex real-time PCR.

PubMed

Carloni, Elisa; Rotundo, Luca; Brandi, Giorgio; Amagliani, Giulia

2018-05-25

The application of rapid, specific, and sensitive methods for pathogen detection and quantification is very advantageous in diagnosis of human pathogens in several applications, including food analysis. The aim of this study was the evaluation of a method for the multiplexed detection and quantification of three significant foodborne pathogenic species (Escherichia coli O157, Salmonella spp., and Listeria monocytogenes). The assay combines specific DNA extraction by multiplex magnetic capture hybridization (mMCH) with multiplex real-time PCR. The amplification assay showed linearity in the range 10 6 -10 genomic units (GU)/PCR for each co-amplified species. The sensitivity corresponded to 1 GU/PCR for E. coli O157 and L. monocytogenes, and 10 GU/PCR for Salmonella spp. The immobilization process and the hybrid capture of the MCH showed good efficiency and reproducibility for all targets, allowing the combination in equal amounts of the different nanoparticle types in mMCH. MCH and mMCH efficiencies were similar. The detection limit of the method was 10 CFU in samples with individual pathogens and 10 2  CFU in samples with combination of the three pathogens in unequal amounts (amount's differences of 2 or 3 log). In conclusion, this multiplex molecular platform can be applied to determine the presence of target species in food samples after culture enrichment. In this way, this method could be a time-saving and sensitive tool to be used in routine diagnosis.

Fast and Adaptive Lossless On-Board Hyperspectral Data Compression System for Space Applications

NASA Technical Reports Server (NTRS)

Aranki, Nazeeh; Bakhshi, Alireza; Keymeulen, Didier; Klimesh, Matthew

2009-01-01

Efficient on-board lossless hyperspectral data compression reduces the data volume necessary to meet NASA and DoD limited downlink capabilities. The techniques also improves signature extraction, object recognition and feature classification capabilities by providing exact reconstructed data on constrained downlink resources. At JPL a novel, adaptive and predictive technique for lossless compression of hyperspectral data was recently developed. This technique uses an adaptive filtering method and achieves a combination of low complexity and compression effectiveness that far exceeds state-of-the-art techniques currently in use. The JPL-developed 'Fast Lossless' algorithm requires no training data or other specific information about the nature of the spectral bands for a fixed instrument dynamic range. It is of low computational complexity and thus well-suited for implementation in hardware, which makes it practical for flight implementations of pushbroom instruments. A prototype of the compressor (and decompressor) of the algorithm is available in software, but this implementation may not meet speed and real-time requirements of some space applications. Hardware acceleration provides performance improvements of 10x-100x vs. the software implementation (about 1M samples/sec on a Pentium IV machine). This paper describes a hardware implementation of the JPL-developed 'Fast Lossless' compression algorithm on a Field Programmable Gate Array (FPGA). The FPGA implementation targets the current state of the art FPGAs (Xilinx Virtex IV and V families) and compresses one sample every clock cycle to provide a fast and practical real-time solution for Space applications.

A vision for ubiquitous sequencing

PubMed Central

Erlich, Yaniv

2015-01-01

Genomics has recently celebrated reaching the $1000 genome milestone, making affordable DNA sequencing a reality. With this goal successfully completed, the next goal of the sequencing revolution can be sequencing sensors—miniaturized sequencing devices that are manufactured for real-time applications and deployed in large quantities at low costs. The first part of this manuscript envisions applications that will benefit from moving the sequencers to the samples in a range of domains. In the second part, the manuscript outlines the critical barriers that need to be addressed in order to reach the goal of ubiquitous sequencing sensors. PMID:26430149

Plasma plume oscillations monitoring during laser welding of stainless steel by discrete wavelet transform application.

PubMed

Sibillano, Teresa; Ancona, Antonio; Rizzi, Domenico; Lupo, Valentina; Tricarico, Luigi; Lugarà, Pietro Mario

2010-01-01

The plasma optical radiation emitted during CO2 laser welding of stainless steel samples has been detected with a Si-PIN photodiode and analyzed under different process conditions. The discrete wavelet transform (DWT) has been used to decompose the optical signal into various discrete series of sequences over different frequency bands. The results show that changes of the process settings may yield different signal features in the range of frequencies between 200 Hz and 30 kHz. Potential applications of this method to monitor in real time the laser welding processes are also discussed.

CMT for biomedical and other applications

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

Spanne, P.

This session includes two presentations describing applications for x-ray tomography using synchrotron radiation for biomedical uses and fluid flow modeling, and outlines advantages for using monoenergetic x-rays. Contrast mechanisms are briefly described and several graphs of absorbed doses and scattering of x-rays are included. Also presented are schematic diagrams of computerized tomographic instrumentation with camera head. A brief description of goals for a real time tomographic system and expected improvements to the system are described. Color photomicrographs of the Berea Sandstone and human bone are provided, as well as a 3-D microtomographic reconstruction of a human vertebra sample.

Smartphone Ownership and Interest in Mobile Applications to Monitor Symptoms of Mental Health Conditions

PubMed Central

Friedman, Rohn; Keshavan, Matcheri

2014-01-01

Background Patient retrospective recollection is a mainstay of assessing symptoms in mental health and psychiatry. However, evidence suggests that these retrospective recollections may not be as accurate as data collection though the experience sampling method (ESM), which captures patient data in “real time” and “real life.” However, the difficulties in practical implementation of ESM data collection have limited its impact in psychiatry and mental health. Smartphones with the capability to run mobile applications may offer a novel method of collecting ESM data that may represent a practical and feasible tool for mental health and psychiatry. Objective This paper aims to provide data on psychiatric patients’ prevalence of smartphone ownership, patterns of use, and interest in utilizing mobile applications to monitor their mental health conditions. Methods One hundred psychiatric outpatients at a large urban teaching hospital completed a paper-and-pencil survey regarding smartphone ownership, use, and interest in utilizing mobile applications to monitor their mental health condition. Results Ninety-seven percent of patients reported owning a phone and 72% reported that their phone was a smartphone. Patients in all age groups indicated greater than 50% interest in using a mobile application on a daily basis to monitor their mental health condition. Conclusions Smartphone and mobile applications represent a practical opportunity to explore new modalities of monitoring, treatment, and research of psychiatric and mental health conditions. PMID:25098314

Smartphone ownership and interest in mobile applications to monitor symptoms of mental health conditions.

PubMed

Torous, John; Friedman, Rohn; Keshavan, Matcheri

2014-01-21

Patient retrospective recollection is a mainstay of assessing symptoms in mental health and psychiatry. However, evidence suggests that these retrospective recollections may not be as accurate as data collection though the experience sampling method (ESM), which captures patient data in "real time" and "real life." However, the difficulties in practical implementation of ESM data collection have limited its impact in psychiatry and mental health. Smartphones with the capability to run mobile applications may offer a novel method of collecting ESM data that may represent a practical and feasible tool for mental health and psychiatry. This paper aims to provide data on psychiatric patients' prevalence of smartphone ownership, patterns of use, and interest in utilizing mobile applications to monitor their mental health conditions. One hundred psychiatric outpatients at a large urban teaching hospital completed a paper-and-pencil survey regarding smartphone ownership, use, and interest in utilizing mobile applications to monitor their mental health condition. Ninety-seven percent of patients reported owning a phone and 72% reported that their phone was a smartphone. Patients in all age groups indicated greater than 50% interest in using a mobile application on a daily basis to monitor their mental health condition. Smartphone and mobile applications represent a practical opportunity to explore new modalities of monitoring, treatment, and research of psychiatric and mental health conditions.

Sexual Behaviour and Interest in Using a Sexual Health Mobile App to Help Improve and Manage College Students' Sexual Health

ERIC Educational Resources Information Center

Richman, Alice R.; Webb, Monica C.; Brinkley, Jason; Martin, Ryan J.

2014-01-01

Many US college students are reported to engage in risky sexual behaviour. Smartphone applications are a popular way to provide users with information in real time. We explored the potential for mobile technology to be used in promoting the sexual health of college students. Using findings from an online survey among a random sample of 5000…

Simultaneous and accurate real-time monitoring of glucose and ethanol in alcoholic drinks, must, and biomass by a dual-amperometric biosensor.

PubMed

Mentana, Annalisa; Palermo, Carmen; Nardiello, Donatella; Quinto, Maurizio; Centonze, Diego

2013-01-09

In this work the optimization and application of a dual-amperometric biosensor for simultaneous monitoring of glucose and ethanol content, as quality markers in drinks and alcoholic fermentation media, are described. The biosensor is based on glucose oxidase (GOD) and alcohol oxidase (AOD) immobilized by co-cross-linking with bovine serum albumin (BSA) and glutaraldehyde (GLU) both onto a dual gold electrode, modified with a permselective overoxidized polypyrrole film (PPYox). Response, rejection of interferents, and stability of the dual biosensor were optimized in terms of PPYox thickness, BSA, and enzyme loading. The biosensor was integrated in a flow injection system coupled with an at-line microdialysis fiber as a sampling tool. Flow rates inside and outside the fiber were optimized in terms of linear responses (0.01-1 and 0.01-1.5 M) and sensitivities (27.6 ± 0.4 and 31.0 ± 0.6 μA·M(-1)·cm(-2)) for glucose and ethanol. Excellent anti-interference characteristics, the total absence of "cross-talk", and good response stability under operational conditions allowed application of the dual biosensor in accurate real-time monitoring (at least 15 samples/h) of alcoholic drinks, white grape must, and woody biomass.

Highly Sensitive GMO Detection Using Real-Time PCR with a Large Amount of DNA Template: Single-Laboratory Validation.

PubMed

Mano, Junichi; Hatano, Shuko; Nagatomi, Yasuaki; Futo, Satoshi; Takabatake, Reona; Kitta, Kazumi

2018-03-01

Current genetically modified organism (GMO) detection methods allow for sensitive detection. However, a further increase in sensitivity will enable more efficient testing for large grain samples and reliable testing for processed foods. In this study, we investigated real-time PCR-based GMO detection methods using a large amount of DNA template. We selected target sequences that are commonly introduced into many kinds of GM crops, i.e., 35S promoter and nopaline synthase (NOS) terminator. This makes the newly developed method applicable to a wide range of GMOs, including some unauthorized ones. The estimated LOD of the new method was 0.005% of GM maize events; to the best of our knowledge, this method is the most sensitive among the GM maize detection methods for which the LOD was evaluated in terms of GMO content. A 10-fold increase in the DNA amount as compared with the amount used under common testing conditions gave an approximately 10-fold reduction in the LOD without PCR inhibition. Our method is applicable to various analytical samples, including processed foods. The use of other primers and fluorescence probes would permit highly sensitive detection of various recombinant DNA sequences besides the 35S promoter and NOS terminator.

Detection of influenza A(H1N1)v virus by real-time RT-PCR.

PubMed

Panning, M; Eickmann, M; Landt, O; Monazahian, M; Olschläger, S; Baumgarte, S; Reischl, U; Wenzel, J J; Niller, H H; Günther, S; Hollmann, B; Huzly, D; Drexler, J F; Helmer, A; Becker, S; Matz, B; Eis-Hübinger, Am; Drosten, C

2009-09-10

Influenza A(H1N1)v virus was first identified in April 2009. A novel real-time RT-PCR for influenza A(H1N1)v virus was set up ad hoc and validated following industry-standard criteria. The lower limit of detection of the assay was 384 copies of viral RNA per ml of viral transport medium (95% confidence interval: 273-876 RNA copies/ml). Specificity was 100% as assessed on a panel of reference samples including seasonal human influenza A virus H1N1 and H3N2, highly pathogenic avian influenza A virus H5N1 and porcine influenza A virus H1N1, H1N2 and H3N2 samples. The real-time RT-PCR assay for the influenza A matrix gene recommended in 2007 by the World Health Organization was modified to work under the same reaction conditions as the influenza A(H1N1)v virus-specific test. Both assays were equally sensitive. Clinical applicability of both assays was demonstrated by screening of almost 2,000 suspected influenza (H1N1)v specimens, which included samples from the first cases of pandemic H1N1 influenza imported to Germany. Measuring influenza A(H1N1)v virus concentrations in 144 laboratory-confirmed samples yielded a median of 4.6 log RNA copies/ml. The new methodology proved its principle and might assist public health laboratories in the upcoming influenza pandemic.

Real-Time Earthquake Monitoring with Spatio-Temporal Fields

NASA Astrophysics Data System (ADS)

Whittier, J. C.; Nittel, S.; Subasinghe, I.

2017-10-01

With live streaming sensors and sensor networks, increasingly large numbers of individual sensors are deployed in physical space. Sensor data streams are a fundamentally novel mechanism to deliver observations to information systems. They enable us to represent spatio-temporal continuous phenomena such as radiation accidents, toxic plumes, or earthquakes almost as instantaneously as they happen in the real world. Sensor data streams discretely sample an earthquake, while the earthquake is continuous over space and time. Programmers attempting to integrate many streams to analyze earthquake activity and scope need to write code to integrate potentially very large sets of asynchronously sampled, concurrent streams in tedious application code. In previous work, we proposed the field stream data model (Liang et al., 2016) for data stream engines. Abstracting the stream of an individual sensor as a temporal field, the field represents the Earth's movement at the sensor position as continuous. This simplifies analysis across many sensors significantly. In this paper, we undertake a feasibility study of using the field stream model and the open source Data Stream Engine (DSE) Apache Spark(Apache Spark, 2017) to implement a real-time earthquake event detection with a subset of the 250 GPS sensor data streams of the Southern California Integrated GPS Network (SCIGN). The field-based real-time stream queries compute maximum displacement values over the latest query window of each stream, and related spatially neighboring streams to identify earthquake events and their extent. Further, we correlated the detected events with an USGS earthquake event feed. The query results are visualized in real-time.

Performance of a New HPV Cervi-Collect Collection and Transportation Kit

PubMed Central

Chernesky, M.; Huang, S.; Jang, D.; Erickson, B.; Salituro, J.; Engel, H.; Gilchrist, J.; Neuscheler, P.; Mak, W. B.; Abravaya, K.

2012-01-01

Background. Liquid-based Pap (L-Pap) media are used for Pap and human papillomavirus (HPV) testing. Objectives. To compare RealTime High Risk (HR) HPV testing of a new collection kit (Cervi-Collect) and PreservCyt L-Pap specimens. To determine ease of use and safety of Cervi-Collect. Methods. L-Pap samples (n = 203) were tested with HC2 and RealTime HR HPV and Cervi-Collect with RealTime HR HPV. Discordant samples were genotyped. Results. L-Pap and Cervi-Collect specimens tested by RealTime HR HPV showed 93.1% agreement (Kappa 0.86). RealTime HR HPV and HC2 on L-Pap had 90.3% agreement (Kappa 0.80). RealTime HR HPV on Cervi-Collect and HC2 on L-Pap showed 88.2% agreement (Kappa 0.76). Sixteen of 21 samples which were HC2 negative and RealTime HR HPV positive on L-Pap or Cervi-Collect contained HR HPV genotypes. Eleven healthcare collectors were in strong agreement on a usability and safety questionnaire. Conclusion. Cervi-Collect samples were easy to collect and showed strong agreement with L-Pap samples tested with RealTime HR HPV or HC2. PMID:22174716

Development of a novel ultrasound-assisted headspace liquid-phase microextraction and its application to the analysis of chlorophenols in real aqueous samples.

PubMed

Xu, Hui; Liao, Ying; Yao, Jinrong

2007-10-05

A new sample pretreatment technique, ultrasound-assisted headspace liquid-phase microextraction was developed as mentioned in this paper. In the technique, the volatile analytes were headspace extracted into a small drop of solvent, which suspended on the bottom of a cone-shaped PCR tube instead of the needle tip of a microsyringe. More solvent could be suspended in the PCR tube than microsyringe due to the larger interfacial tension, thus the analysis sensitivity was significantly improved with the increase of the extractant volume. Moreover, ultrasound-assisted extraction and independent controlling temperature of the extractant and the sample were performed to enhance the extraction efficiency. Following the extraction, the solvent-loaded sample was analyzed by high-performance liquid chromatography. Chlorophenols (2-chlorophenol, 2,4-dichlorophenol and 2,6-dichlorophenol) were chosen as model analytes to investigate the feasibility of the method. The experimental conditions related to the extraction efficiency were systematically studied. Under the optimum experimental conditions, the detection limit (S/N=3), intra- and inter-day RSD were 6 ng mL(-1), 4.6%, 3.9% for 2-chlorophenol, 12 ng mL(-1), 2.4%, 8.8% for 2,4-dichlorophenol and 23 ng mL(-1), 3.3%, 5.3% for 2,6-dichlorophenol, respectively. The proposed method was successfully applied to determine chlorophenols in real aqueous samples. Good recoveries ranging from 84.6% to 100.7% were obtained. In addition, the extraction efficiency of our method and the conventional headspace liquid-phase microextraction were compared; the extraction efficiency of the former was about 21 times higher than that of the latter. The results demonstrated that the proposed method is a promising sample pretreatment approach, its advantages over the conventional headspace liquid-phase microextraction include simple setup, ease of operation, rapidness, sensitivity, precision and no cross-contamination. The method is very suitable for the analysis of trace volatile and semivolatile pollutants in real aqueous sample.

Explicit construction of quadratic Lyapunov functions for the small gain, positivity, circle, and Popov theorems and their application to robust stability

NASA Technical Reports Server (NTRS)

Haddad, Wassim M.; Bernstein, Dennis S.

1991-01-01

Lyapunov function proofs of sufficient conditions for asymptotic stability are given for feedback interconnections of bounded real and positive real transfer functions. Two cases are considered: (1) a proper bounded real (resp., positive real) transfer function with a bounded real (resp., positive real) time-varying memoryless nonlinearity; and (2) two strictly proper bounded real (resp., positive real) transfer functions. A similar treatment is given for the circle and Popov theorems. Application of these results to robust stability with time-varying bounded real, positive real, and sector-bounded uncertainty is discussed.

Moving your laboratories to the field--Advantages and limitations of the use of field portable instruments in environmental sample analysis.

PubMed

Gałuszka, Agnieszka; Migaszewski, Zdzisław M; Namieśnik, Jacek

2015-07-01

The recent rapid progress in technology of field portable instruments has increased their applications in environmental sample analysis. These instruments offer a possibility of cost-effective, non-destructive, real-time, direct, on-site measurements of a wide range of both inorganic and organic analytes in gaseous, liquid and solid samples. Some of them do not require the use of reagents and do not produce any analytical waste. All these features contribute to the greenness of field portable techniques. Several stationary analytical instruments have their portable versions. The most popular ones include: gas chromatographs with different detectors (mass spectrometer (MS), flame ionization detector, photoionization detector), ultraviolet-visible and near-infrared spectrophotometers, X-ray fluorescence spectrometers, ion mobility spectrometers, electronic noses and electronic tongues. The use of portable instruments in environmental sample analysis gives a possibility of on-site screening and a subsequent selection of samples for routine laboratory analyses. They are also very useful in situations that require an emergency response and for process monitoring applications. However, quantification of results is still problematic in many cases. The other disadvantages include: higher detection limits and lower sensitivity than these obtained in laboratory conditions, a strong influence of environmental factors on the instrument performance and a high possibility of sample contamination in the field. This paper reviews recent applications of field portable instruments in environmental sample analysis and discusses their analytical capabilities. Copyright © 2015 Elsevier Inc. All rights reserved.

Frequency of awake bruxism behaviours in the natural environment. A 7-day, multiple-point observation of real-time report in healthy young adults.

PubMed

Bracci, A; Djukic, G; Favero, L; Salmaso, L; Guarda-Nardini, L; Manfredini, D

2018-06-01

The aim of this study was to assess awake bruxism (AB) behaviours in a sample of healthy young adults using a smartphone-based application for a real-time report (ie, ecological momentary assessment [EMA], also called experience sampling method [ESM]). Forty-six dental students used a smartphone application that sent 15 alerts at random intervals during the day for 1 week to collect AB self-reports. They had to answer on time by tapping on the display icon that refers to their current condition of jaw muscles: relaxed; teeth contact; teeth clenching; teeth grinding; jaw clenching without teeth contact (ie, bracing). The average frequency of relaxed jaw muscles, as a percentage of answers over the 7 days, was 71.7%. Teeth contact (14.5%) and jaw clenching (10.0%) were the most frequent AB behaviours. No significant gender differences were detected. Interindividual differences were quite relevant, but the overall frequency was in general only moderately variable from day-to-day. Coefficient of variation (CV) was low for the condition "relaxed jaw muscles" (0.44). At the individual level, teeth contact was the most prevalent behaviour, with a 39.1%-52.2% proportion of subjects reporting it at least once a day. During a 7-day observation period, the frequency of real-time report of AB behaviours in a sample of healthy young adults was 28.3%. The low daily variability in the average frequency value for the relaxed jaw muscles condition suggests that EMA may be a reliable strategy to get deeper into the epidemiology of oral behaviours. This investigation introduced EMA principles to the study of AB and provided data on the frequency of AB behaviours in young adults that could be compared to populations with risk/associated factors and possible clinical consequences. © 2018 John Wiley & Sons Ltd.

Development of a new pentaplex real-time PCR assay for the identification of poly-microbial specimens containing Staphylococcus aureus and other staphylococci, with simultaneous detection of staphylococcal virulence and methicillin resistance markers.

PubMed

Okolie, Charles E; Wooldridge, Karl G; Turner, David P; Cockayne, Alan; James, Richard

2015-06-01

Staphylococcus aureus strains harbouring genes encoding virulence and antibiotic resistance are of public health importance. In clinical samples, pathogenic S. aureus is often mixed with putatively less pathogenic coagulase-negative staphylococci (CoNS), both of which can harbour mecA, the gene encoding staphylococcal methicillin-resistance. There have been previous attempts at distinguishing MRSA from MRCoNS, most of which were based on the detection of one of the pathognomonic markers of S. aureus, such as coa, nuc or spa. That approach might suffice for discrete colonies and mono-microbial samples; it is inadequate for identification of clinical specimens containing mixtures of S. aureus and CoNS. In the present study, a real-time pentaplex PCR assay has been developed which simultaneously detects markers for bacteria (16S rRNA), coagulase-negative staphylococcus (cns), S. aureus (spa), Panton-Valentine leukocidin (pvl) and methicillin resistance (mecA). Staphylococcal and non-staphylococcal bacterial strains (n = 283) were used to validate the new assay. The applicability of this test to clinical samples was evaluated using spiked blood cultures (n = 43) containing S. aureus and CoNS in mono-microbial and poly-microbial models, which showed that the 5 markers were all detected as expected. Cycling completes within 1 h, delivering 100% specificity, NPV and PPV with a detection limit of 1.0 × 10(1) to 3.0 × 10(1) colony forming units (CFU)/ml, suggesting direct applicability in routine diagnostic microbiology. This is the most multiplexed real-time PCR-based PVL-MRSA assay and the first detection of a unique marker for CoNS without recourse to the conventional elimination approach. There was no evidence that this new assay produced invalid/indeterminate test results. Copyright © 2015 Elsevier Ltd. All rights reserved.

23 CFR 511.307 - Eligibility for Federal funding.

Code of Federal Regulations, 2011 CFR

2011-04-01

... the development and implementation of a real-time information program. (b) Those project applications... applications to establish a real-time information program for non-Interstate highways are entitled to a Federal... MANAGEMENT REAL-TIME SYSTEM MANAGEMENT INFORMATION PROGRAM Real-Time System Management Information Program...

Detection of Diarrhea Etiology Among U.S. Military Personnel During Exercise Balikatan 2014, Philippines, Using TaqMan Array Cards.

PubMed

Lertsethtakarn, Paphavee; Nakjarung, Kaewkanya; Silapong, Sasikorn; Neesanant, Pimmnapar; Sakpaisal, Pimmada; Bodhidatta, Ladaporn; Liu, Jie; Houpt, Eric; Velasco, John Mark; Macareo, Louis R; Swierczewski, Brett E; Mason, Carl J

2016-11-01

Military personnel are vulnerable to diarrhea. Diarrheal disease is common when deployed for operations or exercise in developing countries. Although diarrheal disease is transient, cumulative time lost and medical asset can have a significant impact on military operations. Currently, diagnostics of diarrheal etiology typically relies on a mixture of conventional bacteriology, enzyme-linked immunosorbent assay, and polymerase chain reaction (PCR)-based methods including real-time PCR. These methods, however, can be time and labor intensive, although the identification of diarrheal etiology needs to be informative and rapid for treatment and prevention. Real-time PCR has been increasingly used to identify pathogens. Real-time PCR panels of common diarrheal pathogens have been developed, but several diarrheal pathogens are not included in the panel. An expanded and customizable panel to detect diarrhea etiology has been developed employing TaqMan Array Card (TAC) technology. TAC performs 384 real-time PCR reactions simultaneously. As currently configured for diarrheal disease by the University of Virginia, a maximum of 8 samples can be tested simultaneously with approximately 48 target pathogens per sample including bacteria, fungi, helminths, protozoan parasites, and viruses. TAC diarrheal disease panels have been successfully applied to detect pathogens in acute diarrheal stool samples from young children in several international multicenter diarrhea studies. In this study, TAC was applied to stool samples collected under an approved human use protocol from military personnel with acute diarrhea participating in the annual joint military exercise, Balikatan, between the Republic of the Philippines and the United States in 2014. Several established pathogen-specific real-time PCR detection assays were also performed in parallel for comparative purposes. TAC was applied to 7 stool samples. Campylobacter spp. was the most common diarrheal disease pathogen detected. Results from TAC matched 5 out of 6 pathogen specific real-time PCR assays. TAC required a total of 5-6 hours to complete all the procedures from nucleic acid extraction and data analysis, whereas a minimum of 18 hours and 4 hours are required for conventional bacteriology and enzyme-linked immunosorbent assay, respectively, per pathogen. With TAC, pathogen load can be estimated from the amount of nucleic acid present for each pathogen, which can be analyzed further to better determine pathogen attribution and to compare pathogen load between case and control samples. Unfortunately, such correlative analysis was not possible because of the limited sample size available in this study. A larger sample size is needed for further evaluation of TAC on a specific population set, including military personnel. Regardless, TAC was found to be a useful and functional diagnostic platform that is less time-consuming, easy to use with high reproducibility, and costs less per sample compared to the current typically employed methods. The successful application of TAC in acute diarrhea stool samples from a US military population in the Philippines demonstrates its versatility as a potential candidate for a next-generation diagnostics platform. Reprint & Copyright © 2016 Association of Military Surgeons of the U.S.

Separating twin images and locating the center of a microparticle in dense suspensions using correlations among reconstructed fields of two parallel holograms.

PubMed

Ling, Hangjian; Katz, Joseph

2014-09-20

This paper deals with two issues affecting the application of digital holographic microscopy (DHM) for measuring the spatial distribution of particles in a dense suspension, namely discriminating between real and virtual images and accurate detection of the particle center. Previous methods to separate real and virtual fields have involved applications of multiple phase-shifted holograms, combining reconstructed fields of multiple axially displaced holograms, and analysis of intensity distributions of weakly scattering objects. Here, we introduce a simple approach based on simultaneously recording two in-line holograms, whose planes are separated by a short distance from each other. This distance is chosen to be longer than the elongated trace of the particle. During reconstruction, the real images overlap, whereas the virtual images are displaced by twice the distance between hologram planes. Data analysis is based on correlating the spatial intensity distributions of the two reconstructed fields to measure displacement between traces. This method has been implemented for both synthetic particles and a dense suspension of 2 μm particles. The correlation analysis readily discriminates between real and virtual images of a sample containing more than 1300 particles. Consequently, we can now implement DHM for three-dimensional tracking of particles when the hologram plane is located inside the sample volume. Spatial correlations within the same reconstructed field are also used to improve the detection of the axial location of the particle center, extending previously introduced procedures to suspensions of microscopic particles. For each cross section within a particle trace, we sum the correlations among intensity distributions in all planes located symmetrically on both sides of the section. This cumulative correlation has a sharp peak at the particle center. Using both synthetic and recorded particle fields, we show that the uncertainty in localizing the axial location of the center is reduced to about one particle's diameter.

Concurrent measurement of "real-world" stress and arousal in individuals with psychosis: assessing the feasibility and validity of a novel methodology.

PubMed

Kimhy, David; Delespaul, Philippe; Ahn, Hongshik; Cai, Shengnan; Shikhman, Marina; Lieberman, Jeffrey A; Malaspina, Dolores; Sloan, Richard P

2010-11-01

Psychosis has been repeatedly suggested to be affected by increases in stress and arousal. However, there is a dearth of evidence supporting the temporal link between stress, arousal, and psychosis during "real-world" functioning. This paucity of evidence may stem from limitations of current research methodologies. Our aim is to the test the feasibility and validity of a novel methodology designed to measure concurrent stress and arousal in individuals with psychosis during "real-world" daily functioning. Twenty patients with psychosis completed a 36-hour ambulatory assessment of stress and arousal. We used experience sampling method with palm computers to assess stress (10 times per day, 10 AM → 10 PM) along with concurrent ambulatory measurement of cardiac autonomic regulation using a Holter monitor. The clocks of the palm computer and Holter monitor were synchronized, allowing the temporal linking of the stress and arousal data. We used power spectral analysis to determine the parasympathetic contributions to autonomic regulation and sympathovagal balance during 5 minutes before and after each experience sample. Patients completed 79% of the experience samples (75% with a valid concurrent arousal data). Momentary increases in stress had inverse correlation with concurrent parasympathetic activity (ρ = -.27, P < .0001) and positive correlation with sympathovagal balance (ρ = .19, P = .0008). Stress and heart rate were not significantly related (ρ = -.05, P = .3875). The findings support the feasibility and validity of our methodology in individuals with psychosis. The methodology offers a novel way to study in high time resolution the concurrent, "real-world" interactions between stress, arousal, and psychosis. The authors discuss the methodology's potential applications and future research directions.

Photometric classification of type Ia supernovae in the SuperNova Legacy Survey with supervised learning

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

Möller, A.; Ruhlmann-Kleider, V.; Leloup, C.

In the era of large astronomical surveys, photometric classification of supernovae (SNe) has become an important research field due to limited spectroscopic resources for candidate follow-up and classification. In this work, we present a method to photometrically classify type Ia supernovae based on machine learning with redshifts that are derived from the SN light-curves. This method is implemented on real data from the SNLS deferred pipeline, a purely photometric pipeline that identifies SNe Ia at high-redshifts (0.2 < z < 1.1). Our method consists of two stages: feature extraction (obtaining the SN redshift from photometry and estimating light-curve shape parameters)more » and machine learning classification. We study the performance of different algorithms such as Random Forest and Boosted Decision Trees. We evaluate the performance using SN simulations and real data from the first 3 years of the Supernova Legacy Survey (SNLS), which contains large spectroscopically and photometrically classified type Ia samples. Using the Area Under the Curve (AUC) metric, where perfect classification is given by 1, we find that our best-performing classifier (Extreme Gradient Boosting Decision Tree) has an AUC of 0.98.We show that it is possible to obtain a large photometrically selected type Ia SN sample with an estimated contamination of less than 5%. When applied to data from the first three years of SNLS, we obtain 529 events. We investigate the differences between classifying simulated SNe, and real SN survey data. In particular, we find that applying a thorough set of selection cuts to the SN sample is essential for good classification. This work demonstrates for the first time the feasibility of machine learning classification in a high- z SN survey with application to real SN data.« less

Development and validation of a Pneumocystis jirovecii real-time polymerase chain reaction assay for diagnosis of Pneumocystis pneumonia

PubMed Central

Church, Deirdre L; Ambasta, Anshula; Wilmer, Amanda; Williscroft, Holly; Ritchie, Gordon; Pillai, Dylan R; Champagne, Sylvie; Gregson, Daniel G

2015-01-01

BACKGROUND: Pneumocystis jirovecii (PJ), a pathogenic fungus, causes severe interstitial Pneumocystis pneumonia (PCP) among immunocompromised patients. A laboratory-developed real-time polyermase chain reaction (PCR) assay was validated for PJ detection to improve diagnosis of PCP. METHODS: Forty stored bronchoalveolar lavage (BAL) samples (20 known PJ positive [PJ+] and 20 known PJ negative [PJ−]) were initially tested using the molecular assay. Ninety-two sequentially collected BAL samples were then analyzed using an immunofluorescence assay (IFA) and secondarily tested using the PJ real-time PCR assay. Discrepant results were resolved by retesting BAL samples using another real-time PCR assay with a different target. PJ real-time PCR assay performance was compared with the existing gold standard (ie, IFA) and a modified gold standard, in which a true positive was defined as a sample that tested positive in two of three methods in a patient suspected to have PCP. RESULTS: Ninety of 132 (68%) BAL fluid samples were collected from immunocompromised patients. Thirteen of 92 (14%) BALs collected were PJ+ when tested using IFA. A total of 40 BAL samples were PJ+ in the present study including: all IFA positive samples (n=13); all referred PJ+ BAL samples (n=20); and seven additional BAL samples that were IFA negative, but positive using the modified gold standard. Compared with IFA, the PJ real-time PCR had sensitivity, specificity, and positive and negative predictive values of 100%, 91%, 65% and 100%, respectively. Compared with the modified gold standard, PJ real-time PCR had a sensitivity, specificity, and positive and negative predictive values of 100%. CONCLUSION: PJ real-time PCR improved detection of PJ in immunocompromised patients. PMID:26600815

Co-Labeling for Multi-View Weakly Labeled Learning.

PubMed

Xu, Xinxing; Li, Wen; Xu, Dong; Tsang, Ivor W

2016-06-01

It is often expensive and time consuming to collect labeled training samples in many real-world applications. To reduce human effort on annotating training samples, many machine learning techniques (e.g., semi-supervised learning (SSL), multi-instance learning (MIL), etc.) have been studied to exploit weakly labeled training samples. Meanwhile, when the training data is represented with multiple types of features, many multi-view learning methods have shown that classifiers trained on different views can help each other to better utilize the unlabeled training samples for the SSL task. In this paper, we study a new learning problem called multi-view weakly labeled learning, in which we aim to develop a unified approach to learn robust classifiers by effectively utilizing different types of weakly labeled multi-view data from a broad range of tasks including SSL, MIL and relative outlier detection (ROD). We propose an effective approach called co-labeling to solve the multi-view weakly labeled learning problem. Specifically, we model the learning problem on each view as a weakly labeled learning problem, which aims to learn an optimal classifier from a set of pseudo-label vectors generated by using the classifiers trained from other views. Unlike traditional co-training approaches using a single pseudo-label vector for training each classifier, our co-labeling approach explores different strategies to utilize the predictions from different views, biases and iterations for generating the pseudo-label vectors, making our approach more robust for real-world applications. Moreover, to further improve the weakly labeled learning on each view, we also exploit the inherent group structure in the pseudo-label vectors generated from different strategies, which leads to a new multi-layer multiple kernel learning problem. Promising results for text-based image retrieval on the NUS-WIDE dataset as well as news classification and text categorization on several real-world multi-view datasets clearly demonstrate that our proposed co-labeling approach achieves state-of-the-art performance for various multi-view weakly labeled learning problems including multi-view SSL, multi-view MIL and multi-view ROD.

78 FR 21385 - Agency Information Collection Activities; Proposed Collection; Comment Request: Application for...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-10

...: Application for Surplus Federal Real Property Public Benefit Conveyance and BRAC Program for Emergency... Federal real property for public benefit. The purpose of this application is to implement the processes and procedures for the successful, lawful, and expeditious conveyance of real property from the...

Application Exercises Improve Transfer of Statistical Knowledge in Real-World Situations

ERIC Educational Resources Information Center

Daniel, Frances; Braasch, Jason L. G.

2013-01-01

The present research investigated whether real-world application exercises promoted students' abilities to spontaneously transfer statistical knowledge and to recognize the use of statistics in real-world contexts. Over the course of a semester of psychological statistics, two classes completed multiple application exercises designed to mimic…

Detection of bacteria and fungi in blood of patients with febrile neutropenia by real-time PCR with universal primers and probes.

PubMed

Teranishi, Hideto; Ohzono, Nanae; Inamura, Norikazu; Kato, Atsushi; Wakabayashi, Tokio; Akaike, Hiroto; Terada, Kihei; Ouchi, Kazunobu

2015-03-01

Febrile neutropenia is the main treatment-related cause of mortality in cancer patients. During June 2012 to April 2014, 97 blood culture samples were collected from patients receiving chemotherapy for hematological malignancy and cancer with febrile neutropenia episodes (FNEs). The samples were examined for the presence of bacteria and fungi using real-time PCR amplification and sequencing of 16S and 18S rRNA genes. Bacteria were identified in 20 of 97 samples (20.6%) by the real-time PCR assay and in 10 of 97 (10.3%) samples by blood culture. In 6 blood culture-positive samples, the real-time PCR assay detected the same type of bacteria. No fungi were detected by the real-time PCR assay or blood culture. During antibiotic therapy, all samples were negative by blood culture, but the real-time PCR assay yielded a positive result in 2 cases of 2 (100%). The bacterial DNA copy number was not well correlated with the serum C-reactive protein titer of patients with FNEs. We conclude that a real-time PCR assay could provide better detection of causative microbes' in a shorter time, and with a smaller blood sample than blood culture. Using a real-time PCR assay in combination with blood culture could improve microbiological documentation of FNEs. Copyright © 2014 Japanese Society of Chemotherapy and The Japanese Association for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Understanding the Effects of Sampling on Healthcare Risk Modeling for the Prediction of Future High-Cost Patients

NASA Astrophysics Data System (ADS)

Moturu, Sai T.; Liu, Huan; Johnson, William G.

Rapidly rising healthcare costs represent one of the major issues plaguing the healthcare system. Data from the Arizona Health Care Cost Containment System, Arizona's Medicaid program provide a unique opportunity to exploit state-of-the-art machine learning and data mining algorithms to analyze data and provide actionable findings that can aid cost containment. Our work addresses specific challenges in this real-life healthcare application with respect to data imbalance in the process of building predictive risk models for forecasting high-cost patients. We survey the literature and propose novel data mining approaches customized for this compelling application with specific focus on non-random sampling. Our empirical study indicates that the proposed approach is highly effective and can benefit further research on cost containment in the healthcare industry.

Observation uncertainty in reversible Markov chains.

PubMed

Metzner, Philipp; Weber, Marcus; Schütte, Christof

2010-09-01

In many applications one is interested in finding a simplified model which captures the essential dynamical behavior of a real life process. If the essential dynamics can be assumed to be (approximately) memoryless then a reasonable choice for a model is a Markov model whose parameters are estimated by means of Bayesian inference from an observed time series. We propose an efficient Monte Carlo Markov chain framework to assess the uncertainty of the Markov model and related observables. The derived Gibbs sampler allows for sampling distributions of transition matrices subject to reversibility and/or sparsity constraints. The performance of the suggested sampling scheme is demonstrated and discussed for a variety of model examples. The uncertainty analysis of functions of the Markov model under investigation is discussed in application to the identification of conformations of the trialanine molecule via Robust Perron Cluster Analysis (PCCA+) .

Condensed Phase Membrane Introduction Mass Spectrometry with Direct Electron Ionization: On-line Measurement of PAHs in Complex Aqueous Samples

NASA Astrophysics Data System (ADS)

Termopoli, Veronica; Famiglini, Giorgio; Palma, Pierangela; Cappiello, Achille; Vandergrift, Gregory W.; Krogh, Erik T.; Gill, Chris G.

2016-02-01

Polycyclic aromatic hydrocarbons (PAHs) are USEPA regulated priority pollutants. Their low aqueous solubility requires very sensitive analytical methods for their detection, typically involving preconcentration steps. Presented is the first demonstrated `proof of concept' use of condensed phase membrane introduction mass spectrometry (CP-MIMS) coupled with direct liquid electron ionization (DEI) for the direct, on-line measurement of PAHs in aqueous samples. DEI is very well suited for the ionization of PAHs and other nonpolar compounds, and is not significantly influenced by the co-elution of matrix components. Linear calibration data for low ppb levels of aqueous naphthalene, anthracene, and pyrene is demonstrated, with measured detection limits of 4 ppb. Analytical response times (t10%-90% signal rise) ranged from 2.8 min for naphthalene to 4.7 min for pyrene. Both intra- and interday reproducibility has been assessed (<3% and 5% RSD, respectively). Direct measurements of ppb level PAHs spiked in a variety of real, complex environmental sample matrices is examined, including natural waters, sea waters, and a hydrocarbon extraction production waste water sample. For these spiked, complex samples, direct PAH measurement by CP-MIMS-DEI yielded minimal signal suppression from sample matrix effects (81%-104%). We demonstrate the use of this analytical approach to directly monitor real-time changes in aqueous PAH concentrations with potential applications for continuous on-line monitoring strategies and binding/adsorption studies in heterogeneous samples.

Novel quantitative real-time LCR for the sensitive detection of SNP frequencies in pooled DNA: method development, evaluation and application.

PubMed

Psifidi, Androniki; Dovas, Chrysostomos; Banos, Georgios

2011-01-19

Single nucleotide polymorphisms (SNP) have proven to be powerful genetic markers for genetic applications in medicine, life science and agriculture. A variety of methods exist for SNP detection but few can quantify SNP frequencies when the mutated DNA molecules correspond to a small fraction of the wild-type DNA. Furthermore, there is no generally accepted gold standard for SNP quantification, and, in general, currently applied methods give inconsistent results in selected cohorts. In the present study we sought to develop a novel method for accurate detection and quantification of SNP in DNA pooled samples. The development and evaluation of a novel Ligase Chain Reaction (LCR) protocol that uses a DNA-specific fluorescent dye to allow quantitative real-time analysis is described. Different reaction components and thermocycling parameters affecting the efficiency and specificity of LCR were examined. Several protocols, including gap-LCR modifications, were evaluated using plasmid standard and genomic DNA pools. A protocol of choice was identified and applied for the quantification of a polymorphism at codon 136 of the ovine PRNP gene that is associated with susceptibility to a transmissible spongiform encephalopathy in sheep. The real-time LCR protocol developed in the present study showed high sensitivity, accuracy, reproducibility and a wide dynamic range of SNP quantification in different DNA pools. The limits of detection and quantification of SNP frequencies were 0.085% and 0.35%, respectively. The proposed real-time LCR protocol is applicable when sensitive detection and accurate quantification of low copy number mutations in DNA pools is needed. Examples include oncogenes and tumour suppressor genes, infectious diseases, pathogenic bacteria, fungal species, viral mutants, drug resistance resulting from point mutations, and genetically modified organisms in food.

Novel Quantitative Real-Time LCR for the Sensitive Detection of SNP Frequencies in Pooled DNA: Method Development, Evaluation and Application

PubMed Central

Psifidi, Androniki; Dovas, Chrysostomos; Banos, Georgios

2011-01-01

Background Single nucleotide polymorphisms (SNP) have proven to be powerful genetic markers for genetic applications in medicine, life science and agriculture. A variety of methods exist for SNP detection but few can quantify SNP frequencies when the mutated DNA molecules correspond to a small fraction of the wild-type DNA. Furthermore, there is no generally accepted gold standard for SNP quantification, and, in general, currently applied methods give inconsistent results in selected cohorts. In the present study we sought to develop a novel method for accurate detection and quantification of SNP in DNA pooled samples. Methods The development and evaluation of a novel Ligase Chain Reaction (LCR) protocol that uses a DNA-specific fluorescent dye to allow quantitative real-time analysis is described. Different reaction components and thermocycling parameters affecting the efficiency and specificity of LCR were examined. Several protocols, including gap-LCR modifications, were evaluated using plasmid standard and genomic DNA pools. A protocol of choice was identified and applied for the quantification of a polymorphism at codon 136 of the ovine PRNP gene that is associated with susceptibility to a transmissible spongiform encephalopathy in sheep. Conclusions The real-time LCR protocol developed in the present study showed high sensitivity, accuracy, reproducibility and a wide dynamic range of SNP quantification in different DNA pools. The limits of detection and quantification of SNP frequencies were 0.085% and 0.35%, respectively. Significance The proposed real-time LCR protocol is applicable when sensitive detection and accurate quantification of low copy number mutations in DNA pools is needed. Examples include oncogenes and tumour suppressor genes, infectious diseases, pathogenic bacteria, fungal species, viral mutants, drug resistance resulting from point mutations, and genetically modified organisms in food. PMID:21283808

Elemental analysis of urinary calculi by laser induced plasma spectroscopy.

PubMed

Fang, Xiao; Ahmad, S Rafi; Mayo, Mike; Iqbal, Syed

2005-12-01

Laser induced plasma spectroscopy (LIPS) has been applied to analyse and identify elemental constituents of urinary calculi. Measurements on seven different urinary stone samples were conducted and the concentrations of some key elemental species were estimated. The elements detected with the present system were: Calcium, Magnesium, Sodium, Samarium, Potassium and Lead. Absolute concentrations of the species were derived from pre-calibration of the system for each element. Their concentrations were found to be widely different in different samples. It was observed that the samples containing a significant amount of lead have large proportion of calcium. It has been established that LIPS would allow real time clinic measurements of elemental contents and the concentrations in the biomaterials without sample preparation. The technique has the potential for routine clinic applications in urological disorder diagnosis.

Development and use of interactive displays in real-time ground support research facilities

NASA Technical Reports Server (NTRS)

Rhea, Donald C.; Hammons, Kvin R.; Malone, Jacqueline C.; Nesel, Michael C.

1989-01-01

The NASA Western Aeronautical Test Range (WATR) is one of the world's most advanced aeronautical research flight test support facilities. A variety of advanced and often unique real-time interactive displays has been developed for use in the mission control centers (MCC) to support research flight and ground testing. These dispalys consist of applications operating on systems described as real-time interactive graphics super workstations and real-time interactive PC/AT compatible workstations. This paper reviews these two types of workstations and the specific applications operating on each display system. The applications provide examples that demonstrate overall system capability applicable for use in other ground-based real-time research/test facilities.

[Application of transcription mediated amplification and real-time reverse transcription polymerase chain reaction in detection of human immunodeficiency virus RNA].

PubMed

Wu, Daxian; Tao, Shuhui; Liu, Shuiping; Zhou, Jiebin; Tan, Deming; Hou, Zhouhua

2017-07-28

To observe the sensitivity of transcription mediated amplification (TMA), and to compare its performance with real-time reverse transcription polymerase chain reaction (real-time RT-PCR) in detecting human immunodeficiency virus RNA (HIV RNA).
 Methods: TMA system was established with TaqMan probes, specific primers, moloney murine leukemia virus (MMLV) reverse transcriptase, T7 RNA polymerase, and reaction substrates. The sensitivity of TMA was evaluated by amplifying a group of 10-fold diluted HIV RNA standards which were transcribed in vitro. A total of 60 plasma of HIV infected patients were measured by TMA and Cobas Amplicor HIV-1 Monitor test to observe the positive rate. The correlation and concordance of the above two technologies were investigated by linear regression and Bland-Altman analysis.
 Results: TMA system was established successfully and HIV RNA transcribed standards at concentration of equal or more than 10 copies/mL could be detected by TMA technology. Among 60 samples of plasma from HIV infected patients, 46 were positively detected and 12 were negatively amplified by both TMA and Cobas reagents; 2 samples were positively tested by Cobas reagent but negatively tested by TMA system. The concordance rate of the two methods was 97.1% and the difference of positive detection rate between the two methods was not statistically significant (P>0.05). Linear regression was used for 46 samples which were positively detected by both TMA and Cobas reagents and showed an excellent correlation between the two reagents (r=0.997, P<0.001). Bland-Altma analysis revealed that the mean different value of HIV RNA levels for denary logarithm was 0.02. Forty-four samples were included in 95% of credibility interval of concordance.
 Conclusion: TMA system has the potential of high sensitivity. TMA and real-time RT-PCR keep an excellent correlation and consistency in detecting HIV RNA.

Label-free turn-on fluorescent detection of melamine based on the anti-quenching ability of Hg 2+ to gold nanoclusters.

PubMed

Dai, Haichao; Shi, Yan; Wang, Yilin; Sun, Yujing; Hu, Jingting; Ni, Pengjuan; Li, Zhuang

2014-03-15

In this work, we proposed a facile, environmentally friendly and cost-effective assay for melamine with BSA-stabilized gold nanoclusters (AuNCs) as a fluorescence reader. Melamine, which has a multi-nitrogen heterocyclic ring, is prone to coordinate with Hg(2+). This property causes the anti-quenching ability of Hg(2+) to AuNCs through decreasing the metallophilic interaction between Hg(2+) and Au(+). By this method, detection limit down to 0.15 µM is obtained, which is approximately 130 times lower than that of the US food and Drug Administration estimated melamine safety limit of 20 µM. Furthermore, several real samples spiked with melamine, including raw milk and milk powder, are analyzed using the sensing system with excellent recoveries. This gold-nanocluster-based fluorescent method could find applications in highly sensitive detection of melamine in real samples. © 2013 Elsevier B.V. All rights reserved.

Manual control models of industrial management

NASA Technical Reports Server (NTRS)

Crossman, E. R. F. W.

1972-01-01

The industrial engineer is often required to design and implement control systems and organization for manufacturing and service facilities, to optimize quality, delivery, and yield, and minimize cost. Despite progress in computer science most such systems still employ human operators and managers as real-time control elements. Manual control theory should therefore be applicable to at least some aspects of industrial system design and operations. Formulation of adequate model structures is an essential prerequisite to progress in this area; since real-world production systems invariably include multilevel and multiloop control, and are implemented by timeshared human effort. A modular structure incorporating certain new types of functional element, has been developed. This forms the basis for analysis of an industrial process operation. In this case it appears that managerial controllers operate in a discrete predictive mode based on fast time modelling, with sampling interval related to plant dynamics. Successive aggregation causes reduced response bandwidth and hence increased sampling interval as a function of level.

Blood-Based Analyses of Cancer: Circulating Tumor Cells and Circulating Tumor DNA

PubMed Central

Haber, Daniel A.; Velculescu, Victor E.

2015-01-01

The ability to study nonhematologic cancers through noninvasive sampling of blood is one of the most exciting and rapidly advancing fields in cancer diagnostics. This has been driven both by major technologic advances, including the isolation of intact cancer cells and the analysis of cancer cell–derived DNA from blood samples, and by the increasing application of molecularly driven therapeutics, which rely on such accurate and timely measurements of critical biomarkers. Moreover, the dramatic efficacy of these potent cancer therapies drives the selection for additional genetic changes as tumors acquire drug resistance, necessitating repeated sampling of cancer cells to adjust therapy in response to tumor evolution. Together, these advanced noninvasive diagnostic capabilities and their applications in guiding precision cancer therapies are poised to change the ways in which we select and monitor cancer treatments. Significance Recent advances in technologies to analyze circulating tumor cells and circulating tumor DNA are setting the stage for real-time, noninvasive monitoring of cancer and providing novel insights into cancer evolution, invasion, and metastasis. PMID:24801577

DNA recognition by peptide nucleic acid-modified PCFs: from models to real samples

NASA Astrophysics Data System (ADS)

Selleri, S.; Coscelli, E.; Poli, F.; Passaro, D.; Cucinotta, A.; Lantano, C.; Corradini, R.; Marchelli, R.

2010-04-01

The increased concern, emerged in the last few years, on food products safety has stimulated the research on new techniques for traceability of raw food materials. DNA analysis is one of the most powerful tools for the certification of food quality, and it is presently performed through the polymerase chain reaction technique. Photonic crystal fibers, due to the presence of an array of air holes running along their length, can be exploited for performing DNA recognition by derivatizing hole surfaces and checking hybridization of complementary nucledotide chains in the sample. In this paper the application of a suspended core photonic crystal fiber in the recognition of DNA sequences is discussed. The fiber is characterized in terms of electromagnetic properties by means of a full-vector modal solver based on the finite element method. Then, the performances of the fiber in the recognition of mall synthetic oligonucleotides are discussed, together with a test of the possibility to extend this recognition to samples of DNA of applicative interest, such as olive leaves.

Trends in biochemical and biomedical applications of mass spectrometry

NASA Astrophysics Data System (ADS)

Gelpi, Emilio

1992-09-01

This review attempts an in-depth evaluation of progress and achievements made since the last 11th International Mass Spectrometry Conference in the application of mass spectrometric techniques to biochemistry and biomedicine. For this purpose, scientific contributions in this field at major international meetings have been monitored, together with an extensive appraisal of literature data covering the period from 1988 to 1991. A bibliometric evaluation of the MEDLINE database for this period provides a total of almost 4000 entries for mass spectrometry. This allows a detailed study of literature and geographical sources of the most frequent applications, of disciplines where mass spectrometry is most active and of types of sample and instrumentation most commonly used. In this regard major efforts according to number of publications (over 100 literature reports) are concentrated in countries like Canada, France, Germany, Italy, Japan, Sweden, UK and the USA. Also, most of the work using mass spectrometry in biochemistry and biomedicine is centred on studies on biotransformation, metabolism, pharmacology, pharmacokinetics and toxicology, which have been carried out on samples of blood, urine, plasma and tissue, by order of frequency of use. Human and animal studies appear to be evenly distributed in terms of the number of reports published in the literature in which the authors make use of experimental animals or describe work on human samples. Along these lines, special attention is given to the real usefulness of mass spectrometry (MS) technology in routine medical practice. Thus the review concentrates on evaluating the progress made in disease diagnosis and overall patient care. As regards prevailing techniques, GCMS continues to be the mainstay of the state of the art methods for multicomponent analysis, stable isotope tracer studies and metabolic profiling, while HPLC--MS and tandem MS are becoming increasingly important in biomedical research. However, despite the relatively large number of mass spectrometry reports in the biomedical sciences very few true routine applications are described, and recent technological innovations in instrumentation such as FABMS, electrospray, plasma or laser desorption have contributed relatively much more to structural biology, especially in biopolymer studies of macromolecules rather than to real life biomedical applications on patients and clinical problems.

A pipeline VLSI design of fast singular value decomposition processor for real-time EEG system based on on-line recursive independent component analysis.

PubMed

Huang, Kuan-Ju; Shih, Wei-Yeh; Chang, Jui Chung; Feng, Chih Wei; Fang, Wai-Chi

2013-01-01

This paper presents a pipeline VLSI design of fast singular value decomposition (SVD) processor for real-time electroencephalography (EEG) system based on on-line recursive independent component analysis (ORICA). Since SVD is used frequently in computations of the real-time EEG system, a low-latency and high-accuracy SVD processor is essential. During the EEG system process, the proposed SVD processor aims to solve the diagonal, inverse and inverse square root matrices of the target matrices in real time. Generally, SVD requires a huge amount of computation in hardware implementation. Therefore, this work proposes a novel design concept for data flow updating to assist the pipeline VLSI implementation. The SVD processor can greatly improve the feasibility of real-time EEG system applications such as brain computer interfaces (BCIs). The proposed architecture is implemented using TSMC 90 nm CMOS technology. The sample rate of EEG raw data adopts 128 Hz. The core size of the SVD processor is 580×580 um(2), and the speed of operation frequency is 20MHz. It consumes 0.774mW of power during the 8-channel EEG system per execution time.

Optical coherence tomography-current technology and applications in clinical and biomedical research.

PubMed

Marschall, Sebastian; Sander, Birgit; Mogensen, Mette; Jørgensen, Thomas M; Andersen, Peter E

2011-07-01

Optical coherence tomography (OCT) is a noninvasive imaging technique that provides real-time two- and three-dimensional images of scattering samples with micrometer resolution. By mapping the local reflectivity, OCT visualizes the morphology of the sample. In addition, functional properties such as birefringence, motion, or the distributions of certain substances can be detected with high spatial resolution. Its main field of application is biomedical imaging and diagnostics. In ophthalmology, OCT is accepted as a clinical standard for diagnosing and monitoring the treatment of a number of retinal diseases, and OCT is becoming an important instrument for clinical cardiology. New applications are emerging in various medical fields, such as early-stage cancer detection, surgical guidance, and the early diagnosis of musculoskeletal diseases. OCT has also proven its value as a tool for developmental biology. The number of companies involved in manufacturing OCT systems has increased substantially during the last few years (especially due to its success in opthalmology), and this technology can be expected to continue to spread into various fields of application.

The Next-Generation PCR-Based Quantification Method for Ambient Waters: Digital PCR.

PubMed

Cao, Yiping; Griffith, John F; Weisberg, Stephen B

2016-01-01

Real-time quantitative PCR (qPCR) is increasingly being used for ambient water monitoring, but development of digital polymerase chain reaction (digital PCR) has the potential to further advance the use of molecular techniques in such applications. Digital PCR refines qPCR by partitioning the sample into thousands to millions of miniature reactions that are examined individually for binary endpoint results, with DNA density calculated from the fraction of positives using Poisson statistics. This direct quantification removes the need for standard curves, eliminating the labor and materials associated with creating and running standards with each batch, and removing biases associated with standard variability and mismatching amplification efficiency between standards and samples. Confining reactions and binary endpoint measurements to small partitions also leads to other performance advantages, including reduced susceptibility to inhibition, increased repeatability and reproducibility, and increased capacity to measure multiple targets in one analysis. As such, digital PCR is well suited for ambient water monitoring applications and is particularly advantageous as molecular methods move toward autonomous field application.

Hyperspectral anomaly detection using Sony PlayStation 3

NASA Astrophysics Data System (ADS)

Rosario, Dalton; Romano, João; Sepulveda, Rene

2009-05-01

We present a proof-of-principle demonstration using Sony's IBM Cell processor-based PlayStation 3 (PS3) to run-in near real-time-a hyperspectral anomaly detection algorithm (HADA) on real hyperspectral (HS) long-wave infrared imagery. The PS3 console proved to be ideal for doing precisely the kind of heavy computational lifting HS based algorithms require, and the fact that it is a relatively open platform makes programming scientific applications feasible. The PS3 HADA is a unique parallel-random sampling based anomaly detection approach that does not require prior spectra of the clutter background. The PS3 HADA is designed to handle known underlying difficulties (e.g., target shape/scale uncertainties) often ignored in the development of autonomous anomaly detection algorithms. The effort is part of an ongoing cooperative contribution between the Army Research Laboratory and the Army's Armament, Research, Development and Engineering Center, which aims at demonstrating performance of innovative algorithmic approaches for applications requiring autonomous anomaly detection using passive sensors.

Design and application of a synthetic DNA standard for real-time PCR analysis of microbial communities in a biogas digester.

PubMed

May, T; Koch-Singenstreu, M; Ebling, J; Stantscheff, R; Müller, L; Jacobi, F; Polag, D; Keppler, F; König, H

2015-08-01

A synthetic DNA fragment containing primer binding sites for the quantification of ten different microbial groups was constructed and evaluated as a reliable enumeration standard for quantitative real-time PCR (qPCR) analyses. This approach has been exemplary verified for the quantification of several methanogenic orders and families in a series of samples drawn from a mesophilic biogas plant. Furthermore, the total amounts of bacteria as well as the number of sulfate-reducing and propionic acid bacteria as potential methanogenic interaction partners were successfully determined. The obtained results indicated a highly dynamic microbial community structure which was distinctly affected by the organic loading rate, the substrate selection, and the amount of free volatile fatty acids in the fermenter. Methanosarcinales was the most predominant methanogenic order during the 3 months of observation despite fluctuating process conditions. During all trials, the modified quantification standard indicated a maximum of reproducibility and efficiency, enabling this method to open up a wide range of novel application options.

MS-Based Analytical Techniques: Advances in Spray-Based Methods and EI-LC-MS Applications

PubMed Central

Medina, Isabel; Cappiello, Achille; Careri, Maria

2018-01-01

Mass spectrometry is the most powerful technique for the detection and identification of organic compounds. It can provide molecular weight information and a wealth of structural details that give a unique fingerprint for each analyte. Due to these characteristics, mass spectrometry-based analytical methods are showing an increasing interest in the scientific community, especially in food safety, environmental, and forensic investigation areas where the simultaneous detection of targeted and nontargeted compounds represents a key factor. In addition, safety risks can be identified at the early stage through online and real-time analytical methodologies. In this context, several efforts have been made to achieve analytical instrumentation able to perform real-time analysis in the native environment of samples and to generate highly informative spectra. This review article provides a survey of some instrumental innovations and their applications with particular attention to spray-based MS methods and food analysis issues. The survey will attempt to cover the state of the art from 2012 up to 2017. PMID:29850370

Micro-nano-bio acoustic system for the detection of foodborne pathogens in real samples.

PubMed

Papadakis, George; Murasova, Pavla; Hamiot, Audrey; Tsougeni, Katerina; Kaprou, Georgia; Eck, Michael; Rabus, David; Bilkova, Zuzana; Dupuy, Bruno; Jobst, Gerhard; Tserepi, Angeliki; Gogolides, Evangelos; Gizeli, Electra

2018-07-15

The fast and efficient detection of foodborne pathogens is a societal priority, given the large number of food-poisoning outbreaks, and a scientific and technological challenge, given the need to detect as little as 1 viable cell in 25 gr of food. Here, we present the first approach that achieves the above goal, thanks to the use of a micro/nano-technology and the detection capability of acoustic wave sensors. Starting from 1 Salmonella cell in 25 ml of milk, we employ immuno-magnetic beads to capture cells after only 3 h of pre-enrichment and subsequently demonstrate efficient DNA amplification using the Loop Mediated Isothermal Amplification method (LAMP) and acoustic detection in an integrated platform, within an additional ½ h. The demonstrated 4 h sample-to-analysis time comes as a huge improvement to the current need of few days to obtain the same result. In addition, the work presents the first reported Lab-on-Chip platform that comprises an acoustic device as the sensing element, exhibiting impressive analytical features, namely, an acoustic limit of detection of 2 cells/μl or 3 aM of the DNA target and ability to detect in a label-free manner dsDNA amplicons in impure samples. The use of food samples together with the incorporation of the necessary pre-enrichment step and ability for multiple analysis with an internal control, make the proposed methodology highly relevant to real-world applications. Moreover, the work suggests that acoustic wave devices can be used as an attractive alternative to electrochemical sensors in integrated platforms for applications in food safety and the point-of-care diagnostics. Copyright © 2018. Published by Elsevier B.V.

Validation and Application of a PCR Primer Set to Quantify Fungal Communities in the Soil Environment by Real-Time Quantitative PCR

PubMed Central

Chemidlin Prévost-Bouré, Nicolas; Christen, Richard; Dequiedt, Samuel; Mougel, Christophe; Lelièvre, Mélanie; Jolivet, Claudy; Shahbazkia, Hamid Reza; Guillou, Laure; Arrouays, Dominique; Ranjard, Lionel

2011-01-01

Fungi constitute an important group in soil biological diversity and functioning. However, characterization and knowledge of fungal communities is hampered because few primer sets are available to quantify fungal abundance by real-time quantitative PCR (real-time Q-PCR). The aim in this study was to quantify fungal abundance in soils by incorporating, into a real-time Q-PCR using the SYBRGreen® method, a primer set already used to study the genetic structure of soil fungal communities. To satisfy the real-time Q-PCR requirements to enhance the accuracy and reproducibility of the detection technique, this study focused on the 18S rRNA gene conserved regions. These regions are little affected by length polymorphism and may provide sufficiently small targets, a crucial criterion for enhancing accuracy and reproducibility of the detection technique. An in silico analysis of 33 primer sets targeting the 18S rRNA gene was performed to select the primer set with the best potential for real-time Q-PCR: short amplicon length; good fungal specificity and coverage. The best consensus between specificity, coverage and amplicon length among the 33 sets tested was the primer set FR1 / FF390. This in silico analysis of the specificity of FR1 / FF390 also provided additional information to the previously published analysis on this primer set. The specificity of the primer set FR1 / FF390 for Fungi was validated in vitro by cloning - sequencing the amplicons obtained from a real time Q-PCR assay performed on five independent soil samples. This assay was also used to evaluate the sensitivity and reproducibility of the method. Finally, fungal abundance in samples from 24 soils with contrasting physico-chemical and environmental characteristics was examined and ranked to determine the importance of soil texture, organic carbon content, C∶N ratio and land use in determining fungal abundance in soils. PMID:21931659

Assessment of real-time PCR method for detection of EGFR mutation using both supernatant and cell pellet of malignant pleural effusion samples from non-small-cell lung cancer patients.

PubMed

Shin, Saeam; Kim, Juwon; Kim, Yoonjung; Cho, Sun-Mi; Lee, Kyung-A

2017-10-26

EGFR mutation is an emerging biomarker for treatment selection in non-small-cell lung cancer (NSCLC) patients. However, optimal mutation detection is hindered by complications associated with the biopsy procedure, tumor heterogeneity and limited sensitivity of test methodology. In this study, we evaluated the diagnostic utility of real-time PCR using malignant pleural effusion samples. A total of 77 pleural fluid samples from 77 NSCLC patients were tested using the cobas EGFR mutation test (Roche Molecular Systems). Pleural fluid was centrifuged, and separated cell pellets and supernatants were tested in parallel. Results were compared with Sanger sequencing and/or peptide nucleic acid (PNA)-mediated PCR clamping of matched tumor tissue or pleural fluid samples. All samples showed valid real-time PCR results in one or more DNA samples extracted from cell pellets and supernatants. Compared with other molecular methods, the sensitivity of real-time PCR method was 100%. Concordance rate of real-time PCR and Sanger sequencing plus PNA-mediated PCR clamping was 98.7%. We have confirmed that real-time PCR using pleural fluid had a high concordance rate compared to conventional methods, with no failed samples. Our data demonstrated that the parallel real-time PCR testing using supernatant and cell pellet could offer reliable and robust surrogate strategy when tissue is not available.

Designing a Dynamic Data Driven Application System for Estimating Real-Time Load of DOC in a River

NASA Astrophysics Data System (ADS)

Ouyang, Y.; None

2011-12-01

Understanding the dynamics of naturally occurring dissolved organic carbon (DOC) in a river is central to estimating surface water quality, aquatic carbon cycling, and climate change. Currently, determination of DOC in surface water is primarily accomplished by manually collecting samples for laboratory analysis, which requires at least 24 hours. In other words, no effort has been devoted to monitoring real-time variations of DOC in a river due to the lack of suitable and/or cost-effective wireless sensors. However, when considering human health, carbon footprints, and effects of urbanization, industry, and agriculture on water resource supply, timely DOC information may be critical. We have developed here a new paradigm, a dynamic data driven application system (DDDAS), for estimating the real-time load of DOC into a river. This DDDAS consisted of the following four components: (1) a Visual Basic (VB) program for downloading US Geological Survey real-time chlorophyll and discharge data; (2) a STELLA model for evaluating real-time DOC load based on the relationship between chlorophyll a, DOC, and river discharge; (3) a batch file for linking the VB program and STELLA model; and (4) a Microsoft Windows Scheduled Tasks wizard for executing the model and displaying output on a computer screen at selected times. Results show that the real-time load of DOC into the St. Johns River basin near Satsuma, Putnam County, Florida, USA varied over a range from -13,143 to 29,248 kg/h at the selected site in Florida, USA. The negative loads occurred because of the back flow in the estuarine reach of the river. The cumulative load of DOC in the river for the selected site at the end of the simulation (178 hours) was about 1.2 tons. Our results support the utility of the DDDAS developed in this study for estimating the real-time variations of DOC in river ecosystems.

TaqMan based real time PCR assay targeting EML4-ALK fusion transcripts in NSCLC.

PubMed

Robesova, Blanka; Bajerova, Monika; Liskova, Kvetoslava; Skrickova, Jana; Tomiskova, Marcela; Pospisilova, Sarka; Mayer, Jiri; Dvorakova, Dana

2014-07-01

Lung cancer with the ALK rearrangement constitutes only a small fraction of patients with non-small cell lung cancer (NSCLC). However, in the era of molecular-targeted therapy, efficient patient selection is crucial for successful treatment. In this context, an effective method for EML4-ALK detection is necessary. We developed a new highly sensitive variant specific TaqMan based real time PCR assay applicable to RNA from formalin-fixed paraffin-embedded tissue (FFPE). This assay was used to analyze the EML4-ALK gene in 96 non-selected NSCLC specimens and compared with two other methods (end-point PCR and break-apart FISH). EML4-ALK was detected in 33/96 (34%) specimens using variant specific real time PCR, whereas in only 23/96 (24%) using end-point PCR. All real time PCR positive samples were confirmed with direct sequencing. A total of 46 specimens were subsequently analyzed by all three detection methods. Using variant specific real time PCR we identified EML4-ALK transcript in 17/46 (37%) specimens, using end-point PCR in 13/46 (28%) specimens and positive ALK rearrangement by FISH was detected in 8/46 (17.4%) specimens. Moreover, using variant specific real time PCR, 5 specimens showed more than one EML4-ALK variant simultaneously (in 2 cases the variants 1+3a+3b, in 2 specimens the variants 1+3a and in 1 specimen the variant 1+3b). In one case of 96 EML4-ALK fusion gene and EGFR mutation were detected. All simultaneous genetic variants were confirmed using end-point PCR and direct sequencing. Our variant specific real time PCR assay is highly sensitive, fast, financially acceptable, applicable to FFPE and seems to be a valuable tool for the rapid prescreening of NSCLC patients in clinical practice, so, that most patients able to benefit from targeted therapy could be identified. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Paris-Edinburgh cell applications at HPCAT

NASA Astrophysics Data System (ADS)

Park, Changyong; Shen, Guoyin; Wang, Yanbin

2011-06-01

A Paris-Edinburgh cell (model VX-3) has been installed at HPCAT 16BM-B, a bending magnet white X-ray beamline at the Advanced Photon Source. The PE anvil and the heater assembly are specifically designed to contain the sample volume ranging from 0.03 mm3 to >1.2 mm3 while the entire sample volume can be seen through X-ray windows widely open in radial direction. The pressure and temperature of sample can reach up to 7 GPa and 2,300 K, respectively. For diffraction experiment, the maximum momentum transfer, Q = 4 πsin(θ) / λ, can reach up to ~40 Å -1. A real-time white-beam radiography imaging system obtains the absorption contrast images of compressed sample with 7x magnification, 5 μm image resolutions, and update rate of 0.1 msec to 60 sec per frame. A table top channel-cut monochromator which can provide 30-90 keV monochromatic X-rays is also available for transmission measurement. These series of new instrumental developments are expected to widen the range of user sciences at HPCAT with new opportunities for in-situ measurement of real-time radiography, amorphous and liquid structure, ultrasound velocity, density, electrical resistivity and thermal conductivity. Work supported by DOE-NNSA, DOE-BES, and NSF-COMPRESS.

Mesoporous silica based MCM-41 as solid-phase extraction sorbent combined with micro-liquid chromatography-quadrupole-mass spectrometry for the analysis of pharmaceuticals in waters.

PubMed

Dahane, S; Martínez Galera, M; Marchionni, M E; Socías Viciana, M M; Derdour, A; Gil García, M D

2016-05-15

This paper reports the first application of the silica based mesoporous material MCM-41 as a sorbent in solid phase extraction, to pre-concentrate pharmaceuticals of very different polarity (atenolol, nadolol, pindolol, timolol, bisoprolol, metoprolol, betaxolol, ketoprofen, naproxen, ibuprofen, diclofenac, tolfenamic acid, flufenamic acid and meclofenamic acid) in surface waters. The analytes were extracted from 100mL water samples at pH 2.0 (containing 10(-3) mol/L of sodium chloride) by passing the solution through a cartridge filled with 100 mg of MCM-41. Following elution, the pharmaceuticals were determined by micro-liquid chromatography and triple quadrupole-mass spectrometry. Two selected reaction monitoring transitions were monitored per compound, the most intense one being used for quantification and the second one for confirmation. Matrix effect was found in real waters for most analytes and was overcome using the standard addition method, which compared favorably with the matrix matched calibration method. The detection limits in solvent (acetonitrile:water 10:90, v/v) ranged from 0.01 to 1.48 μg/L and in real water extracts from 0.10 to 3.85 μg/L (0.001-0.0385 μg/L in the water samples). The quantitation limits in solvent were in the range 0.02-4.93 μg/L, whereas in real water extracts were between 0.45 and 10.00 μg/L (0.0045 and 0.1000 μg/L in the water samples). When ultrapure water samples were spiked at two concentration levels of each pharmaceutical (0.1 and 0.2 μg/L) and quantified using solvent based calibration graphs, recoveries were near 100%. However, recoveries for most pharmaceuticals were comparable or better than de described above, when river water samples (spiked at the same concentration levels) were quantified by the standard addition method and slightly worse using the matrix matched calibration method. Five real samples (two rivers, one dam and two fountain water samples) were analyzed by the developed method, atenolol, timolol, betaxolol, nadolol and diclofenac being found in some of them, at levels higher than their quantitation limits. Copyright © 2016 Elsevier B.V. All rights reserved.

Investigation of the continuous flow of the sample solution on the performance of electromembrane extraction: Comparison with conventional procedure.

PubMed

Nojavan, Saeed; Sirani, Mahsa; Asadi, Sakine

2017-10-01

In this study, electromembrane extraction from a flowing sample solution, termed as continuous-flow electromembrane extraction, was developed and compared with conventional procedures for the determination of four basic drugs in real samples. Experimental parameters affecting the extraction efficiency were further studied and optimized. Under optimum conditions, linearity of continuous-flow procedure was within 8.0-500 ng/mL, while it was wider for conventional procedures (2.0-500 ng/mL). Moreover, repeatability (percentage relative standard deviation) was found to range between 5.6 and 10.4% (n = 3) for the continuous-flow procedure, with a better repeatability than that of conventional procedures (2.3-5.5% (n = 3)). Also, for the continuous-flow procedure, the estimated detection limit (signal-to-noise ratio = 3) was less than 2.4 ng/mL and extraction recoveries were within 8-10%, while the corresponding figures for conventional procedures were less than 0.6 ng/mL and 42-60%, respectively. Thus, the results showed that both continuous flow and conventional procedures were applicable for the extraction of model compounds. However, the conventional procedure was more convenient to use, and thus it was applied to determine sample drugs in real urine and wastewater samples. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Sensitive Quantification of Aflatoxin B1 in Animal Feeds, Corn Feed Grain, and Yellow Corn Meal Using Immunomagnetic Bead-Based Recovery and Real-Time Immunoquantitative-PCR

PubMed Central

Babu, Dinesh; Muriana, Peter M.

2014-01-01

Aflatoxins are considered unavoidable natural mycotoxins encountered in foods, animal feeds, and feed grains. In this study, we demonstrate the application of our recently developed real-time immunoquantitative PCR (RT iq-PCR) assay for sensitive detection and quantification of aflatoxins in poultry feed, two types of dairy feed (1 and 2), horse feed, whole kernel corn feed grains, and retail yellow ground corn meal. Upon testing methanol/water (60:40) extractions of the above samples using competitive direct enzyme linked immunosorbent assay, the aflatoxin content was found to be <20 μg/kg. The RT iq-PCR assay exhibited high antigen hook effect in samples containing aflatoxin levels higher than the quantification limits (0.1–10 μg/kg), addressed by comparing the quantification results of undiluted and diluted extracts. In testing the reliability of the immuno-PCR assay, samples were spiked with 200 μg/kg of aflatoxin B1, but the recovery of spiked aflatoxin was found to be poor. Considering the significance of determining trace levels of aflatoxins and their serious implications for animal and human health, the RT iq-PCR method described in this study can be useful for quantifying low natural aflatoxin levels in complex matrices of food or animal feed samples without the requirement of extra sample cleanup. PMID:25474493

Sensitive quantification of aflatoxin B1 in animal feeds, corn feed grain, and yellow corn meal using immunomagnetic bead-based recovery and real-time immunoquantitative-PCR.

PubMed

Babu, Dinesh; Muriana, Peter M

2014-12-02

Aflatoxins are considered unavoidable natural mycotoxins encountered in foods, animal feeds, and feed grains. In this study, we demonstrate the application of our recently developed real-time immunoquantitative PCR (RT iq-PCR) assay for sensitive detection and quantification of aflatoxins in poultry feed, two types of dairy feed (1 and 2), horse feed, whole kernel corn feed grains, and retail yellow ground corn meal. Upon testing methanol/water (60:40) extractions of the above samples using competitive direct enzyme linked immunosorbent assay, the aflatoxin content was found to be <20 μg/kg. The RT iq-PCR assay exhibited high antigen hook effect in samples containing aflatoxin levels higher than the quantification limits (0.1-10 μg/kg), addressed by comparing the quantification results of undiluted and diluted extracts. In testing the reliability of the immuno-PCR assay, samples were spiked with 200 μg/kg of aflatoxin B1, but the recovery of spiked aflatoxin was found to be poor. Considering the significance of determining trace levels of aflatoxins and their serious implications for animal and human health, the RT iq-PCR method described in this study can be useful for quantifying low natural aflatoxin levels in complex matrices of food or animal feed samples without the requirement of extra sample cleanup.

On-site identification of meat species in processed foods by a rapid real-time polymerase chain reaction system.

PubMed

Furutani, Shunsuke; Hagihara, Yoshihisa; Nagai, Hidenori

2017-09-01

Correct labeling of foods is critical for consumers who wish to avoid a specific meat species for religious or cultural reasons. Therefore, gene-based point-of-care food analysis by real-time Polymerase Chain Reaction (PCR) is expected to contribute to the quality control in the food industry. In this study, we perform rapid identification of meat species by our portable rapid real-time PCR system, following a very simple DNA extraction method. Applying these techniques, we correctly identified beef, pork, chicken, rabbit, horse, and mutton in processed foods in 20min. Our system was sensitive enough to detect the interfusion of about 0.1% chicken egg-derived DNA in a processed food sample. Our rapid real-time PCR system is expected to contribute to the quality control in food industries because it can be applied for the identification of meat species, and future applications can expand its functionality to the detection of genetically modified organisms or mutations. Copyright © 2017 Elsevier Ltd. All rights reserved.

A Critical Review on Clinical Application of Separation Techniques for Selective Recognition of Uracil and 5-Fluorouracil.

PubMed

Pandey, Khushaboo; Dubey, Rama Shankar; Prasad, Bhim Bali

2016-03-01

The most important objectives that are frequently found in bio-analytical chemistry involve applying tools to relevant medical/biological problems and refining these applications. Developing a reliable sample preparation step, for the medical and biological fields is another primary objective in analytical chemistry, in order to extract and isolate the analytes of interest from complex biological matrices. Since, main inborn errors of metabolism (IEM) diagnosable through uracil analysis and the therapeutic monitoring of toxic 5-fluoruracil (an important anti-cancerous drug) in dihydropyrimidine dehydrogenase deficient patients, require an ultra-sensitive, reproducible, selective, and accurate analytical techniques for their measurements. Therefore, keeping in view, the diagnostic value of uracil and 5-fluoruracil measurements, this article refines several analytical techniques involved in selective recognition and quantification of uracil and 5-fluoruracil from biological and pharmaceutical samples. The prospective study revealed that implementation of molecularly imprinted polymer as a solid-phase material for sample preparation and preconcentration of uracil and 5-fluoruracil had proven to be effective as it could obviates problems related to tedious separation techniques, owing to protein binding and drastic interferences, from the complex matrices in real samples such as blood plasma, serum samples.

Real-time specific surface area measurements via laser-induced breakdown spectroscopy

USGS Publications Warehouse

Washburn, Kathryn E.; Birdwell, Justin E.; Howard, James E.

2017-01-01

From healthcare to cosmetics to environmental science, the specific surface area (SSA) of micro- and mesoporous materials or products can greatly affect their chemical and physical properties. SSA results are also widely used to examine source rocks in conventional and unconventional petroleum resource plays. Despite its importance, current methods to measure SSA are often cumbersome, time-consuming, or require cryogenic consumables (e.g., liquid nitrogen). These methods are not amenable to high-throughput environments, have stringent sample preparation requirements, and are not practical for use in the field. We present a new application of laser-induced breakdown spectroscopy for rapid measurement of SSA. This study evaluates geological samples, specifically organic-rich oil shales, but the approach is expected to be applicable to many other types of materials. The method uses optical emission spectroscopy to examine laser-generated plasma and quantify the amount of argon adsorbed to a sample during an inert gas purge. The technique can accommodate a wide range of sample sizes and geometries and has the potential for field use. These advantages for SSA measurement combined with the simultaneous acquisition of composition information make this a promising new approach for characterizing geologic samples and other materials.

Zero-crossing sampling of Fourier-transform interferograms and spectrum reconstruction using the real-zero interpolation method.

PubMed

Minami, K; Kawata, S; Minami, S

1992-10-10

The real-zero interpolation method is applied to a Fourier-transformed infrared (FT-IR) interferogram. With this method an interferogram is reconstructed from its zero-crossing information only, without the use of a long-word analog-to-digital converter. We installed a phase-locked loop circuit into an FT-IR spectrometer for oversampling the interferogram. Infrared absorption spectra of polystyrene and Mylar films were measured as binary interferograms by the FT-IR spectrometer, which was equipped with the developed circuits, and their Fourier spectra were successfully reconstructed. The relationship of the oversampling ratio to the dynamic range of the reconstructed interferogram was evaluated through computer simulations. We also discuss the problems of this method for practical applications.

Weighted fusion of depth and inertial data to improve view invariance for real-time human action recognition

NASA Astrophysics Data System (ADS)

Chen, Chen; Hao, Huiyan; Jafari, Roozbeh; Kehtarnavaz, Nasser

2017-05-01

This paper presents an extension to our previously developed fusion framework [10] involving a depth camera and an inertial sensor in order to improve its view invariance aspect for real-time human action recognition applications. A computationally efficient view estimation based on skeleton joints is considered in order to select the most relevant depth training data when recognizing test samples. Two collaborative representation classifiers, one for depth features and one for inertial features, are appropriately weighted to generate a decision making probability. The experimental results applied to a multi-view human action dataset show that this weighted extension improves the recognition performance by about 5% over equally weighted fusion deployed in our previous fusion framework.

Utilization of biosensors and chemical sensors for space applications

NASA Technical Reports Server (NTRS)

Bonting, S. L.

1992-01-01

There will be a need for a wide array of chemical sensors for biomedical experimentation and for the monitoring of water and air recycling processes on Space Station Freedom. The infrequent logistics flights of the Space Shuttle will necessitate onboard analysis. The advantages of biosensors and chemical sensors over conventional analysis onboard spacecraft are manifold. They require less crew time, space, and power. Sample treatment is not needed. Real time or near-real time monitoring is possible, in some cases on a continuous basis. Sensor signals in digitized form can be transmitted to the ground. Types and requirements for chemical sensors to be used in biomedical experimentation and monitoring of water recycling during long-term space missions are discussed.

Sequentially Executed Model Evaluation Framework

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

2015-10-20

Provides a message passing framework between generic input, model and output drivers, and specifies an API for developing such drivers. Also provides batch and real-time controllers which step the model and I/O through the time domain (or other discrete domain), and sample I/O drivers. This is a library framework, and does not, itself, solve any problems or execute any modeling. The SeMe framework aids in development of models which operate on sequential information, such as time-series, where evaluation is based on prior results combined with new data for this iteration. Has applications in quality monitoring, and was developed as partmore » of the CANARY-EDS software, where real-time water quality data is being analyzed for anomalies.« less

Efficient Robust Regression via Two-Stage Generalized Empirical Likelihood

PubMed Central

Bondell, Howard D.; Stefanski, Leonard A.

2013-01-01

Large- and finite-sample efficiency and resistance to outliers are the key goals of robust statistics. Although often not simultaneously attainable, we develop and study a linear regression estimator that comes close. Efficiency obtains from the estimator’s close connection to generalized empirical likelihood, and its favorable robustness properties are obtained by constraining the associated sum of (weighted) squared residuals. We prove maximum attainable finite-sample replacement breakdown point, and full asymptotic efficiency for normal errors. Simulation evidence shows that compared to existing robust regression estimators, the new estimator has relatively high efficiency for small sample sizes, and comparable outlier resistance. The estimator is further illustrated and compared to existing methods via application to a real data set with purported outliers. PMID:23976805

A pilot study characterizing real time exposures to particulate matter and carbon monoxide from cookstove related woodsmoke in rural Peru

NASA Astrophysics Data System (ADS)

Commodore, Adwoa A.; Hartinger, Stella M.; Lanata, Claudio F.; Mäusezahl, Daniel; Gil, Ana I.; Hall, Daniel B.; Aguilar-Villalobos, Manuel; Naeher, Luke P.

2013-11-01

Nearly half of the world's population is exposed to household air pollution (HAP) due to long hours spent in close proximity to unvented cooking fires. We aimed to use PM2.5 and CO measurements to characterize exposure to cookstove generated woodsmoke in real time among control (n = 10) and intervention (n = 9) households in San Marcos, Cajamarca Region, Peru. Real time personal particulate matter with an aerodynamic diameter ≤2.5 μm (PM2.5), and personal and kitchen carbon monoxide (CO) samples were taken. Control households used a number of stoves including open fire and chimney stoves while intervention households used study-promoted chimney stoves. Measurements were categorized into lunch (9 am-1 pm) and dinner (3 pm-7 pm) periods, where applicable, to adjust for a wide range of sampling periods (2.8-13.1 h). During the 4-h time periods, mean personal PM2.5 exposures were correlated with personal CO exposures during lunch (r = 0.67 p = 0.024 n = 11) and dinner (r = 0.72 p = 0.0011 n = 17) in all study households. Personal PM2.5 exposures and kitchen CO concentrations were also correlated during lunch (r = 0.76 p = 0.018 n = 9) and dinner (r = 0.60 p = 0.018 n = 15). CO may be a useful indicator of PM during 4-h time scales measured in real time, particularly during high woodsmoke exposures, particularly during residential biomass cooking.

Embedded neural recording with TinyOS-based wireless-enabled processor modules.

PubMed

Farshchi, Shahin; Pesterev, Aleksey; Nuyujukian, Paul; Guenterberg, Eric; Mody, Istvan; Judy, Jack W

2010-04-01

To create a wireless neural recording system that can benefit from the continuous advancements being made in embedded microcontroller and communications technologies, an embedded-system-based architecture for wireless neural recording has been designed, fabricated, and tested. The system consists of commercial-off-the-shelf wireless-enabled processor modules (motes) for communicating the neural signals, and a back-end database server and client application for archiving and browsing the neural signals. A neural-signal-acquisition application has been developed to enable the mote to either acquire neural signals at a rate of 4000 12-bit samples per second, or detect and transmit spike heights and widths sampled at a rate of 16670 12-bit samples per second on a single channel. The motes acquire neural signals via a custom low-noise neural-signal amplifier with adjustable gain and high-pass corner frequency that has been designed, and fabricated in a 1.5-microm CMOS process. In addition to browsing acquired neural data, the client application enables the user to remotely toggle modes of operation (real-time or spike-only), as well as amplifier gain and high-pass corner frequency.

Differential Diagnosis of Malaria on Truelab Uno®, a Portable, Real-Time, MicroPCR Device for Point-Of-Care Applications.

PubMed

Nair, Chandrasekhar Bhaskaran; Manjula, Jagannath; Subramani, Pradeep Annamalai; Nagendrappa, Prakash B; Manoj, Mulakkapurath Narayanan; Malpani, Sukriti; Pullela, Phani Kumar; Subbarao, Pillarisetti Venkata; Ramamoorthy, Siva; Ghosh, Susanta K

2016-01-01

Sensitive and specific detection of malarial parasites is crucial in controlling the significant malaria burden in the developing world. Also important is being able to identify life threatening Plasmodium falciparum malaria quickly and accurately to reduce malaria related mortality. Existing methods such as microscopy and rapid diagnostic tests (RDTs) have major shortcomings. Here, we describe a new real-time PCR-based diagnostic test device at point-of-care service for resource-limited settings. Truenat® Malaria, a chip-based microPCR test, was developed by bigtec Labs, Bangalore, India, for differential identification of Plasmodium falciparum and Plasmodium vivax parasites. The Truenat Malaria tests runs on bigtec's Truelab Uno® microPCR device, a handheld, battery operated, and easy-to-use real-time microPCR device. The performance of Truenat® Malaria was evaluated versus the WHO nested PCR protocol. The Truenat® Malaria was further evaluated in a triple-blinded study design using a sample panel of 281 specimens created from the clinical samples characterized by expert microscopy and a rapid diagnostic test kit by the National Institute of Malaria Research (NIMR). A comparative evaluation was done on the Truelab Uno® and a commercial real-time PCR system. The limit of detection of the Truenat Malaria assay was found to be <5 parasites/μl for both P. falciparum and P. vivax. The Truenat® Malaria test was found to have sensitivity and specificity of 100% each, compared to the WHO nested PCR protocol based on the evaluation of 100 samples. The sensitivity using expert microscopy as the reference standard was determined to be around 99.3% (95% CI: 95.5-99.9) at the species level. Mixed infections were identified more accurately by Truenat Malaria (32 samples identified as mixed) versus expert microscopy and RDTs which detected 4 and 5 mixed samples, respectively. The Truenat® Malaria microPCR test is a valuable diagnostic tool and implementation should be considered not only for malaria diagnosis but also for active surveillance and epidemiological intervention.

Differential Diagnosis of Malaria on Truelab Uno®, a Portable, Real-Time, MicroPCR Device for Point-Of-Care Applications

PubMed Central

Nair, Chandrasekhar Bhaskaran; Manjula, Jagannath; Subramani, Pradeep Annamalai; Nagendrappa, Prakash B.; Manoj, Mulakkapurath Narayanan; Malpani, Sukriti; Pullela, Phani Kumar; Subbarao, Pillarisetti Venkata; Ramamoorthy, Siva; Ghosh, Susanta K.

2016-01-01

Background Sensitive and specific detection of malarial parasites is crucial in controlling the significant malaria burden in the developing world. Also important is being able to identify life threatening Plasmodium falciparum malaria quickly and accurately to reduce malaria related mortality. Existing methods such as microscopy and rapid diagnostic tests (RDTs) have major shortcomings. Here, we describe a new real-time PCR-based diagnostic test device at point-of-care service for resource-limited settings. Methods Truenat® Malaria, a chip-based microPCR test, was developed by bigtec Labs, Bangalore, India, for differential identification of Plasmodium falciparum and Plasmodium vivax parasites. The Truenat Malaria tests runs on bigtec’s Truelab Uno® microPCR device, a handheld, battery operated, and easy-to-use real-time microPCR device. The performance of Truenat® Malaria was evaluated versus the WHO nested PCR protocol. The Truenat® Malaria was further evaluated in a triple-blinded study design using a sample panel of 281 specimens created from the clinical samples characterized by expert microscopy and a rapid diagnostic test kit by the National Institute of Malaria Research (NIMR). A comparative evaluation was done on the Truelab Uno® and a commercial real-time PCR system. Results The limit of detection of the Truenat Malaria assay was found to be <5 parasites/μl for both P. falciparum and P. vivax. The Truenat® Malaria test was found to have sensitivity and specificity of 100% each, compared to the WHO nested PCR protocol based on the evaluation of 100 samples. The sensitivity using expert microscopy as the reference standard was determined to be around 99.3% (95% CI: 95.5–99.9) at the species level. Mixed infections were identified more accurately by Truenat Malaria (32 samples identified as mixed) versus expert microscopy and RDTs which detected 4 and 5 mixed samples, respectively. Conclusion The Truenat® Malaria microPCR test is a valuable diagnostic tool and implementation should be considered not only for malaria diagnosis but also for active surveillance and epidemiological intervention. PMID:26784111

Integrating machine learning techniques into robust data enrichment approach and its application to gene expression data.

PubMed

Erdoğdu, Utku; Tan, Mehmet; Alhajj, Reda; Polat, Faruk; Rokne, Jon; Demetrick, Douglas

2013-01-01

The availability of enough samples for effective analysis and knowledge discovery has been a challenge in the research community, especially in the area of gene expression data analysis. Thus, the approaches being developed for data analysis have mostly suffered from the lack of enough data to train and test the constructed models. We argue that the process of sample generation could be successfully automated by employing some sophisticated machine learning techniques. An automated sample generation framework could successfully complement the actual sample generation from real cases. This argument is validated in this paper by describing a framework that integrates multiple models (perspectives) for sample generation. We illustrate its applicability for producing new gene expression data samples, a highly demanding area that has not received attention. The three perspectives employed in the process are based on models that are not closely related. The independence eliminates the bias of having the produced approach covering only certain characteristics of the domain and leading to samples skewed towards one direction. The first model is based on the Probabilistic Boolean Network (PBN) representation of the gene regulatory network underlying the given gene expression data. The second model integrates Hierarchical Markov Model (HIMM) and the third model employs a genetic algorithm in the process. Each model learns as much as possible characteristics of the domain being analysed and tries to incorporate the learned characteristics in generating new samples. In other words, the models base their analysis on domain knowledge implicitly present in the data itself. The developed framework has been extensively tested by checking how the new samples complement the original samples. The produced results are very promising in showing the effectiveness, usefulness and applicability of the proposed multi-model framework.

Incorporation of support vector machines in the LIBS toolbox for sensitive and robust classification amidst unexpected sample and system variability

PubMed Central

ChariDingari, Narahara; Barman, Ishan; Myakalwar, Ashwin Kumar; Tewari, Surya P.; Kumar, G. Manoj

2012-01-01

Despite the intrinsic elemental analysis capability and lack of sample preparation requirements, laser-induced breakdown spectroscopy (LIBS) has not been extensively used for real world applications, e.g. quality assurance and process monitoring. Specifically, variability in sample, system and experimental parameters in LIBS studies present a substantive hurdle for robust classification, even when standard multivariate chemometric techniques are used for analysis. Considering pharmaceutical sample investigation as an example, we propose the use of support vector machines (SVM) as a non-linear classification method over conventional linear techniques such as soft independent modeling of class analogy (SIMCA) and partial least-squares discriminant analysis (PLS-DA) for discrimination based on LIBS measurements. Using over-the-counter pharmaceutical samples, we demonstrate that application of SVM enables statistically significant improvements in prospective classification accuracy (sensitivity), due to its ability to address variability in LIBS sample ablation and plasma self-absorption behavior. Furthermore, our results reveal that SVM provides nearly 10% improvement in correct allocation rate and a concomitant reduction in misclassification rates of 75% (cf. PLS-DA) and 80% (cf. SIMCA)-when measurements from samples not included in the training set are incorporated in the test data – highlighting its robustness. While further studies on a wider matrix of sample types performed using different LIBS systems is needed to fully characterize the capability of SVM to provide superior predictions, we anticipate that the improved sensitivity and robustness observed here will facilitate application of the proposed LIBS-SVM toolbox for screening drugs and detecting counterfeit samples as well as in related areas of forensic and biological sample analysis. PMID:22292496

Incorporation of support vector machines in the LIBS toolbox for sensitive and robust classification amidst unexpected sample and system variability.

PubMed

Dingari, Narahara Chari; Barman, Ishan; Myakalwar, Ashwin Kumar; Tewari, Surya P; Kumar Gundawar, Manoj

2012-03-20

Despite the intrinsic elemental analysis capability and lack of sample preparation requirements, laser-induced breakdown spectroscopy (LIBS) has not been extensively used for real-world applications, e.g., quality assurance and process monitoring. Specifically, variability in sample, system, and experimental parameters in LIBS studies present a substantive hurdle for robust classification, even when standard multivariate chemometric techniques are used for analysis. Considering pharmaceutical sample investigation as an example, we propose the use of support vector machines (SVM) as a nonlinear classification method over conventional linear techniques such as soft independent modeling of class analogy (SIMCA) and partial least-squares discriminant analysis (PLS-DA) for discrimination based on LIBS measurements. Using over-the-counter pharmaceutical samples, we demonstrate that the application of SVM enables statistically significant improvements in prospective classification accuracy (sensitivity), because of its ability to address variability in LIBS sample ablation and plasma self-absorption behavior. Furthermore, our results reveal that SVM provides nearly 10% improvement in correct allocation rate and a concomitant reduction in misclassification rates of 75% (cf. PLS-DA) and 80% (cf. SIMCA)-when measurements from samples not included in the training set are incorporated in the test data-highlighting its robustness. While further studies on a wider matrix of sample types performed using different LIBS systems is needed to fully characterize the capability of SVM to provide superior predictions, we anticipate that the improved sensitivity and robustness observed here will facilitate application of the proposed LIBS-SVM toolbox for screening drugs and detecting counterfeit samples, as well as in related areas of forensic and biological sample analysis.

Real-time support for high performance aircraft operation

NASA Technical Reports Server (NTRS)

Vidal, Jacques J.

1989-01-01

The feasibility of real-time processing schemes using artificial neural networks (ANNs) is investigated. A rationale for digital neural nets is presented and a general processor architecture for control applications is illustrated. Research results on ANN structures for real-time applications are given. Research results on ANN algorithms for real-time control are also shown.

A Java program for LRE-based real-time qPCR that enables large-scale absolute quantification.

PubMed

Rutledge, Robert G

2011-03-02

Linear regression of efficiency (LRE) introduced a new paradigm for real-time qPCR that enables large-scale absolute quantification by eliminating the need for standard curves. Developed through the application of sigmoidal mathematics to SYBR Green I-based assays, target quantity is derived directly from fluorescence readings within the central region of an amplification profile. However, a major challenge of implementing LRE quantification is the labor intensive nature of the analysis. Utilizing the extensive resources that are available for developing Java-based software, the LRE Analyzer was written using the NetBeans IDE, and is built on top of the modular architecture and windowing system provided by the NetBeans Platform. This fully featured desktop application determines the number of target molecules within a sample with little or no intervention by the user, in addition to providing extensive database capabilities. MS Excel is used to import data, allowing LRE quantification to be conducted with any real-time PCR instrument that provides access to the raw fluorescence readings. An extensive help set also provides an in-depth introduction to LRE, in addition to guidelines on how to implement LRE quantification. The LRE Analyzer provides the automated analysis and data storage capabilities required by large-scale qPCR projects wanting to exploit the many advantages of absolute quantification. Foremost is the universal perspective afforded by absolute quantification, which among other attributes, provides the ability to directly compare quantitative data produced by different assays and/or instruments. Furthermore, absolute quantification has important implications for gene expression profiling in that it provides the foundation for comparing transcript quantities produced by any gene with any other gene, within and between samples.

Optofluidic bioimaging platform for quantitative phase imaging of lab on a chip devices using digital holographic microscopy.

PubMed

Pandiyan, Vimal Prabhu; John, Renu

2016-01-20

We propose a versatile 3D phase-imaging microscope platform for real-time imaging of optomicrofluidic devices based on the principle of digital holographic microscopy (DHM). Lab-on-chip microfluidic devices fabricated on transparent polydimethylsiloxane (PDMS) and glass substrates have attained wide popularity in biological sensing applications. However, monitoring, visualization, and characterization of microfluidic devices, microfluidic flows, and the biochemical kinetics happening in these devices is difficult due to the lack of proper techniques for real-time imaging and analysis. The traditional bright-field microscopic techniques fail in imaging applications, as the microfluidic channels and the fluids carrying biological samples are transparent and not visible in bright light. Phase-based microscopy techniques that can image the phase of the microfluidic channel and changes in refractive indices due to the fluids and biological samples present in the channel are ideal for imaging the fluid flow dynamics in a microfluidic channel at high resolutions. This paper demonstrates three-dimensional imaging of a microfluidic device with nanometric depth precisions and high SNR. We demonstrate imaging of microelectrodes of nanometric thickness patterned on glass substrate and the microfluidic channel. Three-dimensional imaging of a transparent PDMS optomicrofluidic channel, fluid flow, and live yeast cell flow in this channel has been demonstrated using DHM. We also quantify the average velocity of fluid flow through the channel. In comparison to any conventional bright-field microscope, the 3D depth information in the images illustrated in this work carry much information about the biological system under observation. The results demonstrated in this paper prove the high potential of DHM in imaging optofluidic devices; detection of pathogens, cells, and bioanalytes on lab-on-chip devices; and in studying microfluidic dynamics in real time based on phase changes.

A Java Program for LRE-Based Real-Time qPCR that Enables Large-Scale Absolute Quantification

PubMed Central

Rutledge, Robert G.

2011-01-01

Background Linear regression of efficiency (LRE) introduced a new paradigm for real-time qPCR that enables large-scale absolute quantification by eliminating the need for standard curves. Developed through the application of sigmoidal mathematics to SYBR Green I-based assays, target quantity is derived directly from fluorescence readings within the central region of an amplification profile. However, a major challenge of implementing LRE quantification is the labor intensive nature of the analysis. Findings Utilizing the extensive resources that are available for developing Java-based software, the LRE Analyzer was written using the NetBeans IDE, and is built on top of the modular architecture and windowing system provided by the NetBeans Platform. This fully featured desktop application determines the number of target molecules within a sample with little or no intervention by the user, in addition to providing extensive database capabilities. MS Excel is used to import data, allowing LRE quantification to be conducted with any real-time PCR instrument that provides access to the raw fluorescence readings. An extensive help set also provides an in-depth introduction to LRE, in addition to guidelines on how to implement LRE quantification. Conclusions The LRE Analyzer provides the automated analysis and data storage capabilities required by large-scale qPCR projects wanting to exploit the many advantages of absolute quantification. Foremost is the universal perspective afforded by absolute quantification, which among other attributes, provides the ability to directly compare quantitative data produced by different assays and/or instruments. Furthermore, absolute quantification has important implications for gene expression profiling in that it provides the foundation for comparing transcript quantities produced by any gene with any other gene, within and between samples. PMID:21407812

A Method for Estimating View Transformations from Image Correspondences Based on the Harmony Search Algorithm.

PubMed

Cuevas, Erik; Díaz, Margarita

2015-01-01

In this paper, a new method for robustly estimating multiple view relations from point correspondences is presented. The approach combines the popular random sampling consensus (RANSAC) algorithm and the evolutionary method harmony search (HS). With this combination, the proposed method adopts a different sampling strategy than RANSAC to generate putative solutions. Under the new mechanism, at each iteration, new candidate solutions are built taking into account the quality of the models generated by previous candidate solutions, rather than purely random as it is the case of RANSAC. The rules for the generation of candidate solutions (samples) are motivated by the improvisation process that occurs when a musician searches for a better state of harmony. As a result, the proposed approach can substantially reduce the number of iterations still preserving the robust capabilities of RANSAC. The method is generic and its use is illustrated by the estimation of homographies, considering synthetic and real images. Additionally, in order to demonstrate the performance of the proposed approach within a real engineering application, it is employed to solve the problem of position estimation in a humanoid robot. Experimental results validate the efficiency of the proposed method in terms of accuracy, speed, and robustness.

An improved RT-IPCR for detection of pyrene and related polycyclic aromatic hydrocarbons.

PubMed

Meng, X Y; Li, Y S; Zhou, Y; Sun, Y; Qiao, B; Si, C C; Hu, P; Lu, S Y; Ren, H L; Liu, Z S; Qiu, H J; Liu, J Q

2016-04-15

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous homogeneous chemicals which are well known by carcinogens, mutagens and endocrine disorder. Here, an improved real-time immuno-PCR (RT-IPCR) was developed for detection of pyrene and its homologs in water samples. The PAHs in sample compete with pyrene-modified DNA to bind with monoclonal antibody (McAb) coated on PCR plate. The reporter DNA was exponentially amplified by real-time PCR instrument using Fast Start universal SYBR Green Master (ROX) kit. Only two reaction steps were needed to accomplish the detection. The assay had a good linear range from 5 pmol L(-1) to 5 nmol L(-1) with a detection limit of 3.5 pmol L(-1). For application assay, the average recoveries from tap water, lake water and mineral water were 98.4%, 98.2% and 99.7%, respectively which showed a good correlation (R(2)=0.9906) with those from GC-MS. The results indicated that the improved RT-IPCR seems to be a potential method for simple and ultrasensitive detection of pyrene and some homologues in environment water samples. Copyright © 2015 Elsevier B.V. All rights reserved.

Rapid detection of HLA-B*51 by real-time polymerase chain reaction and high-resolution melting analysis.

PubMed

Imperiali, C; Alía-Ramos, P; Padró-Miquel, A

2015-08-01

HLA-B*51, a class I human leukocyte antigen (HLA) molecule, is the strongest known genetic risk factor for Behçet disease. However, there are only few articles reporting methods to determine the presence or absence of HLA-B51. For this reason, we designed and developed an easy, fast, and inexpensive real-time high-resolution melting (HRM) assay to detect HLA-B*51. We genotyped 61 samples by our HRM assay and by conventional polymerase chain reaction, and no discrepancies were found between results. Besides, a subgroup of 25 samples was also genotyped in a different laboratory, and another subgroup of 16 samples was obtained from the International Histocompatibility Working Group DNA Bank, and a full concordance of results was observed with those obtained by HRM. Regarding the identifying system evaluated, we obtained 100% of specificity, sensibility, and repeatability, and 0% of false positive and false negative rates. Therefore, this HRM analysis is easily applicable to the rapid detection of HLA-B*51, exhibits a high speed, and requires a very low budget. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Fast, Safe, Propellant-Efficient Spacecraft Motion Planning Under Clohessy-Wiltshire-Hill Dynamics

NASA Technical Reports Server (NTRS)

Starek, Joseph A.; Schmerling, Edward; Maher, Gabriel D.; Barbee, Brent W.; Pavone, Marco

2016-01-01

This paper presents a sampling-based motion planning algorithm for real-time and propellant-optimized autonomous spacecraft trajectory generation in near-circular orbits. Specifically, this paper leverages recent algorithmic advances in the field of robot motion planning to the problem of impulsively actuated, propellant- optimized rendezvous and proximity operations under the Clohessy-Wiltshire-Hill dynamics model. The approach calls upon a modified version of the FMT* algorithm to grow a set of feasible trajectories over a deterministic, low-dispersion set of sample points covering the free state space. To enforce safety, the tree is only grown over the subset of actively safe samples, from which there exists a feasible one-burn collision-avoidance maneuver that can safely circularize the spacecraft orbit along its coasting arc under a given set of potential thruster failures. Key features of the proposed algorithm include 1) theoretical guarantees in terms of trajectory safety and performance, 2) amenability to real-time implementation, and 3) generality, in the sense that a large class of constraints can be handled directly. As a result, the proposed algorithm offers the potential for widespread application, ranging from on-orbit satellite servicing to orbital debris removal and autonomous inspection missions.

Comparative research of effectiveness of cellulose and fiberglass porous membrane carriers for bio sampling in veterinary and food industry monitoring

NASA Astrophysics Data System (ADS)

Gusev, Alexander; Vasyukova, Inna; Zakharova, Olga; Altabaeva, Yuliya; Saushkin, Nikolai; Samsonova, Jeanne; Kondakov, Sergey; Osipov, Alexander; Snegin, Eduard

2017-11-01

The aim of proposed research is to study the applicability of fiberglass porous membrane materials in a new strip format for dried blood storage in food industry monitoring. A comparative analysis of cellulosic and fiberglass porous membrane materials was carried out to obtain dried samples of serum or blood and the possibility of further species-specific analysis. Blood samples of Sus scrofa were used to study the comparative effectiveness of cellulose and fiberglass porous membrane carriers for long-term biomaterial storage allowing for further DNA detection by real-time polymerase chain reaction (PCR) method. Scanning electron microscopy of various membranes - native and with blood samples - indicate a fundamental difference in the form of dried samples. Membranes based on cellulosic materials sorb the components of the biological fluid on the surface of the fibers of their structure, partially penetrating the cellulose fibers, while in the case of glass fiber membranes the components of the biological fluid dry out as films in the pores of the membrane between the structural filaments. This fundamental difference in the retention mechanisms affects the rate of dissolution of the components of dry samples and contributes to an increase in the efficiency of the desorption process of the sample before subsequent analysis. Detecting of pig DNA in every analyzed sample under the performed Real-time PCR as well as good state of the biomaterial preservation on the glass fiber membranes was clearly demonstrated. Good biomaterials preservation has been revealed on the test cards for 4 days as well as for 1 hour.

Digital micromirror devices: principles and applications in imaging.

PubMed

Bansal, Vivek; Saggau, Peter

2013-05-01

A digital micromirror device (DMD) is an array of individually switchable mirrors that can be used in many advanced optical systems as a rapid spatial light modulator. With a DMD, several implementations of confocal microscopy, hyperspectral imaging, and fluorescence lifetime imaging can be realized. The DMD can also be used as a real-time optical processor for applications such as the programmable array microscope and compressive sensing. Advantages and disadvantages of the DMD for these applications as well as methods to overcome some of the limitations will be discussed in this article. Practical considerations when designing with the DMD and sample optical layouts of a completely DMD-based imaging system and one in which acousto-optic deflectors (AODs) are used in the illumination pathway are also provided.

34 CFR 12.7 - How is surplus Federal real property disposed of when there is more than one applicant?

Code of Federal Regulations, 2010 CFR

2010-07-01

... Education DISPOSAL AND UTILIZATION OF SURPLUS FEDERAL REAL PROPERTY FOR EDUCATIONAL PURPOSES Distribution of...'s proposed educational use at the site of the surplus Federal real property; (2) Considering the quality of each applicant's proposed program and plan of use; and (3) Considering each applicant's ability...

Differentially Private Histogram Publication For Dynamic Datasets: An Adaptive Sampling Approach

PubMed Central

Li, Haoran; Jiang, Xiaoqian; Xiong, Li; Liu, Jinfei

2016-01-01

Differential privacy has recently become a de facto standard for private statistical data release. Many algorithms have been proposed to generate differentially private histograms or synthetic data. However, most of them focus on “one-time” release of a static dataset and do not adequately address the increasing need of releasing series of dynamic datasets in real time. A straightforward application of existing histogram methods on each snapshot of such dynamic datasets will incur high accumulated error due to the composibility of differential privacy and correlations or overlapping users between the snapshots. In this paper, we address the problem of releasing series of dynamic datasets in real time with differential privacy, using a novel adaptive distance-based sampling approach. Our first method, DSFT, uses a fixed distance threshold and releases a differentially private histogram only when the current snapshot is sufficiently different from the previous one, i.e., with a distance greater than a predefined threshold. Our second method, DSAT, further improves DSFT and uses a dynamic threshold adaptively adjusted by a feedback control mechanism to capture the data dynamics. Extensive experiments on real and synthetic datasets demonstrate that our approach achieves better utility than baseline methods and existing state-of-the-art methods. PMID:26973795

Micromagnetic Cancer Cell Immobilization and Release for Real-Time Single Cell Analysis

NASA Astrophysics Data System (ADS)

Jaiswal, Devina; Rad, Armin Tahmasbi; Nieh, Mu-Ping; Claffey, Kevin P.; Hoshino, Kazunori

2017-04-01

Understanding the interaction of live cells with macromolecules is crucial for designing efficient therapies. Considering the functional heterogeneity found in cancer cells, real-time single cell analysis is necessary to characterize responses. In this study, we have designed and fabricated a microfluidic channel with patterned micromagnets which can temporarily immobilize the cells during analysis and release them after measurements. The microchannel is composed of plain coverslip top and bottom panels to facilitate easy microscopic observation and undisturbed application of analytes to the cells. Cells labeled with functionalized magnetic beads were immobilized in the device with an efficiency of 90.8±3.6%. Since the micromagnets are made of soft magnetic material (Ni), they released cells when external magnetic field was turned off from the channel. This allows the reuse of the channel for a new sample. As a model drug analysis, the immobilized breast cancer cells (MCF7) were exposed to fluorescent lipid nanoparticles and association and dissociation were measured through fluorescence analysis. Two concentrations of nanoparticles, 0.06 μg/ml and 0.08 μg/ml were tested and time lapse images were recorded and analyzed. The microfluidic device was able to provide a microenvironment for sample analysis, making it an efficient platform for real-time analysis.

Wireless in-situ Sensor Network for Agriculture and Water Monitoring on a River Basin Scale in Southern Finland: Evaluation from a Data User’s Perspective

PubMed Central

Kotamäki, Niina; Thessler, Sirpa; Koskiaho, Jari; Hannukkala, Asko O.; Huitu, Hanna; Huttula, Timo; Havento, Jukka; Järvenpää, Markku

2009-01-01

Sensor networks are increasingly being implemented for environmental monitoring and agriculture to provide spatially accurate and continuous environmental information and (near) real-time applications. These networks provide a large amount of data which poses challenges for ensuring data quality and extracting relevant information. In the present paper we describe a river basin scale wireless sensor network for agriculture and water monitoring. The network, called SoilWeather, is unique and the first of this type in Finland. The performance of the network is assessed from the user and maintainer perspectives, concentrating on data quality, network maintenance and applications. The results showed that the SoilWeather network has been functioning in a relatively reliable way, but also that the maintenance and data quality assurance by automatic algorithms and calibration samples requires a lot of effort, especially in continuous water monitoring over large areas. We see great benefits on sensor networks enabling continuous, real-time monitoring, while data quality control and maintenance efforts highlight the need for tight collaboration between sensor and sensor network owners to decrease costs and increase the quality of the sensor data in large scale applications. PMID:22574050

Ultrasonic Phased Array Compressive Imaging in Time and Frequency Domain: Simulation, Experimental Verification and Real Application

PubMed Central

Bai, Zhiliang; Chen, Shili; Jia, Lecheng; Zeng, Zhoumo

2018-01-01

Embracing the fact that one can recover certain signals and images from far fewer measurements than traditional methods use, compressive sensing (CS) provides solutions to huge amounts of data collection in phased array-based material characterization. This article describes how a CS framework can be utilized to effectively compress ultrasonic phased array images in time and frequency domains. By projecting the image onto its Discrete Cosine transform domain, a novel scheme was implemented to verify the potentiality of CS for data reduction, as well as to explore its reconstruction accuracy. The results from CIVA simulations indicate that both time and frequency domain CS can accurately reconstruct array images using samples less than the minimum requirements of the Nyquist theorem. For experimental verification of three types of artificial flaws, although a considerable data reduction can be achieved with defects clearly preserved, it is currently impossible to break Nyquist limitation in the time domain. Fortunately, qualified recovery in the frequency domain makes it happen, meaning a real breakthrough for phased array image reconstruction. As a case study, the proposed CS procedure is applied to the inspection of an engine cylinder cavity containing different pit defects and the results show that orthogonal matching pursuit (OMP)-based CS guarantees the performance for real application. PMID:29738452

A study of internet of things real-time data updating based on WebSocket

NASA Astrophysics Data System (ADS)

Wei, Shoulin; Yu, Konglin; Dai, Wei; Liang, Bo; Zhang, Xiaoli

2015-12-01

The Internet of Things (IoT) is gradually entering the industrial stage. Web applications in IoT such as monitoring, instant messaging, real-time quote system changes need to be transmitted in real-time mode to client without client constantly refreshing and sending the request. These applications often need to be as fast as possible and provide nearly real-time components. Real-time data updating is becoming the core part of application layer visualization technology in IoT. With support of data push in server-side, running state of "Things" in IoT could be displayed in real-time mode. This paper discusses several current real-time data updating method and explores the advantages and disadvantages of each method. We explore the use of WebSocket in a new approach for real-time data updating in IoT, since WebSocket provides low delay, low network throughput solutions for full-duplex communication.

Searching for the best real-time RT-PCRs to detect Zika virus infections: the importance of comparing several protocols.

PubMed

de Moraes, F M; Espósito, D L A; Klein, T M; da Fonseca, B A L

2018-01-01

Clinical manifestations of Zika, dengue, and chikungunya virus infections are very similar, making it difficult to reach a diagnosis based only on clinical grounds. In addition, there is an intense cross-reactivity between antibodies directed to Zika virus and other flaviviruses, and an accurate Zika diagnosis is best achieved by real-time RT-PCR. However, some real-time RT-PCR show better performance than others. To reach the best possible Zika diagnosis, the analytic sensitivity of some probe-based real-time RT-PCR amplifying Zika virus RNA was evaluated in spiked and clinical samples. We evaluated primers and probes to detect Zika virus, which had been published before, and tested sensitivity using serum spiked and patient samples by real-time RT-PCR. When tested against spiked samples, the previously described primers showed different sensitivity, with very similar results when samples from patients (serum and urine) were analyzed. Real-time RT-PCR designed to amplify Zika virus NS1 showed the best analytical sensitivity for all samples.

Simultaneous multi-beam planar array IR (pair) spectroscopy

DOEpatents

Elmore, Douglas L.; Rabolt, John F.; Tsao, Mei-Wei

2005-09-13

An apparatus and method capable of providing spatially multiplexed IR spectral information simultaneously in real-time for multiple samples or multiple spatial areas of one sample using IR absorption phenomena requires no moving parts or Fourier Transform during operation, and self-compensates for background spectra and degradation of component performance over time. IR spectral information and chemical analysis of the samples is determined by using one or more IR sources, sampling accessories for positioning the samples, optically dispersive elements, a focal plane array (FPA) arranged to detect the dispersed light beams, and a processor and display to control the FPA, and display an IR spectrograph. Fiber-optic coupling can be used to allow remote sensing. Portability, reliability, and ruggedness is enhanced due to the no-moving part construction. Applications include determining time-resolved orientation and characteristics of materials, including polymer monolayers. Orthogonal polarizers may be used to determine certain material characteristics.

A new real-time PCR protocol for detection of avian haemosporidians.

PubMed

Bell, Jeffrey A; Weckstein, Jason D; Fecchio, Alan; Tkach, Vasyl V

2015-07-19

Birds possess the most diverse assemblage of haemosporidian parasites; including three genera, Plasmodium, Haemoproteus, and Leucocytozoon. Currently there are over 200 morphologically identified avian haemosporidian species, although true species richness is unknown due to great genetic diversity and insufficient sampling in highly diverse regions. Studies aimed at surveying haemosporidian diversity involve collecting and screening samples from hundreds to thousands of individuals. Currently, screening relies on microscopy and/or single or nested standard PCR. Although effective, these methods are time and resource consuming, and in the case of microscopy require substantial expertise. Here we report a newly developed real-time PCR protocol designed to quickly and reliably detect all three genera of avian haemosporidians in a single biochemical reaction. Using available DNA sequences from avian haemosporidians we designed primers R330F and R480RL, which flank a 182 base pair fragment of mitochondrial conserved rDNA. These primers were initially tested using real-time PCR on samples from Malawi, Africa, previously screened for avian haemosporidians using traditional nested PCR. Our real time protocol was further tested on 94 samples from the Cerrado biome of Brazil, previously screened using a single PCR assay for haemosporidian parasites. These samples were also amplified using modified nested PCR protocols, allowing for comparisons between the three different screening methods (single PCR, nested PCR, real-time PCR). The real-time PCR protocol successfully identified all three genera of avian haemosporidians from both single and mixed infections previously detected from Malawi. There was no significant difference between the three different screening protocols used for the 94 samples from the Brazilian Cerrado (χ(2) = 0.3429, df = 2, P = 0.842). After proving effective, the real-time protocol was used to screen 2113 Brazilian samples, identifying 693 positive samples. Our real-time PCR assay proved as effective as two widely used molecular screening techniques, single PCR and nested PCR. However, the real-time protocol has the distinct advantage of detecting all three genera in a single reaction, which significantly increases efficiency by greatly decreasing screening time and cost. Our real-time PCR protocol is therefore a valuable tool in the quickly expanding field of avian haemosporidian research.

Development of an updated PCR assay for detection of African swine fever virus.

PubMed

Luo, Yuzi; Atim, Stella A; Shao, Lina; Ayebazibwe, Chrisostom; Sun, Yuan; Liu, Yan; Ji, Shengwei; Meng, Xing-Yu; Li, Su; Li, Yongfeng; Masembe, Charles; Ståhl, Karl; Widén, Frederik; Liu, Lihong; Qiu, Hua-Ji

2017-01-01

Due to the current unavailability of vaccines or treatments for African swine fever (ASF), which is caused by African swine fever virus (ASFV), rapid and reliable detection of the virus is essential for timely implementation of emergency control measures and differentiation of ASF from other swine diseases with similar clinical presentations. Here, an improved PCR assay was developed and evaluated for sensitive and universal detection of ASFV. Primers specific for ASFV were designed based on the highly conserved region of the vp72 gene sequences of all ASFV strains available in GenBank, and the PCR assay was established and compared with two OIE-validated PCR tests. The analytic detection limit of the PCR assay was 60 DNA copies per reaction. No amplification signal was observed for several other porcine viruses. The novel PCR assay was more sensitive than two OIE-validated PCR assays when testing 14 strains of ASFV representing four genotypes (I, V, VIII and IX) from diverse geographical areas. A total of 62 clinical swine blood samples collected from Uganda were examined by the novel PCR, giving a high agreement (59/62) with a superior sensitive universal probe library-based real-time PCR. Eight out of 62 samples tested positive, and three samples with higher Ct values (39.15, 38.39 and 37.41) in the real-time PCR were negative for ASFV in the novel PCR. In contrast, one (with a Ct value of 29.75 by the real-time PCR) and two (with Ct values of 29.75 and 33.12) ASFV-positive samples were not identified by the two OIE-validated PCR assays, respectively. Taken together, these data show that the novel PCR assay is specific, sensitive, and applicable for molecular diagnosis and surveillance of ASF.

Application of time-resolved fluorescence for direct and continuous probing of release from polymeric delivery vehicles.

PubMed

Viger, Mathieu L; Sheng, Wangzhong; McFearin, Cathryn L; Berezin, Mikhail Y; Almutairi, Adah

2013-11-10

Though accurately evaluating the kinetics of release is critical for validating newly designed therapeutic carriers for in vivo applications, few methods yet exist for release measurement in real time and without the need for any sample preparation. Many of the current approaches (e.g. chromatographic methods, absorption spectroscopy, or NMR spectroscopy) rely on isolation of the released material from the loaded vehicles, which require additional sample purification and can lead to loss of accuracy when probing fast kinetics of release. In this study we describe the use of time-resolved fluorescence for in situ monitoring of small molecule release kinetics from biodegradable polymeric drug delivery systems. This method relies on the observation that fluorescent reporters being released from polymeric drug delivery systems possess distinct excited-state lifetime components, reflecting their different environments in the particle suspensions, i.e., confined in the polymer matrices or free in the aqueous environment. These distinct lifetimes enable real-time quantitative mapping of the relative concentrations of dye in each population to obtain precise and accurate temporal information on the release profile of particular carrier/payload combinations. We found that fluorescence lifetime better distinguishes subtle differences in release profiles (e.g. differences associated with dye loading) than conventional steady-state fluorescence measurements, which represent the averaged dye behavior over the entire scan. Given the method's applicability to both hydrophobic and hydrophilic cargo, it could be employed to model the release of any drug-carrier combination. Copyright © 2013 Elsevier B.V. All rights reserved.

Ambient stable quantitative PCR reagents for the detection of Yersinia pestis.

PubMed

Qu, Shi; Shi, Qinghai; Zhou, Lei; Guo, Zhaobiao; Zhou, Dongsheng; Zhai, Junhui; Yang, Ruifu

2010-03-09

Although assays for detecting Yersinia pestis using TaqMan probe-based real-time PCR have been developed for years, little is reported on room-temperature-stable PCR reagents, which will be invaluable for field epidemic surveillance, immediate response to public health emergencies, counter-bioterrorism investigation, etc. In this work, a set of real-time PCR reagents for rapid detection of Y. pestis was developed with extraordinary stability at 37 degrees C. TaqMan-based real-time PCR assays were developed using the primers and probes targeting the 3a sequence in the chromosome and the F1 antigen gene caf1 in the plasmid pMT1of Y. pestis, respectively. Then, carbohydrate mixtures were added to the PCR reagents, which were later vacuum-dried for stability evaluation. The vacuum-dried reagents were stable at 37 degrees C for at least 49 days for a lower concentration of template DNA (10 copies/microl), and up to 79 days for higher concentrations (> or =10(2) copies/microl). The reagents were used subsequently to detect soil samples spiked with Y. pestis vaccine strain EV76, and 5x10(4) CFU per gram of soil could be detected by both 3a- and caf1-based PCR reagents. In addition, a simple and efficient method for soil sample processing is presented here. The vacuum-dried reagents for real-time PCR maintain accuracy and reproducibility for at least 49 days at 37 degrees C, indicating that they can be easily transported at room temperature for field application if the machine for performing real-time PCR is available. This dry reagent is of great significance for routine plague surveillance.

Design of a portable, intrinsically safe multichannel acquisition system for high-resolution, real-time processing HD-sEMG.

PubMed

Barone, Umberto; Merletti, Roberto

2013-08-01

A compact and portable system for real-time, multichannel, HD-sEMG acquisition is presented. The device is based on a modular, multiboard approach for scalability and to optimize power consumption for battery operating mode. The proposed modular approach allows us to configure the number of sEMG channels from 64 to 424. A plastic-optical-fiber-based 10/100 Ethernet link is implemented on a field-programmable gate array (FPGA)-based board for real-time, safety data transmission toward a personal computer or laptop for data storage and offline analysis. The high-performance A/D conversion stage, based on 24-bit ADC, allows us to automatically serialize the samples and transmits them on a single SPI bus connecting a sequence of up to 14 ADC chips in chain mode. The prototype is configured to work with 64 channels and a sample frequency of 2.441 ksps (derived from 25-MHz clock source), corresponding to a real data throughput of 3 Mbps. The prototype was assembled to demonstrate the available features (e.g., scalability) and evaluate the expected performances. The analog front end board could be dynamically configured to acquire sEMG signals in monopolar or single differential mode by means of FPGA I/O interface. The system can acquire continuously 64 channels for up to 5 h with a lightweight battery pack of 7.5 Vdc/2200 mAh. A PC-based application was also developed, by means of the open source Qt Development Kit from Nokia, for prototype characterization, sEMG measurements, and real-time visualization of 2-D maps.

Ambient Stable Quantitative PCR Reagents for the Detection of Yersinia pestis

PubMed Central

Zhou, Lei; Guo, Zhaobiao; Zhou, Dongsheng; Zhai, Junhui; Yang, Ruifu

2010-01-01

Background Although assays for detecting Yersinia pestis using TaqMan probe-based real-time PCR have been developed for years, little is reported on room-temperature-stable PCR reagents, which will be invaluable for field epidemic surveillance, immediate response to public health emergencies, counter-bioterrorism investigation, etc. In this work, a set of real-time PCR reagents for rapid detection of Y. pestis was developed with extraordinary stability at 37°C. Methods/Principal Findings TaqMan-based real-time PCR assays were developed using the primers and probes targeting the 3a sequence in the chromosome and the F1 antigen gene caf1 in the plasmid pMT1of Y. pestis, respectively. Then, carbohydrate mixtures were added to the PCR reagents, which were later vacuum-dried for stability evaluation. The vacuum-dried reagents were stable at 37°C for at least 49 days for a lower concentration of template DNA (10 copies/µl), and up to 79 days for higher concentrations (≥102 copies/µl). The reagents were used subsequently to detect soil samples spiked with Y. pestis vaccine strain EV76, and 5×104 CFU per gram of soil could be detected by both 3a- and caf1-based PCR reagents. In addition, a simple and efficient method for soil sample processing is presented here. Conclusions/Significance The vacuum-dried reagents for real-time PCR maintain accuracy and reproducibility for at least 49 days at 37°C, indicating that they can be easily transported at room temperature for field application if the machine for performing real-time PCR is available. This dry reagent is of great significance for routine plague surveillance. PMID:20231881

MicroRaman measurements for nuclear fuel reprocessing applications

DOE PAGES

Casella, Amanda; Lines, Amanda; Nelson, Gilbert; ...

2016-12-01

Treatment and reuse of used nuclear fuel is a key component in closing the nuclear fuel cycle. Solvent extraction reprocessing methods that have been developed contain various steps tailored to the separation of specific radionuclides, which are highly dependent upon solution properties. The instrumentation used to monitor these processes must be robust, require little or no maintenance, and be able to withstand harsh environments such as high radiation fields and aggressive chemical matrices. Our group has been investigating the use of optical spectroscopy for the on-line monitoring of actinides, lanthanides, and acid strength within fuel reprocessing streams. This paper willmore » focus on the development and application of a new MicroRaman probe for on-line real-time monitoring of the U(VI)/nitrate ion/nitric acid in solutions relevant to used nuclear fuel reprocessing. Previous research has successfully demonstrated the applicability on the macroscopic scale, using sample probes requiring larger solution volumes. In an effort to minimize waste and reduce dose to personnel, we have modified this technique to allow measurement at the microfluidic scale using a Raman microprobe. Under the current sampling environment, Raman samples typically require upwards of 10 mL and larger. Using the new sampling system, we can sample volumes at 10 μL or less, which is a scale reduction of over 1,000 fold in sample size. Finally, this paper will summarize our current work in this area including: comparisons between the macroscopic and microscopic probes for detection limits, optimized channel focusing, and application in a flow cell with varying levels of HNO 3, and UO 2(NO 3) 2.« less

Evaluation of laboratory powder X-ray micro-diffraction for applications in the fields of cultural heritage and forensic science.

PubMed

Svarcová, Silvie; Kocí, Eva; Bezdicka, Petr; Hradil, David; Hradilová, Janka

2010-09-01

The uniqueness and limited amounts of forensic samples and samples from objects of cultural heritage together with the complexity of their composition requires the application of a wide range of micro-analytical methods, which are non-destructive to the samples, because these must be preserved for potential late revision. Laboratory powder X-ray micro-diffraction (micro-XRD) is a very effective non-destructive technique for direct phase analysis of samples smaller than 1 mm containing crystal constituents. It compliments optical and electron microscopy with elemental micro-analysis, especially in cases of complicated mixtures containing phases with similar chemical composition. However, modification of X-ray diffraction to the micro-scale together with its application for very heterogeneous real samples leads to deviations from the standard procedure. Knowledge of both the limits and the phenomena which can arise during the analysis is crucial for the meaningful and proper application of the method. We evaluated basic limits of micro-XRD equipped with a mono-capillary with an exit diameter of 0.1 mm, for example the size of irradiated area, appropriate grain size, and detection limits allowing identification of given phases. We tested the reliability and accuracy of quantitative phase analysis based on micro-XRD data in comparison with conventional XRD (reflection and transmission), carrying out experiments with two-phase model mixtures simulating historic colour layers. Furthermore, we demonstrate the wide use of micro-XRD for investigation of various types of micro-samples (contact traces, powder traps, colour layers) and we show how to enhance data quality by proper choice of experiment geometry and conditions.

A lab-on-a-chip system with integrated sample preparation and loop-mediated isothermal amplification for rapid and quantitative detection of Salmonella spp. in food samples.

PubMed

Sun, Yi; Quyen, Than Linh; Hung, Tran Quang; Chin, Wai Hoe; Wolff, Anders; Bang, Dang Duong

2015-04-21

Foodborne disease is a major public health threat worldwide. Salmonellosis, an infectious disease caused by Salmonella spp., is one of the most common foodborne diseases. Isolation and identification of Salmonella by conventional bacterial culture or molecular-based methods are time consuming and usually take a few hours to days to complete. In response to the demand for rapid on line or on site detection of pathogens, in this study, we describe for the first time an eight-chamber lab-on-a-chip (LOC) system with integrated magnetic bead-based sample preparation and loop-mediated isothermal amplification (LAMP) for rapid and quantitative detection of Salmonella spp. in food samples. The whole diagnostic procedures including DNA isolation, isothermal amplification, and real-time detection were accomplished in a single chamber. Up to eight samples could be handled simultaneously and the system was capable to detect Salmonella at concentration of 50 cells per test within 40 min. The simple design, together with high level of integration, isothermal amplification, and quantitative analysis of multiple samples in short time, will greatly enhance the practical applicability of the LOC system for rapid on-site screening of Salmonella for applications in food safety control, environmental surveillance, and clinical diagnostics.

Long-wave, infrared laser-induced breakdown (LIBS) spectroscopy emissions from energetic materials.

PubMed

Yang, Clayton S-C; Brown, Ei E; Hommerich, Uwe; Jin, Feng; Trivedi, Sudhir B; Samuels, Alan C; Snyder, A Peter

2012-12-01

Laser-induced breakdown spectroscopy (LIBS) has shown great promise for applications in chemical, biological, and explosives sensing and has significant potential for real-time standoff detection and analysis. In this study, LIBS emissions were obtained in the mid-infrared (MIR) and long-wave infrared (LWIR) spectral regions for potential applications in explosive material sensing. The IR spectroscopy region revealed vibrational and rotational signatures of functional groups in molecules and fragments thereof. The silicon-based detector for conventional ultraviolet-visible LIBS operations was replaced with a mercury-cadmium-telluride detector for MIR-LWIR spectral detection. The IR spectral signature region between 4 and 12 μm was mined for the appearance of MIR and LWIR-LIBS emissions directly indicative of oxygenated breakdown products as well as dissociated, and/or recombined sample molecular fragments. Distinct LWIR-LIBS emission signatures from dissociated-recombination sample molecular fragments between 4 and 12 μm are observed for the first time.

Development and inter-laboratory validation of unlabeled probe melting curve analysis for detection of JAK2 V617F mutation in polycythemia vera.

PubMed

Wu, Zhiyuan; Yuan, Hong; Zhang, Xinju; Liu, Weiwei; Xu, Jinhua; Zhang, Wei; Guan, Ming

2011-01-01

JAK2 V617F, a somatic point mutation that leads to constitutive JAK2 phosphorylation and kinase activation, has been incorporated into the WHO classification and diagnostic criteria of myeloid neoplasms. Although various approaches such as restriction fragment length polymorphism, amplification refractory mutation system and real-time PCR have been developed for its detection, a generic rapid closed-tube method, which can be utilized on routine genetic testing instruments with stability and cost-efficiency, has not been described. Asymmetric PCR for detection of JAK2 V617F with a 3'-blocked unlabeled probe, saturate dye and subsequent melting curve analysis was performed on a Rotor-Gene® Q real-time cycler to establish the methodology. We compared this method to the existing amplification refractory mutation systems and direct sequencing. Hereafter, the broad applicability of this unlabeled probe melting method was also validated on three diverse real-time systems (Roche LightCycler® 480, Applied Biosystems ABI® 7500 and Eppendorf Mastercycler® ep realplex) in two different laboratories. The unlabeled probe melting analysis could genotype JAK2 V617F mutation explicitly with a 3% mutation load detecting sensitivity. At level of 5% mutation load, the intra- and inter-assay CVs of probe-DNA heteroduplex (mutation/wild type) covered 3.14%/3.55% and 1.72%/1.29% respectively. The method could equally discriminate mutant from wild type samples on the other three real-time instruments. With a high detecting sensitivity, unlabeled probe melting curve analysis is more applicable to disclose JAK2 V617F mutation than conventional methodologies. Verified with the favorable inter- and intra-assay reproducibility, unlabeled probe melting analysis provided a generic mutation detecting alternative for real-time instruments.

Pin on disk against ball on disk for the evaluation of wear improvement on cryo-treated metal cutting shears

NASA Astrophysics Data System (ADS)

Jimbert, P.; Iturrondobeitia, M.; Ibarretxe, J.; Fernandez-Martinez, R.

2015-03-01

When talking about trybology, the election of the laboratory experiment type is a common problem of discussion. Laboratory wear methods are not designed to exactly reproduce the real working conditions of the analyzed part itself but serve to engineers and researcher to extrapolate the laboratory results to the real application. In order to shed some light on this issue, two wear tests have been analyzed following an ASTM standard and using the same experimental parameters and testing pair-materials in order to be able to make a comparison: Pin-on-Disk (PoD) against Ball-on-Disk (BoD). Three different tool steel have been analyzed in this study, AISI D2, AISI A8 and AISI H13, used to produce metal cutting shears. Metal on metal dry sliding tests were designed in order to reproduce the tool working conditions. These three materials were cryogenically treated and compared against no cryogenically treated ones to measure the improvement on their wear resistance due to cryogenic treatment. Finally, the wear rates obtained with both laboratory tests were compared against some real production metal cutting tools wear data. Results revealed an improvement of the wear resistance for cryo-treated samples of around 20% with the BoD test and around 6% with the PoD test. Real production tools wear was calculated for one of the tool steels and for two different applications. The improvement was approximately the one revealed by the BoD test. So, for the studied case, the BoD laboratory test gives more realistic prediction of real tool life improvement due to the cryogenic treatment.

A review of microdialysis coupled to microchip electrophoresis for monitoring biological events

PubMed Central

Saylor, Rachel A.; Lunte, Susan M.

2015-01-01

Microdialysis is a powerful sampling technique that enables monitoring of dynamic processes in vitro and in vivo. The combination of microdialysis with chromatographic or electrophoretic methods yields along with selective detection methods yields a “separation-based sensor” capable of monitoring multiple analytes in near real time. Analysis of microdialysis samples requires techniques that are fast (<1 min), have low volume requirements (nL–pL), and, ideally, can be employed on-line. Microchip electrophoresis fulfills these requirements and also permits the possibility of integrating sample preparation and manipulation with detection strategies directly on-chip. Microdialysis coupled to microchip electrophoresis has been employed for monitoring biological events in vivo and in vitro. This review discusses technical considerations for coupling microdialysis sampling and microchip electrophoresis, including various interface designs, and current applications in the field. PMID:25637011

Adaptive Sampling-Based Information Collection for Wireless Body Area Networks.

PubMed

Xu, Xiaobin; Zhao, Fang; Wang, Wendong; Tian, Hui

2016-08-31

To collect important health information, WBAN applications typically sense data at a high frequency. However, limited by the quality of wireless link, the uploading of sensed data has an upper frequency. To reduce upload frequency, most of the existing WBAN data collection approaches collect data with a tolerable error. These approaches can guarantee precision of the collected data, but they are not able to ensure that the upload frequency is within the upper frequency. Some traditional sampling based approaches can control upload frequency directly, however, they usually have a high loss of information. Since the core task of WBAN applications is to collect health information, this paper aims to collect optimized information under the limitation of upload frequency. The importance of sensed data is defined according to information theory for the first time. Information-aware adaptive sampling is proposed to collect uniformly distributed data. Then we propose Adaptive Sampling-based Information Collection (ASIC) which consists of two algorithms. An adaptive sampling probability algorithm is proposed to compute sampling probabilities of different sensed values. A multiple uniform sampling algorithm provides uniform samplings for values in different intervals. Experiments based on a real dataset show that the proposed approach has higher performance in terms of data coverage and information quantity. The parameter analysis shows the optimized parameter settings and the discussion shows the underlying reason of high performance in the proposed approach.

Nonuniform sampling techniques for antenna applications

NASA Technical Reports Server (NTRS)

Rahmat-Samii, Yahya; Cheung, Rudolf Lap-Tung

1987-01-01

A two-dimensional sampling technique, which can employ irregularly spaced samples (amplitude and phase) in order to generate the complete far-field patterns is presented. The technique implements a matrix inversion algorithm, which depends only on the nonuniform sampled data point locations and with no dependence on the actual field values at these points. A powerful simulation algorithm is presented to allow a real-life simulation of many reflector/feed configurations and to determine the usefulness of the nonuniform sampling technique for the copolar and cross-polar patterns. Additionally, an overlapped window concept and a generalized error simulation model are discussed to identify the stability of the technique for recovering the field data among the nonuniform sampled data. Numerical results are tailored for the pattern reconstruction of a 20-m offset reflector antenna operating at L-band. This reflector is planned to be used in a proposed measurement concept of large antenna aboard the Space Shuttle, whereby it would be almost impractical to accurately control the movement of the Shuttle with respect to the RF source in prescribed directions in order to generate uniform sampled points. Also, application of the nonuniform sampling technique to patterns obtained using near-field measured data is demonstrated. Finally, results of an actual far-field measurement are presented for the construction of patterns of a reflector antenna from a set of nonuniformly distributed measured amplitude and phase data.

Adaptive Sampling-Based Information Collection for Wireless Body Area Networks

PubMed Central

Xu, Xiaobin; Zhao, Fang; Wang, Wendong; Tian, Hui

2016-01-01

To collect important health information, WBAN applications typically sense data at a high frequency. However, limited by the quality of wireless link, the uploading of sensed data has an upper frequency. To reduce upload frequency, most of the existing WBAN data collection approaches collect data with a tolerable error. These approaches can guarantee precision of the collected data, but they are not able to ensure that the upload frequency is within the upper frequency. Some traditional sampling based approaches can control upload frequency directly, however, they usually have a high loss of information. Since the core task of WBAN applications is to collect health information, this paper aims to collect optimized information under the limitation of upload frequency. The importance of sensed data is defined according to information theory for the first time. Information-aware adaptive sampling is proposed to collect uniformly distributed data. Then we propose Adaptive Sampling-based Information Collection (ASIC) which consists of two algorithms. An adaptive sampling probability algorithm is proposed to compute sampling probabilities of different sensed values. A multiple uniform sampling algorithm provides uniform samplings for values in different intervals. Experiments based on a real dataset show that the proposed approach has higher performance in terms of data coverage and information quantity. The parameter analysis shows the optimized parameter settings and the discussion shows the underlying reason of high performance in the proposed approach. PMID:27589758

Comparison of sampling sites and laboratory diagnostic tests for S. equi subsp. equi in horses from confirmed strangles outbreaks.

PubMed

Lindahl, S; Båverud, V; Egenvall, A; Aspán, A; Pringle, J

2013-01-01

Strangles is a contagious equine-specific disease caused by Streptococcus equi subsp. equi. Unfortunately, detection of S. equi can fail in up to 40% of horses with strangles. Whereas recent molecular biologic methods and sampling techniques have improved recovery of S. equi optimal sampling methods and laboratory analyses remain ill-defined. To determine the yield of S. equi from horses with acute strangles in confirmed outbreaks by field-sampling methods subjected to culture and biochemical identification, and real-time PCR directly and after culture. Fifty-seven horses of varying breeds and ages from 8 strangles outbreaks. Prospective study. Culture with biochemical identification and real-time PCR directly, and from culture, were performed on nasal swabs, nasopharyngeal swabs, and nasopharyngeal lavages. Real-time PCR directly from samples identified the highest number of infected horses, with 45/57 nasal swabs, 41/57 nasopharyngeal swabs, and 48/57 nasopharyngeal lavages S. equi positive. Biochemical identification (highest positives 22/57) was inferior to real-time PCR for S. equi recovery regardless of sampling method. Real-time PCR of nasopharyngeal lavage directly and after culture yielded 52/57 positives whereas direct real-time PCR of nasopharyngeal lavage combined with either nasopharyngeal swabs or nasal swabs yielded 53/57 positives. Three horses were negative on all samples. Nasopharyngeal lavage analyzed by a combination of real-time PCR directly and after culture or, alternatively, real-time PCR directly on a nasopharyngeal lavage and a nasal/nasopharyngeal swab can identify S. equi in over 90% of acute strangles cases. Copyright © 2013 by the American College of Veterinary Internal Medicine.

Applications of Quantum Cascade Laser Scanners for Remote Detection of Chemical and Biological Threats and Weapons of Mass Destruction

DTIC Science & Technology

2014-07-09

Rivera. Highly Sensitive Filter Paper Substrate for SERS Trace Explosives Detection , International Journal of Spectroscopy, (09 2012): 0. doi: 10.1155...Highly Sensitive Filter Paper Substrate for SERS Field Detection of Trace Threat Chemicals”, PITTCON-2013: Forensic Analysis in the Lab and Crime Scene...the surface. In addition, built-in algorithms were used for nearly real-time sample detection . Trace and bulk concentrations of the other substances

Hybrid system for in vivo real-time planar fluorescence and volumetric optoacoustic imaging

NASA Astrophysics Data System (ADS)

Chen, Zhenyue; Deán-Ben, Xosé Luís.; Gottschalk, Sven; Razansky, Daniel

2018-02-01

Fluorescence imaging is widely employed in all fields of cell and molecular biology due to its high sensitivity, high contrast and ease of implementation. However, the low spatial resolution and lack of depth information, especially in strongly-scattering samples, restrict its applicability for deep-tissue imaging applications. On the other hand, optoacoustic imaging is known to deliver a unique set of capabilities such as high spatial and temporal resolution in three dimensions, deep penetration and spectrally-enriched imaging contrast. Since fluorescent substances can generate contrast in both modalities, simultaneous fluorescence and optoacoustic readings can provide new capabilities for functional and molecular imaging of living organisms. Optoacoustic images can further serve as valuable anatomical references based on endogenous hemoglobin contrast. Herein, we propose a hybrid system for in vivo real-time planar fluorescence and volumetric optoacoustic tomography, both operating in reflection mode, which synergistically combines the advantages of stand-alone systems. Validation of the spatial resolution and sensitivity of the system were first carried out in tissue mimicking phantoms while in vivo imaging was further demonstrated by tracking perfusion of an optical contrast agent in a mouse brain in the hybrid imaging mode. Experimental results show that the proposed system effectively exploits the contrast mechanisms of both imaging modalities, making it especially useful for accurate monitoring of fluorescence-based signal dynamics in highly scattering samples.

Comparison of clinical application of the Abbott HBV PCR kit and the VERSANT HBV DNA 3.0 test to measure serum hepatitis B virus DNA in Taiwanese patients.

PubMed

Yang, Jeng-Fu; Lin, Ya-Yun; Huang, Jee-Fu; Liu, Shu-Fen; Chu, Pei-Yu; Hsieh, Ming-Yen; Lin, Zu-Yau; Chen, Shinn-Cherng; Wang, Liang-Yen; Dai, Chia-Yen; Chuang, Wan-Long; Yu, Ming-Lung

2009-08-01

With an estimated 350-400 million people worldwide chronically infected with hepatitis B virus (HBV), and the subsequent serious complications caused by liver damage including cirrhosis, liver failure, and hepatocellular carcinoma, HBV infection remains a global health issue, particularly in Taiwan, an HBV-hyperendemic area. Sensitive and accurate quantification of HBV DNA is necessary to monitor patients with chronic hepatitis B who are receiving antiviral therapy to determine treatment response and adapt therapy. We evaluated and compared the clinical performance of two HBV DNA assays based on different technologies: the RealArt HBV PCR Kit (Abbott HBV DNA PCR kit, real-time polymerase chain reaction assay, detection limit: 27 IU/mL) and the VERSANT bDNA 3.0 assay (Bayer, branched DNA signal amplification assay, detection limit: 357 IU/mL). Serum levels of HBV DNA in 173 chronic HBV carriers were determined using both the RealArt HBV PCR Kit and the VERSANT bDNA 3.0 test. Of the 173 samples analyzed for baseline viral load detection, HBV DNA was quantifiable in 147 patients (82.1%) by the RealArt HBV PCR Kit, which was significantly higher than the 92 (53.2%) samples quantified by the VERSANT bDNA 3.0 assay. A total of 86 (49.7%) samples were quantifiable by both assays, whereas 25 (14.5%) were below the detection limit of both assays. The HBV DNA quantification values measured by the RealArt HBV PCR Kit and the VERSANT bDNA 3.0 assay were positively correlated (Spearman's rank correlation coefficient r = 0.932, p < 0.001). On average, the results derived from the RealArt HBV PCR Kit were 0.67 log lower than those of the VERSANT bDNA 3.0 assay. HBV DNA concentrations were significantly higher in 63 HBV e antigen (HBeAg)-seropositive patients than in 110 HBeAg-seronegative patients (5.42 +/- 2.34 logs vs. 3.21 +/- 2.27 logs, p < 0.001). The RealArt HBV PCR Kit is more sensitive and has a wider dynamic range than the VERSANT bDNA 3.0 assay in the clinical setting of chronic hepatitis B patients. The sensitivity and wide dynamic range of the PCR assay allow optimal monitoring and timely adaptation of antiviral therapy. Nevertheless, the HBV DNA values measured by the RealArt HBV PCR Kit and the VERSANT bDNA 3.0 assay were significantly correlated.

Comparison of culture, single and multiplex real-time PCR for detection of Sabin poliovirus shedding in recently vaccinated Indian children.

PubMed

Giri, Sidhartha; Rajan, Anand K; Kumar, Nirmal; Dhanapal, Pavithra; Venkatesan, Jayalakshmi; Iturriza-Gomara, Miren; Taniuchi, Mami; John, Jacob; Abraham, Asha Mary; Kang, Gagandeep

2017-08-01

Although, culture is considered the gold standard for poliovirus detection from stool samples, real-time PCR has emerged as a faster and more sensitive alternative. Detection of poliovirus from the stool of recently vaccinated children by culture, single and multiplex real-time PCR was compared. Of the 80 samples tested, 55 (68.75%) were positive by culture compared to 61 (76.25%) and 60 (75%) samples by the single and one step multiplex real-time PCR assays respectively. Real-time PCR (singleplex and multiplex) is more sensitive than culture for poliovirus detection in stool, although the difference was not statistically significant. © 2017 Wiley Periodicals, Inc.

[The establishment and application of the method with virus concentration and detection in drinking water].

PubMed

Ye, Xiao-yan; Xiao, Wen-qing; Huang, Xia-ning; Zhang, Yong-lu; Cao, Yu-guang; Gu, Kang-ding

2012-07-01

This study aimed to construct an effective method to concentrate and detect virus in drinking water, and human adenovirus pollution status in actual water samples was monitored by constructed method. The concentration efficient of NanoCeram filter for the first concentration with source water and drinking water and the concentration efficient of the different concentrations of PEG 8000 for the second concentration were assessed by spiking f₂ bacteriophage into water samples. The standard of human adenovirus for real-time PCR was constructed by T-A clone. The plasmid obtained was identified through sequence analyzing and consistency check comparing to target gene fragment was conducted by using blast algorithm. Then, real-time PCR was constructed to quantify the concentration of human adenovirus using the plasmid as standard. Water samples were concentrated by using NanoCeram filter on the spot and then concentrated for the second time by PEG/NaCl in 2011. The DNA of concentrated samples were extracted for the quantification of human adenovirus in real-time PCR subsequently to monitor the pollution of human adenovirus in water. For the first concentration by NanoCeram filter, the recovery rates were (51.63 ± 26.60)% in source water and (50.27 ± 14.35)% in treated water, respectively. For the second concentration, the highest recovery rate was reached to (90.09 ± 10.50)% at the concentration of 0.13 kg/L of PEG 8000. The sequence identity score of standard of adenovirus for real time PCR and adenovirus gene was 99%, implying that it can be successfully used to quantification with human adenovirus. The levels of human adenovirus in the water samples sampled in 2011 ranged from 4.13×10³ to 2.20×10⁶ copies/L in source water, while range from 5.57×10² to 7.52×10⁵ copies/L in treated water and the removal efficiency range was (75.49 ± 11.71)%. NanoCeram filers combined with PEG/NaCl was an effective method to concentrate virus in aquatic environment. There was a large number of human adenovirus in source water, and it is not sufficient to remove them thoroughly through conventional water treatment processes.

Real-time hyperspectral imaging for food safety applications

USDA-ARS?s Scientific Manuscript database

Multispectral imaging systems with selected bands can commonly be used for real-time applications of food processing. Recent research has demonstrated several image processing methods including binning, noise removal filter, and appropriate morphological analysis in real-time mode can remove most fa...

Optimization of the elution buffer and concentration method for detecting hepatitis E virus in swine liver using a nested reverse transcription-polymerase chain reaction and real-time reverse transcription-polymerase chain reaction.

PubMed

Son, Na Ry; Seo, Dong Joo; Lee, Min Hwa; Seo, Sheungwoo; Wang, Xiaoyu; Lee, Bog-Hieu; Lee, Jeong-Su; Joo, In-Sun; Hwang, In-Gyun; Choi, Changsun

2014-09-01

The aim of this study was to develop an optimal technique for detecting hepatitis E virus (HEV) in swine livers. Here, three elution buffers and two concentration methods were compared with respect to enhancing recovery of HEV from swine liver samples. Real-time reverse transcription-polymerase chain reaction (RT-PCR) and nested RT-PCR were performed to detect HEV RNA. When phosphate-buffered saline (PBS, pH 7.4) was used to concentrate HEV in swine liver samples using ultrafiltration, real-time RT-PCR detected HEV in 6 of the 26 samples. When threonine buffer was used to concentrate HEV using polyethylene glycol (PEG) precipitation and ultrafiltration, real-time RT-PCR detected HEV in 1 and 3 of the 26 samples, respectively. When glycine buffer was used to concentrate HEV using ultrafiltration and PEG precipitation, real-time RT-PCR detected HEV in 1 and 3 samples of the 26 samples, respectively. When nested RT-PCR was used to detect HEV, all samples tested negative regardless of the type of elution buffer or concentration method used. Therefore, the combination of real-time RT-PCR and ultrafiltration with PBS buffer was the most sensitive and reliable method for detecting HEV in swine livers. Copyright © 2014 Elsevier B.V. All rights reserved.

Extracting Cell Stiffness from Real-Time Deformability Cytometry: Theory and Experiment.

PubMed

Mietke, Alexander; Otto, Oliver; Girardo, Salvatore; Rosendahl, Philipp; Taubenberger, Anna; Golfier, Stefan; Ulbricht, Elke; Aland, Sebastian; Guck, Jochen; Fischer-Friedrich, Elisabeth

2015-11-17

Cell stiffness is a sensitive indicator of physiological and pathological changes in cells, with many potential applications in biology and medicine. A new method, real-time deformability cytometry, probes cell stiffness at high throughput by exposing cells to a shear flow in a microfluidic channel, allowing for mechanical phenotyping based on single-cell deformability. However, observed deformations of cells in the channel not only are determined by cell stiffness, but also depend on cell size relative to channel size. Here, we disentangle mutual contributions of cell size and cell stiffness to cell deformation by a theoretical analysis in terms of hydrodynamics and linear elasticity theory. Performing real-time deformability cytometry experiments on both model spheres of known elasticity and biological cells, we demonstrate that our analytical model not only predicts deformed shapes inside the channel but also allows for quantification of cell mechanical parameters. Thereby, fast and quantitative mechanical sampling of large cell populations becomes feasible. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Extracting Cell Stiffness from Real-Time Deformability Cytometry: Theory and Experiment

PubMed Central

Mietke, Alexander; Otto, Oliver; Girardo, Salvatore; Rosendahl, Philipp; Taubenberger, Anna; Golfier, Stefan; Ulbricht, Elke; Aland, Sebastian; Guck, Jochen; Fischer-Friedrich, Elisabeth

2015-01-01

Cell stiffness is a sensitive indicator of physiological and pathological changes in cells, with many potential applications in biology and medicine. A new method, real-time deformability cytometry, probes cell stiffness at high throughput by exposing cells to a shear flow in a microfluidic channel, allowing for mechanical phenotyping based on single-cell deformability. However, observed deformations of cells in the channel not only are determined by cell stiffness, but also depend on cell size relative to channel size. Here, we disentangle mutual contributions of cell size and cell stiffness to cell deformation by a theoretical analysis in terms of hydrodynamics and linear elasticity theory. Performing real-time deformability cytometry experiments on both model spheres of known elasticity and biological cells, we demonstrate that our analytical model not only predicts deformed shapes inside the channel but also allows for quantification of cell mechanical parameters. Thereby, fast and quantitative mechanical sampling of large cell populations becomes feasible. PMID:26588562

Advances in the in Vivo Raman Spectroscopy of Malignant Skin Tumors Using Portable Instrumentation

PubMed Central

Kourkoumelis, Nikolaos; Balatsoukas, Ioannis; Moulia, Violetta; Elka, Aspasia; Gaitanis, Georgios; Bassukas, Ioannis D.

2015-01-01

Raman spectroscopy has emerged as a promising tool for real-time clinical diagnosis of malignant skin tumors offering a number of potential advantages: it is non-intrusive, it requires no sample preparation, and it features high chemical specificity with minimal water interference. However, in vivo tissue evaluation and accurate histopathological classification remain a challenging task for the successful transition from laboratory prototypes to clinical devices. In the literature, there are numerous reports on the applications of Raman spectroscopy to biomedical research and cancer diagnostics. Nevertheless, cases where real-time, portable instrumentations have been employed for the in vivo evaluation of skin lesions are scarce, despite their advantages in use as medical devices in the clinical setting. This paper reviews the advances in real-time Raman spectroscopy for the in vivo characterization of common skin lesions. The translational momentum of Raman spectroscopy towards the clinical practice is revealed by (i) assembling the technical specifications of portable systems and (ii) analyzing the spectral characteristics of in vivo measurements. PMID:26132563

A baroclinic quasigeostrophic open ocean model

NASA Technical Reports Server (NTRS)

Miller, R. N.; Robinson, A. R.; Haidvogel, D. B.

1983-01-01

A baroclinic quasigeostrophic open ocean model is presented, calibrated by a series of test problems, and demonstrated to be feasible and efficient for application to realistic mid-oceanic mesoscale eddy flow regimes. Two methods of treating the depth dependence of the flow, a finite difference method and a collocation method, are tested and intercompared. Sample Rossby wave calculations with and without advection are performed with constant stratification and two levels of nonlinearity, one weaker than and one typical of real ocean flows. Using exact analytical solutions for comparison, the accuracy and efficiency of the model is tabulated as a function of the computational parameters and stability limits set; typically, errors were controlled between 1 percent and 10 percent RMS after two wave periods. Further Rossby wave tests with realistic stratification and wave parameters chosen to mimic real ocean conditions were performed to determine computational parameters for use with real and simulated data. Finally, a prototype calculation with quasiturbulent simulated data was performed successfully, which demonstrates the practicality of the model for scientific use.

Fast contactless vibrating structure characterization using real time field programmable gate array-based digital signal processing: demonstrations with a passive wireless acoustic delay line probe and vision.

PubMed

Goavec-Mérou, G; Chrétien, N; Friedt, J-M; Sandoz, P; Martin, G; Lenczner, M; Ballandras, S

2014-01-01

Vibrating mechanical structure characterization is demonstrated using contactless techniques best suited for mobile and rotating equipments. Fast measurement rates are achieved using Field Programmable Gate Array (FPGA) devices as real-time digital signal processors. Two kinds of algorithms are implemented on FPGA and experimentally validated in the case of the vibrating tuning fork. A first application concerns in-plane displacement detection by vision with sampling rates above 10 kHz, thus reaching frequency ranges above the audio range. A second demonstration concerns pulsed-RADAR cooperative target phase detection and is applied to radiofrequency acoustic transducers used as passive wireless strain gauges. In this case, the 250 ksamples/s refresh rate achieved is only limited by the acoustic sensor design but not by the detection bandwidth. These realizations illustrate the efficiency, interest, and potentialities of FPGA-based real-time digital signal processing for the contactless interrogation of passive embedded probes with high refresh rates.

Real-time terahertz digital holography with a quantum cascade laser

PubMed Central

Locatelli, Massimiliano; Ravaro, Marco; Bartalini, Saverio; Consolino, Luigi; Vitiello, Miriam S.; Cicchi, Riccardo; Pavone, Francesco; De Natale, Paolo

2015-01-01

Coherent imaging in the THz range promises to exploit the peculiar capabilities of these wavelengths to penetrate common materials like plastics, ceramics, paper or clothes with potential breakthroughs in non-destructive inspection and quality control, homeland security and biomedical applications. Up to now, however, THz coherent imaging has been limited by time-consuming raster scanning, point-like detection schemes and by the lack of adequate coherent sources. Here, we demonstrate real-time digital holography (DH) at THz frequencies exploiting the high spectral purity and the mW output power of a quantum cascade laser combined with the high sensitivity and resolution of a microbolometric array. We show that, in a one-shot exposure, phase and amplitude information of whole samples, either in reflection or in transmission, can be recorded. Furthermore, a 200 times reduced sensitivity to mechanical vibrations and a significantly enlarged field of view are observed, as compared to DH in the visible range. These properties of THz DH enable unprecedented holographic recording of real world dynamic scenes. PMID:26315647

Speeding Up Non-Parametric Bootstrap Computations for Statistics Based on Sample Moments in Small/Moderate Sample Size Applications

PubMed Central

Chaibub Neto, Elias

2015-01-01

In this paper we propose a vectorized implementation of the non-parametric bootstrap for statistics based on sample moments. Basically, we adopt the multinomial sampling formulation of the non-parametric bootstrap, and compute bootstrap replications of sample moment statistics by simply weighting the observed data according to multinomial counts instead of evaluating the statistic on a resampled version of the observed data. Using this formulation we can generate a matrix of bootstrap weights and compute the entire vector of bootstrap replications with a few matrix multiplications. Vectorization is particularly important for matrix-oriented programming languages such as R, where matrix/vector calculations tend to be faster than scalar operations implemented in a loop. We illustrate the application of the vectorized implementation in real and simulated data sets, when bootstrapping Pearson’s sample correlation coefficient, and compared its performance against two state-of-the-art R implementations of the non-parametric bootstrap, as well as a straightforward one based on a for loop. Our investigations spanned varying sample sizes and number of bootstrap replications. The vectorized bootstrap compared favorably against the state-of-the-art implementations in all cases tested, and was remarkably/considerably faster for small/moderate sample sizes. The same results were observed in the comparison with the straightforward implementation, except for large sample sizes, where the vectorized bootstrap was slightly slower than the straightforward implementation due to increased time expenditures in the generation of weight matrices via multinomial sampling. PMID:26125965

Photonics-based real-time ultra-high-range-resolution radar with broadband signal generation and processing.

PubMed

Zhang, Fangzheng; Guo, Qingshui; Pan, Shilong

2017-10-23

Real-time and high-resolution target detection is highly desirable in modern radar applications. Electronic techniques have encountered grave difficulties in the development of such radars, which strictly rely on a large instantaneous bandwidth. In this article, a photonics-based real-time high-range-resolution radar is proposed with optical generation and processing of broadband linear frequency modulation (LFM) signals. A broadband LFM signal is generated in the transmitter by photonic frequency quadrupling, and the received echo is de-chirped to a low frequency signal by photonic frequency mixing. The system can operate at a high frequency and a large bandwidth while enabling real-time processing by low-speed analog-to-digital conversion and digital signal processing. A conceptual radar is established. Real-time processing of an 8-GHz LFM signal is achieved with a sampling rate of 500 MSa/s. Accurate distance measurement is implemented with a maximum error of 4 mm within a range of ~3.5 meters. Detection of two targets is demonstrated with a range-resolution as high as 1.875 cm. We believe the proposed radar architecture is a reliable solution to overcome the limitations of current radar on operation bandwidth and processing speed, and it is hopefully to be used in future radars for real-time and high-resolution target detection and imaging.

EasyLCMS: an asynchronous web application for the automated quantification of LC-MS data

PubMed Central

2012-01-01

Background Downstream applications in metabolomics, as well as mathematical modelling, require data in a quantitative format, which may also necessitate the automated and simultaneous quantification of numerous metabolites. Although numerous applications have been previously developed for metabolomics data handling, automated calibration and calculation of the concentrations in terms of μmol have not been carried out. Moreover, most of the metabolomics applications are designed for GC-MS, and would not be suitable for LC-MS, since in LC, the deviation in the retention time is not linear, which is not taken into account in these applications. Moreover, only a few are web-based applications, which could improve stand-alone software in terms of compatibility, sharing capabilities and hardware requirements, even though a strong bandwidth is required. Furthermore, none of these incorporate asynchronous communication to allow real-time interaction with pre-processed results. Findings Here, we present EasyLCMS (http://www.easylcms.es/), a new application for automated quantification which was validated using more than 1000 concentration comparisons in real samples with manual operation. The results showed that only 1% of the quantifications presented a relative error higher than 15%. Using clustering analysis, the metabolites with the highest relative error distributions were identified and studied to solve recurrent mistakes. Conclusions EasyLCMS is a new web application designed to quantify numerous metabolites, simultaneously integrating LC distortions and asynchronous web technology to present a visual interface with dynamic interaction which allows checking and correction of LC-MS raw data pre-processing results. Moreover, quantified data obtained with EasyLCMS are fully compatible with numerous downstream applications, as well as for mathematical modelling in the systems biology field. PMID:22884039

Comparison of a real-time PCR method with a culture method for the detection of Salmonella enterica serotype enteritidis in naturally contaminated environmental samples from integrated poultry houses.

PubMed

Lungu, Bwalya; Waltman, W Douglas; Berghaus, Roy D; Hofacre, Charles L

2012-04-01

Conventional culture methods have traditionally been considered the "gold standard" for the isolation and identification of foodborne bacterial pathogens. However, culture methods are labor-intensive and time-consuming. A Salmonella enterica serotype Enteritidis-specific real-time PCR assay that recently received interim approval by the National Poultry Improvement Plan for the detection of Salmonella Enteritidis was evaluated against a culture method that had also received interim National Poultry Improvement Plan approval for the analysis of environmental samples from integrated poultry houses. The method was validated with 422 field samples collected by either the boot sock or drag swab method. The samples were cultured by selective enrichment in tetrathionate broth followed by transfer onto a modified semisolid Rappaport-Vassiliadis medium and then plating onto brilliant green with novobiocin and xylose lysine brilliant Tergitol 4 plates. One-milliliter aliquots of the selective enrichment broths from each sample were collected for DNA extraction by the commercial PrepSEQ nucleic acid extraction assay and analysis by the Salmonella Enteritidis-specific real-time PCR assay. The real-time PCR assay detected no significant differences between the boot sock and drag swab samples. In contrast, the culture method detected a significantly higher number of positive samples from boot socks. The diagnostic sensitivity of the real-time PCR assay for the field samples was significantly higher than that of the culture method. The kappa value obtained was 0.46, indicating moderate agreement between the real-time PCR assay and the culture method. In addition, the real-time PCR method had a turnaround time of 2 days compared with 4 to 8 days for the culture method. The higher sensitivity as well as the reduction in time and labor makes this real-time PCR assay an excellent alternative to conventional culture methods for diagnostic purposes, surveillance, and research studies to improve food safety.

A Rapid, Low-Cost Method to Determine Travel Times at Managed Aquifer Recharge Operations Using Noble Gas Tracers

NASA Astrophysics Data System (ADS)

Moran, J. E.; Visser, A.; Singleton, M. J.; Esser, B. K.; Halliwell, M.; Hillegonds, D. J.

2012-12-01

Managed aquifer recharge is a key component for the sustainable use of surface water and groundwater in the arid western U.S. When recycled water is a recharge water source, subsurface residence time, required for bacteria and virus deactivation, is best verified by application of an extrinsic tracer. Desirable tracer properties include: no real or perceived health risk, inexpensive even for a large volume of tagged water, large dynamic range, efficient introduction, convenient sampling methods, and rapid, low-cost analysis. We have developed and tested a dissolved noble gas tracer technique ideally suited for tracing large water volumes at managed aquifer recharge facilities. In an application of the method at a water district's facilities in the San Francisco Bay area, Xenon was introduced into a 106 m3 pond over a period of 7 days using a 300 m length of gas-permeable silicone tubing. Samples from the pond, near-field shallow monitoring wells, and production wells about 400 m from the recharge pond were analyzed for dissolved Xe by noble gas membrane inlet mass spectrometry (NGMIMS). The NGMIMS uses a syringe pump, gas-permeable membrane inlet, and quadrupole residual gas analyzer for measurement of noble gas concentrations. Samples are collected in VOA vials, and analysis can be carried out in real-time, with a measurement uncertainty of about 5% for Xe. Tracer first appeared in a production well 136 days after starting the tracer introduction at 0.7% (C/C0) of the peak pond xenon concentration. The cost of the tracer is about US650/106 m3 water, and the NGMIMS was assembled with parts totaling approximately US50,000, making application of the tracer method feasible for most managed aquifer recharge projects. This project is part of the California State Water Resources Control Board Groundwater Ambient Monitoring and Assessment (GAMA) Program.

New Developments of Broadband Cavity Enhanced Spectroscopic Techniques

NASA Astrophysics Data System (ADS)

Walsh, A.; Zhao, D.; Linnartz, H.; Ubachs, W.

2013-06-01

In recent years, cavity enhanced spectroscopic techniques, such as cavity ring-down spectroscopy (CRDS), cavity enhanced absorption spectroscopy (CEAS), and broadband cavity enhanced absorption spectroscopy (BBCEAS), have been widely employed as ultra-sensitive methods for the measurement of weak absorptions and in the real-time detection of trace species. In this contribution, we introduce two new cavity enhanced spectroscopic concepts: a) Optomechanical shutter modulated BBCEAS, a variant of BBCEAS capable of measuring optical absorption in pulsed systems with typically low duty cycles. In conventional BBCEAS applications, the latter substantially reduces the signal-to-noise ratio (S/N), consequently also reducing the detection sensitivity. To overcome this, we incorporate a fast optomechanical shutter as a time gate, modulating the detection scheme of BBCEAS and increasing the effective duty cycle reaches a value close to unity. This extends the applications of BBCEAS into pulsed samples and also in time-resolved studies. b) Cavity enhanced self-absorption spectroscopy (CESAS), a new spectroscopic concept capable of studying light emitting matter (plasma, flames, combustion samples) simultaneously in absorption and emission. In CESAS, a sample (plasma, flame or combustion source) is located in an optically stable cavity consisting of two high reflectivity mirrors, and here it acts both as light source and absorbing medium. A high detection sensitivity of weak absorption is reached without the need of an external light source, such as a laser or broadband lamp. The performance is illustrated by the first CESAS result on a supersonically expanding hydrocarbon plasma. We expect CESAS to become a generally applicable analytical tool for real time and in situ diagnostics. A. Walsh, D. Zhao, W. Ubachs, H. Linnartz, J. Phys. Chem. A, {dx.doi.org/10.1021/jp310392n}, in press, 2013. A. Walsh, D. Zhao, H. Linnartz Rev. Sci. Instrum. {84}(2), 021608 2013. A. Walsh, D. Zhao, H. Linnartz Appl. Phys. Lett. {101}(9), 091111 2012.

A New Generation of Real-Time Systems in the JET Tokamak

NASA Astrophysics Data System (ADS)

Alves, Diogo; Neto, Andre C.; Valcarcel, Daniel F.; Felton, Robert; Lopez, Juan M.; Barbalace, Antonio; Boncagni, Luca; Card, Peter; De Tommasi, Gianmaria; Goodyear, Alex; Jachmich, Stefan; Lomas, Peter J.; Maviglia, Francesco; McCullen, Paul; Murari, Andrea; Rainford, Mark; Reux, Cedric; Rimini, Fernanda; Sartori, Filippo; Stephen, Adam V.; Vega, Jesus; Vitelli, Riccardo; Zabeo, Luca; Zastrow, Klaus-Dieter

2014-04-01

Recently, a new recipe for developing and deploying real-time systems has become increasingly adopted in the JET tokamak. Powered by the advent of x86 multi-core technology and the reliability of JET's well established Real-Time Data Network (RTDN) to handle all real-time I/O, an official Linux vanilla kernel has been demonstrated to be able to provide real-time performance to user-space applications that are required to meet stringent timing constraints. In particular, a careful rearrangement of the Interrupt ReQuests' (IRQs) affinities together with the kernel's CPU isolation mechanism allows one to obtain either soft or hard real-time behavior depending on the synchronization mechanism adopted. Finally, the Multithreaded Application Real-Time executor (MARTe) framework is used for building applications particularly optimised for exploring multi-core architectures. In the past year, four new systems based on this philosophy have been installed and are now part of JET's routine operation. The focus of the present work is on the configuration aspects that enable these new systems' real-time capability. Details are given about the common real-time configuration of these systems, followed by a brief description of each system together with results regarding their real-time performance. A cycle time jitter analysis of a user-space MARTe based application synchronizing over a network is also presented. The goal is to compare its deterministic performance while running on a vanilla and on a Messaging Real time Grid (MRG) Linux kernel.

Moving your laboratories to the field – Advantages and limitations of the use of field portable instruments in environmental sample analysis

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

Gałuszka, Agnieszka, E-mail: Agnieszka.Galuszka@ujk.edu.pl; Migaszewski, Zdzisław M.; Namieśnik, Jacek

The recent rapid progress in technology of field portable instruments has increased their applications in environmental sample analysis. These instruments offer a possibility of cost-effective, non-destructive, real-time, direct, on-site measurements of a wide range of both inorganic and organic analytes in gaseous, liquid and solid samples. Some of them do not require the use of reagents and do not produce any analytical waste. All these features contribute to the greenness of field portable techniques. Several stationary analytical instruments have their portable versions. The most popular ones include: gas chromatographs with different detectors (mass spectrometer (MS), flame ionization detector, photoionization detector),more » ultraviolet–visible and near-infrared spectrophotometers, X-ray fluorescence spectrometers, ion mobility spectrometers, electronic noses and electronic tongues. The use of portable instruments in environmental sample analysis gives a possibility of on-site screening and a subsequent selection of samples for routine laboratory analyses. They are also very useful in situations that require an emergency response and for process monitoring applications. However, quantification of results is still problematic in many cases. The other disadvantages include: higher detection limits and lower sensitivity than these obtained in laboratory conditions, a strong influence of environmental factors on the instrument performance and a high possibility of sample contamination in the field. This paper reviews recent applications of field portable instruments in environmental sample analysis and discusses their analytical capabilities. - Highlights: • Field portable instruments are widely used in environmental sample analysis. • Field portable instruments are indispensable for analysis in emergency response. • Miniaturization of field portable instruments reduces resource consumption. • In situ analysis is in agreement with green analytical chemistry principles. • Performance requirements in field analysis stimulate technological progress.« less

Assessment of SCAR markers to design real-time PCR primers for rhizosphere quantification of Azospirillum brasilense phytostimulatory inoculants of maize.

PubMed

Couillerot, O; Poirier, M-A; Prigent-Combaret, C; Mavingui, P; Caballero-Mellado, J; Moënne-Loccoz, Y

2010-08-01

To assess the applicability of sequence characterized amplified region (SCAR) markers obtained from BOX, ERIC and RAPD fragments to design primers for real-time PCR quantification of the phytostimulatory maize inoculants Azospirillum brasilense UAP-154 and CFN-535 in the rhizosphere. Primers were designed based on strain-specific SCAR markers and were screened for successful amplification of target strain and absence of cross-reaction with other Azospirillum strains. The specificity of primers thus selected was verified under real-time PCR conditions using genomic DNA from strain collection and DNA from rhizosphere samples. The detection limit was 60 fg DNA with pure cultures and 4 x 10(3) (for UAP-154) and 4 x 10(4) CFU g(-1) (for CFN-535) in the maize rhizosphere. Inoculant quantification was effective from 10(4) to 10(8) CFU g(-1) soil. BOX-based SCAR markers were useful to find primers for strain-specific real-time PCR quantification of each A. brasilense inoculant in the maize rhizosphere. Effective root colonization is a prerequisite for successful Azospirillum phytostimulation, but cultivation-independent monitoring methods were lacking. The real-time PCR methods developed here will help understand the effect of environmental conditions on root colonization and phytostimulation by A. brasilense UAP-154 and CFN-535.

REAL-TIME ENVIRONMENTAL MONITORING: APPLICATIONS FOR HOMELAND SECURITY

EPA Science Inventory

Real-time monitoring technology developed as part of the EMPACT program has a variety of potential applications. These tools can measure a variety of potential contaminants in the air, water, in buildings, or in the soil. Real-time monitoring technology allows these detection sys...

Network protocols for real-time applications

NASA Technical Reports Server (NTRS)

Johnson, Marjory J.

1987-01-01

The Fiber Distributed Data Interface (FDDI) and the SAE AE-9B High Speed Ring Bus (HSRB) are emerging standards for high-performance token ring local area networks. FDDI was designed to be a general-purpose high-performance network. HSRB was designed specifically for military real-time applications. A workshop was conducted at NASA Ames Research Center in January, 1987 to compare and contrast these protocols with respect to their ability to support real-time applications. This report summarizes workshop presentations and includes an independent comparison of the two protocols. A conclusion reached at the workshop was that current protocols for the upper layers of the Open Systems Interconnection (OSI) network model are inadequate for real-time applications.

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

Jamieson, Kevin; Davis, IV, Warren L.

Active learning methods automatically adapt data collection by selecting the most informative samples in order to accelerate machine learning. Because of this, real-world testing and comparing active learning algorithms requires collecting new datasets (adaptively), rather than simply applying algorithms to benchmark datasets, as is the norm in (passive) machine learning research. To facilitate the development, testing and deployment of active learning for real applications, we have built an open-source software system for large-scale active learning research and experimentation. The system, called NEXT, provides a unique platform for realworld, reproducible active learning research. This paper details the challenges of building themore » system and demonstrates its capabilities with several experiments. The results show how experimentation can help expose strengths and weaknesses of active learning algorithms, in sometimes unexpected and enlightening ways.« less

A flange on electron spectromicroscope with spherical deflector analyzer--simultaneous imaging of reciprocal and real spaces.

PubMed

Grzelakowski, Krzysztof P

2013-07-01

An instrumental realization of the idea for the electron emission spectromicroscope based on the newly developed imaging energy filter called α-SDA (Spherical Deflector Analyzer) is reported. Its compact design enables the realization of the flange-on spectromicroscope concept. It is equipped with two independent energy selective imaging channels: one for real and another for reciprocal space visualization. These images can be acquired quasi-simultaneousely by means of the software based on the switching on and off potentials of the energy filter. An electron gun located inside the immersion objective lens allows a new kind of sample illumination by high energy primary electrons and thus, opens a new application field for electron spectromicroscopy under laboratory conditions. Copyright © 2013 Elsevier B.V. All rights reserved.

Fast Filtration of Bacterial or Mammalian Suspension Cell Cultures for Optimal Metabolomics Results

PubMed Central

Bordag, Natalie; Janakiraman, Vijay; Nachtigall, Jonny; González Maldonado, Sandra; Bethan, Bianca; Laine, Jean-Philippe; Fux, Elie

2016-01-01

The metabolome offers real time detection of the adaptive, multi-parametric response of the organisms to environmental changes, pathophysiological stimuli or genetic modifications and thus rationalizes the optimization of cell cultures in bioprocessing. In bioprocessing the measurement of physiological intracellular metabolite levels is imperative for successful applications. However, a sampling method applicable to all cell types with little to no validation effort which simultaneously offers high recovery rates, high metabolite coverage and sufficient removal of extracellular contaminations is still missing. Here, quenching, centrifugation and fast filtration were compared and fast filtration in combination with a stabilizing washing solution was identified as the most promising sampling method. Different influencing factors such as filter type, vacuum pressure, washing solutions were comprehensively tested. The improved fast filtration method (MxP® FastQuench) followed by routine lipid/polar extraction delivers a broad metabolite coverage and recovery reflecting well physiological intracellular metabolite levels for different cell types, such as bacteria (Escherichia coli) as well as mammalian cells chinese hamster ovary (CHO) and mouse myeloma cells (NS0).The proposed MxP® FastQuench allows sampling, i.e. separation of cells from medium with washing and quenching, in less than 30 seconds and is robustly designed to be applicable to all cell types. The washing solution contains the carbon source respectively the 13C-labeled carbon source to avoid nutritional stress during sampling. This method is also compatible with automation which would further reduce sampling times and the variability of metabolite profiling data. PMID:27438065

Detection of Brucella spp. in milk from seronegative cows by real-time polymerase chain reaction in the region of Batna, Algeria

PubMed Central

Sabrina, Rabehi; Mossadak, Hamdi Taha; Bakir, Mamache; Asma, Meghezzi; Khaoula, Boushaba

2018-01-01

Aim: The aim of this study was to detect Brucella spp. DNA in milk samples collected from seronegative cows using the real-time polymerase chain reaction (PCR) assay for diagnosis of brucellosis in seronegative dairy cows to prevent transmission of disease to humans and to reduce economic losses in animal production. Materials and Methods: In this study, 65 milk samples were investigated for the detection of Brucella spp. The detection of the IS711 gene in all samples was done by real-time PCR assay by comparative cycle threshold method. Results: The results show that of the 65 DNA samples tested, 2 (3.08%) were positive for Brucella infection. The mean cyclic threshold values of IS711 real-time PCR test were 37.97 and 40.48, indicating a positive reaction. Conclusion: The results of the present study indicated that the real-time PCR appears to offer several advantages over serological tests. For this reason, the real-time PCR should be validated on representative numbers of Brucella-infected and free samples before being implemented in routine diagnosis in human and animal brucellosis for controlling this disease. PMID:29657430

Hair analysis for cocaine: factors in laboratory contamination studies and their relevance to proficiency sample preparation and hair testing practices.

PubMed

Hill, Virginia; Cairns, Thomas; Schaffer, Michael

2008-03-21

Hair samples were contaminated by rubbing with cocaine (COC) followed by sweat application, multiple shampoo treatments and storage. The samples were then washed with isopropanol for 15min, followed by sequential aqueous washes totaling 3.5h. The amount of drug in the last wash was used to calculate a wash criterion to determine whether samples were positive due to use or contamination. Analyses of cocaine and metabolites were done by LC/MS/MS. These procedures were applied to samples produced by a U.S. government-sponsored cooperative study, in which this laboratory participated, and to samples in a parallel in-house study. All contaminated samples in both studies were correctly identified as contaminated by cutoff, benzoylecgonine (BE) presence, BE ratio, and/or the wash criterion. A method for determining hair porosity was applied to samples in both studies, and porosity characteristics of hair are discussed as they relate to experimental and real-world contamination of hair, preparation of proficiency survey samples, and analysis of unknown hair samples.

A Simulation Approach to Assessing Sampling Strategies for Insect Pests: An Example with the Balsam Gall Midge

PubMed Central

Carleton, R. Drew; Heard, Stephen B.; Silk, Peter J.

2013-01-01

Estimation of pest density is a basic requirement for integrated pest management in agriculture and forestry, and efficiency in density estimation is a common goal. Sequential sampling techniques promise efficient sampling, but their application can involve cumbersome mathematics and/or intensive warm-up sampling when pests have complex within- or between-site distributions. We provide tools for assessing the efficiency of sequential sampling and of alternative, simpler sampling plans, using computer simulation with “pre-sampling” data. We illustrate our approach using data for balsam gall midge (Paradiplosis tumifex) attack in Christmas tree farms. Paradiplosis tumifex proved recalcitrant to sequential sampling techniques. Midge distributions could not be fit by a common negative binomial distribution across sites. Local parameterization, using warm-up samples to estimate the clumping parameter k for each site, performed poorly: k estimates were unreliable even for samples of n∼100 trees. These methods were further confounded by significant within-site spatial autocorrelation. Much simpler sampling schemes, involving random or belt-transect sampling to preset sample sizes, were effective and efficient for P. tumifex. Sampling via belt transects (through the longest dimension of a stand) was the most efficient, with sample means converging on true mean density for sample sizes of n∼25–40 trees. Pre-sampling and simulation techniques provide a simple method for assessing sampling strategies for estimating insect infestation. We suspect that many pests will resemble P. tumifex in challenging the assumptions of sequential sampling methods. Our software will allow practitioners to optimize sampling strategies before they are brought to real-world applications, while potentially avoiding the need for the cumbersome calculations required for sequential sampling methods. PMID:24376556

Brief Report: Development of a Robotic Intervention Platform for Young Children with ASD.

PubMed

Warren, Zachary; Zheng, Zhi; Das, Shuvajit; Young, Eric M; Swanson, Amy; Weitlauf, Amy; Sarkar, Nilanjan

2015-12-01

Increasingly researchers are attempting to develop robotic technologies for children with autism spectrum disorder (ASD). This pilot study investigated the development and application of a novel robotic system capable of dynamic, adaptive, and autonomous interaction during imitation tasks with embedded real-time performance evaluation and feedback. The system was designed to incorporate both a humanoid robot and a human examiner. We compared child performance within system across these conditions in a sample of preschool children with ASD (n = 8) and a control sample of typically developing children (n = 8). The system was well-tolerated in the sample, children with ASD exhibited greater attention to the robotic system than the human administrator, and for children with ASD imitation performance appeared superior during the robotic interaction.

Antibiotic resistance of microorganisms in agricultural soils in Russia

NASA Astrophysics Data System (ADS)

Danilova, N. V.; Galitskaya, P. Yu; Selivanovskaya, S. Yu

2018-01-01

Antibiotics are medicines that are widely used in livestock production not only for the prevention and treatment of infectious diseases, but also for accelerating the growth of animals. The application of manure for fertilizing agricultural soils leads to the entry into the soil ecosystem not only of the antibiotics themselves, but also the resistance genes to them. In this study, 30 samples of arable soils were tested for the presence of the tet(X) gene, which encodes bacterial resistance to antibiotics of the tetracycline group. Using real-time PCR, it was found that 27 out of 30 soil samples contained tet(X). 52% of these samples were heavily contaminated, 34% had a medium level of contamination and 14% were slightly contaminated by the resistance gene tet(X).

Monitoring airborne molecular contamination: a quantitative and qualitative comparison of real-time and grab-sampling techniques

NASA Astrophysics Data System (ADS)

Shupp, Aaron M.; Rodier, Dan; Rowley, Steven

2007-03-01

Monitoring and controlling Airborne Molecular Contamination (AMC) has become essential in deep ultraviolet (DUV) photolithography for both optimizing yields and protecting tool optics. A variety of technologies have been employed for both real-time and grab-sample monitoring. Real-time monitoring has the advantage of quickly identifying "spikes" and upset conditions, while 2 - 24 hour plus grab sampling allows for extremely low detection limits by concentrating the mass of the target contaminant over a period of time. Employing a combination of both monitoring techniques affords the highest degree of control, lowest detection limits, and the most detailed data possible in terms of speciation. As happens with many technologies, there can be concern regarding the accuracy and agreement between real-time and grab-sample methods. This study utilizes side by side comparisons of two different real-time monitors operating in parallel with both liquid impingers and dry sorbent tubes to measure NIST traceable gas standards as well as real world samples. By measuring in parallel, a truly valid comparison is made between methods while verifying the results against a certified standard. The final outcome for this investigation is that a dry sorbent tube grab-sample technique produced results that agreed in terms of accuracy with NIST traceable standards as well as the two real-time techniques Ion Mobility Spectrometry (IMS) and Pulsed Fluorescence Detection (PFD) while a traditional liquid impinger technique showed discrepancies.

Development of a copula-based particle filter (CopPF) approach for hydrologic data assimilation under consideration of parameter interdependence

NASA Astrophysics Data System (ADS)

Fan, Y. R.; Huang, G. H.; Baetz, B. W.; Li, Y. P.; Huang, K.

2017-06-01

In this study, a copula-based particle filter (CopPF) approach was developed for sequential hydrological data assimilation by considering parameter correlation structures. In CopPF, multivariate copulas are proposed to reflect parameter interdependence before the resampling procedure with new particles then being sampled from the obtained copulas. Such a process can overcome both particle degeneration and sample impoverishment. The applicability of CopPF is illustrated with three case studies using a two-parameter simplified model and two conceptual hydrologic models. The results for the simplified model indicate that model parameters are highly correlated in the data assimilation process, suggesting a demand for full description of their dependence structure. Synthetic experiments on hydrologic data assimilation indicate that CopPF can rejuvenate particle evolution in large spaces and thus achieve good performances with low sample size scenarios. The applicability of CopPF is further illustrated through two real-case studies. It is shown that, compared with traditional particle filter (PF) and particle Markov chain Monte Carlo (PMCMC) approaches, the proposed method can provide more accurate results for both deterministic and probabilistic prediction with a sample size of 100. Furthermore, the sample size would not significantly influence the performance of CopPF. Also, the copula resampling approach dominates parameter evolution in CopPF, with more than 50% of particles sampled by copulas in most sample size scenarios.

An Efficient Silent Data Corruption Detection Method with Error-Feedback Control and Even Sampling for HPC Applications

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

Di, Sheng; Berrocal, Eduardo; Cappello, Franck

The silent data corruption (SDC) problem is attracting more and more attentions because it is expected to have a great impact on exascale HPC applications. SDC faults are hazardous in that they pass unnoticed by hardware and can lead to wrong computation results. In this work, we formulate SDC detection as a runtime one-step-ahead prediction method, leveraging multiple linear prediction methods in order to improve the detection results. The contributions are twofold: (1) we propose an error feedback control model that can reduce the prediction errors for different linear prediction methods, and (2) we propose a spatial-data-based even-sampling method tomore » minimize the detection overheads (including memory and computation cost). We implement our algorithms in the fault tolerance interface, a fault tolerance library with multiple checkpoint levels, such that users can conveniently protect their HPC applications against both SDC errors and fail-stop errors. We evaluate our approach by using large-scale traces from well-known, large-scale HPC applications, as well as by running those HPC applications on a real cluster environment. Experiments show that our error feedback control model can improve detection sensitivity by 34-189% for bit-flip memory errors injected with the bit positions in the range [20,30], without any degradation on detection accuracy. Furthermore, memory size can be reduced by 33% with our spatial-data even-sampling method, with only a slight and graceful degradation in the detection sensitivity.« less

Industrial Raman gas sensing for real-time system control

NASA Astrophysics Data System (ADS)

Buric, M.; Mullen, J.; Chorpening, B.; Woodruff, S.

2014-06-01

Opportunities exist to improve on-line process control in energy applications with a fast, non-destructive measurement of gas composition. Here, we demonstrate a Raman sensing system which is capable of reporting the concentrations of numerous species simultaneously with sub-percent accuracy and sampling times below one-second for process control applications in energy or chemical production. The sensor is based upon a hollow-core capillary waveguide with a 300 micron bore with reflective thin-film metal and dielectric linings. The effect of using such a waveguide in a Raman process is to integrate Raman photons along the length of the sample-filled waveguide, thus permitting the acquisition of very large Raman signals for low-density gases in a short time. The resultant integrated Raman signals can then be used for quick and accurate analysis of a gaseous mixture. The sensor is currently being tested for energy applications such as coal gasification, turbine control, well-head monitoring for exploration or production, and non-conventional gas utilization. In conjunction with an ongoing commercialization effort, the researchers have recently completed two prototype instruments suitable for hazardous area operation and testing. Here, we report pre-commercialization testing of those field prototypes for control applications in gasification or similar processes. Results will be discussed with respect to accuracy, calibration requirements, gas sampling techniques, and possible control strategies of industrial significance.

Supercritical and Transcritical Real-Fluid Mixing in Diesel Engine Applications

DTIC Science & Technology

2015-09-01

ARL-RP-0551 ● SEP 2015 US Army Research Laboratory Supercritical and Transcritical Real-Fluid Mixing in Diesel Engine...ARL-RP-0551 ● SEP 2015 US Army Research Laboratory Supercritical and Transcritical Real-Fluid Mixing in Diesel Engine Applications by...COVERED (From - To) 1 January 2014–30 September 2014 4. TITLE AND SUBTITLE Supercritical and Transcritical Real-Fluid Mixing in Diesel Engine

Wavelet-Based Interpolation and Representation of Non-Uniformly Sampled Spacecraft Mission Data

NASA Technical Reports Server (NTRS)

Bose, Tamal

2000-01-01

A well-documented problem in the analysis of data collected by spacecraft instruments is the need for an accurate, efficient representation of the data set. The data may suffer from several problems, including additive noise, data dropouts, an irregularly-spaced sampling grid, and time-delayed sampling. These data irregularities render most traditional signal processing techniques unusable, and thus the data must be interpolated onto an even grid before scientific analysis techniques can be applied. In addition, the extremely large volume of data collected by scientific instrumentation presents many challenging problems in the area of compression, visualization, and analysis. Therefore, a representation of the data is needed which provides a structure which is conducive to these applications. Wavelet representations of data have already been shown to possess excellent characteristics for compression, data analysis, and imaging. The main goal of this project is to develop a new adaptive filtering algorithm for image restoration and compression. The algorithm should have low computational complexity and a fast convergence rate. This will make the algorithm suitable for real-time applications. The algorithm should be able to remove additive noise and reconstruct lost data samples from images.

Medical Device Integrated Vital Signs Monitoring Application with Real-Time Clinical Decision Support.

PubMed

Moqeem, Aasia; Baig, Mirza; Gholamhosseini, Hamid; Mirza, Farhaan; Lindén, Maria

2018-01-01

This research involves the design and development of a novel Android smartphone application for real-time vital signs monitoring and decision support. The proposed application integrates market available, wireless and Bluetooth connected medical devices for collecting vital signs. The medical device data collected by the app includes heart rate, oxygen saturation and electrocardiograph (ECG). The collated data is streamed/displayed on the smartphone in real-time. This application was designed by adopting six screens approach (6S) mobile development framework and focused on user-centered approach and considered clinicians-as-a-user. The clinical engagement, consultations, feedback and usability of the application in the everyday practices were considered critical from the initial phase of the design and development. Furthermore, the proposed application is capable to deliver rich clinical decision support in real-time using the integrated medical device data.

Design of smart sensing components for volcano monitoring

USGS Publications Warehouse

Xu, M.; Song, W.-Z.; Huang, R.; Peng, Y.; Shirazi, B.; LaHusen, R.; Kiely, A.; Peterson, N.; Ma, A.; Anusuya-Rangappa, L.; Miceli, M.; McBride, D.

2009-01-01

In a volcano monitoring application, various geophysical and geochemical sensors generate continuous high-fidelity data, and there is a compelling need for real-time raw data for volcano eruption prediction research. It requires the network to support network synchronized sampling, online configurable sensing and situation awareness, which pose significant challenges on sensing component design. Ideally, the resource usages shall be driven by the environment and node situations, and the data quality is optimized under resource constraints. In this paper, we present our smart sensing component design, including hybrid time synchronization, configurable sensing, and situation awareness. Both design details and evaluation results are presented to show their efficiency. Although the presented design is for a volcano monitoring application, its design philosophy and framework can also apply to other similar applications and platforms. ?? 2009 Elsevier B.V.

Achieving AFRL Universal FADEC Vision With Open Architecture Addressing Capability and Obsolescence for Military and Commercial Applications (Preprint)

DTIC Science & Technology

2006-11-01

engines will involve a family of common components. It will consist of a real - time operating system and partitioned application software (AS...system will employ a standard hardware and software architecture. It will consist of a real time operating system and partitioned application...Inputs - Enables Large Cost Reduction 3. Software - FAA Certified Auto Code - Real Time Operating System - Commercial

Improving Mid-Course Flight Through an Application of Real-Time Optimal Control

DTIC Science & Technology

2017-12-01

COURSE FLIGHT THROUGH AN APPLICATION OF REAL- TIME OPTIMAL CONTROL by Mark R. Roncoroni December 2017 Thesis Advisor: Ronald Proulx Co...collection of information is estimated to average 1 hour per response, including the time for reviewing instruction, searching existing data sources...AND DATES COVERED Master’s thesis 4. TITLE AND SUBTITLE IMPROVING MID-COURSE FLIGHT THROUGH AN APPLICATION OF REAL- TIME OPTIMAL CONTROL 5. FUNDING

Application of Structured Light System Technique for Authentication of Wooden Panel Paintings.

PubMed

Buchón-Moragues, Fernando; Bravo, José María; Ferri, Marcelino; Redondo, Javier; Sánchez-Pérez, Juan Vicente

2016-06-14

This paper presents a new application of photogrammetric techniques for protecting cultural heritage. The accuracy of the method and the fact that it can be used to carry out different tests without contact between the sample and the instruments can make this technique very useful for authenticating and cataloging artworks. The application focuses on the field of pictorial artworks, and wooden panel paintings in particular. In these works, the orography formed by the brushstrokes can be easily digitalized using a photogrammetric technique, called Structured Light System, with submillimeter accuracy. Thus, some of the physical characteristics of the brushstrokes, like minimum and maximum heights or slopes become a fingerprint of the painting. We explain in detail the general principles of the Structured Light System Technique and the specific characteristics of the commercial set-up used in this work. Some experiments are carried out on a sample painted by us to check the accuracy limits of the technique and to propose some tests that can help to stablish a methodology for authentication purposes. Finally, some preliminary results obtained on a real pictorial artwork are presented, providing geometrical information of its metric features as an example of the possibilities of this application.

Application of Structured Light System Technique for Authentication of Wooden Panel Paintings

PubMed Central

Buchón-Moragues, Fernando; Bravo, José María; Ferri, Marcelino; Redondo, Javier; Sánchez-Pérez, Juan Vicente

2016-01-01

This paper presents a new application of photogrammetric techniques for protecting cultural heritage. The accuracy of the method and the fact that it can be used to carry out different tests without contact between the sample and the instruments can make this technique very useful for authenticating and cataloging artworks. The application focuses on the field of pictorial artworks, and wooden panel paintings in particular. In these works, the orography formed by the brushstrokes can be easily digitalized using a photogrammetric technique, called Structured Light System, with submillimeter accuracy. Thus, some of the physical characteristics of the brushstrokes, like minimum and maximum heights or slopes become a fingerprint of the painting. We explain in detail the general principles of the Structured Light System Technique and the specific characteristics of the commercial set-up used in this work. Some experiments are carried out on a sample painted by us to check the accuracy limits of the technique and to propose some tests that can help to stablish a methodology for authentication purposes. Finally, some preliminary results obtained on a real pictorial artwork are presented, providing geometrical information of its metric features as an example of the possibilities of this application. PMID:27314353

Development of recombinase polymerase amplification assays for the rapid detection of peste des petits ruminants virus.

PubMed

Zhang, Yongning; Wang, Jianchang; Zhang, Zhou; Mei, Lin; Wang, Jinfeng; Wu, Shaoqiang; Lin, Xiangmei

2018-04-01

Peste des petits ruminants (PPR) is a severe infectious disease of small ruminants caused by PPR virus (PPRV). Rapid and sensitive detection of PPRV is critical for controlling PPR. This report describes the development and evaluation of a conventional reverse transcription recombinase polymerase amplification (RT-RPA) assay and a real-time RT-RPA assay, targeting the PPRV N gene. Sensitivity analysis revealed that the conventional RT-RPA assay could detect 852 copies of standard PPRV RNA per reaction at 95% probability within 20 min at 41 °C, and the real-time RT-RPA assay could detect 103 copies of RNA molecules per reaction at 95% probability. Specificity analysis showed that both assays have no cross-reactivity with nucleic acid templates prepared from other selected viruses or common pathogens. Clinical evaluation using 162 ovine and hircine serum and nasal swab samples showed that the performance of both the real-time RT-RPA assay and the conventional RT-RPA assay were comparable to that of real-time RT-PCR. The overall agreements between real-time RT-PCR and real-time RT-RPA, and conventional RT-RPA were 99.4% (161/162) and 98.8% (160/162), respectively. The R 2 value of real-time RT-RPA and real-time RT-PCR was 0.900 by linear regression analysis. Our results suggest that both RT-RPA assays have a potential application in the rapid, sensitive and specific detection of PPRV. Copyright © 2018 Elsevier B.V. All rights reserved.

Development of laser-induced breakdown spectroscopy sensor to assess groundwater quality impacts resulting from geologic carbon sequestration

NASA Astrophysics Data System (ADS)

Carson, Cantwell G.; Goueguel, Christian; Jain, Jinesh; McIntyre, Dustin

2015-05-01

The injection of CO2 into deep aquifers can potentially affect the quality of groundwater supplies were leakage to occur from the injection formation or fluids. Therefore, the detection of CO2 and/or entrained contaminants that migrate into shallow groundwater aquifers is important both to assess storage permanence and to evaluate impacts on water resources. Naturally occurring elements (i.e., Li, Sr) in conjunction with isotope ratios can be used to detect such leakage. We propose the use of laser induced breakdown spectroscopy (LIBS) as an analytical technique to detect a suite of elements in water samples. LIBS has real time monitoring capabilities and can be applied for elemental and isotopic analysis of solid, liquid, and gas samples. The flexibility of probe design and use of fiber optics make it a suitable technique for real time measurements in harsh conditions and in hard to reach places. The laboratory scale experiments to measure Li, K, Ca, and Sr composition of water samples indicate that the technique produces rapid and reliable data. Since CO2 leakage from saline aquifers may accompany a brine solution, we studied the effect of sodium salts on the accuracy of LIBS analysis. This work specifically also details the fabrication and application of a miniature ruggedized remotely operated diode pumped solid state passively Q-switched laser system for use as the plasma excitation source for a real time LIBS analysis. This work also proposes the optical distribution of many laser spark sources across a wide area for widespread leak detection and basin monitoring.

Detection of Listeria monocytogenes in ready-to-eat food by Step One real-time polymerase chain reaction.

PubMed

Pochop, Jaroslav; Kačániová, Miroslava; Hleba, Lukáš; Lopasovský, L'ubomír; Bobková, Alica; Zeleňáková, Lucia; Stričík, Michal

2012-01-01

The aim of this study was to follow contamination of ready-to-eat food with Listeria monocytogenes by using the Step One real time polymerase chain reaction (PCR). We used the PrepSEQ Rapid Spin Sample Preparation Kit for isolation of DNA and MicroSEQ® Listeria monocytogenes Detection Kit for the real-time PCR performance. In 30 samples of ready-to-eat milk and meat products without incubation we detected strains of Listeria monocytogenes in five samples (swabs). Internal positive control (IPC) was positive in all samples. Our results indicated that the real-time PCR assay developed in this study could sensitively detect Listeria monocytogenes in ready-to-eat food without incubation.

Unsupervised Bayesian linear unmixing of gene expression microarrays.

PubMed

Bazot, Cécile; Dobigeon, Nicolas; Tourneret, Jean-Yves; Zaas, Aimee K; Ginsburg, Geoffrey S; Hero, Alfred O

2013-03-19

This paper introduces a new constrained model and the corresponding algorithm, called unsupervised Bayesian linear unmixing (uBLU), to identify biological signatures from high dimensional assays like gene expression microarrays. The basis for uBLU is a Bayesian model for the data samples which are represented as an additive mixture of random positive gene signatures, called factors, with random positive mixing coefficients, called factor scores, that specify the relative contribution of each signature to a specific sample. The particularity of the proposed method is that uBLU constrains the factor loadings to be non-negative and the factor scores to be probability distributions over the factors. Furthermore, it also provides estimates of the number of factors. A Gibbs sampling strategy is adopted here to generate random samples according to the posterior distribution of the factors, factor scores, and number of factors. These samples are then used to estimate all the unknown parameters. Firstly, the proposed uBLU method is applied to several simulated datasets with known ground truth and compared with previous factor decomposition methods, such as principal component analysis (PCA), non negative matrix factorization (NMF), Bayesian factor regression modeling (BFRM), and the gradient-based algorithm for general matrix factorization (GB-GMF). Secondly, we illustrate the application of uBLU on a real time-evolving gene expression dataset from a recent viral challenge study in which individuals have been inoculated with influenza A/H3N2/Wisconsin. We show that the uBLU method significantly outperforms the other methods on the simulated and real data sets considered here. The results obtained on synthetic and real data illustrate the accuracy of the proposed uBLU method when compared to other factor decomposition methods from the literature (PCA, NMF, BFRM, and GB-GMF). The uBLU method identifies an inflammatory component closely associated with clinical symptom scores collected during the study. Using a constrained model allows recovery of all the inflammatory genes in a single factor.

Rapid determination of anti-estrogens by gas chromatography/mass spectrometry in urine: Method validation and application to real samples.

PubMed

Gerace, E; Salomone, A; Abbadessa, G; Racca, S; Vincenti, M

2012-02-01

A fast screening protocol was developed for the simultaneous determination of nine anti-estrogenic agents (aminoglutethimide, anastrozole, clomiphene, drostanolone, formestane, letrozole, mesterolone, tamoxifen, testolactone) plus five of their metabolites in human urine. After an enzymatic hydrolysis, these compounds can be extracted simultaneously from urine with a simple liquid-liquid extraction at alkaline conditions. The analytes were subsequently analyzed by fast-gas chromatography/mass spectrometry (fast-GC/MS) after derivatization. The use of a short column, high-flow carrier gas velocity and fast temperature ramping produced an efficient separation of all analytes in about 4 min, allowing a processing rate of 10 samples/h. The present analytical method was validated according to UNI EN ISO/IEC 17025 guidelines for qualitative methods. The range of investigated parameters included the limit of detection, selectivity, linearity, repeatability, robustness and extraction efficiency. High MS-sampling rate, using a benchtop quadrupole mass analyzer, resulted in accurate peak shape definition under both scan and selected ion monitoring modes, and high sensitivity in the latter mode. Therefore, the performances of the method are comparable to the ones obtainable from traditional GC/MS analysis. The method was successfully tested on real samples arising from clinical treatments of hospitalized patients and could profitably be used for clinical studies on anti-estrogenic drug administration.

Rapid determination of anti-estrogens by gas chromatography/mass spectrometry in urine: Method validation and application to real samples

PubMed Central

Gerace, E.; Salomone, A.; Abbadessa, G.; Racca, S.; Vincenti, M.

2011-01-01

A fast screening protocol was developed for the simultaneous determination of nine anti-estrogenic agents (aminoglutethimide, anastrozole, clomiphene, drostanolone, formestane, letrozole, mesterolone, tamoxifen, testolactone) plus five of their metabolites in human urine. After an enzymatic hydrolysis, these compounds can be extracted simultaneously from urine with a simple liquid–liquid extraction at alkaline conditions. The analytes were subsequently analyzed by fast-gas chromatography/mass spectrometry (fast-GC/MS) after derivatization. The use of a short column, high-flow carrier gas velocity and fast temperature ramping produced an efficient separation of all analytes in about 4 min, allowing a processing rate of 10 samples/h. The present analytical method was validated according to UNI EN ISO/IEC 17025 guidelines for qualitative methods. The range of investigated parameters included the limit of detection, selectivity, linearity, repeatability, robustness and extraction efficiency. High MS-sampling rate, using a benchtop quadrupole mass analyzer, resulted in accurate peak shape definition under both scan and selected ion monitoring modes, and high sensitivity in the latter mode. Therefore, the performances of the method are comparable to the ones obtainable from traditional GC/MS analysis. The method was successfully tested on real samples arising from clinical treatments of hospitalized patients and could profitably be used for clinical studies on anti-estrogenic drug administration. PMID:29403714

A human fecal contamination score for ranking recreational sites using the HF183/BacR287 quantitative real-time PCR method.

PubMed

Cao, Yiping; Sivaganesan, Mano; Kelty, Catherine A; Wang, Dan; Boehm, Alexandria B; Griffith, John F; Weisberg, Stephen B; Shanks, Orin C

2018-01-01

Human fecal pollution of recreational waters remains a public health concern worldwide. As a result, there is a growing interest in the application of human-associated fecal source identification quantitative real-time PCR (qPCR) technologies for water quality research and management. However, there are currently no standardized approaches for field implementation and interpretation of qPCR data. In this study, a standardized HF183/BacR287 qPCR method was combined with a water sampling strategy and a novel Bayesian weighted average approach to establish a human fecal contamination score (HFS) that can be used to prioritize sampling sites for remediation based on measured human waste levels. The HFS was then used to investigate 975 study design scenarios utilizing different combinations of sites with varying sampling intensities (daily to once per week) and number of qPCR replicates per sample (2-14 replicates). Findings demonstrate that site prioritization with HFS is feasible and that both sampling intensity and number of qPCR replicates influence reliability of HFS estimates. The novel data analysis strategy presented here provides a prescribed approach for the implementation and interpretation of human-associated HF183/BacR287 qPCR data with the goal of site prioritization based on human fecal pollution levels. In addition, information is provided for future users to customize study designs for optimal HFS performance. Published by Elsevier Ltd.

From Ions to Bits - Developing the IT infrastructure around the CAMECA IMS 1280-HR SIMS lab at GFZ Potsdam

NASA Astrophysics Data System (ADS)

Galkin, A.; Klump, J.; Wiedenbeck, M.

2012-04-01

Secondary Ion Mass Spectrometers (SIMS) is an highly sensitive technique for analyzing the surfaces of solids and thin film samples, but has the major drawback that such instruments are both rare and expensive. The Virtual SIMS project aims to design, develop and operate the IT infrastructure around the CAMECA IMS 1280-HR SIMS at GFZ Potsdam. The system will cover the whole spectrum of the procedures in the lab - from the online application for measurement time, to the remote access to the instrument and finally the maintenance of the data for publishing and future re-use. A virtual lab infrastructure around the IMS 1280 will enable remote access to the instrument and make measurement time available to the broadest possible user community. Envisioned is that the IT infrastructure would consist of the following: web portal, data repository, sample repository, project management software, communication arrangements between the lab staff and distant researcher and remote access to the instruments. The web portal will handle online applications for the measurement time. The data from the experiments, the monitoring sensor logs and the lab logbook entries are to be stored and archived. Researchers will be able to access their data remotely in real time, thus imposing a user rights management strucuture. Also planned is that all samples and the standards will be assigned a unique International GeoSample Number (IGSN) and that the images of the samples will be stored and made accessible in addition to any additional documents which might be uploaded by the researcher. The project management application will schedule the application process, the measurements times, notifications and alerts. A video conference capability is forseen for communication between the Potsdam staff and the remote researcher. The remote access to the instruments requires a sophisticated client-server solution. This highly sensitive instrument has to be controlled in real-time with latencies diminished to a minimum. Also, failures and shortages of the internet connection, as well as possible outages on the client side, have to be considered and safe fallbacks for such events must be provided. The level of skills of the researcher remotely operating the instrument will define the scope of control given during an operating session. An important aspect of the project is the design of the virtual lab system in collaboration with the laboratory operators and the researchers who will use the instrument and its peripherals. Different approaches for the IT solutions will be tested and evaluated, so imporved guidelines can evolve from obsperved operating performance.

Stability of gametocyte-specific Pfs25-mRNA in dried blood spots on filter paper subjected to different storage conditions

PubMed Central

2012-01-01

Background Real-time quantitative nucleic acid sequence-based amplification (QT-NASBA) is a sensitive method for detection of sub-microscopic gametocytaemia by measuring gametocyte-specific mRNA. Performing analysis on fresh whole blood samples is often not feasible in remote and resource-poor areas. Convenient methods for sample storage and transport are urgently needed. Methods Real-time QT-NASBA was performed on whole blood spiked with a dilution series of purified in-vitro cultivated gametocytes. The blood was either freshly processed or spotted on filter papers. Gametocyte detection sensitivity for QT-NASBA was determined and controlled by microscopy. Dried blood spot (DBS) samples were subjected to five different storage conditions and the loss of sensitivity over time was investigated. A formula to approximate the loss of Pfs25-mRNA due to different storage conditions and time was developed. Results Pfs25-mRNA was measured in time to positivity (TTP) and correlated well with the microscopic counts and the theoretical concentrations of the dilution series. TTP results constantly indicated higher amounts of RNA in filter paper samples extracted after 24 hours than in immediately extracted fresh blood. Among investigated storage conditions freezing at −20°C performed best with 98.7% of the Pfs25-mRNA still detectable at day 28 compared to fresh blood samples. After 92 days, the RNA detection rate was only slightly decreased to 92.9%. Samples stored at 37°C showed most decay with only 64.5% of Pfs25-mRNA detectable after one month. The calculated theoretical detection limit for 24 h-old DBS filter paper samples was 0.0095 (95% CI: 0.0025 to 0.0380) per μl. Conclusions The results suggest that the application of DBS filter papers for quantification of Plasmodium falciparum gametocytes with real-time QT-NASBA is practical and recommendable. This method proved sensitive enough for detection of sub-microscopic densities even after prolonged storage. Decay rates can be predicted for different storage conditions as well as durations. PMID:22545954

Integral-equation based methods for parameter estimation in output pulses of radiation detectors: Application in nuclear medicine and spectroscopy

NASA Astrophysics Data System (ADS)

Mohammadian-Behbahani, Mohammad-Reza; Saramad, Shahyar

2018-04-01

Model based analysis methods are relatively new approaches for processing the output data of radiation detectors in nuclear medicine imaging and spectroscopy. A class of such methods requires fast algorithms for fitting pulse models to experimental data. In order to apply integral-equation based methods for processing the preamplifier output pulses, this article proposes a fast and simple method for estimating the parameters of the well-known bi-exponential pulse model by solving an integral equation. The proposed method needs samples from only three points of the recorded pulse as well as its first and second order integrals. After optimizing the sampling points, the estimation results were calculated and compared with two traditional integration-based methods. Different noise levels (signal-to-noise ratios from 10 to 3000) were simulated for testing the functionality of the proposed method, then it was applied to a set of experimental pulses. Finally, the effect of quantization noise was assessed by studying different sampling rates. Promising results by the proposed method endorse it for future real-time applications.

Hierarchical Bayesian sparse image reconstruction with application to MRFM.

PubMed

Dobigeon, Nicolas; Hero, Alfred O; Tourneret, Jean-Yves

2009-09-01

This paper presents a hierarchical Bayesian model to reconstruct sparse images when the observations are obtained from linear transformations and corrupted by an additive white Gaussian noise. Our hierarchical Bayes model is well suited to such naturally sparse image applications as it seamlessly accounts for properties such as sparsity and positivity of the image via appropriate Bayes priors. We propose a prior that is based on a weighted mixture of a positive exponential distribution and a mass at zero. The prior has hyperparameters that are tuned automatically by marginalization over the hierarchical Bayesian model. To overcome the complexity of the posterior distribution, a Gibbs sampling strategy is proposed. The Gibbs samples can be used to estimate the image to be recovered, e.g., by maximizing the estimated posterior distribution. In our fully Bayesian approach, the posteriors of all the parameters are available. Thus, our algorithm provides more information than other previously proposed sparse reconstruction methods that only give a point estimate. The performance of the proposed hierarchical Bayesian sparse reconstruction method is illustrated on synthetic data and real data collected from a tobacco virus sample using a prototype MRFM instrument.

Microstructural changes in a cementitious membrane due to the application of a DC electric field.

PubMed

Covelo, Alba; Diaz, Belen; Freire, Lorena; Novoa, X Ramon; Perez, M Consuelo

2008-07-01

The use of electromigration techniques to accelerate chloride ions motion is commonly employed to characterise the permeability of cementitious samples to chlorides, a relevant parameter in reinforced concrete corrosion. This paper is devoted to the study of microstructure's changes occurring in mortar samples when submitted to natural diffusion and migration experiments. The application of an electric field reduces testing time in about one order of magnitude with respect to natural diffusion experiments. Nevertheless, the final sample's microstructure differs in both tests. Impedance Spectroscopy is employed for real time monitoring of microstructural changes. During migration experiments the global impedance undergoes important increase in shorter period of time compared to natural diffusion tests. So, the forced motion of ions through the concrete membrane induces significant variations in the porous structure, as confirmed by Mercury Intrusion Porosimetry. After migration experiments, an important increase in the capillary pore size (10-100 nm) was detected. Conversely, no relevant variations are found after natural diffusion tests. Results presented in this work cast doubt on the significance of diffusion coefficient values obtained under accelerated conditions.

Development and validation of a method for the determination of low-ppb levels of macrocyclic lactones in butter, using HPLC-fluorescence.

PubMed

Macedo, Fabio; Marsico, Eliane Teixeira; Conte-Júnior, Carlos Adam; de Resende, Michele Fabri; Brasil, Taila Figueiredo; Pereira Netto, Annibal Duarte

2015-07-15

An analytical method was developed and validated for the simultaneous determination of four macrocyclic lactones (ML) (abamectin, doramectin, ivermectin and moxidectin) in butter, using liquid chromatography with fluorescence detection. The method employed heated liquid-liquid extraction and a mixture of acetonitrile, ethyl acetate and water, with preconcentration and derivatization, to produce stable fluorescent derivatives. The chromatographic run time was <12.5 min, with excellent separation. The method validation followed international guidelines and employed fortified butter samples. The figures of merit obtained, e.g. recovery (72.4-106.5%), repeatability (8.8%), within-laboratory reproducibility (15.7%) and limits of quantification (0.09-0.16 μg kg(-1)) were satisfactory for the desired application. The application of the method to real samples showed that ML residues were present in six of the ten samples evaluated. The method proved to be simple, easy and appropriate for simultaneous determination of ML residues in butter. To our knowledge, this is the first method described for the evaluation of ML in butter. Copyright © 2015. Published by Elsevier Ltd.

Microcomputer data acquisition and control.

PubMed

East, T D

1986-01-01

In medicine and biology there are many tasks that involve routine well defined procedures. These tasks are ideal candidates for computerized data acquisition and control. As the performance of microcomputers rapidly increases and cost continues to go down the temptation to automate the laboratory becomes great. To the novice computer user the choices of hardware and software are overwhelming and sadly most of the computer sales persons are not at all familiar with real-time applications. If you want to bill your patients you have hundreds of packaged systems to choose from; however, if you want to do real-time data acquisition the choices are very limited and confusing. The purpose of this chapter is to provide the novice computer user with the basics needed to set up a real-time data acquisition system with the common microcomputers. This chapter will cover the following issues necessary to establish a real time data acquisition and control system: Analysis of the research problem: Definition of the problem; Description of data and sampling requirements; Cost/benefit analysis. Choice of Microcomputer hardware and software: Choice of microprocessor and bus structure; Choice of operating system; Choice of layered software. Digital Data Acquisition: Parallel Data Transmission; Serial Data Transmission; Hardware and software available. Analog Data Acquisition: Description of amplitude and frequency characteristics of the input signals; Sampling theorem; Specification of the analog to digital converter; Hardware and software available; Interface to the microcomputer. Microcomputer Control: Analog output; Digital output; Closed-Loop Control. Microcomputer data acquisition and control in the 21st Century--What is in the future? High speed digital medical equipment networks; Medical decision making and artificial intelligence.

Real-Time Food Authentication Using a Miniature Mass Spectrometer.

PubMed

Gerbig, Stefanie; Neese, Stephan; Penner, Alexander; Spengler, Bernhard; Schulz, Sabine

2017-10-17

Food adulteration is a threat to public health and the economy. In order to determine food adulteration efficiently, rapid and easy-to-use on-site analytical methods are needed. In this study, a miniaturized mass spectrometer in combination with three ambient ionization methods was used for food authentication. The chemical fingerprints of three milk types, five fish species, and two coffee types were measured using electrospray ionization, desorption electrospray ionization, and low temperature plasma ionization. Minimum sample preparation was needed for the analysis of liquid and solid food samples. Mass spectrometric data was processed using the laboratory-built software MS food classifier, which allows for the definition of specific food profiles from reference data sets using multivariate statistical methods and the subsequent classification of unknown data. Applicability of the obtained mass spectrometric fingerprints for food authentication was evaluated using different data processing methods, leave-10%-out cross-validation, and real-time classification of new data. Classification accuracy of 100% was achieved for the differentiation of milk types and fish species, and a classification accuracy of 96.4% was achieved for coffee types in cross-validation experiments. Measurement of two milk mixtures yielded correct classification of >94%. For real-time classification, the accuracies were comparable. Functionality of the software program and its performance is described. Processing time for a reference data set and a newly acquired spectrum was found to be 12 s and 2 s, respectively. These proof-of-principle experiments show that the combination of a miniaturized mass spectrometer, ambient ionization, and statistical analysis is suitable for on-site real-time food authentication.

Application of TaqMan fluorescent probe-based quantitative real-time PCR assay for the environmental survey of Legionella spp. and Legionella pneumophila in drinking water reservoirs in Taiwan.

PubMed

Kao, Po-Min; Hsu, Bing-Mu; Hsu, Tsui-Kang; Ji, Wen-Tsai; Huang, Po-Hsiang; Hsueh, Chih-Jen; Chiang, Chuen-Sheue; Huang, Shih-Wei; Huang, Yu-Li

2014-08-15

In this study, TaqMan fluorescent quantitative real-time PCR was performed to quantify Legionella species in reservoirs. Water samples were collected from 19 main reservoirs in Taiwan, and 12 (63.2%) were found to contain Legionella spp. The identified species included uncultured Legionella spp., L. pneumophila, L. jordanis, and L. drancourtii. The concentrations of Legionella spp. and L. pneumophila in the water samples were in the range of 1.8×10(2)-2.6×10(3) and 1.6×10(2)-2.4×10(2) cells/L, respectively. The presence and absence of Legionella spp. in the reservoir differed significantly in pH values. These results highlight the importance that L. pneumophila, L. jordanis, and L. drancourtii are potential pathogens in the reservoirs. The presence of L. pneumophila in reservoirs may be a potential public health concern that must be further examined. Copyright © 2014 Elsevier B.V. All rights reserved.

Proteomic Characterization of Dermal Interstitial Fluid Extracted Using a Novel Microneedle-Assisted Technique.

PubMed

Tran, Bao Quoc; Miller, Philip R; Taylor, Robert M; Boyd, Gabrielle; Mach, Phillip M; Rosenzweig, C Nicole; Baca, Justin T; Polsky, Ronen; Glaros, Trevor

2018-01-05

As wearable fitness devices have gained commercial acceptance, interest in real-time monitoring of an individual's physiological status using noninvasive techniques has grown. Microneedles have been proposed as a minimally invasive technique for sampling the dermal interstitial fluid (ISF) for clinical monitoring and diagnosis, but little is known about its composition. In this study, a novel microneedle array was used to collect dermal ISF from three healthy human donors and compared with matching serum and plasma samples. Using a shotgun quantitative proteomic approach, 407 proteins were quantified with at least one unique peptide, and of those, 135 proteins were differently expressed at least 2-fold. Collectively, these proteins tended to originate from the cytoplasm, membrane bound vesicles, and extracellular vesicular exosomes. Proteomic analysis confirmed previously published work that indicates that ISF is highly similar to both plasma and serum. In this study, less than one percent of proteins were uniquely identified in ISF. Taken together, ISF could serve as a minimally invasive alternative for blood-derived fluids with potential for real-time monitoring applications.

Global preamplification simplifies targeted mRNA quantification

PubMed Central

Kroneis, Thomas; Jonasson, Emma; Andersson, Daniel; Dolatabadi, Soheila; Ståhlberg, Anders

2017-01-01

The need to perform gene expression profiling using next generation sequencing and quantitative real-time PCR (qPCR) on small sample sizes and single cells is rapidly expanding. However, to analyse few molecules, preamplification is required. Here, we studied global and target-specific preamplification using 96 optimised qPCR assays. To evaluate the preamplification strategies, we monitored the reactions in real-time using SYBR Green I detection chemistry followed by melting curve analysis. Next, we compared yield and reproducibility of global preamplification to that of target-specific preamplification by qPCR using the same amount of total RNA. Global preamplification generated 9.3-fold lower yield and 1.6-fold lower reproducibility than target-specific preamplification. However, the performance of global preamplification is sufficient for most downstream applications and offers several advantages over target-specific preamplification. To demonstrate the potential of global preamplification we analysed the expression of 15 genes in 60 single cells. In conclusion, we show that global preamplification simplifies targeted gene expression profiling of small sample sizes by a flexible workflow. We outline the pros and cons for global preamplification compared to target-specific preamplification. PMID:28332609

Curcumin-cysteine and curcumin-tryptophan conjugate as fluorescence turn on sensors for picric Acid in aqueous media.

PubMed

Gogoi, Bedanta; Sen Sarma, Neelotpal

2015-06-03

Rapid detection of picric acid in real sample is of outmost importance from the perspective of health, safety, and environment. In this study, a very simple and cost-effective detection of picric acid is accomplished by developing a couple of biobased conjugates curcumin-cysteine (CC) and curcumin-tryptophan (CT), which undergo efficient fluorescence turn on toward picric acid in aqueous media. Both the probes experience about 26.5-fold fluorescence enhancements at 70 nM concentration of the analyte. Here, the fluorescence turn on process is governed by the aggregation induced emission, which is induced from the electrostatic interaction between the conjugates with picric acid. The detection limit of CC and CT are about 13.51 and 13.54 nM of picric acid, respectively. Importantly, both the probes exhibit high selectivity and low interference of other analogues toward the detection of picric acid. In addition, the probes are highly photostable, show low response time and are practically applicable for sensing picric acid in real environmental samples, which is the ultimate goal of this work.

Long-Term Persistence of Pesticides and TPs in Archived Agricultural Soil Samples and Comparison with Pesticide Application.

PubMed

Chiaia-Hernandez, Aurea C; Keller, Armin; Wächter, Daniel; Steinlin, Christine; Camenzuli, Louise; Hollender, Juliane; Krauss, Martin

2017-09-19

For polar and more degradable pesticides, not many data on long-term persistence in soil under field conditions and real application practices exist. To assess the persistence of pesticides in soil, a multiple-compound screening method (log K ow 1.7-5.5) was developed based on pressurized liquid extraction, QuEChERS and LC-HRMS. The method was applied to study 80 polar pesticides and >90 transformation products (TPs) in archived topsoil samples from the Swiss Soil Monitoring Network (NABO) from 1995 to 2008 with known pesticide application patterns. The results reveal large variations between crop type and field sites. For the majority of the sites 10-15 pesticides were identified with a detection rate of 45% at concentrations between 1 and 330 μg/kg dw in soil. Furthermore, TPs were detected in 47% of the cases where the "parent-compound" was applied. Overall, residues of about 80% of all applied pesticides could be detected with half of these found as TPs with a persistence of more than a decade.

The NWRA Classification Infrastructure: description and extension to the Discriminant Analysis Flare Forecasting System (DAFFS)

NASA Astrophysics Data System (ADS)

Leka, K. D.; Barnes, Graham; Wagner, Eric

2018-04-01

A classification infrastructure built upon Discriminant Analysis (DA) has been developed at NorthWest Research Associates for examining the statistical differences between samples of two known populations. Originating to examine the physical differences between flare-quiet and flare-imminent solar active regions, we describe herein some details of the infrastructure including: parametrization of large datasets, schemes for handling "null" and "bad" data in multi-parameter analysis, application of non-parametric multi-dimensional DA, an extension through Bayes' theorem to probabilistic classification, and methods invoked for evaluating classifier success. The classifier infrastructure is applicable to a wide range of scientific questions in solar physics. We demonstrate its application to the question of distinguishing flare-imminent from flare-quiet solar active regions, updating results from the original publications that were based on different data and much smaller sample sizes. Finally, as a demonstration of "Research to Operations" efforts in the space-weather forecasting context, we present the Discriminant Analysis Flare Forecasting System (DAFFS), a near-real-time operationally-running solar flare forecasting tool that was developed from the research-directed infrastructure.

Elemental labelling combined with liquid chromatography inductively coupled plasma mass spectrometry for quantification of biomolecules: A review

PubMed Central

Kretschy, Daniela; Koellensperger, Gunda; Hann, Stephan

2012-01-01

This article reviews novel quantification concepts where elemental labelling is combined with flow injection inductively coupled plasma mass spectrometry (FI-ICP-MS) or liquid chromatography inductively coupled plasma mass spectrometry (LC–ICP-MS), and employed for quantification of biomolecules such as proteins, peptides and related molecules in challenging sample matrices. In the first sections an overview on general aspects of biomolecule quantification, as well as of labelling will be presented emphasizing the potential, which lies in such methodological approaches. In this context, ICP-MS as detector provides high sensitivity, selectivity and robustness in biological samples and offers the capability for multiplexing and isotope dilution mass spectrometry (IDMS). Fundamental methodology of elemental labelling will be highlighted and analytical, as well as biomedical applications will be presented. A special focus will lie on established applications underlining benefits and bottlenecks of such approaches for the implementation in real life analysis. Key research made in this field will be summarized and a perspective for future developments including sophisticated and innovative applications will given. PMID:23062431

Development of a Laboratory Synchrophasor Network and an Application to Estimate Transmission Line Parameters in Real Time

NASA Astrophysics Data System (ADS)

Almiron Bonnin, Rubens Eduardo

The development of an experimental synchrophasors network and application of synchrophasors for real-time transmission line parameter monitoring are presented in this thesis. In the laboratory setup, a power system is simulated in a RTDS real-time digital simulator, and the simulated voltages and currents are input to hardware phasor measurement units (PMUs) through the analog outputs of the simulator. Time synchronizing signals for the PMU devices are supplied from a common GPS clock. The real time data collected from PMUs are sent to a phasor data concentrator (PDC) through Ethernet using the TCP/IP protocol. A real-time transmission line parameter monitoring application program that uses the synchrophasor data provided by the PDC is implemented and validated. The experimental synchrophasor network developed in this thesis is expected to be used in research on synchrophasor applications as well as in graduate and undergraduate teaching.

Piezoelectric and Electrostrictive Materials for Transducer Applications. Volume 1

DTIC Science & Technology

1990-01-31

by non-stoichiometry or by doping with aleovalent ions. For doped materials the aging is very similar to that in PLZT, again affecting the dispersive...during aging looks similar to that in MnO doped PMNPT.? Figure 8 shows the Cole-Cole plot for different aging time in the quenched sample. CL~ m ~ m rmt... parameters show that the angle of tilt of the arc from the real axis a and the average time constant r decrease during aging . The Cole-Cole plot become

Apparatus and method for quantitative determination of materials contained in fluids

DOEpatents

Radziemski, Leon J.; Cremers, David A.

1985-01-01

Apparatus and method for near real-time in-situ monitoring of particulates and vapors contained in fluids. Initial filtration of a known volume of the fluid sample is combined with laser-induced dielectric breakdown spectroscopy of the filter employed to obtain qualitative and quantitative information with high sensitivity. Application of the invention to monitoring of beryllium, beryllium oxide, or other beryllium-alloy dusts is demonstrated. Significant shortening of analysis time is achieved from those of the usual chemical techniques of analysis.

Apparatus and method for quantitative determination of materials contained in fluids

DOEpatents

Radziemski, L.J.; Cremers, D.A.

1982-09-07

Apparatus and method for near real-time in-situ monitoring of particulates and vapors contained in fluids are described. Initial filtration of a known volume of the fluid sample is combined with laser-induced dielectric breakdown spectroscopy of the filter employed to obtain qualitative and quantitative information with high sensitivity. Application of the invention to monitoring of beryllium, beryllium oxide, or other beryllium-alloy dusts is shown. Significant shortening of analysis time is achieved from the usual chemical techniques of analysis.

Applications of virtual reality technology in pathology.

PubMed

Grimes, G J; McClellan, S A; Goldman, J; Vaughn, G L; Conner, D A; Kujawski, E; McDonald, J; Winokur, T; Fleming, W

1997-01-01

TelePath(SM) a telerobotic system utilizing virtual microscope concepts based on high quality still digital imaging and aimed at real-time support for surgery by remote diagnosis of frozen sections. Many hospitals and clinics have an application for the remote practice of pathology, particularly in the area of reading frozen sections in support of surgery, commonly called anatomic pathology. The goal is to project the expertise of the pathologist into the remote setting by giving the pathologist access to the microscope slides with an image quality and human interface comparable to what the pathologist would experience at a real rather than a virtual microscope. A working prototype of a virtual microscope has been defined and constructed which has the needed performance in both the image quality and human interface areas for a pathologist to work remotely. This is accomplished through the use of telerobotics and an image quality which provides the virtual microscope the same diagnostic capabilities as a real microscope. The examination of frozen sections is performed a two-dimensional world. The remote pathologist is in a virtual world with the same capabilities as a "real" microscope, but response times may be slower depending on the specific computing and telecommunication environments. The TelePath system has capabilities far beyond a normal biological microscope, such as the ability to create a low power image of the entire sample using multiple images digitally matched together; the ability to digitally retrace a viewing trajectory; and the ability to archive images using CD ROM and other mass storage devices.

A Survey of Recent MARTe Based Systems

NASA Astrophysics Data System (ADS)

Neto, André C.; Alves, Diogo; Boncagni, Luca; Carvalho, Pedro J.; Valcarcel, Daniel F.; Barbalace, Antonio; De Tommasi, Gianmaria; Fernandes, Horácio; Sartori, Filippo; Vitale, Enzo; Vitelli, Riccardo; Zabeo, Luca

2011-08-01

The Multithreaded Application Real-Time executor (MARTe) is a data driven framework environment for the development and deployment of real-time control algorithms. The main ideas which led to the present version of the framework were to standardize the development of real-time control systems, while providing a set of strictly bounded standard interfaces to the outside world and also accommodating a collection of facilities which promote the speed and ease of development, commissioning and deployment of such systems. At the core of every MARTe based application, is a set of independent inter-communicating software blocks, named Generic Application Modules (GAM), orchestrated by a real-time scheduler. The platform independence of its core library provides MARTe the necessary robustness and flexibility for conveniently testing applications in different environments including non-real-time operating systems. MARTe is already being used in several machines, each with its own peculiarities regarding hardware interfacing, supervisory control configuration, operating system and target control application. This paper presents and compares the most recent results of systems using MARTe: the JET Vertical Stabilization system, which uses the Real Time Application Interface (RTAI) operating system on Intel multi-core processors; the COMPASS plasma control system, driven by Linux RT also on Intel multi-core processors; ISTTOK real-time tomography equilibrium reconstruction which shares the same support configuration of COMPASS; JET error field correction coils based on VME, PowerPC and VxWorks; FTU LH reflected power system running on VME, Intel with RTAI.

A Robust Kalman Framework with Resampling and Optimal Smoothing

PubMed Central

Kautz, Thomas; Eskofier, Bjoern M.

2015-01-01

The Kalman filter (KF) is an extremely powerful and versatile tool for signal processing that has been applied extensively in various fields. We introduce a novel Kalman-based analysis procedure that encompasses robustness towards outliers, Kalman smoothing and real-time conversion from non-uniformly sampled inputs to a constant output rate. These features have been mostly treated independently, so that not all of their benefits could be exploited at the same time. Here, we present a coherent analysis procedure that combines the aforementioned features and their benefits. To facilitate utilization of the proposed methodology and to ensure optimal performance, we also introduce a procedure to calculate all necessary parameters. Thereby, we substantially expand the versatility of one of the most widely-used filtering approaches, taking full advantage of its most prevalent extensions. The applicability and superior performance of the proposed methods are demonstrated using simulated and real data. The possible areas of applications for the presented analysis procedure range from movement analysis over medical imaging, brain-computer interfaces to robot navigation or meteorological studies. PMID:25734647

Fast, multi-channel real-time processing of signals with microsecond latency using graphics processing units.

PubMed

Rath, N; Kato, S; Levesque, J P; Mauel, M E; Navratil, G A; Peng, Q

2014-04-01

Fast, digital signal processing (DSP) has many applications. Typical hardware options for performing DSP are field-programmable gate arrays (FPGAs), application-specific integrated DSP chips, or general purpose personal computer systems. This paper presents a novel DSP platform that has been developed for feedback control on the HBT-EP tokamak device. The system runs all signal processing exclusively on a Graphics Processing Unit (GPU) to achieve real-time performance with latencies below 8 μs. Signals are transferred into and out of the GPU using PCI Express peer-to-peer direct-memory-access transfers without involvement of the central processing unit or host memory. Tests were performed on the feedback control system of the HBT-EP tokamak using forty 16-bit floating point inputs and outputs each and a sampling rate of up to 250 kHz. Signals were digitized by a D-TACQ ACQ196 module, processing done on an NVIDIA GTX 580 GPU programmed in CUDA, and analog output was generated by D-TACQ AO32CPCI modules.

Real-air data reduction procedures based on flow parameters measured in the test section of supersonic and hypersonic facilities

NASA Technical Reports Server (NTRS)

Miller, C. G., III; Wilder, S. E.

1972-01-01

Data-reduction procedures for determining free stream and post-normal shock kinetic and thermodynamic quantities are derived. These procedures are applicable to imperfect real air flows in thermochemical equilibrium for temperatures to 15 000 K and a range of pressures from 0.25 N/sq m to 1 GN/sq m. Although derived primarily to meet the immediate needs of the 6-inch expansion tube, these procedures are applicable to any supersonic or hypersonic test facility where combinations of three of the following flow parameters are measured in the test section: (1) Stagnation pressure behind normal shock; (2) freestream static pressure; (3) stagnation point heat transfer rate; (4) free stream velocity; (5) stagnation density behind normal shock; and (6) free stream density. Limitations of the nine procedures and uncertainties in calculated flow quantities corresponding to uncertainties in measured input data are discussed. A listing of the computer program is presented, along with a description of the inputs required and a sample of the data printout.

75 FR 24722 - Agency Information Collection Activities: Submission for OMB Review; Comment Request, OMB No...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-05

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41 CFR 102-75.1205 - What action must be taken on approved applications?

Code of Federal Regulations, 2010 CFR

2010-07-01

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41 CFR 102-75.1205 - What action must be taken on approved applications?

Code of Federal Regulations, 2011 CFR

2011-01-01

... taken on approved applications? 102-75.1205 Section 102-75.1205 Public Contracts and Property Management Federal Property Management Regulations System (Continued) FEDERAL MANAGEMENT REGULATION REAL PROPERTY 75-REAL PROPERTY DISPOSAL Use of Federal Real Property to Assist the Homeless Action on Approved...

Quantification of the biocontrol agent Trichoderma harzianum with real-time TaqMan PCR and its potential extrapolation to the hyphal biomass.

PubMed

López-Mondéjar, Rubén; Antón, Anabel; Raidl, Stefan; Ros, Margarita; Pascual, José Antonio

2010-04-01

The species of the genus Trichoderma are used successfully as biocontrol agents against a wide range of phytopathogenic fungi. Among them, Trichoderma harzianum is especially effective. However, to develop more effective fungal biocontrol strategies in organic substrates and soil, tools for monitoring the control agents are required. Real-time PCR is potentially an effective tool for the quantification of fungi in environmental samples. The aim of this study consisted of the development and application of a real-time PCR-based method to the quantification of T. harzianum, and the extrapolation of these data to fungal biomass values. A set of primers and a TaqMan probe for the ITS region of the fungal genome were designed and tested, and amplification was correlated to biomass measurements obtained with optical microscopy and image analysis, of the hyphal length of the mycelium of the colony. A correlation of 0.76 between ITS copies and biomass was obtained. The extrapolation of the quantity of ITS copies, calculated based on real-time PCR data, into quantities of fungal biomass provides potentially a more accurate value of the quantity of soil fungi. Copyright 2009 Elsevier Ltd. All rights reserved.

Effective real-time vehicle tracking using discriminative sparse coding on local patches

NASA Astrophysics Data System (ADS)

Chen, XiangJun; Ye, Feiyue; Ruan, Yaduan; Chen, Qimei

2016-01-01

A visual tracking framework that provides an object detector and tracker, which focuses on effective and efficient visual tracking in surveillance of real-world intelligent transport system applications, is proposed. The framework casts the tracking task as problems of object detection, feature representation, and classification, which is different from appearance model-matching approaches. Through a feature representation of discriminative sparse coding on local patches called DSCLP, which trains a dictionary on local clustered patches sampled from both positive and negative datasets, the discriminative power and robustness has been improved remarkably, which makes our method more robust to a complex realistic setting with all kinds of degraded image quality. Moreover, by catching objects through one-time background subtraction, along with offline dictionary training, computation time is dramatically reduced, which enables our framework to achieve real-time tracking performance even in a high-definition sequence with heavy traffic. Experiment results show that our work outperforms some state-of-the-art methods in terms of speed, accuracy, and robustness and exhibits increased robustness in a complex real-world scenario with degraded image quality caused by vehicle occlusion, image blur of rain or fog, and change in viewpoint or scale.

Online Detection of Driver Fatigue Using Steering Wheel Angles for Real Driving Conditions

PubMed Central

Li, Zuojin; Li, Shengbo Eben; Li, Renjie; Cheng, Bo; Shi, Jinliang

2017-01-01

This paper presents a drowsiness on-line detection system for monitoring driver fatigue level under real driving conditions, based on the data of steering wheel angles (SWA) collected from sensors mounted on the steering lever. The proposed system firstly extracts approximate entropy (ApEn) features from fixed sliding windows on real-time steering wheel angles time series. After that, this system linearizes the ApEn features series through an adaptive piecewise linear fitting using a given deviation. Then, the detection system calculates the warping distance between the linear features series of the sample data. Finally, this system uses the warping distance to determine the drowsiness state of the driver according to a designed binary decision classifier. The experimental data were collected from 14.68 h driving under real road conditions, including two fatigue levels: “wake” and “drowsy”. The results show that the proposed system is capable of working online with an average 78.01% accuracy, 29.35% false detections of the “awake” state, and 15.15% false detections of the “drowsy” state. The results also confirm that the proposed method based on SWA signal is valuable for applications in preventing traffic accidents caused by driver fatigue. PMID:28257094

Sample Training Based Wildfire Segmentation by 2D Histogram θ-Division with Minimum Error

PubMed Central

Dong, Erqian; Sun, Mingui; Jia, Wenyan; Zhang, Dengyi; Yuan, Zhiyong

2013-01-01

A novel wildfire segmentation algorithm is proposed with the help of sample training based 2D histogram θ-division and minimum error. Based on minimum error principle and 2D color histogram, the θ-division methods were presented recently, but application of prior knowledge on them has not been explored. For the specific problem of wildfire segmentation, we collect sample images with manually labeled fire pixels. Then we define the probability function of error division to evaluate θ-division segmentations, and the optimal angle θ is determined by sample training. Performances in different color channels are compared, and the suitable channel is selected. To further improve the accuracy, the combination approach is presented with both θ-division and other segmentation methods such as GMM. Our approach is tested on real images, and the experiments prove its efficiency for wildfire segmentation. PMID:23878526

Demonstrating the Value of Near Real-time Satellite-based Earth Observations in a Research and Education Framework

NASA Astrophysics Data System (ADS)

Chiu, L.; Hao, X.; Kinter, J. L.; Stearn, G.; Aliani, M.

2017-12-01

The launch of GOES-16 series provides an opportunity to advance near real-time applications in natural hazard detection, monitoring and warning. This study demonstrates the capability and values of receiving real-time satellite-based Earth observations over a fast terrestrial networks and processing high-resolution remote sensing data in a university environment. The demonstration system includes 4 components: 1) Near real-time data receiving and processing; 2) data analysis and visualization; 3) event detection and monitoring; and 4) information dissemination. Various tools are developed and integrated to receive and process GRB data in near real-time, produce images and value-added data products, and detect and monitor extreme weather events such as hurricane, fire, flooding, fog, lightning, etc. A web-based application system is developed to disseminate near-real satellite images and data products. The images are generated with GIS-compatible format (GeoTIFF) to enable convenient use and integration in various GIS platforms. This study enhances the capacities for undergraduate and graduate education in Earth system and climate sciences, and related applications to understand the basic principles and technology in real-time applications with remote sensing measurements. It also provides an integrated platform for near real-time monitoring of extreme weather events, which are helpful for various user communities.

Field application of a planted fixed bed reactor (PFR) for support media and rhizosphere investigation using undisturbed samples from full-scale constructed wetlands.

PubMed

Barreto, A B; Vasconcellos, G R; von Sperling, M; Kuschk, P; Kappelmeyer, U; Vasel, J L

2015-01-01

This study presents a novel method for investigations on undisturbed samples from full-scale horizontal subsurface-flow constructed wetlands (HSSFCW). The planted fixed bed reactor (PFR), developed at the Helmholtz Center for Environmental Research (UFZ), is a universal test unit for planted soil filters that reproduces the operational conditions of a constructed wetland (CW) system in laboratory scale. The present research proposes modifications on the PFR original configuration in order to allow its operation in field conditions. A mobile device to obtain undisturbed samples from real-scale HSSFCW was also developed. The experimental setting is presented with two possible operational configurations. The first allows the removal and replacement of undisturbed samples in the CW bed for laboratory investigations, guaranteeing sample integrity with a mobile device. The second allows the continuous operation of the PFR and undisturbed samples as a fraction of the support media, reproducing the same environmental conditions outside the real-scale system. Investigations on the hydrodynamics of the adapted PFR were carried out with saline tracer tests, validating the proposed adaptation. Six adapted PFR units were installed next to full-scale HSSFCW beds and fed with interstitial liquid pumped from two regions of planted and unplanted support media. Fourteen points were monitored along the system, covering carbon fractions, nitrogen and sulfate. The results indicate the method as a promising tool for investigations on CW support media, rhizosphere and open space for studies on CW modeling, respirometry, kinetic parameters, microbial communities, redox potential and plant influence on HSSFCW.

Model-based vision for space applications

NASA Technical Reports Server (NTRS)

Chaconas, Karen; Nashman, Marilyn; Lumia, Ronald

1992-01-01

This paper describes a method for tracking moving image features by combining spatial and temporal edge information with model based feature information. The algorithm updates the two-dimensional position of object features by correlating predicted model features with current image data. The results of the correlation process are used to compute an updated model. The algorithm makes use of a high temporal sampling rate with respect to spatial changes of the image features and operates in a real-time multiprocessing environment. Preliminary results demonstrate successful tracking for image feature velocities between 1.1 and 4.5 pixels every image frame. This work has applications for docking, assembly, retrieval of floating objects and a host of other space-related tasks.

The bivariate regression model and its application

NASA Astrophysics Data System (ADS)

Pratikno, B.; Sulistia, L.; Saniyah

2018-03-01

The paper studied a bivariate regression model (BRM) and its application. The maximum power and minimum size are used to choose the eligible tests using non-sample prior information (NSPI). In the simulation study on real data, we used Wilk’s lamda to determine the best model of the BRM. The result showed that the power of the pre-test-test (PTT) on the NSPI is a significant choice of the tests among unrestricted test (UT) and restricted test (RT), and the best model of the BRM is Y (1) = ‑894 + 46X and Y (2) = 78 + 0.2X with significant Wilk’s lamda 0.88 < 0.90 (Wilk’s table).

On a useful functional representation of control system structure

NASA Technical Reports Server (NTRS)

Malchow, Harvey L.

1988-01-01

An alternative structure for control systems is proposed. The structure is represented by a three-element block diagram and three functional definitions. It is argued that the three functional elements form a canonical set. The set includes the functions description, estimation and control. General overlay of the structure on parallel state and nested-state control systems is discussed. Breakdown of two real nested-state control systems into the proposed functional format is displayed. Application of the process to the mapping of complex control systems R and D efforts is explained with the Mars Rover Sample and Return mission as an example. A previous application of this basic functional structure to Space Station performance requirements organization is discussed.

Layout Study and Application of Mobile App Recommendation Approach Based On Spark Streaming Framework

NASA Astrophysics Data System (ADS)

Wang, H. T.; Chen, T. T.; Yan, C.; Pan, H.

2018-05-01

For App recommended areas of mobile phone software, made while using conduct App application recommended combined weighted Slope One algorithm collaborative filtering algorithm items based on further improvement of the traditional collaborative filtering algorithm in cold start, data matrix sparseness and other issues, will recommend Spark stasis parallel algorithm platform, the introduction of real-time streaming streaming real-time computing framework to improve real-time software applications recommended.

Designing and Using Projects with Real World Application in a MBA Managerial Accounting Class: The Case of The Balanced Scorecard

ERIC Educational Resources Information Center

Houke, Charlotte

2017-01-01

This paper explores the purpose of designing and using projects with real world application in a M.B.A. managerial accounting class. Included is a discussion of how and why the Balanced Scorecard (BSC) Project has been used in classes to link theory with practice by providing real world application of the BSC framework. M.B.A. students represent a…

Evaluation of non-extracted genital swabs for real-time HSV PCR.

PubMed

Miari, Victoria F; Wall, Gavin R; Clark, Duncan A

2015-01-01

Nucleic acid extraction of clinical samples is accepted as a key requirement in molecular diagnostics. At Barts Health NHS Trust, swabs taken from patients with clinical suspicion of HSV infection were routinely extracted on the Qiagen MDx BioRobot prior to testing with a real-time triplex PCR for HSV1, HSV2, and VZV. The aim of this study was to adapt an existing HSV1/HSV2/VZV real-time PCR by replacing VZV with phocine herpesvirus 1 (PhHV) as an internal control (IC) and evaluate whether this adapted assay required the nucleic acid extraction step for predominantly genital swabs. First 313 non-extracted and extracted swabs were tested in parallel with the existing triplex HSV1/HSV2/VZV real-time PCR. The second stage involved testing 176 non-extracted swabs using a triplex real-time PCR for HSV1, HSV2, and PhHV and comparing the results with the samples extracted and tested by the original triplex assay. The results correlated well when the existing assay was used, with only three non-extracted samples that would have been reported as negative compared to the extracted sample result (Cq s 33, 39, 35-two samples HSV1, one sample HSV2). In the evaluation using the adapted assay containing the IC, two of 176 samples were discordant, where a HSV negative non-extracted sample result would have been reported differently to the extracted sample result (Cq s 32, 33-both HSV1). This study demonstrated that it is feasible to test non-extracted swabs for HSV in a real-time PCR that includes an IC. J. Med. Virol. 87: 125-129, 2015. © 2014 Wiley Periodicals, Inc. © 2014 Wiley Periodicals, Inc.

Rapid, Real-time Methane Detection in Ground Water Using a New Gas-Water Equilibrator Design

NASA Astrophysics Data System (ADS)

Ruybal, C. J.; DiGiulio, D. C.; Wilkin, R. T.; Hargrove, K. D.; McCray, J. E.

2014-12-01

Recent increases in unconventional gas development have been accompanied by public concern for methane contamination in drinking water wells near production areas. Although not a regulated pollutant, methane may be a marker contaminant for others that are less mobile in groundwater and thus may be detected later, or at a location closer to the source. In addition, methane poses an explosion hazard if exsolved concentrations reach 5 - 15% volume in air. Methods for determining dissolved gases, such as methane, have evolved over 60 years. However, the response time of these methods is insufficient to monitor trends in methane concentration in real-time. To enable rapid, real-time monitoring of aqueous methane concentrations during ground water purging, a new gas-water equilibrator (GWE) was designed that increases gas-water mass exchange rates of methane for measurement. Monitoring of concentration trends allows a comparison of temporal trends between sampling events and comparison of baseline conditions with potential post-impact conditions. These trends may be a result of removal of stored casing water, pre-purge ambient borehole flow, formation physical and chemical heterogeneity, or flow outside of well casing due to inadequate seals. Real-time information in the field can help focus an investigation, aid in determining when to collect a sample, save money by limiting costs (e.g. analytical, sample transport and storage), and provide an immediate assessment of local methane concentrations. Four domestic water wells, one municipal water well, and one agricultural water well were sampled for traditional laboratory analysis and compared to the field GWE results. Aqueous concentrations measured on the GWE ranged from non-detect to 1,470 μg/L methane. Some trends in aqueous methane concentrations measured on the GWE were observed during purging. Applying a paired t-test comparing the new GWE method and traditional laboratory analysis yielded a p-value 0.383, suggesting no significant difference between the two methods for the current study. Additional field and laboratory experimentation are necessary to justify use beyond screening. However, early GWE use suggests promising results and applications.

Recent progress on gas sensor based on quantum cascade lasers and hollow fiber waveguides

NASA Astrophysics Data System (ADS)

Liu, Ningwu; Sun, Juan; Deng, Hao; Ding, Junya; Zhang, Lei; Li, Jingsong

2017-02-01

Mid-infrared laser spectroscopy provides an ideal platform for trace gas sensing applications. Despite this potential, early MIR sensing applications were limited due to the size of the involved optical components, e.g. light sources and sample cells. A potential solution to this demand is the integration of hollow fiber waveguide with novelty quantum cascade lasers.Recently QCLs had great improvements in power, efficiency and wavelength range, which made the miniaturized platforms for gas sensing maintaining or even enhancing the achievable sensitivity conceivable. So that the miniaturization of QCLs and HWGs can be evolved into a mini sensor, which may be tailored to a variety of real-time and in situ applications ranging from environmental monitoring to workplace safety surveillance. In this article, we introduce QCLs and HWGs, display the applications of HWG based on QCL gas sensing and discuss future strategies for hollow fiber coupled quantum cascade laser gas sensor technology.

Improved Safety for Molecular Diagnosis of Classical Rabies Viruses by Use of a TaqMan Real-Time Reverse Transcription-PCR “Double Check” Strategy▿ †

PubMed Central

Hoffmann, B.; Freuling, C. M.; Wakeley, P. R.; Rasmussen, T. B.; Leech, S.; Fooks, A. R.; Beer, M.; Müller, T.

2010-01-01

To improve the diagnosis of classical rabies virus with molecular methods, a validated, ready-to-use, real-time reverse transcription-PCR (RT-PCR) assay was developed. In a first step, primers and 6-carboxyfluorescien-labeled TaqMan probes specific for rabies virus were selected from the consensus sequence of the nucleoprotein gene of 203 different rabies virus sequences derived from GenBank. The selected primer-probe combination was highly specific and sensitive. During validation using a sample set of rabies virus strains from the virus archives of the Friedrich-Loeffler-Institut (FLI; Germany), the Veterinary Laboratories Agency (VLA; United Kingdom), and the DTU National Veterinary Institute (Lindholm, Denmark), covering the global diversity of rabies virus lineages, it was shown that both the newly developed assay and a previously described one had some detection failures. This was overcome by a combined assay that detected all samples as positive. In addition, the introduction of labeled positive controls (LPC) increased the diagnostic safety of the single as well as the combined assay. Based on the newly developed, alternative assay for the detection of rabies virus and the application of LPCs, an improved diagnostic sensitivity and reliability can be ascertained for postmortem and intra vitam real-time RT-PCR analyses in rabies reference laboratories. PMID:20739489

Analyzing the carbon dynamics in north western Portugal: calibration and application of Forest-BGC

NASA Astrophysics Data System (ADS)

Rodrigues, M. A.; Lopes, D. M.; Leite, S. M.; Tabuada, V. M.

2010-04-01

Net primary production (NPP) is an important variable that allows monitoring forestry ecosystems fixation of atmospheric Carbon. The importance of monitoring the sequestred carbon is related to the binding commitments established by the Kyoto Protocol. There are ecophysiologic models, as Forest-BGC that allow for estimating NPP. In a first stage, this study aims to analyze the climate evolution at the Vila Real administrative district during the last decades. The historical information will be observed in order to detect the past tendencies of evolution. Past will help us to predict future. In a next stage these tendencies will be used to infer the impact of these change scenarios on the net primary production of the forest ecosystems from this study area. For a parameterization and validation of the FOREST-BGC, this study was carried on based on 500 m2 sampling plots from the National Forest Inventory 2006 and are located in several County Halls of the district of Vila Real (Montalegre, Chaves, Valpaços, Boticas, Vila Pouca de Aguiar, Murça, Mondim de Basto, Alijó, Sabrosa and Vila Real). In order to quantify Biomass dinamics, we have selected 45 sampling plots: 19 from Pinus pinaster stands, 17 from Quercus pyrenaica and 10 from mixed of Quercus pyrenaica with Pinus pinaster. Adaptation strategies for climate change impacts can be proposed based on these research results.

Innovative qPCR using interfacial effects to enable low threshold cycle detection and inhibition relief

PubMed Central

Harshman, Dustin K.; Rao, Brianna M.; McLain, Jean E.; Watts, George S.; Yoon, Jeong-Yeol

2015-01-01

Molecular diagnostics offers quick access to information but fails to operate at a speed required for clinical decision-making. Our novel methodology, droplet-on-thermocouple silhouette real-time polymerase chain reaction (DOTS qPCR), uses interfacial effects for droplet actuation, inhibition relief, and amplification sensing. DOTS qPCR has sample-to-answer times as short as 3 min 30 s. In infective endocarditis diagnosis, DOTS qPCR demonstrates reproducibility, differentiation of antibiotic susceptibility, subpicogram limit of detection, and thermocycling speeds of up to 28 s/cycle in the presence of tissue contaminants. Langmuir and Gibbs adsorption isotherms are used to describe the decreasing interfacial tension upon amplification. Moreover, a log-linear relationship with low threshold cycles is presented for real-time quantification by imaging the droplet-on-thermocouple silhouette with a smartphone. DOTS qPCR resolves several limitations of commercially available real-time PCR systems, which rely on fluorescence detection, have substantially higher threshold cycles, and require expensive optical components and extensive sample preparation. Due to the advantages of low threshold cycle detection, we anticipate extending this technology to biological research applications such as single cell, single nucleus, and single DNA molecule analyses. Our work is the first demonstrated use of interfacial effects for sensing reaction progress, and it will enable point-of-care molecular diagnosis of infections. PMID:26601245

Improved safety for molecular diagnosis of classical rabies viruses by use of a TaqMan real-time reverse transcription-PCR "double check" strategy.

PubMed

Hoffmann, B; Freuling, C M; Wakeley, P R; Rasmussen, T B; Leech, S; Fooks, A R; Beer, M; Müller, T

2010-11-01

To improve the diagnosis of classical rabies virus with molecular methods, a validated, ready-to-use, real-time reverse transcription-PCR (RT-PCR) assay was developed. In a first step, primers and 6-carboxyfluorescien-labeled TaqMan probes specific for rabies virus were selected from the consensus sequence of the nucleoprotein gene of 203 different rabies virus sequences derived from GenBank. The selected primer-probe combination was highly specific and sensitive. During validation using a sample set of rabies virus strains from the virus archives of the Friedrich-Loeffler-Institut (FLI; Germany), the Veterinary Laboratories Agency (VLA; United Kingdom), and the DTU National Veterinary Institute (Lindholm, Denmark), covering the global diversity of rabies virus lineages, it was shown that both the newly developed assay and a previously described one had some detection failures. This was overcome by a combined assay that detected all samples as positive. In addition, the introduction of labeled positive controls (LPC) increased the diagnostic safety of the single as well as the combined assay. Based on the newly developed, alternative assay for the detection of rabies virus and the application of LPCs, an improved diagnostic sensitivity and reliability can be ascertained for postmortem and intra vitam real-time RT-PCR analyses in rabies reference laboratories.

Continuous-flow water sampler for real-time isotopic water measurements

NASA Astrophysics Data System (ADS)

Carter, J.; Dennis, K.

2013-12-01

Measuring the stable isotopes of liquid water (δ18O and δD) is a tool familiar to many Earth scientists, but most current techniques require discrete sampling. For example, isotope ratio mass spectrometry requires the collection of aliquots of water that are then converted to CO2, CO or H2 for analysis. Similarly, laser-based techniques, such as Cavity Ring-Down Spectroscopy (CRDS) convert discrete samples (typically < 2μL) of liquid water to water vapor using a flash vaporization process. By requiring the use of discrete samples fine-scale spatial and temporal studies of changes in δ18O and δD are limited. Here we present a continuous-flow water sampler that will enable scientists to probe isotopic changes in real-time, with applications including, but not limited to, quantification of the 'amount effect' (Dansgaard, 1964) during an individual precipitation event or storm track, real-time mixing of water in river systems, and shipboard continuous water measurements (Munksgaard et al., 2012). Due to the inherent ability of CRDS to measure a continuous flow of water vapor it is an ideal candidate for interfacing with a continuous water sampling system. Here we present results from the first commercially available continuous-flow water sampler, developed by engineers at Picarro. This peripheral device is compatible with Picarro CRDS isotopic water analyzers, allowing real-time, continuous isotopic measurements of liquid water. The new device, which expands upon the design of Munskgaard et al. (2011), utilizes expanded polytetrafluoroethylene (ePTFE) membrane technology to continuously generate gas-phase water, while liquid water is pumped through the system. The water vapor subsequently travels to the CRDS analyzer where the isotopic ratios are measured and recorded. The generation of water vapor using membrane technology is sensitive to environmental conditions, which if not actively control, lead to sustainable experimental noise and drift. Consequently, our continuous-flow water sample employs active control for all pertinent parameters, significantly increasing its stability and usability. We will present data from controlled laboratory experiments demonstrating sample-to-sample precision and long-term stability. We will also show experimental data that highlights the instrumental sample-to-sample memory, which we have decreased significantly from previous implementations of this technology. Additionally, we will present field results from the Sacramento River, CA. Dansgaard, W. (1964) 'Stable isotopes in precipitation', Tellus, 16(4), p. 436-468. Munksgaard, N.C., Wurster, C.M., Bass, A., Zagorskis, I., and Bird, M.I. (2012) 'First continuous shipboard d18O and dD measurements in seawater by diffusion sampling--cavity ring-down spectrometry', Environmental Chemistry Letters, 10, p.301-307. Munksgaard, N.C., Wurster, C.M., and Bird, M.I., (2011), 'Continuous analysis of δ18O and δD values of water by diffusion sampling cavity ring-down spectrometry: a novel sampling device for unattended field monitoring of precipitation, ground and surface waters', Rapid Communications in Mass Spectrometry, 25, p. 3706-3712.

Multiplex Real-Time PCR Method for Simultaneous Identification and Toxigenic Type Characterization of Clostridium difficile From Stool Samples

PubMed Central

Alam, Mohammad J.; Tisdel, Naradah L.; Shah, Dhara N.; Yapar, Mehmet; Lasco, Todd M.; Garey, Kevin W.

2015-01-01

Background The aim of this study was to develop and validate a multiplex real-time PCR assay for simultaneous identification and toxigenic type characterization of Clostridium difficile. Methods The multiplex real-time PCR assay targeted and simultaneously detected triose phosphate isomerase (tpi) and binary toxin (cdtA) genes, and toxin A (tcdA) and B (tcdB) genes in the first and sec tubes, respectively. The results of multiplex real-time PCR were compared to those of the BD GeneOhm Cdiff assay, targeting the tcdB gene alone. The toxigenic culture was used as the reference, where toxin genes were detected by multiplex real-time PCR. Results A total of 351 stool samples from consecutive patients were included in the study. Fifty-five stool samples (15.6%) were determined to be positive for the presence of C. difficile by using multiplex real-time PCR. Of these, 48 (87.2%) were toxigenic (46 tcdA and tcdB-positive, two positive for only tcdB) and 11 (22.9%) were cdtA-positive. The sensitivity, specificity, negative predictive value (NPV), and positive predictive value (PPV) of the multiplex real-time PCR compared with the toxigenic culture were 95.6%, 98.6%, 91.6%, and 99.3%, respectively. The analytical sensitivity of the multiplex real-time PCR assay was determined to be 103colonyforming unit (CFU)/g spiked stool sample and 0.0625 pg genomic DNA from culture. Analytical specificity determined by using 15 enteric and non-clostridial reference strains was 100%. Conclusions The multiplex real-time PCR assay accurately detected C. difficile isolates from diarrheal stool samples and characterized its toxin genes in a single PCR run. PMID:25932438

Designing robust watermark barcodes for multiplex long-read sequencing.

PubMed

Ezpeleta, Joaquín; Krsticevic, Flavia J; Bulacio, Pilar; Tapia, Elizabeth

2017-03-15

To attain acceptable sample misassignment rates, current approaches to multiplex single-molecule real-time sequencing require upstream quality improvement, which is obtained from multiple passes over the sequenced insert and significantly reduces the effective read length. In order to fully exploit the raw read length on multiplex applications, robust barcodes capable of dealing with the full single-pass error rates are needed. We present a method for designing sequencing barcodes that can withstand a large number of insertion, deletion and substitution errors and are suitable for use in multiplex single-molecule real-time sequencing. The manuscript focuses on the design of barcodes for full-length single-pass reads, impaired by challenging error rates in the order of 11%. The proposed barcodes can multiplex hundreds or thousands of samples while achieving sample misassignment probabilities as low as 10-7 under the above conditions, and are designed to be compatible with chemical constraints imposed by the sequencing process. Software tools for constructing watermark barcode sets and demultiplexing barcoded reads, together with example sets of barcodes and synthetic barcoded reads, are freely available at www.cifasis-conicet.gov.ar/ezpeleta/NS-watermark . ezpeleta@cifasis-conicet.gov.ar. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Optimization of chemical and instrumental parameters in hydride generation laser-induced breakdown spectrometry for the determination of arsenic, antimony, lead and germanium in aqueous samples.

PubMed

Yeşiller, Semira Unal; Yalçın, Serife

2013-04-03

A laser induced breakdown spectrometry hyphenated with on-line continuous flow hydride generation sample introduction system, HG-LIBS, has been used for the determination of arsenic, antimony, lead and germanium in aqueous environments. Optimum chemical and instrumental parameters governing chemical hydride generation, laser plasma formation and detection were investigated for each element under argon and nitrogen atmosphere. Arsenic, antimony and germanium have presented strong enhancement in signal strength under argon atmosphere while lead has shown no sensitivity to ambient gas type. Detection limits of 1.1 mg L(-1), 1.0 mg L(-1), 1.3 mg L(-1) and 0.2 mg L(-1) were obtained for As, Sb, Pb and Ge, respectively. Up to 77 times enhancement in detection limit of Pb were obtained, compared to the result obtained from the direct analysis of liquids by LIBS. Applicability of the technique to real water samples was tested through spiking experiments and recoveries higher than 80% were obtained. Results demonstrate that, HG-LIBS approach is suitable for quantitative analysis of toxic elements and sufficiently fast for real time continuous monitoring in aqueous environments. Copyright © 2013 Elsevier B.V. All rights reserved.

A Method for Estimating View Transformations from Image Correspondences Based on the Harmony Search Algorithm

PubMed Central

Cuevas, Erik; Díaz, Margarita

2015-01-01

In this paper, a new method for robustly estimating multiple view relations from point correspondences is presented. The approach combines the popular random sampling consensus (RANSAC) algorithm and the evolutionary method harmony search (HS). With this combination, the proposed method adopts a different sampling strategy than RANSAC to generate putative solutions. Under the new mechanism, at each iteration, new candidate solutions are built taking into account the quality of the models generated by previous candidate solutions, rather than purely random as it is the case of RANSAC. The rules for the generation of candidate solutions (samples) are motivated by the improvisation process that occurs when a musician searches for a better state of harmony. As a result, the proposed approach can substantially reduce the number of iterations still preserving the robust capabilities of RANSAC. The method is generic and its use is illustrated by the estimation of homographies, considering synthetic and real images. Additionally, in order to demonstrate the performance of the proposed approach within a real engineering application, it is employed to solve the problem of position estimation in a humanoid robot. Experimental results validate the efficiency of the proposed method in terms of accuracy, speed, and robustness. PMID:26339228

Simultaneous determination of 30 hormones illegally added to anti-ageing functional foods using UPLC-MS/MS coupled with SPE clean-up.

PubMed

He, Xiaoqin; Xi, Cunxian; Tang, Bobin; Wang, Guomin; Chen, Dongdong; Peng, Tao; Mu, Zhaode

2014-01-01

A novel analytical method employing solid-phase extraction (SPE) coupled with ultra-high-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) was developed for the simultaneous determination of 30 hormones in anti-ageing functional foods (capsules, powders and tablets). The analytes were extracted with acetic acid-acetonitrile (1-99 v/v), methanol and acetone, respectively. The extract was purified using a combined column, followed by analyte detection with electrospray ionisation in positive- or negative-ion modes. The results indicated that the 30 compounds had good linear correlations in the range of 1-1000 μg kg⁻¹, and the correlation coefficients were above 0.99. The limits of detection (LOD) and limits of quantification (LOQ) were 0.03-2 and 0.1-5 μg kg⁻¹, respectively. The average recovery of 30 compounds at the three spiked levels varied from 74.7% to 124.1%, and the relative standard deviation (RSD) was 2.4-15.0%. This method was applied to the analysis of hormones in 14 real samples of which seven hormones (such as estrone, dienestrol) were detected in four samples, but the remainder of the hormones were not detected. The developed method is sensitive, efficient, reliable and applicable to real samples.

Superhydrophobic analyte concentration utilizing colloid-pillar array SERS substrates.

PubMed

Wallace, Ryan A; Charlton, Jennifer J; Kirchner, Teresa B; Lavrik, Nickolay V; Datskos, Panos G; Sepaniak, Michael J

2014-12-02

The ability to detect a few molecules present in a large sample is of great interest for the detection of trace components in both medicinal and environmental samples. Surface enhanced Raman spectroscopy (SERS) is a technique that can be utilized to detect molecules at very low absolute numbers. However, detection at trace concentration levels in real samples requires properly designed delivery and detection systems. The following work involves superhydrophobic surfaces that have as a framework deterministic or stochastic silicon pillar arrays formed by lithographic or metal dewetting protocols, respectively. In order to generate the necessary plasmonic substrate for SERS detection, simple and flow stable Ag colloid was added to the functionalized pillar array system via soaking. Native pillars and pillars with hydrophobic modification are used. The pillars provide a means to concentrate analyte via superhydrophobic droplet evaporation effects. A ≥ 100-fold concentration of analyte was estimated, with a limit of detection of 2.9 × 10(-12) M for mitoxantrone dihydrochloride. Additionally, analytes were delivered to the surface via a multiplex approach in order to demonstrate an ability to control droplet size and placement for scaled-up uses in real world applications. Finally, a concentration process involving transport and sequestration based on surface treatment selective wicking is demonstrated.

Power requirements and environmental impact of a pedelec. A case study based on real-life applications

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

Abagnale, Carmelina, E-mail: c.abagnale@unina.it; Cardone, Massimo, E-mail: massimo.cardone@unina.it; Iodice, Paolo, E-mail: paolo.iodice@unina.it

2015-07-15

This paper describes the methodologies to appraise the power requests and environmental analysis of an electrically assisted bicycle under real driving conditions, also containing regulations and technical-science-related aspects. For this purpose, in this study, the on-road test program of an electrically assisted bicycle was executed in the urban area of Naples on different test tracks, so a general assessment about its driving behavior under several driving conditions was performed. The power requirements in different typical riding situations were estimated by a procedure based on the experimental kinematic parameters that characterize the driving dynamics collected during the real-life applications. An environmentalmore » analysis was also performed, with a methodology that takes into account the environmental assessment of a moped by measuring the experimental moped exhaust emissions of the regulated pollutants. Starting from the results acquired during the different test samples, besides, an assessment of the electric traction offered by this pedelec on the driving comfort was evaluated for different riding situations. - Highlights: • The power requirements of a pedelec in typical riding conditions were identified. • The estimated electricity consumption for battery recharging was defined. • An environmental valuation of the tested pedelec and of a moped was performed. • Emissions that could be saved utilizing a pedelec instead of a moped were derived.« less

Identification of the origin of faecal contamination in estuarine oysters using Bacteroidales and F-specific RNA bacteriophage markers.

PubMed

Mieszkin, S; Caprais, M P; Le Mennec, C; Le Goff, M; Edge, T A; Gourmelon, M

2013-09-01

The aim of this study was to identify the origin of faecal pollution impacting the Elorn estuary (Brittany, France) by applying microbial source tracking (MST) markers in both oysters and estuarine waters. The MST markers used were as follows: (i) human-, ruminant- and pig-associated Bacteroidales markers by real-time PCR and (ii) human genogroup II and animal genogroup I of F-specific RNA bacteriophages (FRNAPH) by culture/genotyping and by direct real-time reverse-transcriptase PCR. The higher occurrence of the human genogroup II of F-specific RNA bacteriophages using a culture/genotyping method, and human-associated Bacteroidales marker by real-time PCR, allowed the identification of human faecal contamination as the predominant source of contamination in oysters (total of 18 oyster batches tested) and waters (total of 24 water samples tested). The importance of using the intravalvular liquids instead of digestive tissues, when applying host-associated Bacteroidales markers in oysters, was also revealed. This study has shown that the application of a MST toolbox of diverse bacterial and viral methods can provide multiple lines of evidence to identify the predominant source of faecal contamination in shellfish from an estuarine environment. Application of this MST toolbox is a useful approach to understand the origin of faecal contamination in shellfish harvesting areas in an estuarine setting. © 2013 The Society for Applied Microbiology.

Finite Adaptation and Multistep Moves in the Metropolis-Hastings Algorithm for Variable Selection in Genome-Wide Association Analysis

PubMed Central

Peltola, Tomi; Marttinen, Pekka; Vehtari, Aki

2012-01-01

High-dimensional datasets with large amounts of redundant information are nowadays available for hypothesis-free exploration of scientific questions. A particular case is genome-wide association analysis, where variations in the genome are searched for effects on disease or other traits. Bayesian variable selection has been demonstrated as a possible analysis approach, which can account for the multifactorial nature of the genetic effects in a linear regression model. Yet, the computation presents a challenge and application to large-scale data is not routine. Here, we study aspects of the computation using the Metropolis-Hastings algorithm for the variable selection: finite adaptation of the proposal distributions, multistep moves for changing the inclusion state of multiple variables in a single proposal and multistep move size adaptation. We also experiment with a delayed rejection step for the multistep moves. Results on simulated and real data show increase in the sampling efficiency. We also demonstrate that with application specific proposals, the approach can overcome a specific mixing problem in real data with 3822 individuals and 1,051,811 single nucleotide polymorphisms and uncover a variant pair with synergistic effect on the studied trait. Moreover, we illustrate multimodality in the real dataset related to a restrictive prior distribution on the genetic effect sizes and advocate a more flexible alternative. PMID:23166669

Application of laser spectroscopy for measurement of exhaled ethane in patients with lung cancer.

PubMed

Skeldon, K D; McMillan, L C; Wyse, C A; Monk, S D; Gibson, G; Patterson, C; France, T; Longbottom, C; Padgett, M J

2006-02-01

There is increasing interest in ethane (C(2)H(6)) in exhaled breath as a non-invasive marker of oxidative stress (OS) and thereby a potential indicator of disease. However, the lack of real-time measurement techniques has limited progress in the field. Here we report on a novel Tunable Diode Laser Spectrometer (TDLS) applied to the analysis of exhaled ethane in patients with lung cancer. The patient group (n=52) comprised randomly selected patients presenting at a respiratory clinic. Of these, a sub-group (n=12) was subsequently diagnosed with lung cancer. An age-matched group (n=12) corresponding to the lung cancer group was taken from a larger control group of healthy adults (n=58). The concentration of ethane in a single exhaled breath sample collected from all subjects was later measured using the TDLS. This technique is capable of real-time analysis of samples with accuracy 0.1 parts per billion (ppb), over 10 times less than typical ambient levels in the northern hemisphere. After correcting for ambient background, ethane in the control group (26% smokers) ranged from 0 to 10.54 ppb (median of 1.9 ppb) while ethane in the lung cancer patients (42% smokers) ranged from 0 to 7.6 ppb (median of 0.7 ppb). Ethane among the non-lung cancer patients presenting for investigation of respiratory disease ranged from 0 to 25 ppb (median 1.45 ppb). We conclude that, while the TDLS proved effective for accurate and rapid sample analysis, there was no significant difference in exhaled ethane among any of the subject groups. Comments are made on the suitability of the technique for monitoring applications.