A simple method to measure critical angles for high-sensitivity differential refractometry.

PubMed

Zilio, S C

2012-01-16

A total internal reflection-based differencial refractometer, capable of measuring the real and imaginary parts of the complex refractive index in real time, is presented. The device takes advantage of the phase difference acquired by s- and p-polarized light to generate an easily detectable minimum at the reflected profile. The method allows to sensitively measuring transparent and turbid liquid samples.

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.

Weighted fractional permutation entropy and fractional sample entropy for nonlinear Potts financial dynamics

NASA Astrophysics Data System (ADS)

Xu, Kaixuan; Wang, Jun

2017-02-01

In this paper, recently introduced permutation entropy and sample entropy are further developed to the fractional cases, weighted fractional permutation entropy (WFPE) and fractional sample entropy (FSE). The fractional order generalization of information entropy is utilized in the above two complexity approaches, to detect the statistical characteristics of fractional order information in complex systems. The effectiveness analysis of proposed methods on the synthetic data and the real-world data reveals that tuning the fractional order allows a high sensitivity and more accurate characterization to the signal evolution, which is useful in describing the dynamics of complex systems. Moreover, the numerical research on nonlinear complexity behaviors is compared between the returns series of Potts financial model and the actual stock markets. And the empirical results confirm the feasibility of the proposed model.

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.

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.

Nonlinearly Activated Neural Network for Solving Time-Varying Complex Sylvester Equation.

PubMed

Li, Shuai; Li, Yangming

2013-10-28

The Sylvester equation is often encountered in mathematics and control theory. For the general time-invariant Sylvester equation problem, which is defined in the domain of complex numbers, the Bartels-Stewart algorithm and its extensions are effective and widely used with an O(n³) time complexity. When applied to solving the time-varying Sylvester equation, the computation burden increases intensively with the decrease of sampling period and cannot satisfy continuous realtime calculation requirements. For the special case of the general Sylvester equation problem defined in the domain of real numbers, gradient-based recurrent neural networks are able to solve the time-varying Sylvester equation in real time, but there always exists an estimation error while a recently proposed recurrent neural network by Zhang et al [this type of neural network is called Zhang neural network (ZNN)] converges to the solution ideally. The advancements in complex-valued neural networks cast light to extend the existing real-valued ZNN for solving the time-varying real-valued Sylvester equation to its counterpart in the domain of complex numbers. In this paper, a complex-valued ZNN for solving the complex-valued Sylvester equation problem is investigated and the global convergence of the neural network is proven with the proposed nonlinear complex-valued activation functions. Moreover, a special type of activation function with a core function, called sign-bi-power function, is proven to enable the ZNN to converge in finite time, which further enhances its advantage in online processing. In this case, the upper bound of the convergence time is also derived analytically. Simulations are performed to evaluate and compare the performance of the neural network with different parameters and activation functions. Both theoretical analysis and numerical simulations validate the effectiveness of the proposed method.

Improved assemblies using a source-agnostic pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of contigs

DOE PAGES

Scholz, Matthew; Lo, Chien -Chi; Chain, Patrick S. G.

2014-10-01

Assembly of metagenomic samples is a very complex process, with algorithms designed to address sequencing platform-specific issues, (read length, data volume, and/or community complexity), while also faced with genomes that differ greatly in nucleotide compositional biases and in abundance. To address these issues, we have developed a post-assembly process: MetaGenomic Assembly by Merging (MeGAMerge). We compare this process to the performance of several assemblers, using both real, and in-silico generated samples of different community composition and complexity. MeGAMerge consistently outperforms individual assembly methods, producing larger contigs with an increased number of predicted genes, without replication of data. MeGAMerge contigs aremore » supported by read mapping and contig alignment data, when using synthetically-derived and real metagenomic data, as well as by gene prediction analyses and similarity searches. Ultimately, MeGAMerge is a flexible method that generates improved metagenome assemblies, with the ability to accommodate upcoming sequencing platforms, as well as present and future assembly algorithms.« less

Chemodosimetric analysis in food-safety monitoring: design, synthesis, and application of a bimetallic Re(I)-Pt(II) complex for detection of dimethyl sulfide in foods.

PubMed

Chow, Cheuk-Fai; Gong, Fu-Wen; Gong, Cheng-Bin

2014-09-21

Detection of neutral biogenic sulfides plays a crucial role in food safety. A new heterobimetallic Re(I)-Pt(II) donor-acceptor complex--[Re(biq)(CO)3(CN)]-[Pt(DMSO)(Cl)2] (1, biq = 2,2'-biquinoline)--was synthesized and characterized. The X-ray crystallographic and photophysical data for 1 are reported in this study. Complex 1 indicated the luminescent chemodosimetric selectivity for dimethyl sulfide, which persisted even in the presence of a variety of interfering vapors, with a detection limit as low as 0.96 ppm. The binding constant (log K) of 1 toward dimethyl sulfide was 3.63 ± 0.03. The analyte selectivity of the complexes was found to be dependent on the ligand coordinated to the Re(I) center. Real samples (beef, chicken, and pork) were monitored real-time for gaseous dimethyl sulfide. Complex 1 shows a linear spectrofluorimetric response with increasing storage time of the meats at 30 °C.

Real-Time, Single-Step Bioassay Using Nanoplasmonic Resonator With Ultra-High Sensitivity

NASA Technical Reports Server (NTRS)

Zhang, Xiang (Inventor); Chen, Fanqing Frank (Inventor); Su, Kai-Hang (Inventor); Wei, Qi-Huo (Inventor); Ellman, Jonathan A. (Inventor); Sun, Cheng (Inventor)

2014-01-01

A nanoplasmonic resonator (NPR) comprising a metallic nanodisk with alternating shielding layer(s), having a tagged biomolecule conjugated or tethered to the surface of the nanoplasmonic resonator for highly sensitive measurement of enzymatic activity. NPRs enhance Raman signals in a highly reproducible manner, enabling fast detection of protease and enzyme activity, such as Prostate Specific Antigen (paPSA), in real-time, at picomolar sensitivity levels. Experiments on extracellular fluid (ECF) from paPSA-positive cells demonstrate specific detection in a complex bio-fluid background in real-time single-step detection in very small sample volumes.

Real-time, single-step bioassay using nanoplasmonic resonator with ultra-high sensitivity

DOEpatents

Zhang, Xiang; Ellman, Jonathan A; Chen, Fanqing Frank; Su, Kai-Hang; Wei, Qi-Huo; Sun, Cheng

2014-04-01

A nanoplasmonic resonator (NPR) comprising a metallic nanodisk with alternating shielding layer(s), having a tagged biomolecule conjugated or tethered to the surface of the nanoplasmonic resonator for highly sensitive measurement of enzymatic activity. NPRs enhance Raman signals in a highly reproducible manner, enabling fast detection of protease and enzyme activity, such as Prostate Specific Antigen (paPSA), in real-time, at picomolar sensitivity levels. Experiments on extracellular fluid (ECF) from paPSA-positive cells demonstrate specific detection in a complex bio-fluid background in real-time single-step detection in very small sample volumes.

Two alternative DNA extraction methods to improve the detection of Mycobacterium-tuberculosis-complex members in cattle and red deer tissue samples.

PubMed

Fell, Shari; Bröckl, Stephanie; Büttner, Mathias; Rettinger, Anna; Zimmermann, Pia; Straubinger, Reinhard K

2016-09-15

Bovine tuberculosis (bTB), which is caused by Mycobacterium bovis and M. caprae, is a notifiable animal disease in Germany. Diagnostic procedure is based on a prescribed protocol that is published in the framework of German bTB legislation. In this protocol small sample volumes are used for DNA extraction followed by real-time PCR analyses. As mycobacteria tend to concentrate in granuloma and the infected tissue in early stages of infection does not necessarily show any visible lesions, it is likely that DNA extraction from only small tissue samples (20-40 mg) of a randomly chosen spot from the organ and following PCR testing may result in false negative results. In this study two DNA extraction methods were developed to process larger sample volumes to increase the detection sensitivity of mycobacterial DNA in animal tissue. The first extraction method is based on magnetic capture, in which specific capture oligonucleotides were utilized. These nucleotides are linked to magnetic particles and capture Mycobacterium-tuberculosis-complex (MTC) DNA released from 10 to 15 g of tissue material. In a second approach remaining sediments from the magnetic capture protocol were further processed with a less complex extraction protocol that can be used in daily routine diagnostics. A total number of 100 tissue samples from 34 cattle (n = 74) and 18 red deer (n = 26) were analyzed with the developed protocols and results were compared to the prescribed protocol. All three extraction methods yield reliable results by the real-time PCR analysis. The use of larger sample volume led to a sensitivity increase of DNA detection which was shown by the decrease of Ct-values. Furthermore five samples which were tested negative or questionable by the official extraction protocol were detected positive by real time PCR when the alternative extraction methods were used. By calculating the kappa index, the three extraction protocols resulted in a moderate (0.52; protocol 1 vs 3) to almost perfect agreement (1.00; red deer sample testing with all protocols). Both new methods yielded increased detection rates for MTC DNA detection in large sample volumes and consequently improve the official diagnostic protocol.

Direct Sequence Spread Spectrum (DSSS) Receiver, User Manual

DTIC Science & Technology

2008-01-01

sampled data is clocked in to correlator data registers and a comparison is made between the code and data register contents, producing a correlation ...symbol (equal to the processing gain Gp ) but need not be otherwise synchronised with the spreading codes . This allows a very long and noise- like PRBS...and Q channels are independently but synchronously sampled . Complex Real ADC FIR Filter Interpolator Acquisition Correlators

Quantification of Campylobacter spp. in pig feces by direct real-time PCR with an internal control of extraction and amplification.

PubMed

Leblanc-Maridor, Mily; Garénaux, Amélie; Beaudeau, François; Chidaine, Bérangère; Seegers, Henri; Denis, Martine; Belloc, Catherine

2011-04-01

The rapid and direct quantification of Campylobacter spp. in complex substrates like feces or environmental samples is crucial to facilitate epidemiological studies on Campylobacter in pig production systems. We developed a real-time PCR assay for detecting and quantifying Campylobacter spp. directly in pig feces with the use of an internal control. Campylobacter spp. and Yersinia ruckeri primers-probes sets were designed and checked for specificity with diverse Campylobacter, related organisms, and other bacterial pathogens before being used in field samples. The quantification of Campylobacter spp. by the real-time PCR then was realized on 531 fecal samples obtained from experimentally and naturally infected pigs; the numeration of Campylobacter on Karmali plate was done in parallel. Yersinia ruckeri, used as bacterial internal control, was added to the samples before DNA extraction to control DNA-extraction and PCR-amplification. The sensitivity of the PCR assay was 10 genome copies. The established Campylobacter real-time PCR assay showed a 7-log-wide linear dynamic range of quantification (R²=0.99) with a detection limit of 200 Colony Forming Units of Campylobacter per gram of feces. A high correlation was found between the results obtained by real-time PCR and those by culture at both qualitative and quantitative levels. Moreover, DNA extraction followed by real-time PCR reduced the time needed for analysis to a few hours (within a working day). In conclusion, the real-time PCR developed in this study provides new tools for further epidemiological surveys to investigate the carriage and excretion of Campylobacter by pigs. Copyright © 2011 Elsevier B.V. All rights reserved.

[Automated RNA amplification for the rapid identification of Mycobacterium tuberculosis complex in respiratory specimens].

PubMed

Drouillon, V; Houriez, F; Buze, M; Lagrange, P; Herrmann, J-L

2006-01-01

Rapid and sensitive detection of Mycobacterium tuberculosis complex (MTB) directly on clinical respiratory specimens is essential for a correct management of patients suspected of tuberculosis. For this purpose PCR-based kits are available to detect MTB in respiratory specimen but most of them need at least 4 hours to be completed. New methods, based on TRC method (TRC: Transcription Reverse transcription Concerted--TRCRapid M. Tuberculosis--Tosoh Bioscience, Tokyo, Japon) and dedicated monitor have been developed. A new kit (TRC Rapid M. tuberculosis and Real-time monitor TRCRapid-160, Tosoh Corporation, Japan) enabling one step amplification and real-time detection of MTB 16S rRNA by a combination of intercalative dye oxazole yellow-linked DNA probe and isothermal RNA amplification directly on respiratory specimens has been tested in our laboratory. 319 respiratory specimens were tested in this preliminary study and results were compared to smear and culture. Fourteen had a positive culture for MTB. Among theses samples, smear was positive in 11 cases (78.6%) and TRC process was positive in 8 cases (57.1%). Overall sensitivity of TRC compared to smear positive samples is 73%. Theses first results demonstrated that a rapid identification of MTB was possible (less than 2 processing hours for 14 specimens and about 1 hour for 1 specimen) in most cases of smear positive samples using ready to use reagents for real time detection of MTB rRNA in clinical samples. New pretreatment and extraction reagents kits to increase the stability of the sputum RNA and the extraction efficiency are now tested in our laboratory.

KSC-2014-3135

NASA Image and Video Library

2014-07-03

CAPE CANAVERAL, Fla. – Samples of Earth rocks and real meteorites are featured in an interactive display at the new Great Balls of Fire exhibit at NASA’s Kennedy Space Center Visitor Complex in Florida. The grand opening featured remarks by former NASA astronaut Tom Jones, and Therrin Protze, chief operating officer at Delaware North Parks and Resorts at the visitor complex. Great Balls of Fire shares the story of the origins of our solar system, asteroids and comets and their possible impacts and risks. The 1,500-square-foot exhibit, located in the East Gallery of the IMAX theatre at the visitor complex, features several interactive displays, real meteorites and replica asteroid models. The exhibit is a production of The Space Science Institute's National Center for Interactive Learning. It is a traveling exhibition that also receives funding from NASA and the National Science Foundation. Photo credit: NASA/Daniel Casper

Arsenic distribution and valence state variation studied by fast hierarchical length-scale morphological, compositional, and speciation imaging at the Nanoscopium, Synchrotron Soleil

NASA Astrophysics Data System (ADS)

Somogyi, Andrea; Medjoubi, Kadda; Sancho-Tomas, Maria; Visscher, P. T.; Baranton, Gil; Philippot, Pascal

2017-09-01

The understanding of real complex geological, environmental and geo-biological processes depends increasingly on in-depth non-invasive study of chemical composition and morphology. In this paper we used scanning hard X-ray nanoprobe techniques in order to study the elemental composition, morphology and As speciation in complex highly heterogeneous geological samples. Multivariate statistical analytical techniques, such as principal component analysis and clustering were used for data interpretation. These measurements revealed the quantitative and valance state inhomogeneity of As and its relation to the total compositional and morphological variation of the sample at sub-μm scales.

Challenges associated with the sampling and analysis of organosulfur compounds in air using real-time PTR-ToF-MS and off-line GC-FID

NASA Astrophysics Data System (ADS)

Perraud, V.; Meinardi, S.; Blake, D. R.; Finlayson-Pitts, B. J.

2015-12-01

Organosulfur compounds (OSC) are naturally emitted via various processes involving phytoplankton and algae in marine regions, from animal metabolism and from biomass decomposition inland. These compounds are malodorant and reactive. Their oxidation to methanesulfonic and sulfuric acids leads to the formation and growth of atmospheric particles, which are known to have negative effects on visibility, climate and human health. In order to predict particle formation events, accurate measurements of the OSC precursors are essential. Here, two different approaches, proton-transfer reaction time-of-flight mass spectrometry (PTR-ToF-MS) and canister sampling coupled with GC-FID are compared for both laboratory standards [dimethyl sulfide (DMS), dimethyl disulfide (DMDS), dimethyl trisulfide (DMTS) and methanethiol (MTO)] and for a complex sample. Results show that both techniques produce accurate quantification of DMS. While PTR-ToF-MS provides real-time measurements of all four OSCs individually, significant fragmentation of DMDS and DMTS occurs, which can complicate their identification in complex mixtures. Canister sampling coupled with GC-FID provides excellent sensitivity for DMS, DMDS and DMTS. However, MTO was observed to react on metal surfaces to produce DMDS and, in the presence of hydrogen sulfide, even DMTS. Avoiding metal in sampling systems seems to be necessary for measuring all but dimethyl sulfide in air.

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

INTEGRATED AND REAL-TIME DIFFUSION DENUDER SAMPLE FOR PM2.5. (R825367)

EPA Science Inventory

Abstract

Particulate matter (PM) is a complex mixture of stable condensed phases, adsorbed or dissolved gases, and semi-volatile materials, i.e. compounds that transfer between the gas and condensed phases. Fine particles in both rural and urban environments contain su...

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.

Single-protein nanomechanical mass spectrometry in real time

PubMed Central

Hanay, M.S.; Kelber, S.; Naik, A.K.; Chi, D.; Hentz, S.; Bullard, E.C.; Colinet, E.; Duraffourg, L.; Roukes, M.L.

2012-01-01

Nanoelectromechanical systems (NEMS) resonators can detect mass with exceptional sensitivity. Previously, mass spectra from several hundred adsorption events were assembled in NEMS-based mass spectrometry using statistical analysis. Here, we report the first realization of single-molecule NEMS-based mass spectrometry in real time. As each molecule in the sample adsorbs upon the NEMS resonator, its mass and the position-of-adsorption are determined by continuously tracking two driven vibrational modes of the device. We demonstrate the potential of multimode NEMS-based mass spectrometry by analyzing IgM antibody complexes in real-time. NEMS-MS is a unique and promising new form of mass spectrometry: it can resolve neutral species, provides resolving power that increases markedly for very large masses, and allows acquisition of spectra, molecule-by-molecule, in real-time. PMID:22922541

Method for Hot Real-Time Analysis of Pyrolysis Vapors at Pilot Scale

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

Pomeroy, Marc D

Pyrolysis oils contain more than 400 compounds, up to 60% of which do not re-volatilize for subsequent chemical analysis. Vapor chemical composition is also complicated as additional condensation reactions occur during quenching and collection of the product. Due to the complexity of the pyrolysis oil, and a desire to catalytically upgrade the vapor composition before condensation, online real-time analytical techniques such as Molecular Beam Mass Spectrometry (MBMS) are of great use. However, in order to properly sample hot pyrolysis vapors at the pilot scale, many challenges must be overcome.

Selective and Sensitive Fluorescent Detection of Picric Acid by New Pyrene and Anthracene Based Copper Complexes.

PubMed

Reddy, Kumbam Lingeshwar; Kumar, Anabathula Manoj; Dhir, Abhimanew; Krishnan, Venkata

2016-11-01

New pyrene and anthracene based copper complexes 4 and 7 respectively were designed, synthesized and characterized. The fluorescence behaviour of both 4 and 7 were evaluated towards nitro aromatics and anions. Both 4 and 7 possess high selectivity for the detection of well-known explosive picric acid (PA) by showing maximum fluorescence affinity. Furthermore, complex 4 showed similar sensing efficiency towards PA at different pH ranges. It was also used for real world applications, as illustrated by the very fast detection of PA from soil samples observed directly by naked eye.

Comparison of DNA Microarray, Loop-Mediated Isothermal Amplification (LAMP) and Real-Time PCR with DNA Sequencing for Identification of Fusarium spp. Obtained from Patients with Hematologic Malignancies.

PubMed

de Souza, Marcela; Matsuzawa, Tetsuhiro; Sakai, Kanae; Muraosa, Yasunori; Lyra, Luzia; Busso-Lopes, Ariane Fidelis; Levin, Anna Sara Shafferman; Schreiber, Angélica Zaninelli; Mikami, Yuzuru; Gonoi, Tohoru; Kamei, Katsuhiko; Moretti, Maria Luiza; Trabasso, Plínio

2017-08-01

The performance of three molecular biology techniques, i.e., DNA microarray, loop-mediated isothermal amplification (LAMP), and real-time PCR were compared with DNA sequencing for properly identification of 20 isolates of Fusarium spp. obtained from blood stream as etiologic agent of invasive infections in patients with hematologic malignancies. DNA microarray, LAMP and real-time PCR identified 16 (80%) out of 20 samples as Fusarium solani species complex (FSSC) and four (20%) as Fusarium spp. The agreement among the techniques was 100%. LAMP exhibited 100% specificity, while DNA microarray, LAMP and real-time PCR showed 100% sensitivity. The three techniques had 100% agreement with DNA sequencing. Sixteen isolates were identified as FSSC by sequencing, being five Fusarium keratoplasticum, nine Fusarium petroliphilum and two Fusarium solani. On the other hand, sequencing identified four isolates as Fusarium non-solani species complex (FNSSC), being three isolates as Fusarium napiforme and one isolate as Fusarium oxysporum. Finally, LAMP proved to be faster and more accessible than DNA microarray and real-time PCR, since it does not require a thermocycler. Therefore, LAMP signalizes as emerging and promising methodology to be used in routine identification of Fusarium spp. among cases of invasive fungal infections.

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.

Complexity and multifractal behaviors of multiscale-continuum percolation financial system for Chinese stock markets

NASA Astrophysics Data System (ADS)

Zeng, Yayun; Wang, Jun; Xu, Kaixuan

2017-04-01

A new financial agent-based time series model is developed and investigated by multiscale-continuum percolation system, which can be viewed as an extended version of continuum percolation system. In this financial model, for different parameters of proportion and density, two Poisson point processes (where the radii of points represent the ability of receiving or transmitting information among investors) are applied to model a random stock price process, in an attempt to investigate the fluctuation dynamics of the financial market. To validate its effectiveness and rationality, we compare the statistical behaviors and the multifractal behaviors of the simulated data derived from the proposed model with those of the real stock markets. Further, the multiscale sample entropy analysis is employed to study the complexity of the returns, and the cross-sample entropy analysis is applied to measure the degree of asynchrony of return autocorrelation time series. The empirical results indicate that the proposed financial model can simulate and reproduce some significant characteristics of the real stock markets to a certain extent.

A Modular Low-Complexity ECG Delineation Algorithm for Real-Time Embedded Systems.

PubMed

Bote, Jose Manuel; Recas, Joaquin; Rincon, Francisco; Atienza, David; Hermida, Roman

2018-03-01

This work presents a new modular and low-complexity algorithm for the delineation of the different ECG waves (QRS, P and T peaks, onsets, and end). Involving a reduced number of operations per second and having a small memory footprint, this algorithm is intended to perform real-time delineation on resource-constrained embedded systems. The modular design allows the algorithm to automatically adjust the delineation quality in runtime to a wide range of modes and sampling rates, from a ultralow-power mode when no arrhythmia is detected, in which the ECG is sampled at low frequency, to a complete high-accuracy delineation mode, in which the ECG is sampled at high frequency and all the ECG fiducial points are detected, in the case of arrhythmia. The delineation algorithm has been adjusted using the QT database, providing very high sensitivity and positive predictivity, and validated with the MIT database. The errors in the delineation of all the fiducial points are below the tolerances given by the Common Standards for Electrocardiography Committee in the high-accuracy mode, except for the P wave onset, for which the algorithm is above the agreed tolerances by only a fraction of the sample duration. The computational load for the ultralow-power 8-MHz TI MSP430 series microcontroller ranges from 0.2% to 8.5% according to the mode used.

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.

Environmental and human monitoring of Americium-241 utilizing extraction chromatography and alpha-spectrometry.

PubMed

Goldstein, S J; Hensley, C A; Armenta, C E; Peters, R J

1997-03-01

Recent developments in extraction chromatography have simplified the separation of americium from complex matrices in preparation for alpha-spectroscopy relative to traditional methods. Here we present results of procedures developed/adapted for water, air, and bioassay samples with less than 1 g of inorganic residue. Prior analytical methods required the use of a complex, multistage procedure for separation of americium from these matrices. The newer, simplified procedure requires only a single 2 mL extraction chromatographic separation for isolation of Am and lanthanides from other components of the sample. This method has been implemented on an extensive variety of "real" environmental and bioassay samples from the Los Alamos area, and consistently reliable and accurate results with appropriate detection limits have been obtained. The new method increases analytical throughput by a factor of approximately 2 and decreases environmental hazards from acid and mixed-waste generation relative to the prior technique. Analytical accuracy, reproducibility, and reliability are also significantly improved over the more complex and laborious method used previously.

Toward cost-efficient sampling methods

NASA Astrophysics Data System (ADS)

Luo, Peng; Li, Yongli; Wu, Chong; Zhang, Guijie

2015-09-01

The sampling method has been paid much attention in the field of complex network in general and statistical physics in particular. This paper proposes two new sampling methods based on the idea that a small part of vertices with high node degree could possess the most structure information of a complex network. The two proposed sampling methods are efficient in sampling high degree nodes so that they would be useful even if the sampling rate is low, which means cost-efficient. The first new sampling method is developed on the basis of the widely used stratified random sampling (SRS) method and the second one improves the famous snowball sampling (SBS) method. In order to demonstrate the validity and accuracy of two new sampling methods, we compare them with the existing sampling methods in three commonly used simulation networks that are scale-free network, random network, small-world network, and also in two real networks. The experimental results illustrate that the two proposed sampling methods perform much better than the existing sampling methods in terms of achieving the true network structure characteristics reflected by clustering coefficient, Bonacich centrality and average path length, especially when the sampling rate is low.

Technique for Performing Dielectric Property Measurements at Microwave Frequencies

NASA Technical Reports Server (NTRS)

Barmatz, Martin B.; Jackson, Henry W.

2010-01-01

A paper discusses the need to perform accurate dielectric property measurements on larger sized samples, particularly liquids at microwave frequencies. These types of measurements cannot be obtained using conventional cavity perturbation methods, particularly for liquids or powdered or granulated solids that require a surrounding container. To solve this problem, a model has been developed for the resonant frequency and quality factor of a cylindrical microwave cavity containing concentric cylindrical samples. This model can then be inverted to obtain the real and imaginary dielectric constants of the material of interest. This approach is based on using exact solutions to Maxwell s equations for the resonant properties of a cylindrical microwave cavity and also using the effective electrical conductivity of the cavity walls that is estimated from the measured empty cavity quality factor. This new approach calculates the complex resonant frequency and associated electromagnetic fields for a cylindrical microwave cavity with lossy walls that is loaded with concentric, axially aligned, lossy dielectric cylindrical samples. In this approach, the calculated complex resonant frequency, consisting of real and imaginary parts, is related to the experimentally measured quantities. Because this approach uses Maxwell's equations to determine the perturbed electromagnetic fields in the cavity with the material(s) inserted, one can calculate the expected wall losses using the fields for the loaded cavity rather than just depending on the value of the fields obtained from the empty cavity quality factor. These additional calculations provide a more accurate determination of the complex dielectric constant of the material being studied. The improved approach will be particularly important when working with larger samples or samples with larger dielectric constants that will further perturb the cavity electromagnetic fields. Also, this approach enables the ability to have a larger sample of interest, such as a liquid or powdered or granulated solid, inside a cylindrical container.

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

Usefulness of real-time PCR as a complementary tool to the monitoring of Legionella spp. and Legionella pneumophila by culture in industrial cooling systems.

PubMed

Touron-Bodilis, A; Pougnard, C; Frenkiel-Lebossé, H; Hallier-Soulier, S

2011-08-01

This study was designed to evaluate the usefulness of quantification by real-time PCR as a management tool to monitor concentrations of Legionella spp. and Legionella pneumophila in industrial cooling systems and its ability to anticipate culture trends by the French standard method (AFNOR T90-431). Quantifications of Legionella bacteria were achieved by both methods on samples from nine cooling systems with different water qualities. Proportion of positive samples for L. pneumophila quantified by PCR was clearly lower in deionized or river waters submitted to a biocide treatment than in raw river waters, while positive samples for Legionella spp. were quantified for almost all the samples. For some samples containing PCR inhibitors, high quantification limits (up to 4·80 × 10(5) GU l(-1) ) did not allow us to quantify L. pneumophila, when they were quantified by culture. Finally, the monitoring of concentrations of L. pneumophila by both methods showed similar trends for 57-100% of the samples. These results suggest that, if some methodological steps designed to reduce inhibitory problems and thus decrease the quantification limits, could be developed to quantify Legionella in complex waters, the real-time PCR could be a valuable complementary tool to monitor the evolution of L. pneumophila concentrations. This study shows the possibility of using real-time PCR to monitor L. pneumophila proliferations in cooling systems and the importance to adapt nucleic acid extraction and purification protocols to raw waters. Journal of Applied Microbiology © 2011 The Society for Applied Microbiology. No claim to French Government works.

User's Manual for PCSMS (Parallel Complex Sparse Matrix Solver). Version 1.

NASA Technical Reports Server (NTRS)

Reddy, C. J.

2000-01-01

PCSMS (Parallel Complex Sparse Matrix Solver) is a computer code written to make use of the existing real sparse direct solvers to solve complex, sparse matrix linear equations. PCSMS converts complex matrices into real matrices and use real, sparse direct matrix solvers to factor and solve the real matrices. The solution vector is reconverted to complex numbers. Though, this utility is written for Silicon Graphics (SGI) real sparse matrix solution routines, it is general in nature and can be easily modified to work with any real sparse matrix solver. The User's Manual is written to make the user acquainted with the installation and operation of the code. Driver routines are given to aid the users to integrate PCSMS routines in their own codes.

Schistosoma real-time PCR as diagnostic tool for international travellers and migrants.

PubMed

Cnops, Lieselotte; Tannich, Egbert; Polman, Katja; Clerinx, Jan; Van Esbroeck, Marjan

2012-10-01

To evaluate the use of a genus-specific PCR that combines high sensitivity with the detection of different Schistosoma species for diagnosis in international travellers and migrants in comparison to standard microscopy. The genus-specific real-time PCR was developed to target the 28S ribosomal RNA gene of the major human Schistosoma species. It was validated for analytical specificity and reproducibility and demonstrated an analytical sensitivity of 0.2 eggs per gram of faeces. Its diagnostic performance was further evaluated on 152 faecal, 32 urine and 38 serum samples from patients presenting at the outpatient clinic of the Institute of Tropical Medicine in Antwerp (Belgium). We detected Schistosoma DNA in 76 faecal (50.0%) and five urine (15.6%) samples of which, respectively, nine and one were not detected by standard microscopy. Only two of the 38 serum samples of patients with confirmed schistosomiasis were positive with the presently developed PCR. Sequence analysis on positive faecal samples allowed identification of the Schistosoma species complex. The real-time PCR is highly sensitive and may offer added value in diagnosing imported schistosomiasis. The genus-specific PCR can detect all schistosome species that are infectious to humans and performs very well with faeces and urine, but not in serum. © 2012 Blackwell Publishing Ltd.

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.

Real-time pathogen monitoring during enrichment: a novel nanotechnology-based approach to food safety testing.

PubMed

Weidemaier, Kristin; Carruthers, Erin; Curry, Adam; Kuroda, Melody; Fallows, Eric; Thomas, Joseph; Sherman, Douglas; Muldoon, Mark

2015-04-02

We describe a new approach for the real-time detection and identification of pathogens in food and environmental samples undergoing culture. Surface Enhanced Raman Scattering (SERS) nanoparticles are combined with a novel homogeneous immunoassay to allow sensitive detection of pathogens in complex samples such as stomached food without the need for wash steps or extensive sample preparation. SERS-labeled immunoassay reagents are present in the cultural enrichment vessel, and the signal is monitored real-time through the wall of the vessel while culture is ongoing. This continuous monitoring of pathogen load throughout the enrichment process enables rapid, hands-free detection of food pathogens. Furthermore, the integration of the food pathogen immunoassay directly into the enrichment vessel enables fully biocontained food safety testing, thereby significantly reducing the risk of contaminating the surrounding environment with enriched pathogens. Here, we present experimental results showing the detection of E. coli, Salmonella, or Listeria in several matrices (raw ground beef, raw ground poultry, chocolate milk, tuna salad, spinach, brie cheese, hot dogs, deli turkey, orange juice, cola, and swabs and sponges used to sample a stainless steel surface) using the SERS system and demonstrate the accuracy of the approach compared to plating results. Copyright © 2014 Elsevier B.V. All rights reserved.

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.

Petroleum accounting principles, procedures, and issues

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

Brock, H.R.; Klingstedt, J.P.; Jones, D.M.

1985-01-01

This book begins with the basics and leads one through the complexities of accounting and reporting for the industry. It presents the material one needs as an accountant in the petroleum industry. Examples deal with real problems and issues. It also includes numerous illustrations and examples, as well as sample forms, lease agreements, and industry and governmental regulations.

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

Wang, Shi-bing, E-mail: wang-shibing@dlut.edu.cn, E-mail: wangxy@dlut.edu.cn; Faculty of Electronic Information and Electrical Engineering, Dalian University of Technology, Dalian 116024; Wang, Xing-yuan, E-mail: wang-shibing@dlut.edu.cn, E-mail: wangxy@dlut.edu.cn

With comprehensive consideration of generalized synchronization, combination synchronization and adaptive control, this paper investigates a novel adaptive generalized combination complex synchronization (AGCCS) scheme for different real and complex nonlinear systems with unknown parameters. On the basis of Lyapunov stability theory and adaptive control, an AGCCS controller and parameter update laws are derived to achieve synchronization and parameter identification of two real drive systems and a complex response system, as well as two complex drive systems and a real response system. Two simulation examples, namely, ACGCS for chaotic real Lorenz and Chen systems driving a hyperchaotic complex Lü system, and hyperchaoticmore » complex Lorenz and Chen systems driving a real chaotic Lü system, are presented to verify the feasibility and effectiveness of the proposed scheme.« less

Evaluation of the Abbott RealTime MTB and RealTime MTB INH/RIF Assays for Direct Detection of Mycobacterium tuberculosis Complex and Resistance Markers in Respiratory and Extrapulmonary Specimens.

PubMed

Hofmann-Thiel, Sabine; Molodtsov, Nikolay; Antonenka, Uladzimir; Hoffmann, Harald

2016-12-01

The Abbott RealTime MTB (RT MTB) assay is a new automated nucleic acid amplification test for the detection of Mycobacterium tuberculosis complex (MTBC) in clinical specimens. In combination with the RealTime MTB INH/RIF (RT MTB INH/RIF) resistance assay, which can be applied to RT MTB-positive specimens as an add-on assay, the tests also indicate the genetic markers of resistance to isoniazid (INH) and rifampin (RIF). We aimed to evaluate the diagnostic sensitivity and specificity of RT MTB using different types of respiratory and extrapulmonary specimens and to compare performance characteristics directly with those of the FluoroType MTB assay. The resistance results obtained by RT MTB INH/RIF were compared to those from the GenoType MTBDRplus and from phenotypic drug susceptibility testing. A total of 715 clinical specimens were analyzed. Compared to culture, the overall sensitivity of RT MTB was 92.1%; the sensitivity rates for smear-positive and smear-negative samples were 100% and 76.2%, respectively. The sensitivities of smear-negative specimens were almost identical for respiratory (76.3%) and extrapulmonary (76%) specimens. Specificity rates were 100% and 95.8% for culture-negative specimens and those that grew nontuberculous mycobacteria, respectively. RT MTB INH/RIF was applied to 233 RT MTB-positive samples and identified resistance markers in 7.7% of samples. Agreement with phenotypic and genotypic drug susceptibility testing was 99.5%. In conclusion, RT MTB and RT MTB INH/RIF allow for the rapid and accurate diagnosis of tuberculosis (TB) in different types of specimens and reliably indicate resistance markers. The strengths of this system are the comparably high sensitivity with paucibacillary specimens, its ability to detect INH and RIF resistance, and its high-throughput capacities. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

A real time QRS detection using delay-coordinate mapping for the microcontroller implementation.

PubMed

Lee, Jeong-Whan; Kim, Kyeong-Seop; Lee, Bongsoo; Lee, Byungchae; Lee, Myoung-Ho

2002-01-01

In this article, we propose a new algorithm using the characteristics of reconstructed phase portraits by delay-coordinate mapping utilizing lag rotundity for a real-time detection of QRS complexes in ECG signals. In reconstructing phase portrait the mapping parameters, time delay, and mapping dimension play important roles in shaping of portraits drawn in a new dimensional space. Experimentally, the optimal mapping time delay for detection of QRS complexes turned out to be 20 ms. To explore the meaning of this time delay and the proper mapping dimension, we applied a fill factor, mutual information, and autocorrelation function algorithm that were generally used to analyze the chaotic characteristics of sampled signals. From these results, we could find the fact that the performance of our proposed algorithms relied mainly on the geometrical property such as an area of the reconstructed phase portrait. For the real application, we applied our algorithm for designing a small cardiac event recorder. This system was to record patients' ECG and R-R intervals for 1 h to investigate HRV characteristics of the patients who had vasovagal syncope symptom and for the evaluation, we implemented our algorithm in C language and applied to MIT/BIH arrhythmia database of 48 subjects. Our proposed algorithm achieved a 99.58% detection rate of QRS complexes.

Electrochemical pesticide detection with AutoDip--a portable platform for automation of crude sample analyses.

PubMed

Drechsel, Lisa; Schulz, Martin; von Stetten, Felix; Moldovan, Carmen; Zengerle, Roland; Paust, Nils

2015-02-07

Lab-on-a-chip devices hold promise for automation of complex workflows from sample to answer with minimal consumption of reagents in portable devices. However, complex, inhomogeneous samples as they occur in environmental or food analysis may block microchannels and thus often cause malfunction of the system. Here we present the novel AutoDip platform which is based on the movement of a solid phase through the reagents and sample instead of transporting a sequence of reagents through a fixed solid phase. A ball-pen mechanism operated by an external actuator automates unit operations such as incubation and washing by consecutively dipping the solid phase into the corresponding liquids. The platform is applied to electrochemical detection of organophosphorus pesticides in real food samples using an acetylcholinesterase (AChE) biosensor. Minimal sample preparation and an integrated reagent pre-storage module hold promise for easy handling of the assay. Detection of the pesticide chlorpyrifos-oxon (CPO) spiked into apple samples at concentrations of 10(-7) M has been demonstrated. This concentration is below the maximum residue level for chlorpyrifos in apples defined by the European Commission.

Real-Time Cytotoxicity Assay for Rapid and Sensitive Detection of Ricin from Complex Matrices

PubMed Central

Pauly, Diana; Worbs, Sylvia; Kirchner, Sebastian; Shatohina, Olena; Dorner, Martin B.; Dorner, Brigitte G.

2012-01-01

Background In the context of a potential bioterrorist attack sensitive and fast detection of functionally active toxins such as ricin from complex matrices is necessary to be able to start timely countermeasures. One of the functional detection methods currently available for ricin is the endpoint cytotoxicity assay, which suffers from a number of technical deficits. Methodology/Findings This work describes a novel online cytotoxicity assay for the detection of active ricin and Ricinus communis agglutinin, that is based on a real-time cell electronic sensing system and impedance measurement. Characteristic growth parameters of Vero cells were monitored online and used as standardized viability control. Upon incubation with toxin the cell status and the cytotoxic effect were visualized using a characteristic cell index–time profile. For ricin, tested in concentrations of 0.06 ng/mL or above, a concentration-dependent decrease of cell index correlating with cytotoxicity was recorded between 3.5 h and 60 h. For ricin, sensitive detection was determined after 24 h, with an IC50 of 0.4 ng/mL (for agglutinin, an IC50 of 30 ng/mL was observed). Using functionally blocking antibodies, the specificity for ricin and agglutinin was shown. For detection from complex matrices, ricin was spiked into several food matrices, and an IC50 ranging from 5.6 to 200 ng/mL was observed. Additionally, the assay proved to be useful in detecting active ricin in environmental sample materials, as shown for organic fertilizer containing R. communis material. Conclusions/Significance The cell-electrode impedance measurement provides a sensitive online detection method for biologically active cytotoxins such as ricin. As the cell status is monitored online, the assay can be standardized more efficiently than previous approaches based on endpoint measurement. More importantly, the real-time cytotoxicity assay provides a fast and easy tool to detect active ricin in complex sample matrices. PMID:22532852

Method for Hot Real-Time Sampling of Gasification Products

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

Pomeroy, Marc D

The Thermochemical Process Development Unit (TCPDU) at the National Renewable Energy Laboratory (NREL) is a highly instrumented half-ton/day pilot scale plant capable of demonstrating industrially relevant thermochemical technologies from lignocellulosic biomass conversion, including gasification. Gasification creates primarily Syngas (a mixture of Hydrogen and Carbon Monoxide) that can be utilized with synthesis catalysts to form transportation fuels and other valuable chemicals. Biomass derived gasification products are a very complex mixture of chemical components that typically contain Sulfur and Nitrogen species that can act as catalysis poisons for tar reforming and synthesis catalysts. Real-time hot online sampling techniques, such as Molecular Beammore » Mass Spectrometry (MBMS), and Gas Chromatographs with Sulfur and Nitrogen specific detectors can provide real-time analysis providing operational indicators for performance. Sampling typically requires coated sampling lines to minimize trace sulfur interactions with steel surfaces. Other materials used inline have also shown conversion of sulfur species into new components and must be minimized. Sample line Residence time within the sampling lines must also be kept to a minimum to reduce further reaction chemistries. Solids from ash and char contribute to plugging and must be filtered at temperature. Experience at NREL has shown several key factors to consider when designing and installing an analytical sampling system for biomass gasification products. They include minimizing sampling distance, effective filtering as close to source as possible, proper line sizing, proper line materials or coatings, even heating of all components, minimizing pressure drops, and additional filtering or traps after pressure drops.« less

Occupational exposure to fungi and particles in animal feed industry.

PubMed

Viegas, Carla; Faria, Tiago; Carolino, Elisabete; Sabino, Raquel; Gomes, Anita Quintal; Viegas, Susana

Very few studies regarding fungal and particulate matter (PM) exposure in feed industry have been reported, although such contaminants are likely to be a significant contributing factor to several symptoms reported among workers. The purpose of this study has been to characterize fungal and dust exposure in one Portuguese feed industry. Air and surface samples were collected and subject to further macro- and microscopic observations. In addition we collected other air samples in order to perform real-time quantitative polymerase chain reaction (PCR) amplification of genes from Aspergillus fumigatus and Aspergillus flavus complexes as well as Stachybotrys chartarum. Additionally, two exposure metrics were considered - particle mass concentration (PMC), measured in 5 different sizes (PM0.5, PM1, PM2.5, PM5, PM10), and particle number concentration (PNC) based on results given in 6 different sizes in terms of diameter (0.3 μm, 0.5 μm, 1 μm, 2.5 μm, 5 μm and 10 μm). Species from the Aspergillus fumigatus complex were the most abundant in air (46.6%) and in surfaces, Penicillium genus was the most frequently found (32%). The only DNA was detected from A. fumigatus complex. The most prevalent in dust samples were smaller particles which may reach deep into the respiratory system and trigger not only local effects but also the systemic ones. Future research work must be developed aiming at assessing the real health effects of these co-exposures. Med Pr 2016;67(2):143-154. This work is available in Open Access model and licensed under a CC BY-NC 3.0 PL license.

A novel multilayer model for missing link prediction and future link forecasting in dynamic complex networks

NASA Astrophysics Data System (ADS)

Yasami, Yasser; Safaei, Farshad

2018-02-01

The traditional complex network theory is particularly focused on network models in which all network constituents are dealt with equivalently, while fail to consider the supplementary information related to the dynamic properties of the network interactions. This is a main constraint leading to incorrect descriptions of some real-world phenomena or incomplete capturing the details of certain real-life problems. To cope with the problem, this paper addresses the multilayer aspects of dynamic complex networks by analyzing the properties of intrinsically multilayered co-authorship networks, DBLP and Astro Physics, and presenting a novel multilayer model of dynamic complex networks. The model examines the layers evolution (layers birth/death process and lifetime) throughout the network evolution. Particularly, this paper models the evolution of each node's membership in different layers by an Infinite Factorial Hidden Markov Model considering feature cascade, and thereby formulates the link generation process for intra-layer and inter-layer links. Although adjacency matrixes are useful to describe the traditional single-layer networks, such a representation is not sufficient to describe and analyze the multilayer dynamic networks. This paper also extends a generalized mathematical infrastructure to address the problems issued by multilayer complex networks. The model inference is performed using some Markov Chain Monte Carlo sampling strategies, given synthetic and real complex networks data. Experimental results indicate a tremendous improvement in the performance of the proposed multilayer model in terms of sensitivity, specificity, positive and negative predictive values, positive and negative likelihood ratios, F1-score, Matthews correlation coefficient, and accuracy for two important applications of missing link prediction and future link forecasting. The experimental results also indicate the strong predictivepower of the proposed model for the application of cascade prediction in terms of accuracy.

Code Samples Used for Complexity and Control

NASA Astrophysics Data System (ADS)

Ivancevic, Vladimir G.; Reid, Darryn J.

2015-11-01

The following sections are included: * MathematicaⓇ Code * Generic Chaotic Simulator * Vector Differential Operators * NLS Explorer * 2C++ Code * C++ Lambda Functions for Real Calculus * Accelerometer Data Processor * Simple Predictor-Corrector Integrator * Solving the BVP with the Shooting Method * Linear Hyperbolic PDE Solver * Linear Elliptic PDE Solver * Method of Lines for a Set of the NLS Equations * C# Code * Iterative Equation Solver * Simulated Annealing: A Function Minimum * Simple Nonlinear Dynamics * Nonlinear Pendulum Simulator * Lagrangian Dynamics Simulator * Complex-Valued Crowd Attractor Dynamics * Freeform Fortran Code * Lorenz Attractor Simulator * Complex Lorenz Attractor * Simple SGE Soliton * Complex Signal Presentation * Gaussian Wave Packet * Hermitian Matrices * Euclidean L2-Norm * Vector/Matrix Operations * Plain C-Code: Levenberg-Marquardt Optimizer * Free Basic Code: 2D Crowd Dynamics with 3000 Agents

Novel Multiplex Real-Time PCR Diagnostic Assay for Identification and Differentiation of Mycobacterium tuberculosis, Mycobacterium canettii, and Mycobacterium tuberculosis Complex Strains▿†

PubMed Central

Reddington, Kate; O'Grady, Justin; Dorai-Raj, Siobhan; Maher, Majella; van Soolingen, Dick; Barry, Thomas

2011-01-01

Tuberculosis (TB) in humans is caused by members of the Mycobacterium tuberculosis complex (MTC). Rapid detection of the MTC is necessary for the timely initiation of antibiotic treatment, while differentiation between members of the complex may be important to guide the appropriate antibiotic treatment and provide epidemiological information. In this study, a multiplex real-time PCR diagnostics assay using novel molecular targets was designed to identify the MTC while simultaneously differentiating between M. tuberculosis and M. canettii. The lepA gene was targeted for the detection of members of the MTC, the wbbl1 gene was used for the differentiation of M. tuberculosis and M. canettii from the remainder of the complex, and a unique region of the M. canettii genome, a possible novel region of difference (RD), was targeted for the specific identification of M. canettii. The multiplex real-time PCR assay was tested using 125 bacterial strains (64 MTC isolates, 44 nontuberculosis mycobacteria [NTM], and 17 other bacteria). The assay was determined to be 100% specific for the mycobacteria tested. Limits of detection of 2.2, 2.17, and 0.73 cell equivalents were determined for M. tuberculosis/M. canettii, the MTC, and M. canettii, respectively, using probit regression analysis. Further validation of this diagnostics assay, using clinical samples, should demonstrate its potential for the rapid, accurate, and sensitive diagnosis of TB caused by M. tuberculosis, M. canettii, and the other members of the MTC. PMID:21123525

Microcontroller-based real-time QRS detection.

PubMed

Sun, Y; Suppappola, S; Wrublewski, T A

1992-01-01

The authors describe the design of a system for real-time detection of QRS complexes in the electrocardiogram based on a single-chip microcontroller (Motorola 68HC811). A systematic analysis of the instrumentation requirements for QRS detection and of the various design techniques is also given. Detection algorithms using different nonlinear transforms for the enhancement of QRS complexes are evaluated by using the ECG database of the American Heart Association. The results show that the nonlinear transform involving multiplication of three adjacent, sign-consistent differences in the time domain gives a good performance and a quick response. When implemented with an appropriate sampling rate, this algorithm is also capable of rejecting pacemaker spikes. The eight-bit single-chip microcontroller provides sufficient throughput and shows a satisfactory performance. Implementation of multiple detection algorithms in the same system improves flexibility and reliability. The low chip count in the design also favors maintainability and cost-effectiveness.

A one-step colorimetric acid-base titration sensor using a complementary color changing coordination system.

PubMed

Cho, Hui Hun; Kim, Si Hyun; Heo, Jun Hyuk; Moon, Young Eel; Choi, Young Hun; Lim, Dong Cheol; Han, Kwon-Hoon; Lee, Jung Heon

2016-06-21

We report the development of a colorimetric sensor that allows for the quantitative measurement of the acid content via acid-base titration in a single-step. In order to create the sensor, we used a cobalt coordination system (Co-complex sensor) that changes from greenish blue colored Co(H2O)4(OH)2 to pink colored Co(H2O)6(2+) after neutralization. Greenish blue and pink are two complementary colors with a strong contrast. As a certain amount of acid is introduced to the Co-complex sensor, a portion of greenish blue colored Co(H2O)4(OH)2 changes to pink colored Co(H2O)6(2+), producing a different color. As the ratio of greenish blue and pink in the Co-complex sensor is determined by the amount of neutralization reaction occurring between Co(H2O)4(OH)2 and an acid, the sensor produced a spectrum of green, yellow green, brown, orange, and pink colors depending on the acid content. In contrast, the color change appeared only beyond the end point for normal acid-base titration. When we mixed this Co-complex sensor with different concentrations of citric acid, tartaric acid, and malic acid, three representative organic acids in fruits, we observed distinct color changes for each sample. This color change could also be observed in real fruit juice. When we treated the Co-complex sensor with real tangerine juice, it generated diverse colors depending on the concentration of citric acid in each sample. These results provide a new angle on simple but quantitative measurements of analytes for on-site usage in various applications, such as in food, farms, and the drug industry.

A microcontroller-based microwave free-space measurement system for permittivity determination of lossy liquid materials.

PubMed

Hasar, U C

2009-05-01

A microcontroller-based noncontact and nondestructive microwave free-space measurement system for real-time and dynamic determination of complex permittivity of lossy liquid materials has been proposed. The system is comprised of two main sections--microwave and electronic. While the microwave section provides for measuring only the amplitudes of reflection coefficients, the electronic section processes these data and determines the complex permittivity using a general purpose microcontroller. The proposed method eliminates elaborate liquid sample holder preparation and only requires microwave components to perform reflection measurements from one side of the holder. In addition, it explicitly determines the permittivity of lossy liquid samples from reflection measurements at different frequencies without any knowledge on sample thickness. In order to reduce systematic errors in the system, we propose a simple calibration technique, which employs simple and readily available standards. The measurement system can be a good candidate for industrial-based applications.

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

Gentry, T.; Schadt, C.; Zhou, J.

Microarray technology has the unparalleled potential tosimultaneously determine the dynamics and/or activities of most, if notall, of the microbial populations in complex environments such as soilsand sediments. Researchers have developed several types of arrays thatcharacterize the microbial populations in these samples based on theirphylogenetic relatedness or functional genomic content. Several recentstudies have used these microarrays to investigate ecological issues;however, most have only analyzed a limited number of samples withrelatively few experiments utilizing the full high-throughput potentialof microarray analysis. This is due in part to the unique analyticalchallenges that these samples present with regard to sensitivity,specificity, quantitation, and data analysis. Thismore » review discussesspecific applications of microarrays to microbial ecology research alongwith some of the latest studies addressing the difficulties encounteredduring analysis of complex microbial communities within environmentalsamples. With continued development, microarray technology may ultimatelyachieve its potential for comprehensive, high-throughput characterizationof microbial populations in near real-time.« less

Novel Bioluminescent Quantitative Detection of Nucleic Acid Amplification in Real-Time

PubMed Central

Gandelman, Olga A.; Church, Vicki L.; Moore, Cathy A.; Kiddle, Guy; Carne, Christopher A.; Parmar, Surendra; Jalal, Hamid; Tisi, Laurence C.; Murray, James A. H.

2010-01-01

Background The real-time monitoring of polynucleotide amplification is at the core of most molecular assays. This conventionally relies on fluorescent detection of the amplicon produced, requiring complex and costly hardware, often restricting it to specialised laboratories. Principal Findings Here we report the first real-time, closed-tube luminescent reporter system for nucleic acid amplification technologies (NAATs) enabling the progress of amplification to be continuously monitored using simple light measuring equipment. The Bioluminescent Assay in Real-Time (BART) continuously reports through bioluminescent output the exponential increase of inorganic pyrophosphate (PPi) produced during the isothermal amplification of a specific nucleic acid target. BART relies on the coupled conversion of inorganic pyrophosphate (PPi) produced stoichiometrically during nucleic acid synthesis to ATP by the enzyme ATP sulfurylase, and can therefore be coupled to a wide range of isothermal NAATs. During nucleic acid amplification, enzymatic conversion of PPi released during DNA synthesis into ATP is continuously monitored through the bioluminescence generated by thermostable firefly luciferase. The assay shows a unique kinetic signature for nucleic acid amplifications with a readily identifiable light output peak, whose timing is proportional to the concentration of original target nucleic acid. This allows qualitative and quantitative analysis of specific targets, and readily differentiates between negative and positive samples. Since quantitation in BART is based on determination of time-to-peak rather than absolute intensity of light emission, complex or highly sensitive light detectors are not required. Conclusions The combined chemistries of the BART reporter and amplification require only a constant temperature maintained by a heating block and are shown to be robust in the analysis of clinical samples. Since monitoring the BART reaction requires only a simple light detector, the iNAAT-BART combination is ideal for molecular diagnostic assays in both laboratory and low resource settings. PMID:21152399

Molecular-level evaluation of selected periodontal pathogens from subgingival regions in canines and humans with periodontal disease

PubMed Central

Polkowska, Izabela; Bartoszcze-Tomaszewska, Małgorzata; Sobczyńska-Rak, Aleksandra; Matuszewski, Łukasz

2017-01-01

Dogs commonly serve as a model for various human conditions, including periodontal diseases. The aim of this study was to identify the anaerobic bacteria that colonize the subgingival areas in dogs and humans by using rapid real-time polymerase chain reaction (RT-PCR)-based tests and to compare the results obtained in each species. Bacterial microflora evaluations, both quantitative and qualitative, were performed by applying ready-made tests on twelve dogs and twelve humans. Five samples were collected from each subject's deepest gingival pockets and joined to form a collective sample. The results of the study revealed interspecies similarities in the prevalences of Porphyromonas (P.) gingivalis, Treponema denticola, Tannerella forsythia, and Fusobacterium nucleatum. Red complex bacteria comprised the largest portion of the studied bacterial complexes in all study groups, with P. gingivalis being the most commonly isolated bacterium. The results show similarities in the prevalence of bacterial microflora in dogs and humans. Microbiological analysis of gingival pockets by using rapid real-time PCR-based tests in clinical practice, both veterinary and human, can facilitate the choice of appropriate pharmacological treatment and can provide a basis for subsequent verification of the treatment's effectiveness. PMID:27297417

Molecular-level evaluation of selected periodontal pathogens from subgingival regions in canines and humans with periodontal disease.

PubMed

Gołyńska, Magdalena; Polkowska, Izabela; Bartoszcze-Tomaszewska, Małgorzata; Sobczyńska-Rak, Aleksandra; Matuszewski, Łukasz

2017-03-30

Dogs commonly serve as a model for various human conditions, including periodontal diseases. The aim of this study was to identify the anaerobic bacteria that colonize the subgingival areas in dogs and humans by using rapid real-time polymerase chain reaction (RT-PCR)-based tests and to compare the results obtained in each species. Bacterial microflora evaluations, both quantitative and qualitative, were performed by applying ready-made tests on twelve dogs and twelve humans. Five samples were collected from each subject's deepest gingival pockets and joined to form a collective sample. The results of the study revealed interspecies similarities in the prevalences of Porphyromonas ( P .) gingivalis, Treponema denticola, Tannerella forsythia , and Fusobacterium nucleatum . Red complex bacteria comprised the largest portion of the studied bacterial complexes in all study groups, with P. gingivalis being the most commonly isolated bacterium. The results show similarities in the prevalence of bacterial microflora in dogs and humans. Microbiological analysis of gingival pockets by using rapid real-time PCR-based tests in clinical practice, both veterinary and human, can facilitate the choice of appropriate pharmacological treatment and can provide a basis for subsequent verification of the treatment's effectiveness.

Design and synthesis of heterobimetallic Ru(II)-Ln(III) complexes as chemodosimetric ensembles for the detection of biogenic amine odorants.

PubMed

Chow, Cheuk-Fai; Lam, Michael H W; Wong, Wai-Yeung

2013-09-03

The detection of neutral biogenic amines plays a crucial role in food safety. Three new heterobimetallic Ru(II)-Ln(III) donor-acceptor complexes, KPrRu, KNdRu, and KSmRu, K{[Ru((II))((t)Bubpy)(CN)4]2-Ln((III))(H2O)4} (where (t)Bubpy = 4,4'-di-tert-butyl-2,2'-bipyridine), have been synthesized and characterized. Their photophysical and X-ray crystallographic data were reported in this study. These complexes were found to be selective for biogenic amine vapors, such as histamine, putrescine, and spermidine, with a detection limit down to the ppb level. The sensitivities of these complexes to the amines were recorded as ~log K = 3.6-5.0. Submicron rods of the complexes, with a nanoscale diameter and microscale length, were obtained through a simple precipitation process. Free-standing polymeric films with different degrees of porosity were fabricated by blending the submicron rods with polystyrene polymer. The polymer with the highest level of porosity exhibited the strongest luminescence enhancement after amine exposure. Real time monitoring of gaseous biogenic amines was applied to real fish samples (Atlantic mackerel) by studying the spectrofluorimetric responses of the Ru(II)-Ln(III) blended polymer film.

Dembo polymerase chain reaction technique for detection of bovine abortion, diarrhea, and respiratory disease complex infectious agents in potential vectors and reservoirs.

PubMed

Rahpaya, Sayed Samim; Tsuchiaka, Shinobu; Kishimoto, Mai; Oba, Mami; Katayama, Yukie; Nunomura, Yuka; Kokawa, Saki; Kimura, Takashi; Kobayashi, Atsushi; Kirino, Yumi; Okabayashi, Tamaki; Nonaka, Nariaki; Mekata, Hirohisa; Aoki, Hiroshi; Shiokawa, Mai; Umetsu, Moeko; Morita, Tatsushi; Hasebe, Ayako; Otsu, Keiko; Asai, Tetsuo; Yamaguchi, Tomohiro; Makino, Shinji; Murata, Yoshiteru; Abi, Ahmad Jan; Omatsu, Tsutomu; Mizutani, Tetsuya

2018-05-31

Bovine abortion, diarrhea, and respiratory disease complexes, caused by infectious agents, result in high and significant economic losses for the cattle industry. These pathogens are likely transmitted by various vectors and reservoirs including insects, birds, and rodents. However, experimental data supporting this possibility are scarce. We collected 117 samples and screened them for 44 bovine abortive, diarrheal, and respiratory disease complex pathogens by using Dembo polymerase chain reaction (PCR), which is based on TaqMan real-time PCR. Fifty-seven samples were positive for at least one pathogen, including bovine viral diarrhea virus, bovine enterovirus, Salmonella enterica ser. Dublin, Salmonella enterica ser. Typhimurium, and Neospora caninum ; some samples were positive for multiple pathogens. Bovine viral diarrhea virus and bovine enterovirus were the most frequently detected pathogens, especially in flies, suggesting an important role of flies in the transmission of these viruses. Additionally, we detected the N. caninum genome from a cockroach sample for the first time. Our data suggest that insects (particularly flies), birds, and rodents are potential vectors and reservoirs of abortion, diarrhea, and respiratory infectious agents, and that they may transmit more than one pathogen at the same time.

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

Real-time high dynamic range laser scanning microscopy

NASA Astrophysics Data System (ADS)

Vinegoni, C.; Leon Swisher, C.; Fumene Feruglio, P.; Giedt, R. J.; Rousso, D. L.; Stapleton, S.; Weissleder, R.

2016-04-01

In conventional confocal/multiphoton fluorescence microscopy, images are typically acquired under ideal settings and after extensive optimization of parameters for a given structure or feature, often resulting in information loss from other image attributes. To overcome the problem of selective data display, we developed a new method that extends the imaging dynamic range in optical microscopy and improves the signal-to-noise ratio. Here we demonstrate how real-time and sequential high dynamic range microscopy facilitates automated three-dimensional neural segmentation. We address reconstruction and segmentation performance on samples with different size, anatomy and complexity. Finally, in vivo real-time high dynamic range imaging is also demonstrated, making the technique particularly relevant for longitudinal imaging in the presence of physiological motion and/or for quantification of in vivo fast tracer kinetics during functional imaging.

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.

Environmental and human monitoring of Americium-241 utilizing extraction chromatography and {alpha}-Spectrometry

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

Goldstein, S.J.; Hensley, C.A.; Armenta, C.E.

1997-03-01

Recent developments in extraction chromatography have simplified the separation of americium from complex matrices in preparation for {alpha}-spectroscopy relative to traditional methods. Here we present results of procedures developed/adapted for water, air, and bioassay samples with less than 1 g of inorganic residue. Prior analytical methods required the use of a complex, multistage procedure for separation of americium from these matrices. The newer, simplified procedure requires only a single 2 mL extraction chromatographic separation for isolation of Am and lanthanides from other components of the sample. This method has been implemented on an extensive variety of `real` environmental and bioassaymore » samples from the Los Alamos area, and consistently reliable and accurate results with appropriate detection limits have been obtained. The new method increases analytical throughput by a factor of {approx}2 and decreases environmental hazards from acid and mixed-waste generation relative to the prior technique. Analytical accuracy, reproducibility, and reliability are also significantly improved over the more complex and laborious method used previously. 24 refs., 2 figs., 2 tabs.« less

Real-time PCR assays for the detection and quantification of carbapenemase genes (bla KPC, bla NDM, and bla OXA-48) in environmental samples.

PubMed

Subirats, Jèssica; Royo, Elena; Balcázar, José Luis; Borrego, Carles M

2017-03-01

In this study, we have developed real-time PCR assays using SYBR Green chemistry to detect all known alleles of bla KPC , bla NDM , and bla OXA-48 -like carbapenemase genes in water, sediment, and biofilm samples collected from hospital and wastewater treatment plant (WWTP) effluents and rivers receiving chronic WWTP discharges. The amplification of bla KPC , bla NDM , and bla OXA-48 DNA was linear over 7 log dilutions (R 2 between 0.995 and 0.997) and showing efficiencies ranging from 92.6% to 100.3%. The analytical sensitivity indicated that the reaction for bla KPC , bla NDM , and bla OXA-48 -like genes was able to detect 35, 16, and 19 copy numbers per assay, respectively. The three carbapenemase genes were detected in hospital effluents, whereas only the bla KPC and bla NDM genes were detected in biofilm and sediment samples collected from wastewater-impacted rivers. The detection of bla KPC , bla NDM , and bla OXA-48 -like genes in different matrices suggests that carbapenem-resistant bacteria occur in both planktonic and benthic habitats thus expanding the range of resistance reservoirs for last-resort antibiotics. We believe that these real-time PCR assays would be a powerful tool for the rapid detection and quantification of bla KPC , bla NDM , and bla OXA-48 -like genes in complex environmental samples.

The complexity of the HANG SENG Index and its constituencies during the 2007-2008 Great Recession

NASA Astrophysics Data System (ADS)

Argyroudis, G.; Siokis, F.

2018-04-01

We apply the multifractal detrended moving average (MF-DMA) procedure to the daily data from HANG SENG Index (HSI) and two sub-indices, the Properties Index which consists of 10 Real Estate Companies and the Finance Index with 12 companies respectively. Two major events are considered: the 2007 and the 1997 crises. Based on scaling exponents and the singularity spectrum analysis, we show that both events reveal multiscaling and the results are robust across different indices. Furthermore, by dividing the data into two equal sub-samples for prior and after the crisis periods, we reveal that for the 2007-2008 crisis, the complexity of the HSI and Properties index remain the same between periods, while for the Finance Index, the after crisis period exhibits richer multifractality and higher complexity. Especially for the Properties Index, the results indicate that the Real Estate sector was not affected as much, by the transitory shocks of the Great Recession. As for the 1997 event, the HS Index is impacted greatly in the after period crisis exhibiting higher degree of multifractality and heterogeneity.

Feature extraction using first and second derivative extrema (FSDE) for real-time and hardware-efficient spike sorting.

PubMed

Paraskevopoulou, Sivylla E; Barsakcioglu, Deren Y; Saberi, Mohammed R; Eftekhar, Amir; Constandinou, Timothy G

2013-04-30

Next generation neural interfaces aspire to achieve real-time multi-channel systems by integrating spike sorting on chip to overcome limitations in communication channel capacity. The feasibility of this approach relies on developing highly efficient algorithms for feature extraction and clustering with the potential of low-power hardware implementation. We are proposing a feature extraction method, not requiring any calibration, based on first and second derivative features of the spike waveform. The accuracy and computational complexity of the proposed method are quantified and compared against commonly used feature extraction methods, through simulation across four datasets (with different single units) at multiple noise levels (ranging from 5 to 20% of the signal amplitude). The average classification error is shown to be below 7% with a computational complexity of 2N-3, where N is the number of sample points of each spike. Overall, this method presents a good trade-off between accuracy and computational complexity and is thus particularly well-suited for hardware-efficient implementation. Copyright © 2013 Elsevier B.V. All rights reserved.

Systolic Processor Array For Recognition Of Spectra

NASA Technical Reports Server (NTRS)

Chow, Edward T.; Peterson, John C.

1995-01-01

Spectral signatures of materials detected and identified quickly. Spectral Analysis Systolic Processor Array (SPA2) relatively inexpensive and satisfies need to analyze large, complex volume of multispectral data generated by imaging spectrometers to extract desired information: computational performance needed to do this in real time exceeds that of current supercomputers. Locates highly similar segments or contiguous subsegments in two different spectra at time. Compares sampled spectra from instruments with data base of spectral signatures of known materials. Computes and reports scores that express degrees of similarity between sampled and data-base spectra.

Determination of effective complex refractive index of a turbid liquid with surface plasmon resonance phase detection.

PubMed

Yingying, Zhang; Jiancheng, Lai; Cheng, Yin; Zhenhua, Li

2009-03-01

The dependence of the surface plasmon resonance (SPR) phase difference curve on the complex refractive index of a sample in Kretschmann configuration is discussed comprehensively, based on which a new method is proposed to measure the complex refractive index of turbid liquid. A corresponding experiment setup was constructed to measure the SPR phase difference curve, and the complex refractive index of turbid liquid was determined. By using the setup, the complex refractive indices of Intralipid solutions with concentrations of 5%, 10%, 15%, and 20% are obtained to be 1.3377+0.0005 i, 1.3427+0.0028 i, 1.3476+0.0034 i, and 1.3496+0.0038 i, respectively. Furthermore, the error analysis indicates that the root-mean-square errors of both the real and the imaginary parts of the measured complex refractive index are less than 5x10(-5).

Rapid identification and quantification of Campylobacter coli and Campylobacter jejuni by real-time PCR in pure cultures and in complex samples

PubMed Central

2011-01-01

Background Campylobacter spp., especially Campylobacter jejuni (C. jejuni) and Campylobacter coli (C. coli), are recognized as the leading human foodborne pathogens in developed countries. Livestock animals carrying Campylobacter pose an important risk for human contamination. Pigs are known to be frequently colonized with Campylobacter, especially C. coli, and to excrete high numbers of this pathogen in their faeces. Molecular tools, notably real-time PCR, provide an effective, rapid, and sensitive alternative to culture-based methods for the detection of C. coli and C. jejuni in various substrates. In order to serve as a diagnostic tool supporting Campylobacter epidemiology, we developed a quantitative real-time PCR method for species-specific detection and quantification of C. coli and C. jejuni directly in faecal, feed, and environmental samples. Results With a sensitivity of 10 genome copies and a linear range of seven to eight orders of magnitude, the C. coli and C. jejuni real-time PCR assays allowed a precise quantification of purified DNA from C. coli and C. jejuni. The assays were highly specific and showed a 6-log-linear dynamic range of quantification with a quantitative detection limit of approximately 2.5 × 102 CFU/g of faeces, 1.3 × 102 CFU/g of feed, and 1.0 × 103 CFU/m2 for the environmental samples. Compared to the results obtained by culture, both C. coli and C. jejuni real-time PCR assays exhibited a specificity of 96.2% with a kappa of 0.94 and 0.89 respectively. For faecal samples of experimentally infected pigs, the coefficients of correlation between the C. coli or C. jejuni real-time PCR assay and culture enumeration were R2 = 0.90 and R2 = 0.93 respectively. Conclusion The C. coli and C. jejuni real-time quantitative PCR assays developed in this study provide a method capable of directly detecting and quantifying C. coli and C. jejuni in faeces, feed, and environmental samples. These assays represent a new diagnostic tool for studying the epidemiology of Campylobacter by, for instance, investigating the carriage and excretion of C. coli and C. jejuni by pigs from conventional herds. PMID:21600037

A nonuniform popularity-similarity optimization (nPSO) model to efficiently generate realistic complex networks with communities

NASA Astrophysics Data System (ADS)

Muscoloni, Alessandro; Vittorio Cannistraci, Carlo

2018-05-01

The investigation of the hidden metric space behind complex network topologies is a fervid topic in current network science and the hyperbolic space is one of the most studied, because it seems associated to the structural organization of many real complex systems. The popularity-similarity-optimization (PSO) model simulates how random geometric graphs grow in the hyperbolic space, generating realistic networks with clustering, small-worldness, scale-freeness and rich-clubness. However, it misses to reproduce an important feature of real complex networks, which is the community organization. The geometrical-preferential-attachment (GPA) model was recently developed in order to confer to the PSO also a soft community structure, which is obtained by forcing different angular regions of the hyperbolic disk to have a variable level of attractiveness. However, the number and size of the communities cannot be explicitly controlled in the GPA, which is a clear limitation for real applications. Here, we introduce the nonuniform PSO (nPSO) model. Differently from GPA, the nPSO generates synthetic networks in the hyperbolic space where heterogeneous angular node attractiveness is forced by sampling the angular coordinates from a tailored nonuniform probability distribution (for instance a mixture of Gaussians). The nPSO differs from GPA in other three aspects: it allows one to explicitly fix the number and size of communities; it allows one to tune their mixing property by means of the network temperature; it is efficient to generate networks with high clustering. Several tests on the detectability of the community structure in nPSO synthetic networks and wide investigations on their structural properties confirm that the nPSO is a valid and efficient model to generate realistic complex networks with communities.

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.

Factorials of real negative and imaginary numbers - A new perspective.

PubMed

Thukral, Ashwani K

2014-01-01

Presently, factorials of real negative numbers and imaginary numbers, except for zero and negative integers are interpolated using the Euler's gamma function. In the present paper, the concept of factorials has been generalised as applicable to real and imaginary numbers, and multifactorials. New functions based on Euler's factorial function have been proposed for the factorials of real negative and imaginary numbers. As per the present concept, the factorials of real negative numbers, are complex numbers. The factorials of real negative integers have their imaginary part equal to zero, thus are real numbers. Similarly, the factorials of imaginary numbers are complex numbers. The moduli of the complex factorials of real negative numbers, and imaginary numbers are equal to their respective real positive number factorials. Fractional factorials and multifactorials have been defined in a new perspective. The proposed concept has also been extended to Euler's gamma function for real negative numbers and imaginary numbers, and beta function.

Topography-Assisted Electromagnetic Platform for Blood-to-PCR in a Droplet

PubMed Central

Chiou, Chi-Han; Shin, Dong Jin; Zhang, Yi; Wang, Tza-Huei

2013-01-01

This paper presents an electromagnetically actuated platform for automated sample preparation and detection of nucleic acids. The proposed platform integrates nucleic acid extraction using silica-coated magnetic particles with real-time polymerase chain reaction (PCR) on a single cartridge. Extraction of genomic material was automated by manipulating magnetic particles in droplets using a series of planar coil electromagnets assisted by topographical features, enabling efficient fluidic processing over a variety of buffers and reagents. The functionality of the platform was demonstrated by performing nucleic acid extraction from whole blood, followed by real-time PCR detection of KRAS oncogene. Automated sample processing from whole blood to PCR-ready droplet was performed in 15 minutes. We took a modular approach of decoupling the modules of magnetic manipulation and optical detection from the device itself, enabling a low-complexity cartridge that operates in tandem with simple external instruments. PMID:23835223

Determination of the complex refractive index segments of turbid sample with multispectral spatially modulated structured light and models approximation

NASA Astrophysics Data System (ADS)

Meitav, Omri; Shaul, Oren; Abookasis, David

2017-09-01

Spectral data enabling the derivation of a biological tissue sample's complex refractive index (CRI) can provide a range of valuable information in the clinical and research contexts. Specifically, changes in the CRI reflect alterations in tissue morphology and chemical composition, enabling its use as an optical marker during diagnosis and treatment. In the present work, we report a method for estimating the real and imaginary parts of the CRI of a biological sample using Kramers-Kronig (KK) relations in the spatial frequency domain. In this method, phase-shifted sinusoidal patterns at single high spatial frequency are serially projected onto the sample surface at different near-infrared wavelengths while a camera mounted normal to the sample surface acquires the reflected diffuse light. In the offline analysis pipeline, recorded images at each wavelength are converted to spatial phase maps using KK analysis and are then calibrated against phase-models derived from diffusion approximation. The amplitude of the reflected light, together with phase data, is then introduced into Fresnel equations to resolve both real and imaginary segments of the CRI at each wavelength. The technique was validated in tissue-mimicking phantoms with known optical parameters and in mouse models of ischemic injury and heat stress. Experimental data obtained indicate variations in the CRI among brain tissue suffering from injury. CRI fluctuations correlated with alterations in the scattering and absorption coefficients of the injured tissue are demonstrated. This technique for deriving dynamic changes in the CRI of tissue may be further developed as a clinical diagnostic tool and for biomedical research applications. To the best of our knowledge, this is the first report of the estimation of the spectral CRI of a mouse head following injury obtained in the spatial frequency domain.

Predictable and Adaptable Complex Real-Time Systems

DTIC Science & Technology

1993-09-30

Predictable and Adaptable Complex Real - Time Systems Grant or Contract Number: N00014-92-J-1048 Reporting Period: 1 Oct 91 - 30 Sep 93 1... Real - Time Systems Grant or Contract Number: N00014-92-J-1048 Reporting Period: 1 Oct 91 - 30 Sep 93 2. Summary of Technical Progress Our...cs.umass.edu Grant or Contract Title: Predictable and Adaptable Complex Real - Time Systems Grant or Contract Number: N00014-92-J-1048 Reporting Period: 1 Oct 91

Sampling-based real-time motion planning under state uncertainty for autonomous micro-aerial vehicles in GPS-denied environments.

PubMed

Li, Dachuan; Li, Qing; Cheng, Nong; Song, Jingyan

2014-11-18

This paper presents a real-time motion planning approach for autonomous vehicles with complex dynamics and state uncertainty. The approach is motivated by the motion planning problem for autonomous vehicles navigating in GPS-denied dynamic environments, which involves non-linear and/or non-holonomic vehicle dynamics, incomplete state estimates, and constraints imposed by uncertain and cluttered environments. To address the above motion planning problem, we propose an extension of the closed-loop rapid belief trees, the closed-loop random belief trees (CL-RBT), which incorporates predictions of the position estimation uncertainty, using a factored form of the covariance provided by the Kalman filter-based estimator. The proposed motion planner operates by incrementally constructing a tree of dynamically feasible trajectories using the closed-loop prediction, while selecting candidate paths with low uncertainty using efficient covariance update and propagation. The algorithm can operate in real-time, continuously providing the controller with feasible paths for execution, enabling the vehicle to account for dynamic and uncertain environments. Simulation results demonstrate that the proposed approach can generate feasible trajectories that reduce the state estimation uncertainty, while handling complex vehicle dynamics and environment constraints.

Sampling-Based Real-Time Motion Planning under State Uncertainty for Autonomous Micro-Aerial Vehicles in GPS-Denied Environments

PubMed Central

Li, Dachuan; Li, Qing; Cheng, Nong; Song, Jingyan

2014-01-01

This paper presents a real-time motion planning approach for autonomous vehicles with complex dynamics and state uncertainty. The approach is motivated by the motion planning problem for autonomous vehicles navigating in GPS-denied dynamic environments, which involves non-linear and/or non-holonomic vehicle dynamics, incomplete state estimates, and constraints imposed by uncertain and cluttered environments. To address the above motion planning problem, we propose an extension of the closed-loop rapid belief trees, the closed-loop random belief trees (CL-RBT), which incorporates predictions of the position estimation uncertainty, using a factored form of the covariance provided by the Kalman filter-based estimator. The proposed motion planner operates by incrementally constructing a tree of dynamically feasible trajectories using the closed-loop prediction, while selecting candidate paths with low uncertainty using efficient covariance update and propagation. The algorithm can operate in real-time, continuously providing the controller with feasible paths for execution, enabling the vehicle to account for dynamic and uncertain environments. Simulation results demonstrate that the proposed approach can generate feasible trajectories that reduce the state estimation uncertainty, while handling complex vehicle dynamics and environment constraints. PMID:25412217

pH Sensing Properties of Flexible, Bias-Free Graphene Microelectrodes in Complex Fluids: From Phosphate Buffer Solution to Human Serum.

PubMed

Ping, Jinglei; Blum, Jacquelyn E; Vishnubhotla, Ramya; Vrudhula, Amey; Naylor, Carl H; Gao, Zhaoli; Saven, Jeffery G; Johnson, Alan T Charlie

2017-08-01

Advances in techniques for monitoring pH in complex fluids can have a significant impact on analytical and biomedical applications. This study develops flexible graphene microelectrodes (GEs) for rapid (<5 s), very-low-power (femtowatt) detection of the pH of complex biofluids by measuring real-time Faradaic charge transfer between the GE and a solution at zero electrical bias. For an idealized sample of phosphate buffer solution (PBS), the Faradaic current is varied monotonically and systematically with the pH, with a resolution of ≈0.2 pH unit. The current-pH dependence is well described by a hybrid analytical-computational model, where the electric double layer derives from an intrinsic, pH-independent (positive) charge associated with the graphene-water interface and ionizable (negative) charged groups. For ferritin solution, the relative Faradaic current, defined as the difference between the measured current response and a baseline response due to PBS, shows a strong signal associated with ferritin disassembly and the release of ferric ions at pH ≈2.0. For samples of human serum, the Faradaic current shows a reproducible rapid (<20 s) response to pH. By combining the Faradaic current and real-time current variation, the methodology is potentially suitable for use to detect tumor-induced changes in extracellular pH. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Analyte quantification with comprehensive two-dimensional gas chromatography: assessment of methods for baseline correction, peak delineation, and matrix effect elimination for real samples.

PubMed

Samanipour, Saer; Dimitriou-Christidis, Petros; Gros, Jonas; Grange, Aureline; Samuel Arey, J

2015-01-02

Comprehensive two-dimensional gas chromatography (GC×GC) is used widely to separate and measure organic chemicals in complex mixtures. However, approaches to quantify analytes in real, complex samples have not been critically assessed. We quantified 7 PAHs in a certified diesel fuel using GC×GC coupled to flame ionization detector (FID), and we quantified 11 target chlorinated hydrocarbons in a lake water extract using GC×GC with electron capture detector (μECD), further confirmed qualitatively by GC×GC with electron capture negative chemical ionization time-of-flight mass spectrometer (ENCI-TOFMS). Target analyte peak volumes were determined using several existing baseline correction algorithms and peak delineation algorithms. Analyte quantifications were conducted using external standards and also using standard additions, enabling us to diagnose matrix effects. We then applied several chemometric tests to these data. We find that the choice of baseline correction algorithm and peak delineation algorithm strongly influence the reproducibility of analyte signal, error of the calibration offset, proportionality of integrated signal response, and accuracy of quantifications. Additionally, the choice of baseline correction and the peak delineation algorithm are essential for correctly discriminating analyte signal from unresolved complex mixture signal, and this is the chief consideration for controlling matrix effects during quantification. The diagnostic approaches presented here provide guidance for analyte quantification using GC×GC. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

Real-time high dynamic range laser scanning microscopy

PubMed Central

Vinegoni, C.; Leon Swisher, C.; Fumene Feruglio, P.; Giedt, R. J.; Rousso, D. L.; Stapleton, S.; Weissleder, R.

2016-01-01

In conventional confocal/multiphoton fluorescence microscopy, images are typically acquired under ideal settings and after extensive optimization of parameters for a given structure or feature, often resulting in information loss from other image attributes. To overcome the problem of selective data display, we developed a new method that extends the imaging dynamic range in optical microscopy and improves the signal-to-noise ratio. Here we demonstrate how real-time and sequential high dynamic range microscopy facilitates automated three-dimensional neural segmentation. We address reconstruction and segmentation performance on samples with different size, anatomy and complexity. Finally, in vivo real-time high dynamic range imaging is also demonstrated, making the technique particularly relevant for longitudinal imaging in the presence of physiological motion and/or for quantification of in vivo fast tracer kinetics during functional imaging. PMID:27032979

Developing a complex independent component analysis technique to extract non-stationary patterns from geophysical time-series

NASA Astrophysics Data System (ADS)

Forootan, Ehsan; Kusche, Jürgen

2016-04-01

Geodetic/geophysical observations, such as the time series of global terrestrial water storage change or sea level and temperature change, represent samples of physical processes and therefore contain information about complex physical interactionswith many inherent time scales. Extracting relevant information from these samples, for example quantifying the seasonality of a physical process or its variability due to large-scale ocean-atmosphere interactions, is not possible by rendering simple time series approaches. In the last decades, decomposition techniques have found increasing interest for extracting patterns from geophysical observations. Traditionally, principal component analysis (PCA) and more recently independent component analysis (ICA) are common techniques to extract statistical orthogonal (uncorrelated) and independent modes that represent the maximum variance of observations, respectively. PCA and ICA can be classified as stationary signal decomposition techniques since they are based on decomposing the auto-covariance matrix or diagonalizing higher (than two)-order statistical tensors from centered time series. However, the stationary assumption is obviously not justifiable for many geophysical and climate variables even after removing cyclic components e.g., the seasonal cycles. In this paper, we present a new decomposition method, the complex independent component analysis (CICA, Forootan, PhD-2014), which can be applied to extract to non-stationary (changing in space and time) patterns from geophysical time series. Here, CICA is derived as an extension of real-valued ICA (Forootan and Kusche, JoG-2012), where we (i) define a new complex data set using a Hilbert transformation. The complex time series contain the observed values in their real part, and the temporal rate of variability in their imaginary part. (ii) An ICA algorithm based on diagonalization of fourth-order cumulants is then applied to decompose the new complex data set in (i). (iii) Dominant non-stationary patterns are recognized as independent complex patterns that can be used to represent the space and time amplitude and phase propagations. We present the results of CICA on simulated and real cases e.g., for quantifying the impact of large-scale ocean-atmosphere interaction on global mass changes. Forootan (PhD-2014) Statistical signal decomposition techniques for analyzing time-variable satellite gravimetry data, PhD Thesis, University of Bonn, http://hss.ulb.uni-bonn.de/2014/3766/3766.htm Forootan and Kusche (JoG-2012) Separation of global time-variable gravity signals into maximally independent components, Journal of Geodesy 86 (7), 477-497, doi: 10.1007/s00190-011-0532-5

Solid-state nanopore detection of protein complexes: applications in healthcare and protein kinetics.

PubMed

Freedman, Kevin J; Bastian, Arangassery R; Chaiken, Irwin; Kim, Min Jun

2013-03-11

Protein conjugation provides a unique look into many biological phenomena and has been used for decades for molecular recognition purposes. In this study, the use of solid-state nanopores for the detection of gp120-associated complexes are investigated. They exhibit monovalent and multivalent binding to anti-gp120 antibody monomer and dimers. In order to investigate the feasibility of many practical applications related to nanopores, detection of specific protein complexes is attempted within a heterogeneous protein sample, and the role of voltage on complexed proteins is researched. It is found that the electric field within the pore can result in unbinding of a freely translocating protein complex within the transient event durations measured experimentally. The strong dependence of the unbinding time with voltage can be used to improve the detection capability of the nanopore system by adding an additional level of specificity that can be probed. These data provide a strong framework for future protein-specific detection schemes, which are shown to be feasible in the realm of a 'real-world' sample and an automated multidimensional method of detecting events. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Using machine learning tools to model complex toxic interactions with limited sampling regimes.

PubMed

Bertin, Matthew J; Moeller, Peter; Guillette, Louis J; Chapman, Robert W

2013-03-19

A major impediment to understanding the impact of environmental stress, including toxins and other pollutants, on organisms, is that organisms are rarely challenged by one or a few stressors in natural systems. Thus, linking laboratory experiments that are limited by practical considerations to a few stressors and a few levels of these stressors to real world conditions is constrained. In addition, while the existence of complex interactions among stressors can be identified by current statistical methods, these methods do not provide a means to construct mathematical models of these interactions. In this paper, we offer a two-step process by which complex interactions of stressors on biological systems can be modeled in an experimental design that is within the limits of practicality. We begin with the notion that environment conditions circumscribe an n-dimensional hyperspace within which biological processes or end points are embedded. We then randomly sample this hyperspace to establish experimental conditions that span the range of the relevant parameters and conduct the experiment(s) based upon these selected conditions. Models of the complex interactions of the parameters are then extracted using machine learning tools, specifically artificial neural networks. This approach can rapidly generate highly accurate models of biological responses to complex interactions among environmentally relevant toxins, identify critical subspaces where nonlinear responses exist, and provide an expedient means of designing traditional experiments to test the impact of complex mixtures on biological responses. Further, this can be accomplished with an astonishingly small sample size.

Measuring Complexity and Predictability of Time Series with Flexible Multiscale Entropy for Sensor Networks

PubMed Central

Zhou, Renjie; Yang, Chen; Wan, Jian; Zhang, Wei; Guan, Bo; Xiong, Naixue

2017-01-01

Measurement of time series complexity and predictability is sometimes the cornerstone for proposing solutions to topology and congestion control problems in sensor networks. As a method of measuring time series complexity and predictability, multiscale entropy (MSE) has been widely applied in many fields. However, sample entropy, which is the fundamental component of MSE, measures the similarity of two subsequences of a time series with either zero or one, but without in-between values, which causes sudden changes of entropy values even if the time series embraces small changes. This problem becomes especially severe when the length of time series is getting short. For solving such the problem, we propose flexible multiscale entropy (FMSE), which introduces a novel similarity function measuring the similarity of two subsequences with full-range values from zero to one, and thus increases the reliability and stability of measuring time series complexity. The proposed method is evaluated on both synthetic and real time series, including white noise, 1/f noise and real vibration signals. The evaluation results demonstrate that FMSE has a significant improvement in reliability and stability of measuring complexity of time series, especially when the length of time series is short, compared to MSE and composite multiscale entropy (CMSE). The proposed method FMSE is capable of improving the performance of time series analysis based topology and traffic congestion control techniques. PMID:28383496

Measuring Complexity and Predictability of Time Series with Flexible Multiscale Entropy for Sensor Networks.

PubMed

Zhou, Renjie; Yang, Chen; Wan, Jian; Zhang, Wei; Guan, Bo; Xiong, Naixue

2017-04-06

Measurement of time series complexity and predictability is sometimes the cornerstone for proposing solutions to topology and congestion control problems in sensor networks. As a method of measuring time series complexity and predictability, multiscale entropy (MSE) has been widely applied in many fields. However, sample entropy, which is the fundamental component of MSE, measures the similarity of two subsequences of a time series with either zero or one, but without in-between values, which causes sudden changes of entropy values even if the time series embraces small changes. This problem becomes especially severe when the length of time series is getting short. For solving such the problem, we propose flexible multiscale entropy (FMSE), which introduces a novel similarity function measuring the similarity of two subsequences with full-range values from zero to one, and thus increases the reliability and stability of measuring time series complexity. The proposed method is evaluated on both synthetic and real time series, including white noise, 1/f noise and real vibration signals. The evaluation results demonstrate that FMSE has a significant improvement in reliability and stability of measuring complexity of time series, especially when the length of time series is short, compared to MSE and composite multiscale entropy (CMSE). The proposed method FMSE is capable of improving the performance of time series analysis based topology and traffic congestion control techniques.

Visualising the Complex Roots of Quadratic Equations with Real Coefficients

ERIC Educational Resources Information Center

Bardell, Nicholas S.

2012-01-01

The roots of the general quadratic equation y = ax[superscript 2] + bx + c (real a, b, c) are known to occur in the following sets: (i) real and distinct; (ii) real and coincident; and (iii) a complex conjugate pair. Case (iii), which provides the focus for this investigation, can only occur when the values of the real coefficients a, b, and c are…

Cavity-enhanced measurements for determining dielectric-membrane thickness and complex index of refraction.

PubMed

Stambaugh, Corey; Durand, Mathieu; Kemiktarak, Utku; Lawall, John

2014-08-01

The material properties of silicon nitride (SiN) play an important role in the performance of SiN membranes used in optomechanical applications. An optimum design of a subwavelength high-contrast grating requires accurate knowledge of the membrane thickness and index of refraction, and its performance is ultimately limited by material absorption. Here we describe a cavity-enhanced method to measure the thickness and complex index of refraction of dielectric membranes with small, but nonzero, absorption coefficients. By determining Brewster's angle and an angle at which reflection is minimized by means of destructive interference, both the real part of the index of refraction and the sample thickness can be measured. A comparison of the losses in the empty cavity and the cavity containing the dielectric sample provides a measurement of the absorption.

Revealing physical interaction networks from statistics of collective dynamics

PubMed Central

Nitzan, Mor; Casadiego, Jose; Timme, Marc

2017-01-01

Revealing physical interactions in complex systems from observed collective dynamics constitutes a fundamental inverse problem in science. Current reconstruction methods require access to a system’s model or dynamical data at a level of detail often not available. We exploit changes in invariant measures, in particular distributions of sampled states of the system in response to driving signals, and use compressed sensing to reveal physical interaction networks. Dynamical observations following driving suffice to infer physical connectivity even if they are temporally disordered, are acquired at large sampling intervals, and stem from different experiments. Testing various nonlinear dynamic processes emerging on artificial and real network topologies indicates high reconstruction quality for existence as well as type of interactions. These results advance our ability to reveal physical interaction networks in complex synthetic and natural systems. PMID:28246630

Seafloor geology and benthic habitats, San Pedro Shelf, southern California

USGS Publications Warehouse

Wong, Florence L.; Dartnell, Peter; Edwards, Brian D.; Phillips, Eleyne L.

2012-01-01

Seafloor samples, videography, still photography, and real-time descriptions of geologic and biologic constituents at or near the seafloor of the San Pedro Shelf, southern California, advance the study of natural and man-made processes on this coastal area off the metropolitan Los Angeles area. Multibeam echo-sounder data collected by the U.S. Geological Survey in 1998 and 1999 guided sampling and camera work in 2004 resulting in a new seafloor character map that shows possible benthic habitats in much higher resolution (4- and 16-m pixels) than previously available. The seafloor is characterized by primarily muddy sand and sand with outcrops of Miocene and Pliocene bedrock along the Palos Verdes Fault Zone. Observed benthic populations indicate low abiotic complexity, low biotic complexity, and low biotic coverage. The data are provided for use in geographic information systems (GIS).

Inferring general relations between network characteristics from specific network ensembles.

PubMed

Cardanobile, Stefano; Pernice, Volker; Deger, Moritz; Rotter, Stefan

2012-01-01

Different network models have been suggested for the topology underlying complex interactions in natural systems. These models are aimed at replicating specific statistical features encountered in real-world networks. However, it is rarely considered to which degree the results obtained for one particular network class can be extrapolated to real-world networks. We address this issue by comparing different classical and more recently developed network models with respect to their ability to generate networks with large structural variability. In particular, we consider the statistical constraints which the respective construction scheme imposes on the generated networks. After having identified the most variable networks, we address the issue of which constraints are common to all network classes and are thus suitable candidates for being generic statistical laws of complex networks. In fact, we find that generic, not model-related dependencies between different network characteristics do exist. This makes it possible to infer global features from local ones using regression models trained on networks with high generalization power. Our results confirm and extend previous findings regarding the synchronization properties of neural networks. Our method seems especially relevant for large networks, which are difficult to map completely, like the neural networks in the brain. The structure of such large networks cannot be fully sampled with the present technology. Our approach provides a method to estimate global properties of under-sampled networks in good approximation. Finally, we demonstrate on three different data sets (C. elegans neuronal network, R. prowazekii metabolic network, and a network of synonyms extracted from Roget's Thesaurus) that real-world networks have statistical relations compatible with those obtained using regression models.

Continuous, Real-Time Monitoring of Cocaine in Undiluted Blood Serum via a Microfluidic, Electrochemical Aptamer-Based Sensor

PubMed Central

Swensen, James S.; Xiao, Yi; Ferguson, Brian S.; Lubin, Arica A.; Lai, Rebecca Y.; Heeger, Alan J.; Plaxco, Kevin W.; Soh, H. Tom.

2009-01-01

The development of a biosensor system capable of continuous, real-time measurement of small-molecule analytes directly in complex, unprocessed aqueous samples has been a significant challenge, and successful implementation has been achieved for only a limited number of targets. Towards a general solution to this problem, we report here the Microfluidic Electrochemical Aptamer-based Sensor (MECAS) chip wherein we integrate target-specific DNA aptamers that fold, and thus generate an electrochemical signal, in response to the analyte with a microfluidic detection system. As a model, we demonstrate the continuous, real-time (~1 minute time resolution) detection of the small molecule drug cocaine at near physiological, low micromolar concentrations directly in undiluted, otherwise unmodified blood serum. We believe our approach of integrating folding-based electrochemical sensors with miniaturized detection systems may lay the ground work for the real-time, point-of-care detection of a wide variety of molecular targets. PMID:19271708

Bat white-nose syndrome: a real-time TaqMan polymerase chain reaction test targeting the intergenic spacer region of Geomyces destructanstructans.

USGS Publications Warehouse

Muller, Laura K.; Lorch, Jeffrey M.; Lindner, Daniel L.; O'Connor, Michael; Gargas, Andrea; Blehert, David S.

2013-01-01

The fungus Geomyces destructans is the causative agent of white-nose syndrome (WNS), a disease that has killed millions of North American hibernating bats. We describe a real-time TaqMan PCR test that detects DNA from G. destructans by targeting a portion of the multicopy intergenic spacer region of the rRNA gene complex. The test is highly sensitive, consistently detecting as little as 3.3 fg of genomic DNA from G. destructans. The real-time PCR test specifically amplified genomic DNA from G. destructans but did not amplify target sequence from 54 closely related fungal isolates (including 43 Geomyces spp. isolates) associated with bats. The test was further qualified by analyzing DNA extracted from 91 bat wing skin samples, and PCR results matched histopathology findings. These data indicate the real-time TaqMan PCR method described herein is a sensitive, specific, and rapid test to detect DNA from G. destructans and provides a valuable tool for WNS diagnostics and research.

Dielectric relaxation spectroscopy of aqueous solutions of diclofenac potassium over the frequency range of 20 Hz to 2 MHz at 303.15 K temperature

NASA Astrophysics Data System (ADS)

Karakthala, J. B.; Vankar, H. P.; Rana, V. A.

2018-05-01

The complex relative dielectric function ɛ*(ω) = ɛ' - jɛ″ of aqueous solutions of diclofenac potassium (DK) in the frequency range 20 Hz to 2 MHz at 303.15 K was measured using a precision LCR meter. The electrical/dielectric properties of the solutions samples were represented in terms of complex relative dielectric function ɛ*(ω) real part σ'(ω) of complex ac conductivity and dc conductivity. These types of studies can be used to explore various mechanism contributed in the absorption, transportation of drug through tissues and membranes of body as well as interactions of drug with body fluid and blood plasma.

Documentation Driven Development for Complex Real-Time Systems

DTIC Science & Technology

2004-12-01

This paper presents a novel approach for development of complex real - time systems , called the documentation-driven development (DDD) approach. This... time systems . DDD will also support automated software generation based on a computational model and some relevant techniques. DDD includes two main...stakeholders to be easily involved in development processes and, therefore, significantly improve the agility of software development for complex real

Vibrational spectroscopy for imaging single microbial cells in complex biological samples

DOE PAGES

Harrison, Jesse P.; Berry, David

2017-04-13

Here, vibrational spectroscopy is increasingly used for the rapid and non-destructive imaging of environmental and medical samples. Both Raman and Fourier-transform infrared (FT-IR) imaging have been applied to obtain detailed information on the chemical composition of biological materials, ranging from single microbial cells to tissues. Due to its compatibility with methods such as stable isotope labeling for the monitoring of cellular activities, vibrational spectroscopy also holds considerable power as a tool in microbial ecology. Chemical imaging of undisturbed biological systems (such as live cells in their native habitats) presents unique challenges due to the physical and chemical complexity of themore » samples, potential for spectral interference, and frequent need for real-time measurements. This Mini Review provides a critical synthesis of recent applications of Raman and FT-IR spectroscopy for characterizing complex biological samples, with a focus on developments in single-cell imaging. We also discuss how new spectroscopic methods could be used to overcome current limitations of singlecell analyses. Given the inherent complementarity of Raman and FT-IR spectroscopic methods, we discuss how combining these approaches could enable us to obtain new insights into biological activities either in situ or under conditions that simulate selected properties of the natural environment.« less

Vibrational spectroscopy for imaging single microbial cells in complex biological samples

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

Harrison, Jesse P.; Berry, David

Here, vibrational spectroscopy is increasingly used for the rapid and non-destructive imaging of environmental and medical samples. Both Raman and Fourier-transform infrared (FT-IR) imaging have been applied to obtain detailed information on the chemical composition of biological materials, ranging from single microbial cells to tissues. Due to its compatibility with methods such as stable isotope labeling for the monitoring of cellular activities, vibrational spectroscopy also holds considerable power as a tool in microbial ecology. Chemical imaging of undisturbed biological systems (such as live cells in their native habitats) presents unique challenges due to the physical and chemical complexity of themore » samples, potential for spectral interference, and frequent need for real-time measurements. This Mini Review provides a critical synthesis of recent applications of Raman and FT-IR spectroscopy for characterizing complex biological samples, with a focus on developments in single-cell imaging. We also discuss how new spectroscopic methods could be used to overcome current limitations of singlecell analyses. Given the inherent complementarity of Raman and FT-IR spectroscopic methods, we discuss how combining these approaches could enable us to obtain new insights into biological activities either in situ or under conditions that simulate selected properties of the natural environment.« less

THE REAL McCOIL: A method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites

PubMed Central

Chang, Hsiao-Han; Worby, Colin J.; Yeka, Adoke; Nankabirwa, Joaniter; Kamya, Moses R.; Staedke, Sarah G.; Hubbart, Christina; Amato, Roberto; Kwiatkowski, Dominic P.

2017-01-01

As many malaria-endemic countries move towards elimination of Plasmodium falciparum, the most virulent human malaria parasite, effective tools for monitoring malaria epidemiology are urgent priorities. P. falciparum population genetic approaches offer promising tools for understanding transmission and spread of the disease, but a high prevalence of multi-clone or polygenomic infections can render estimation of even the most basic parameters, such as allele frequencies, challenging. A previous method, COIL, was developed to estimate complexity of infection (COI) from single nucleotide polymorphism (SNP) data, but relies on monogenomic infections to estimate allele frequencies or requires external allele frequency data which may not available. Estimates limited to monogenomic infections may not be representative, however, and when the average COI is high, they can be difficult or impossible to obtain. Therefore, we developed THE REAL McCOIL, Turning HEterozygous SNP data into Robust Estimates of ALelle frequency, via Markov chain Monte Carlo, and Complexity Of Infection using Likelihood, to incorporate polygenomic samples and simultaneously estimate allele frequency and COI. This approach was tested via simulations then applied to SNP data from cross-sectional surveys performed in three Ugandan sites with varying malaria transmission. We show that THE REAL McCOIL consistently outperforms COIL on simulated data, particularly when most infections are polygenomic. Using field data we show that, unlike with COIL, we can distinguish epidemiologically relevant differences in COI between and within these sites. Surprisingly, for example, we estimated high average COI in a peri-urban subregion with lower transmission intensity, suggesting that many of these cases were imported from surrounding regions with higher transmission intensity. THE REAL McCOIL therefore provides a robust tool for understanding the molecular epidemiology of malaria across transmission settings. PMID:28125584

Nonlinear stochastic interacting dynamics and complexity of financial gasket fractal-like lattice percolation

NASA Astrophysics Data System (ADS)

Zhang, Wei; Wang, Jun

2018-05-01

A novel nonlinear stochastic interacting price dynamics is proposed and investigated by the bond percolation on Sierpinski gasket fractal-like lattice, aim to make a new approach to reproduce and study the complexity dynamics of real security markets. Fractal-like lattices correspond to finite graphs with vertices and edges, which are similar to fractals, and Sierpinski gasket is a well-known example of fractals. Fractional ordinal array entropy and fractional ordinal array complexity are introduced to analyze the complexity behaviors of financial signals. To deeper comprehend the fluctuation characteristics of the stochastic price evolution, the complexity analysis of random logarithmic returns and volatility are preformed, including power-law distribution, fractional sample entropy and fractional ordinal array complexity. For further verifying the rationality and validity of the developed stochastic price evolution, the actual security market dataset are also studied with the same statistical methods for comparison. The empirical results show that this stochastic price dynamics can reconstruct complexity behaviors of the actual security markets to some extent.

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.

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.

The assessment of pi-pi selective stationary phases for two-dimensional HPLC analysis of foods: application to the analysis of coffee.

PubMed

Mnatsakanyan, Mariam; Stevenson, Paul G; Shock, David; Conlan, Xavier A; Goodie, Tiffany A; Spencer, Kylie N; Barnett, Neil W; Francis, Paul S; Shalliker, R Andrew

2010-09-15

Differences between alkyl, dipole-dipole, hydrogen bonding, and pi-pi selective surfaces represented by non-resonance and resonance pi-stationary phases have been assessed for the separation of 'Ristretto' café espresso by employing 2DHPLC techniques with C18 phase selectivity detection. Geometric approach to factor analysis (GAFA) was used to measure the detected peaks (N), spreading angle (beta), correlation, practical peak capacity (n(p)) and percentage usage of the separations space, as an assessment of selectivity differences between regional quadrants of the two-dimensional separation plane. Although all tested systems were correlated to some degree to the C18 dimension, regional measurement of separation divergence revealed that performance of specific systems was better for certain sample components. The results illustrate that because of the complexity of the 'real' sample obtaining a truly orthogonal two-dimensional system for complex samples of natural origin may be practically impossible. Copyright (c) 2010 Elsevier B.V. All rights reserved.

Dielectric Relaxation In Complex Perovskite Sm(Ni{sub 1/2}Ti{sub 1/2})O{sub 3}

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

Kumar, Nishant; Prasad, S.; Sinha, T. P.

2011-11-22

The complex perovskite oxide Samarium nickel titenate, Sm(Ni{sub 1/2}Ti{sub 1/2})O{sub 3}(SNT) is synthesized by a solid-state reaction technique. The X-ray diffraction of the sample at room temperature shows a monoclinic phase. The scanning micrograph of the sample shows the average grain size{approx_equal}0.6{mu}m The field dependence of dielectric response and the loss tangent of the sample are measured in a frequency range from 100Hz to 1MHz and in a temperature range from 313 K to 673 K. An analysis of the real and imaginary parts of the dielectric permittivity with frequency is performed, assuming a distribution of relaxation times as confirmedmore » by Cole-Cole plots. The frequency dependent electrical data are analyzed in the framework of conductivity formalism. The frequency dependent conductivity data are fitted to the universal power law. All these formalisms provided for qualitative similarities in the relaxation times.« less

A real-time fluorescent sensor specific to Mg2+: crystallographic evidence, DFT calculation and its use for quantitative determination of magnesium in drinking water.

PubMed

Men, Guangwen; Chen, Chunrong; Zhang, Shitong; Liang, Chunshuang; Wang, Ying; Deng, Mengyu; Shang, Hongxing; Yang, Bing; Jiang, Shimei

2015-02-14

An "off-the-shelf" fluorescence "turn-on" Mg(2+) chemosensor 3,5-dichlorosalicylaldehyde (BCSA) was rationally designed and developed. This proposed sensor works based on Mg(2+)-induced formation of the 2 : 1 BCSA-Mg(2+) complex. The coordination of BSCA to Mg(2+) increases its structural rigidity generating a chelation-enhanced fluorescence (CHEF) effect which was confirmed by single crystal XRD studies of the BSCA-Mg(2+) complex and TD/DFT calculations. This sensor exhibits high sensitivity and selectivity for the quantitative monitoring of Mg(2+) with a wide detection range (0-40 μM), a low detection limit (2.89 × 10(-7) mol L(-1)) and a short response time (<0.5 s). It can also resist the interference from the other co-existing metal ions, especially Ca(2+). Consequently, this fluorescent sensor can be utilized to monitor Mg(2+) in real time within actual samples from drinking water.

Simulation of the Vortex Dynamics in a Real Pinning Landscape of YBa 2 Cu 3 O 7 - δ Coated Conductors

DOE PAGES

Sadovskyy, I. A.; Koshelev, A. E.; Glatz, A.; ...

2016-01-01

The ability of high-temperature superconductors (HTSs) to carry very large currents with almost no dissipation makes them irreplaceable for high-power applications. The development and further improvement of HTS-based cables require an in-depth understanding of the superconducting vortex dynamics in the presence of complex pinning landscapes. We present a critical current analysis of a real HTS sample in a magnetic field by combining state-of-the-art large-scale Ginzburg-Landau simulations with reconstructive three-dimensional scanning-transmission-electron-microscopy tomography of the pinning landscape in Dy-doped YBa 2Cu 3O 7-δ. This methodology provides a unique look at the vortex dynamics in the presence of a complex pinning landscape responsiblemore » for the high-current-carrying-capacity characteristic of commercial HTS wires. Finally, our method demonstrates very good functional and quantitative agreement of the critical current between simulation and experiment, providing a new predictive tool for HTS wire designs.« less

Simulation of the Vortex Dynamics in a Real Pinning Landscape of YBa 2 Cu 3 O 7 - δ Coated Conductors

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

Sadovskyy, I. A.; Koshelev, A. E.; Glatz, A.

The ability of high-temperature superconductors (HTSs) to carry very large currents with almost no dissipation makes them irreplaceable for high-power applications. The development and further improvement of HTS-based cables require an in-depth understanding of the superconducting vortex dynamics in the presence of complex pinning landscapes. We present a critical current analysis of a real HTS sample in a magnetic field by combining state-of-the-art large-scale Ginzburg-Landau simulations with reconstructive three-dimensional scanning-transmission-electron-microscopy tomography of the pinning landscape in Dy-doped YBa 2Cu 3O 7-δ. This methodology provides a unique look at the vortex dynamics in the presence of a complex pinning landscape responsiblemore » for the high-current-carrying-capacity characteristic of commercial HTS wires. Finally, our method demonstrates very good functional and quantitative agreement of the critical current between simulation and experiment, providing a new predictive tool for HTS wire designs.« less

Simulation of the Vortex Dynamics in a Real Pinning Landscape of YBa 2 Cu 3 O 7 - δ Coated Conductors

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

Sadovskyy, I. A.; Koshelev, A. E.; Glatz, A.

Tmore » he ability of high-temperature superconductors (HSs) to carry very large currents with almost no dissipation makes them irreplaceable for high-power applications. he development and further improvement of HS-based cables require an in-depth understanding of the superconducting vortex dynamics in the presence of complex pinning landscapes. Here, we present a critical current analysis of a real HS sample in a magnetic field by combining state-of-the-art large-scale Ginzburg-Landau simulations with reconstructive three-dimensional scanning-transmission-electron-microscopy tomography of the pinning landscape in Dy-doped YBa 2 Cu 3 O 7 - δ . his methodology provides a unique look at the vortex dynamics in the presence of a complex pinning landscape responsible for the high-current-carrying-capacity characteristic of commercial HS wires. Our method demonstrates very good functional and quantitative agreement of the critical current between simulation and experiment, providing a new predictive tool for HS wire designs.« less

Ion-selective electrodes in potentiometric titrations; a new method for processing and evaluating titration data.

PubMed

Granholm, Kim; Sokalski, Tomasz; Lewenstam, Andrzej; Ivaska, Ari

2015-08-12

A new method to convert the potential of an ion-selective electrode to concentration or activity in potentiometric titration is proposed. The advantage of this method is that the electrode standard potential and the slope of the calibration curve do not have to be known. Instead two activities on the titration curve have to be estimated e.g. the starting activity before the titration begins and the activity at the end of the titration in the presence of large excess of titrant. This new method is beneficial when the analyte is in a complexed matrix or in a harsh environment which affects the properties of the electrode and the traditional calibration procedure with standard solutions cannot be used. The new method was implemented both in a method of linearization based on the Grans's plot and in determination of the stability constant of a complex and the concentration of the complexing ligand in the sample. The new method gave accurate results when using titrations data from experiments with samples of known composition and with real industrial harsh black liquor sample. A complexometric titration model was also developed. Copyright © 2015 Elsevier B.V. All rights reserved.

Resonant Acoustic Determination of Complex Elastic Moduli

NASA Technical Reports Server (NTRS)

Brown, David A.; Garrett, Steven L.

1991-01-01

A simple, inexpensive, yet accurate method for measuring the dynamic complex modulus of elasticity is described. Using a 'free-free' bar selectively excited in three independent vibrational modes, the shear modulus is obtained by measuring the frequency of the torsional resonant mode and the Young's modulus is determined from measurement of either the longitudinal or flexural mode. The damping properties are obtained by measuring the quality factor (Q) for each mode. The Q is inversely proportional to the loss tangent. The viscoelastic behavior of the sample can be obtained by tracking a particular resonant mode (and thus a particular modulus) using a phase locked loop (PLL) and by changing the temperature of the sample. The change in the damping properties is obtained by measuring the in-phase amplitude of the PLL which is proportional to the Q of the material. The real and imaginary parts or the complex modulus can be obtained continuously as a function of parameters such as temperature, pressure, or humidity. For homogeneous and isotropic samples only two independent moduli are needed in order to characterize the complete set of elastic constants, thus, values can be obtained for the dynamic Poisson's ratio, bulk modulus, Lame constants, etc.

Time-Based Indicators of Emotional Complexity: Interrelations and Correlates

PubMed Central

Grühn, Daniel; Lumley, Mark A.; Diehl, Manfred; Labouvie-Vief, Gisela

2012-01-01

Emotional complexity has been regarded as one correlate of adaptive emotion regulation in adulthood. One novel and potentially valuable approach to operationalizing emotional complexity is to use reports of emotions obtained repeatedly in real time, which can generate a number of potential time-based indicators of emotional complexity. It is not known, however, how these indicators relate to each other, to other measures of affective complexity, such as those derived from a cognitive-developmental view of emotional complexity, or to measures of adaptive functioning, such as well-being. A sample of 109 adults, aged 23 to 90 years, participated in an experience-sampling study and reported their negative and positive affect five times a day for one week. Based on these reports, we calculated nine different time-based indicators potentially reflecting emotional complexity. Analyses showed three major findings: First, the indicators showed a diverse pattern of interrelations suggestive of four distinct components of emotional complexity. Second, age was generally not related to time-based indicators of emotional complexity; however, older adults showed overall low variability in negative affect. Third, time-based indicators of emotional complexity were either unrelated or inversely related to measures of adaptive functioning; that is, these measures tended to predict a less adaptive profile, such as lower subjective and psychological well-being. In sum, time-based indicators of emotional complexity displayed a more complex and less beneficial picture than originally thought. In particular, variability in negative affect seems to indicate suboptimal adjustments. Future research would benefit from collecting empirical data for the interrelations and correlates of time-based indicators of emotional complexity in different contexts. PMID:23163712

An advanced real-time digital signal processing system for linear systems emulation, with special emphasis on network and acoustic response characterization

NASA Astrophysics Data System (ADS)

Gaydecki, Patrick; Fernandes, Bosco

2003-11-01

A fast digital signal processing (DSP) system is described that can perform real-time emulation of a wide variety of linear audio-bandwidth systems and networks, such as reverberant spaces, musical instrument bodies and very high order filter networks. The hardware design is based upon a Motorola DSP56309 operating at 110 million multiplication-accumulations per second and a dual-channel 24 bit codec with a maximum sampling frequency of 192 kHz. High level software has been developed to express complex vector frequency responses as both infinite impulse response (IIR) and finite impulse response (FIR) coefficients, in a form suitable for real-time convolution by the firmware installed in the DSP system memory. An algorithm has also been devised to express IIR filters as equivalent FIR structures, thereby obviating the potential instabilities associated with recursive equations and negating the traditional deficiencies of FIR filters respecting equivalent analogue designs. The speed and dynamic range of the system is such that, when sampling at 48 kHz, the frequency response can be specified to a spectral precision of 22 Hz when sampling at 10 kHz, this resolution increases to 0.9 Hz. Moreover, it is also possible to control the phase of any frequency band with a theoretical precision of 10-5 degrees in all cases. The system has been applied in the study of analogue filter networks, real-time Hilbert transformation, phase-shift systems and musical instrument body emulation, where it is providing valuable new insights into the understanding of psychoacoustic mechanisms.

Monitoring diesel particulate matter and calculating diesel particulate densities using Grimm model 1.109 real-time aerosol monitors in underground mines.

PubMed

Kimbal, Kyle C; Pahler, Leon; Larson, Rodney; VanDerslice, Jim

2012-01-01

Currently, there is no Mine Safety and Health Administration (MSHA)-approved sampling method that provides real-time results for ambient concentrations of diesel particulates. This study investigated whether a commercially available aerosol spectrometer, the Grimm Portable Aerosol Spectrometer Model 1.109, could be used during underground mine operations to provide accurate real-time diesel particulate data relative to MSHA-approved cassette-based sampling methods. A subset was to estimate size-specific diesel particle densities to potentially improve the diesel particulate concentration estimates using the aerosol monitor. Concurrent sampling was conducted during underground metal mine operations using six duplicate diesel particulate cassettes, according to the MSHA-approved method, and two identical Grimm Model 1.109 instruments. Linear regression was used to develop adjustment factors relating the Grimm results to the average of the cassette results. Statistical models using the Grimm data produced predicted diesel particulate concentrations that highly correlated with the time-weighted average cassette results (R(2) = 0.86, 0.88). Size-specific diesel particulate densities were not constant over the range of particle diameters observed. The variance of the calculated diesel particulate densities by particle diameter size supports the current understanding that diesel emissions are a mixture of particulate aerosols and a complex host of gases and vapors not limited to elemental and organic carbon. Finally, diesel particulate concentrations measured by the Grimm Model 1.109 can be adjusted to provide sufficiently accurate real-time air monitoring data for an underground mining environment.

The New Maia Detector System: Methods For High Definition Trace Element Imaging Of Natural Material

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

Ryan, C. G.; School of Physics, University of Melbourne, Parkville VIC; CODES Centre of Excellence, University of Tasmania, Hobart TAS

2010-04-06

Motivated by the need for megapixel high definition trace element imaging to capture intricate detail in natural material, together with faster acquisition and improved counting statistics in elemental imaging, a large energy-dispersive detector array called Maia has been developed by CSIRO and BNL for SXRF imaging on the XFM beamline at the Australian Synchrotron. A 96 detector prototype demonstrated the capacity of the system for real-time deconvolution of complex spectral data using an embedded implementation of the Dynamic Analysis method and acquiring highly detailed images up to 77 M pixels spanning large areas of complex mineral sample sections.

The New Maia Detector System: Methods For High Definition Trace Element Imaging Of Natural Material

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

Ryan, C.G.; Siddons, D.P.; Kirkham, R.

2010-05-25

Motivated by the need for megapixel high definition trace element imaging to capture intricate detail in natural material, together with faster acquisition and improved counting statistics in elemental imaging, a large energy-dispersive detector array called Maia has been developed by CSIRO and BNL for SXRF imaging on the XFM beamline at the Australian Synchrotron. A 96 detector prototype demonstrated the capacity of the system for real-time deconvolution of complex spectral data using an embedded implementation of the Dynamic Analysis method and acquiring highly detailed images up to 77 M pixels spanning large areas of complex mineral sample sections.

Real-time and high accuracy frequency measurements for intermediate frequency narrowband signals

NASA Astrophysics Data System (ADS)

Tian, Jing; Meng, Xiaofeng; Nie, Jing; Lin, Liwei

2018-01-01

Real-time and accurate measurements of intermediate frequency signals based on microprocessors are difficult due to the computational complexity and limited time constraints. In this paper, a fast and precise methodology based on the sigma-delta modulator is designed and implemented by first generating the twiddle factors using the designed recursive scheme. This scheme requires zero times of multiplications and only half amounts of addition operations by using the discrete Fourier transform (DFT) and the combination of the Rife algorithm and Fourier coefficient interpolation as compared with conventional methods such as DFT and Fast Fourier Transform. Experimentally, when the sampling frequency is 10 MHz, the real-time frequency measurements with intermediate frequency and narrowband signals have a measurement mean squared error of ±2.4 Hz. Furthermore, a single measurement of the whole system only requires approximately 0.3 s to achieve fast iteration, high precision, and less calculation time.

A novel ultrasonic phased array inspection system to NDT for offshore platform structures

NASA Astrophysics Data System (ADS)

Wang, Hua; Shan, Baohua; Wang, Xin; Ou, Jinping

2007-01-01

A novel ultrasonic phased array detection system is developed for nondestructive testing (NDT). The purpose of the system is to make acquisition of data in real-time from 64-element ultrasonic phased array transducer, and to enable real- time processing of the acquired data. The system is composed of five main parts: master unit, main board, eight transmit/receive units, a 64-element transducer and an external PC. The system can be used with 64 element transducers, excite 32 elements, receive and sample echo signals form 32 elements simultaneously at 62.5MHz with 8 bit precision. The external PC is used as the user interface showing the real time images and controls overall operation of the system through USB serial link. The use of Universal Serial Bus (USB) improves the transform speed and reduces hardware interface complexity. The program of the system is written in Visual C++.NET and is platform independent.

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.

Molecular detection and species identification of Alexandrium (Dinophyceae) causing harmful algal blooms along the Chilean coastline

PubMed Central

Jedlicki, Ana; Fernández, Gonzalo; Astorga, Marcela; Oyarzún, Pablo; Toro, Jorge E.; Navarro, Jorge M.; Martínez, Víctor

2012-01-01

Background and aims On the basis of morphological evidence, the species involved in South American Pacific coast harmful algal blooms (HABs) has been traditionally recognized as Alexandrium catenella (Dinophyceae). However, these observations have not been confirmed using evidence based on genomic sequence variability. Our principal objective was to accurately determine the species of Alexandrium involved in local HABs in order to implement a real-time polymerase chain reaction (PCR) assay for its rapid and easy detection on filter-feeding shellfish, such as mussels. Methodology For species-specific determination, the intergenic spacer 1 (ITS1), 5.8S subunit, ITS2 and the hypervariable genomic regions D1–D5 of the large ribosomal subunit of local strains were sequenced and compared with two data sets of other Alexandrium sequences. Species-specific primers were used to amplify signature sequences within the genomic DNA of the studied species by conventional and real-time PCR. Principal results Phylogenetic analysis determined that the Chilean strain falls into Group I of the tamarensis complex. Our results support the allocation of the Chilean Alexandrium species as a toxic Alexandrium tamarense rather than A. catenella, as currently defined. Once local species were determined to belong to Group I of the tamarensis complex, a highly sensitive and accurate real-time PCR procedure was developed to detect dinoflagellate presence in Mytilus spp. (Bivalvia) samples after being fed (challenged) in vitro with the Chilean Alexandrium strain. The results show that real-time PCR is useful to detect Alexandrium intake in filter-feeding molluscs. Conclusions It has been shown that the classification of local Alexandrium using morphological evidence is not very accurate. Molecular methods enabled the HAB dinoflagellate species of the Chilean coast to be assigned as A. tamarense rather than A. catenella. Real-time PCR analysis based on A. tamarense primers allowed the detection of dinoflagellate DNA in Mytilus spp. samples exposed to this alga. Through the specific assignment of dinoflagellate species involved in HABs, more reliable preventive policies can be implemented. PMID:23259043

Quantification of intestinal bacterial populations by real-time PCR with a universal primer set and minor groove binder probes: a global approach to the enteric flora.

PubMed

Ott, Stephan J; Musfeldt, Meike; Ullmann, Uwe; Hampe, Jochen; Schreiber, Stefan

2004-06-01

The composition of the human intestinal flora is important for the health status of the host. The global composition and the presence of specific pathogens are relevant to the effects of the flora. Therefore, accurate quantification of all major bacterial populations of the enteric flora is needed. A TaqMan real-time PCR-based method for the quantification of 20 dominant bacterial species and groups of the intestinal flora has been established on the basis of 16S ribosomal DNA taxonomy. A PCR with conserved primers was used for all reactions. In each real-time PCR, a universal probe for quantification of total bacteria and a specific probe for the species in question were included. PCR with conserved primers and the universal probe for total bacteria allowed relative and absolute quantification. Minor groove binder probes increased the sensitivity of the assays 10- to 100-fold. The method was evaluated by cross-reaction experiments and quantification of bacteria in complex clinical samples from healthy patients. A sensitivity of 10(1) to 10(3) bacterial cells per sample was achieved. No significant cross-reaction was observed. The real-time PCR assays presented may facilitate understanding of the intestinal bacterial flora through a normalized global estimation of the major contributing species.

A tool for modeling concurrent real-time computation

NASA Technical Reports Server (NTRS)

Sharma, D. D.; Huang, Shie-Rei; Bhatt, Rahul; Sridharan, N. S.

1990-01-01

Real-time computation is a significant area of research in general, and in AI in particular. The complexity of practical real-time problems demands use of knowledge-based problem solving techniques while satisfying real-time performance constraints. Since the demands of a complex real-time problem cannot be predicted (owing to the dynamic nature of the environment) powerful dynamic resource control techniques are needed to monitor and control the performance. A real-time computation model for a real-time tool, an implementation of the QP-Net simulator on a Symbolics machine, and an implementation on a Butterfly multiprocessor machine are briefly described.

A molecular approach for the rapid, selective and sensitive detection of Exophiala jeanselmei in environmental samples: development and performance assessment of a real-time PCR assay.

PubMed

Libert, X; Chasseur, C; Packeu, A; Bureau, F; Roosens, N H; De Keersmaecker, S J C

2016-02-01

Exophiala jeanselmei is an opportunistic pathogenic black yeast growing in humid environments such as water reservoirs of air-conditioning systems. Because this fungal contaminant could be vaporized into the air and subsequently cause health problems, its monitoring is recommended. Currently, this monitoring is based on culture and microscopic identification which are complex, sometimes ambiguous and time-demanding, i.e., up to 21 days. Therefore, molecular, culture-independent methods could be more advantageous for the monitoring of E. jeanselmei. In this study, we developed a SYBR®green real-time PCR assay based on the internal transcribed spacer 2 from the 18S ribosomal DNA complex for the specific detection of E. jeanselmei. The selectivity (100 %), PCR efficiency (95.5 %), dynamic range and repeatability of this qPCR assay were subsequently evaluated. The limit of detection for this qPCR assay was determined to be 1 copy of genomic DNA of E. jeanselmei. Finally, water samples collected from cooling reservoirs were analyzed using this qPCR assay to deliver a proof of concept for the molecular detection of E. jeanselmei in environmental samples. The results obtained by molecular analysis were compared with those of classical methods (i.e., culture and microscopic identification) used in routine analysis and were 100 % matching. This comparison demonstrated that this SYBR®green qPCR assay can be used as a molecular alternative for monitoring and routine investigation of samples contaminated by E. jeanselmei, while eliminating the need for culturing and thereby considerably decreasing the required analysis time to 2 days.

Combined use of direct analysis in real-time/Orbitrap mass spectrometry and micro-Raman spectroscopy for the comprehensive characterization of real explosive samples.

PubMed

Bridoux, Maxime C; Schwarzenberg, Adrián; Schramm, Sébastien; Cole, Richard B

2016-08-01

Direct Analysis in Real Time (DART™) high-resolution Orbitrap™ mass spectrometry (HRMS) in combination with Raman microscopy was used for the detailed molecular level characterization of explosives including not only the charge but also the complex matrix of binders, plasticizers, polymers, and other possible organic additives. A total of 15 defused military weapons including grenades, mines, rockets, submunitions, and mortars were examined. Swabs and wipes were used to collect trace (residual) amounts of explosives and their organic constituents from the defused military weapons and micrometer-size explosive particles were transferred using a vacuum suction-impact collection device (vacuum impactor) from wipe and swap samples to an impaction plate made of carbon. The particles deposited on the carbon plate were then characterized using micro-Raman spectroscopy followed by DART-HRMS providing fingerprint signatures of orthogonal nature. The optical microscope of the micro-Raman spectrometer was first used to localize and characterize the explosive charge on the impaction plate which was then targeted for identification by DART-HRMS analysis in both the negative and positive modes. Raman spectra of the explosives TNT, RDX and PETN were acquired from micrometer size particles and characterized by the presence of their characteristic Raman bands obtained directly at the surface of the impaction plate nondestructively without further sample preparation. Negative mode DART-HRMS confirmed the types of charges contained in the weapons (mainly TNT, RDX, HMX, and PETN; either as individual components or as mixtures). These energetic compounds were mainly detected as deprotonated species [M-H](-), or as adduct [M + (35)Cl](-), [M + (37)Cl](-), or [M + NO3](-) anions. Chloride adducts were promoted in the heated DART reagent gas by adding chloroform vapors to the helium stream using an "in-house" delivery method. When the polarity was switched to positive mode, DART-HRMS revealed a very complex distribution of polymeric binders (mainly polyethylene glycols and polypropylene glycols), plasticizers (e.g., dioctyl sebacate, tributyl phosphate), as well as wax-like compounds whose structural features could not be precisely assigned. In positive mode, compounds were identified either as protonated molecules or ammonium adduct species. These results clearly demonstrate the complementarity of micro-Raman microscopy combined with DART-MS. The former technique provides structural information on the type of explosives present at the surface of the sample, whereas the latter provides not only a confirmation of the nature of the explosive charge but also useful additional information regarding the nature of the complex organic matrix of binders, plasticizers, polymers, oils, and potentially other organic additives and contaminants present in the sample. Combining these two techniques provides a powerful tool for the screening, comprehensive characterization, and differentiation of particulate explosive samples for forensic sciences and homeland security applications. Graphical Abstract Comprehensive characterization of explosive particles collected from swipe samples by micro-Raman and DART™-HRMS.

Simultaneous Detection of Metalloprotease Activities in Complex Biological Samples Using the PrAMA (Proteolytic Activity Matrix Assay) Method.

PubMed

Conrad, Catharina; Miller, Miles A; Bartsch, Jörg W; Schlomann, Uwe; Lauffenburger, Douglas A

2017-01-01

Proteolytic Activity Matrix Analysis (PrAMA) is a method for simultaneously determining the activities of specific Matrix Metalloproteinases (MMPs) and A Disintegrin and Metalloproteinases (ADAMs) in complex biological samples. In mixtures of unknown proteases, PrAMA infers selective metalloproteinase activities by using a panel of moderately specific FRET-based polypeptide protease substrates in parallel, typically monitored by a plate-reader in a 96-well format. Fluorescence measurements are then quantitatively compared to a standard table of catalytic efficiencies measured from purified mixtures of individual metalloproteinases and FRET substrates. Computational inference of specific activities is performed with an easily used Matlab program, which is provided herein. Thus, we describe PrAMA as a combined experimental and mathematical approach to determine real-time metalloproteinase activities, which has previously been applied to live-cell cultures, cellular lysates, cell culture supernatants, and body fluids from patients.

Detection of Multiple Pathogens in Serum Using Silica-Encapsulated Nanotags in a Surface-Enhanced Raman Scattering-Based Immunoassay.

PubMed

Neng, Jing; Li, Yina; Driscoll, Ashley J; Wilson, William C; Johnson, Patrick A

2018-06-06

A robust immunoassay based on surface-enhanced Raman scattering (SERS) has been developed to simultaneously detect trace quantities of multiple pathogenic antigens from West Nile virus, Rift Valley fever virus, and Yersinia pestis in fetal bovine serum. Antigens were detected by capture with silica-encapsulated nanotags and magnetic nanoparticles conjugated with polyclonal antibodies. The magnetic pull-down resulted in aggregation of the immune complexes, and the silica-encapsulated nanotags provided distinct spectra corresponding to each antigen captured. The limit of detection was ∼10 pg/mL in 20% fetal bovine serum, a significant improvement over previous studies in terms of sensitivity, level of multiplexing, and medium complexity. This highly sensitive multiplex immunoassay platform provides a promising method to detect various antigens directly in crude serum samples without the tedious process of sample preparation, which is desirable for on-site diagnostic testing and real-time disease monitoring.

Fast identification of microplastics in complex environmental samples by a thermal degradation method.

PubMed

Dümichen, Erik; Eisentraut, Paul; Bannick, Claus Gerhard; Barthel, Anne-Kathrin; Senz, Rainer; Braun, Ulrike

2017-05-01

In order to determine the relevance of microplastic particles in various environmental media, comprehensive investigations are needed. However, no analytical method exists for fast identification and quantification. At present, optical spectroscopy methods like IR and RAMAN imaging are used. Due to their time consuming procedures and uncertain extrapolation, reliable monitoring is difficult. For analyzing polymers Py-GC-MS is a standard method. However, due to a limited sample amount of about 0.5 mg it is not suited for analysis of complex sample mixtures like environmental samples. Therefore, we developed a new thermoanalytical method as a first step for identifying microplastics in environmental samples. A sample amount of about 20 mg, which assures the homogeneity of the sample, is subjected to complete thermal decomposition. The specific degradation products of the respective polymer are adsorbed on a solid-phase adsorber and subsequently analyzed by thermal desorption gas chromatography mass spectrometry. For certain identification, the specific degradation products for the respective polymer were selected first. Afterwards real environmental samples from the aquatic (three different rivers) and the terrestrial (bio gas plant) systems were screened for microplastics. Mainly polypropylene (PP), polyethylene (PE) and polystyrene (PS) were identified for the samples from the bio gas plant and PE and PS from the rivers. However, this was only the first step and quantification measurements will follow. Copyright © 2017 Elsevier Ltd. All rights reserved.

Real-time generation of the Wigner distribution of complex functions using phase conjugation in photorefractive materials.

PubMed

Sun, P C; Fainman, Y

1990-09-01

An optical processor for real-time generation of the Wigner distribution of complex amplitude functions is introduced. The phase conjugation of the input signal is accomplished by a highly efficient self-pumped phase conjugator based on a 45 degrees -cut barium titanate photorefractive crystal. Experimental results on the real-time generation of Wigner distribution slices for complex amplitude two-dimensional optical functions are presented and discussed.

Real-Time Tracking the Synthesis and Degradation of Albumin in Complex Biological Systems with a near-Infrared Fluorescent Probe.

PubMed

Jin, Qiang; Feng, Lei; Zhang, Shui-Jun; Wang, Dan-Dan; Wang, Fang-Jun; Zhang, Yi; Cui, Jing-Nan; Guo, Wen-Zhi; Ge, Guang-Bo; Yang, Ling

2017-09-19

In this study, a novel fluorescent detection system for biological sensing of human albumin (HA) was developed on the basis of the pseudoesterase activity and substrate preference of HA. The designed near-infrared (NIR) fluorescent probe (DDAP) could be effectively hydrolyzed by HA, accompanied by significant changes in both color and fluorescence spectrum. The sensing mechanism was fully investigated by fluorescence spectroscopy, NMR, and mass spectra. DDAP exhibited excellent selectivity and sensitivity toward HA over a variety of human plasma proteins, hydrolases, and abundant biomolecules found in human body. The probe has been successfully applied to measure native HA in diluted plasma samples and the secreted HA in the hepatocyte culture supernatant. DDAP has also been used for fluorescence imaging of HA reabsorption in living renal cells, and the results show that the probe exhibits good cell permeability, low cytotoxicity and high imaging resolution. Furthermore, DDAP has been successfully used for real-time tracking the uptaking and degradation of albumin in ex vivo mouse kidney models for the first time. All these results clearly demonstrated that DDAP-based assay held great promise for real-time sensing and tracking HA in complex biological systems, which would be very useful for basic researches and clinical diagnosis of HA-associated diseases.

Porous Silicon-Based Biosensors: Towards Real-Time Optical Detection of Target Bacteria in the Food Industry

PubMed Central

Massad-Ivanir, Naama; Shtenberg, Giorgi; Raz, Nitzan; Gazenbeek, Christel; Budding, Dries; Bos, Martine P.; Segal, Ester

2016-01-01

Rapid detection of target bacteria is crucial to provide a safe food supply and to prevent foodborne diseases. Herein, we present an optical biosensor for identification and quantification of Escherichia coli (E. coli, used as a model indicator bacteria species) in complex food industry process water. The biosensor is based on a nanostructured, oxidized porous silicon (PSi) thin film which is functionalized with specific antibodies against E. coli. The biosensors were exposed to water samples collected directly from process lines of fresh-cut produce and their reflectivity spectra were collected in real time. Process water were characterized by complex natural micro-flora (microbial load of >107 cell/mL), in addition to soil particles and plant cell debris. We show that process water spiked with culture-grown E. coli, induces robust and predictable changes in the thin-film optical interference spectrum of the biosensor. The latter is ascribed to highly specific capture of the target cells onto the biosensor surface, as confirmed by real-time polymerase chain reaction (PCR). The biosensors were capable of selectively identifying and quantifying the target cells, while the target cell concentration is orders of magnitude lower than that of other bacterial species, without any pre-enrichment or prior processing steps. PMID:27901131

Porous Silicon-Based Biosensors: Towards Real-Time Optical Detection of Target Bacteria in the Food Industry.

PubMed

Massad-Ivanir, Naama; Shtenberg, Giorgi; Raz, Nitzan; Gazenbeek, Christel; Budding, Dries; Bos, Martine P; Segal, Ester

2016-11-30

Rapid detection of target bacteria is crucial to provide a safe food supply and to prevent foodborne diseases. Herein, we present an optical biosensor for identification and quantification of Escherichia coli (E. coli, used as a model indicator bacteria species) in complex food industry process water. The biosensor is based on a nanostructured, oxidized porous silicon (PSi) thin film which is functionalized with specific antibodies against E. coli. The biosensors were exposed to water samples collected directly from process lines of fresh-cut produce and their reflectivity spectra were collected in real time. Process water were characterized by complex natural micro-flora (microbial load of >10 7  cell/mL), in addition to soil particles and plant cell debris. We show that process water spiked with culture-grown E. coli, induces robust and predictable changes in the thin-film optical interference spectrum of the biosensor. The latter is ascribed to highly specific capture of the target cells onto the biosensor surface, as confirmed by real-time polymerase chain reaction (PCR). The biosensors were capable of selectively identifying and quantifying the target cells, while the target cell concentration is orders of magnitude lower than that of other bacterial species, without any pre-enrichment or prior processing steps.

Porous Silicon-Based Biosensors: Towards Real-Time Optical Detection of Target Bacteria in the Food Industry

NASA Astrophysics Data System (ADS)

Massad-Ivanir, Naama; Shtenberg, Giorgi; Raz, Nitzan; Gazenbeek, Christel; Budding, Dries; Bos, Martine P.; Segal, Ester

2016-11-01

Rapid detection of target bacteria is crucial to provide a safe food supply and to prevent foodborne diseases. Herein, we present an optical biosensor for identification and quantification of Escherichia coli (E. coli, used as a model indicator bacteria species) in complex food industry process water. The biosensor is based on a nanostructured, oxidized porous silicon (PSi) thin film which is functionalized with specific antibodies against E. coli. The biosensors were exposed to water samples collected directly from process lines of fresh-cut produce and their reflectivity spectra were collected in real time. Process water were characterized by complex natural micro-flora (microbial load of >107 cell/mL), in addition to soil particles and plant cell debris. We show that process water spiked with culture-grown E. coli, induces robust and predictable changes in the thin-film optical interference spectrum of the biosensor. The latter is ascribed to highly specific capture of the target cells onto the biosensor surface, as confirmed by real-time polymerase chain reaction (PCR). The biosensors were capable of selectively identifying and quantifying the target cells, while the target cell concentration is orders of magnitude lower than that of other bacterial species, without any pre-enrichment or prior processing steps.

Evaluation of the cognitive effects of travel technique in complex real and virtual environments.

PubMed

Suma, Evan A; Finkelstein, Samantha L; Reid, Myra; V Babu, Sabarish; Ulinski, Amy C; Hodges, Larry F

2010-01-01

We report a series of experiments conducted to investigate the effects of travel technique on information gathering and cognition in complex virtual environments. In the first experiment, participants completed a non-branching multilevel 3D maze at their own pace using either real walking or one of two virtual travel techniques. In the second experiment, we constructed a real-world maze with branching pathways and modeled an identical virtual environment. Participants explored either the real or virtual maze for a predetermined amount of time using real walking or a virtual travel technique. Our results across experiments suggest that for complex environments requiring a large number of turns, virtual travel is an acceptable substitute for real walking if the goal of the application involves learning or reasoning based on information presented in the virtual world. However, for applications that require fast, efficient navigation or travel that closely resembles real-world behavior, real walking has advantages over common joystick-based virtual travel techniques.

Real rock-microfluidic flow cell: A test bed for real-time in situ analysis of flow, transport, and reaction in a subsurface reactive transport environment.

PubMed

Singh, Rajveer; Sivaguru, Mayandi; Fried, Glenn A; Fouke, Bruce W; Sanford, Robert A; Carrera, Martin; Werth, Charles J

2017-09-01

Physical, chemical, and biological interactions between groundwater and sedimentary rock directly control the fundamental subsurface properties such as porosity, permeability, and flow. This is true for a variety of subsurface scenarios, ranging from shallow groundwater aquifers to deeply buried hydrocarbon reservoirs. Microfluidic flow cells are now commonly being used to study these processes at the pore scale in simplified pore structures meant to mimic subsurface reservoirs. However, these micromodels are typically fabricated from glass, silicon, or polydimethylsiloxane (PDMS), and are therefore incapable of replicating the geochemical reactivity and complex three-dimensional pore networks present in subsurface lithologies. To address these limitations, we developed a new microfluidic experimental test bed, herein called the Real Rock-Microfluidic Flow Cell (RR-MFC). A porous 500μm-thick real rock sample of the Clair Group sandstone from a subsurface hydrocarbon reservoir of the North Sea was prepared and mounted inside a PDMS microfluidic channel, creating a dynamic flow-through experimental platform for real-time tracking of subsurface reactive transport. Transmitted and reflected microscopy, cathodoluminescence microscopy, Raman spectroscopy, and confocal laser microscopy techniques were used to (1) determine the mineralogy, geochemistry, and pore networks within the sandstone inserted in the RR-MFC, (2) analyze non-reactive tracer breakthrough in two- and (depth-limited) three-dimensions, and (3) characterize multiphase flow. The RR-MFC is the first microfluidic experimental platform that allows direct visualization of flow and transport in the pore space of a real subsurface reservoir rock sample, and holds potential to advance our understandings of reactive transport and other subsurface processes relevant to pollutant transport and cleanup in groundwater, as well as energy recovery. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

Quadtree of TIN: a new algorithm of dynamic LOD

NASA Astrophysics Data System (ADS)

Zhang, Junfeng; Fei, Lifan; Chen, Zhen

2009-10-01

Currently, Real-time visualization of large-scale digital elevation model mainly employs the regular structure of GRID based on quadtree and triangle simplification methods based on irregular triangulated network (TIN). TIN is a refined means to express the terrain surface in the computer science, compared with GRID. However, the data structure of TIN model is complex, and is difficult to realize view-dependence representation of level of detail (LOD) quickly. GRID is a simple method to realize the LOD of terrain, but contains more triangle count. A new algorithm, which takes full advantage of the two methods' merit, is presented in this paper. This algorithm combines TIN with quadtree structure to realize the view-dependence LOD controlling over the irregular sampling point sets, and holds the details through the distance of viewpoint and the geometric error of terrain. Experiments indicate that this approach can generate an efficient quadtree triangulation hierarchy over any irregular sampling point sets and achieve dynamic and visual multi-resolution performance of large-scale terrain at real-time.

In-situ and real-time growth observation of high-quality protein crystals under quasi-microgravity on earth.

PubMed

Nakamura, Akira; Ohtsuka, Jun; Kashiwagi, Tatsuki; Numoto, Nobutaka; Hirota, Noriyuki; Ode, Takahiro; Okada, Hidehiko; Nagata, Koji; Kiyohara, Motosuke; Suzuki, Ei-Ichiro; Kita, Akiko; Wada, Hitoshi; Tanokura, Masaru

2016-02-26

Precise protein structure determination provides significant information on life science research, although high-quality crystals are not easily obtained. We developed a system for producing high-quality protein crystals with high throughput. Using this system, gravity-controlled crystallization are made possible by a magnetic microgravity environment. In addition, in-situ and real-time observation and time-lapse imaging of crystal growth are feasible for over 200 solution samples independently. In this paper, we also report results of crystallization experiments for two protein samples. Crystals grown in the system exhibited magnetic orientation and showed higher and more homogeneous quality compared with the control crystals. The structural analysis reveals that making use of the magnetic microgravity during the crystallization process helps us to build a well-refined protein structure model, which has no significant structural differences with a control structure. Therefore, the system contributes to improvement in efficiency of structural analysis for "difficult" proteins, such as membrane proteins and supermolecular complexes.

Real-time PCR detection of Didemnum perlucidum (Monniot, 1983) and Didemnum vexillum (Kott, 2002) in an applied routine marine biosecurity context.

PubMed

Simpson, Tiffany J S; Dias, P Joana; Snow, Michael; Muñoz, Julieta; Berry, Tina

2017-05-01

Prevention and early detection are well recognized as the best strategies for minimizing the risks posed by nonindigenous species (NIS) that have the potential to become marine pests. Central to this is the ability to rapidly and accurately identify the presence of NIS, often from complex environmental samples like biofouling and ballast water. Molecular tools have been increasingly applied to assist with the identification of NIS and can prove particularly useful for taxonomically difficult groups like ascidians. In this study, we have developed real-time PCR assays suited to the specific identification of the ascidians Didemnum perlucidum and Didemnum vexillum. Despite being recognized as important global pests, this is the first time specific molecular detection methods have been developed that can support the early identification and detection of these species from a broad range of environmental sample types. These fast, robust and high-throughput assays represent powerful tools for routine marine biosecurity surveillance, as detection and confirmation of the early presence of species could assist in the timely establishment of emergency responses and control strategies. This study applied the developed assays to confirm the ability to detect Didemnid eDNA in water samples. While previous work has focused on detection of marine larvae from water samples, the development of real-time PCR assays specifically aimed at detecting eDNA of sessile invertebrate species in the marine environment represents a world first and a significant step forwards in applied marine biosecurity surveillance. Demonstrated success in the detection of D. perlucidum eDNA from water samples at sites where it could not be visually identified suggests value in incorporating such assays into biosecurity survey designs targeting Didemnid species. © 2016 John Wiley & Sons Ltd.

Simultaneous detection and serotyping of dengue infection using single tube multiplex CDC Dengue Real-Time RT-PCR from India.

PubMed

Sharma, Shashi; Tandel, Kundan; Danwe, Surabhi; Bhatt, Puneet; Dash, P K; Ranjan, Praveer; Rathi, K R; Gupta, Rajiv Mohan; Parida, M M

2018-03-01

Four antigenically different dengue virus serotypes (DENV-1, DENV-2, DENV-3 and DENV-4) are known to cause infections in humans. Some of these are known to cause more severe disease than the others. Chances for developing Dengue hemorrhagic fever-dengue shock syndrome (DHF-DSS) increases significantly with history of previous infection with one of the four serotypes. Therefore, early diagnosis, serotyping and providing early warning of dengue fever epidemics to concerned authorities becomes very important for better patient outcome and to curb the rapid spread in the community. During the 2014 outbreak, a total of 100 samples from suspected cases of dengue were collected. NS1 antigen based rapid test was used for serological diagnosis. Dengue complex one step reverse transcription-polymerase chain reaction was performed to look for presence of viral RNA. Single tube multiplex RT-PCR was also performed to look for infecting serotype. CDC Dengue Multiplex Real Time PCR assay was performed for rapid diagnosis and simultaneous serotyping of the dengue virus. Out of the 100 samples screened, 69 were found to be positive by NS1Ag Rapid test. 34 samples were found positive by dengue consensus RT-PCR assay. 22 samples were found to be positive by single tube Dengue multiplex RT-PCR assay. Serotype DEN-2 was present in maximum numbers followed by DEN-3. 44 samples were found positive by DENV CDC Multiplex Real time PCR assay. DEN-2 was found in maximum numbers followed by DEN-1. Dengue remains to be an important health problem in India and across the globe. Few serotypes of dengue are more dangerous than the others. Rapid diagnosis and serotyping remains the key for better patient management and prevention of disease spreading in the community. Highly sensitive, specific and rapid CDC real time RT-PCR assay was found to be most promising tool among all available molecular diagnostic methods. This will serve a rapid and reliable simultaneous dengue virus detection as well serotyping assay in near future for rapid identification of dengue suspected sample screening.

Application of a surfactant-assisted dispersive liquid-liquid microextraction method along with central composite design for micro-volume based spectrophotometric determination of low level of Cr(VI) ions in aquatic samples.

PubMed

Sobhi, Hamid Reza; Azadikhah, Efat; Behbahani, Mohammad; Esrafili, Ali; Ghambarian, Mahnaz

2018-05-09

A fast, simple, low cost surfactant-assisted dispersive liquid-liquid microextraction method along with central composite design for the determination of low level of Cr(VI) ions in several aquatic samples has been developed. Initially, Cr(VI) ions present in the aqueous sample were readily reacted with 1,5‑diphenylcarbazide (DPC) in acidic medium through complexation. Sodium dodecyl sulfate (SDS), as an anionic surfactant, was then employed as an ion-pair agent to convert the cationic complex into the neutral one. Following on, the whole aqueous phase underwent a dispersive liquid-liquid microextraction (DLLME) leading to the transfer of the neutral complex into the fine droplet of organic extraction phase. A micro-volume spectrophotometer was used to determine Cr(VI) concentrations. Under the optimized conditions predicted by the statistical design, the limit of quantification (LOQ) obtained was reported to be 5.0 μg/L, and the calibration curve was linear over the concentration range of 5-100 μg/L. Finally, the method was successfully implemented for the determination of low levels of Cr(VI) ions in various real aquatic samples and the accuracies fell within the range of 83-102%, while the precision varied in the span of 1.7-5.2%. Copyright © 2018. Published by Elsevier B.V.

Complex mixture analysis by photoionization mass spectrometry with a VUV hydrogen laser source

NASA Astrophysics Data System (ADS)

Huth, T. C.; Denton, M. B.

1985-12-01

Trace organic analysis in complex matrix presents one of the most challenging problems in analytical mass spectrometry. When ionization is accomplished non-selectively using electron impact, extensive sample clean-up is often necessary in order to isolate the analyte from the matrix. Sample preparation can be greatly reduced when the VUV H2 laser is used to selectively photoionize only a small fraction of compounds introduced into the ion source. This device produces parent ions only for all compounds whose ionization potentials lie below a threshold value determined by the photon energy of 7.8 eV. The only observed interference arises from electron impact ionization, when scattered laser radiation interacts with metal surfaces, producing electrons which are then accelerated by potential fields inside the source. These can be suppressed to levels acceptable for practical analysis through proper instrumental design. Results are presented which indicate the ability of this ion source to discriminate against interfering matrix components, in simple extracts from a variety of complex real world matrices, such as brewed coffee, beer, and urine.

A DUAL PLATFORM FOR SELECTIVE ANALYTE ENRICHMENT AND IONIZATION IN MASS SPECTROMETRY USING APTAMER-CONJUGATED GRAPHENE OXIDE

PubMed Central

Gulbakan, Basri; Yasun, Emir; Shukoor, M. Ibrahim; Zhu, Zhi; You, Mingxu; Tan, Xiaohong; Sanchez, Hernan; Powell, David H.; Dai, Hongjie; Tan, Weihong

2010-01-01

This study demonstrates the use of aptamer-conjugated graphene oxide as an affinity extraction and detection platform for analytes from complex biological media. We have shown that cocaine and adenosine can be selectively enriched from plasma samples and that direct mass spectrometric readout can be obtained without a matrix and with greatly improved signal-to-noise ratios. The aptamer conjugated graphene oxide has clear advantages in target enrichment and in generating highly efficient ionization of target molecules for mass spectrometry. These results demonstrate the utility of the approach for analysis of small molecules in real biological samples. PMID:21090719

Advanced Kalman Filter for Real-Time Responsiveness in Complex Systems

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

Welch, Gregory Francis; Zhang, Jinghe

2014-06-10

Complex engineering systems pose fundamental challenges in real-time operations and control because they are highly dynamic systems consisting of a large number of elements with severe nonlinearities and discontinuities. Today’s tools for real-time complex system operations are mostly based on steady state models, unable to capture the dynamic nature and too slow to prevent system failures. We developed advanced Kalman filtering techniques and the formulation of dynamic state estimation using Kalman filtering techniques to capture complex system dynamics in aiding real-time operations and control. In this work, we looked at complex system issues including severe nonlinearity of system equations, discontinuitiesmore » caused by system controls and network switches, sparse measurements in space and time, and real-time requirements of power grid operations. We sought to bridge the disciplinary boundaries between Computer Science and Power Systems Engineering, by introducing methods that leverage both existing and new techniques. While our methods were developed in the context of electrical power systems, they should generalize to other large-scale scientific and engineering applications.« less

Video Game Telemetry as a Critical Tool in the Study of Complex Skill Learning

PubMed Central

Thompson, Joseph J.; Blair, Mark R.; Chen, Lihan; Henrey, Andrew J.

2013-01-01

Cognitive science has long shown interest in expertise, in part because prediction and control of expert development would have immense practical value. Most studies in this area investigate expertise by comparing experts with novices. The reliance on contrastive samples in studies of human expertise only yields deep insight into development where differences are important throughout skill acquisition. This reliance may be pernicious where the predictive importance of variables is not constant across levels of expertise. Before the development of sophisticated machine learning tools for data mining larger samples, and indeed, before such samples were available, it was difficult to test the implicit assumption of static variable importance in expertise development. To investigate if this reliance may have imposed critical restrictions on the understanding of complex skill development, we adopted an alternative method, the online acquisition of telemetry data from a common daily activity for many: video gaming. Using measures of cognitive-motor, attentional, and perceptual processing extracted from game data from 3360 Real-Time Strategy players at 7 different levels of expertise, we identified 12 variables relevant to expertise. We show that the static variable importance assumption is false - the predictive importance of these variables shifted as the levels of expertise increased - and, at least in our dataset, that a contrastive approach would have been misleading. The finding that variable importance is not static across levels of expertise suggests that large, diverse datasets of sustained cognitive-motor performance are crucial for an understanding of expertise in real-world contexts. We also identify plausible cognitive markers of expertise. PMID:24058656

Pooled assembly of marine metagenomic datasets: enriching annotation through chimerism.

PubMed

Magasin, Jonathan D; Gerloff, Dietlind L

2015-02-01

Despite advances in high-throughput sequencing, marine metagenomic samples remain largely opaque. A typical sample contains billions of microbial organisms from thousands of genomes and quadrillions of DNA base pairs. Its derived metagenomic dataset underrepresents this complexity by orders of magnitude because of the sparseness and shortness of sequencing reads. Read shortness and sequencing errors pose a major challenge to accurate species and functional annotation. This includes distinguishing known from novel species. Often the majority of reads cannot be annotated and thus cannot help our interpretation of the sample. Here, we demonstrate quantitatively how careful assembly of marine metagenomic reads within, but also across, datasets can alleviate this problem. For 10 simulated datasets, each with species complexity modeled on a real counterpart, chimerism remained within the same species for most contigs (97%). For 42 real pyrosequencing ('454') datasets, assembly increased the proportion of annotated reads, and even more so when datasets were pooled, by on average 1.6% (max 6.6%) for species, 9.0% (max 28.7%) for Pfam protein domains and 9.4% (max 22.9%) for PANTHER gene families. Our results outline exciting prospects for data sharing in the metagenomics community. While chimeric sequences should be avoided in other areas of metagenomics (e.g. biodiversity analyses), conservative pooled assembly is advantageous for annotation specificity and sensitivity. Intriguingly, our experiment also found potential prospects for (low-cost) discovery of new species in 'old' data. dgerloff@ffame.org Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Video game telemetry as a critical tool in the study of complex skill learning.

PubMed

Thompson, Joseph J; Blair, Mark R; Chen, Lihan; Henrey, Andrew J

2013-01-01

Cognitive science has long shown interest in expertise, in part because prediction and control of expert development would have immense practical value. Most studies in this area investigate expertise by comparing experts with novices. The reliance on contrastive samples in studies of human expertise only yields deep insight into development where differences are important throughout skill acquisition. This reliance may be pernicious where the predictive importance of variables is not constant across levels of expertise. Before the development of sophisticated machine learning tools for data mining larger samples, and indeed, before such samples were available, it was difficult to test the implicit assumption of static variable importance in expertise development. To investigate if this reliance may have imposed critical restrictions on the understanding of complex skill development, we adopted an alternative method, the online acquisition of telemetry data from a common daily activity for many: video gaming. Using measures of cognitive-motor, attentional, and perceptual processing extracted from game data from 3360 Real-Time Strategy players at 7 different levels of expertise, we identified 12 variables relevant to expertise. We show that the static variable importance assumption is false--the predictive importance of these variables shifted as the levels of expertise increased--and, at least in our dataset, that a contrastive approach would have been misleading. The finding that variable importance is not static across levels of expertise suggests that large, diverse datasets of sustained cognitive-motor performance are crucial for an understanding of expertise in real-world contexts. We also identify plausible cognitive markers of expertise.

Low-power grating detection system chip for high-speed low-cost length and angle precision measurement

NASA Astrophysics Data System (ADS)

Hou, Ligang; Luo, Rengui; Wu, Wuchen

2006-11-01

This paper forwards a low power grating detection chip (EYAS) on length and angle precision measurement. Traditional grating detection method, such as resister chain divide or phase locked divide circuit are difficult to design and tune. The need of an additional CPU for control and display makes these methods' implementation more complex and costly. Traditional methods also suffer low sampling speed for the complex divide circuit scheme and CPU software compensation. EYAS is an application specific integrated circuit (ASIC). It integrates micro controller unit (MCU), power management unit (PMU), LCD controller, Keyboard interface, grating detection unit and other peripherals. Working at 10MHz, EYAS can afford 5MHz internal sampling rate and can handle 1.25MHz orthogonal signal from grating sensor. With a simple control interface by keyboard, sensor parameter, data processing and system working mode can be configured. Two LCD controllers can adapt to dot array LCD or segment bit LCD, which comprised output interface. PMU alters system between working and standby mode by clock gating technique to save power. EYAS in test mode (system action are more frequently than real world use) consumes 0.9mw, while 0.2mw in real world use. EYAS achieved the whole grating detection system function, high-speed orthogonal signal handling in a single chip with very low power consumption.

Visual format for detection of Mycobacterium tuberculosis and M. bovis in clinical samples using molecular beacons.

PubMed

Kumar, Parameet; Nath, Kapili; Rath, Bimba; Sen, Manas K; Vishalakshi, Potharuju; Chauhan, Devender S; Katoch, Vishwa M; Singh, Sarman; Tyagi, Sanjay; Sreenivas, Vishnubhatla; Prasad, Hanumanthappa K

2009-09-01

A real-time polymerase chain reaction (PCR) assay for the direct identification of Mycobacterium tuberculosis and M. bovis using molecular beacons was developed. The assay was modified for use in regular thermal cyclers. Molecular beacons that were specific for M. tuberculosis (Tb-B) and M. bovis (Bo-B) were designed. The fluorescence of the target PCR product-molecular beacon probe complex was detected visually using a transilluminator. The results were then compared with those of conventional multiplex PCR (CM-PCR) assays and biochemical identification. The detection limit of Tb-B and Bo-B beacons was 500 fg and 50 fg by the visual format and real-time PCR assay, respectively, compared with 5 pg by CM-PCR assay. Pulmonary and extrapulmonary samples were examined. The agreement between culture and the two assays was very good in sputum samples and fair in extrapulmonary samples. The agreement between clinical diagnoses with the two assays was moderate in extrapulmonary samples. There was very good agreement between CM-PCR and visual format assays for all samples used in the study. Concordance in the identification of isolates by the visual, CM-PCR assay, and biochemical identification was seen. Hence, the use of molecular beacon detection of M. tuberculosis and M. bovis in clinical samples is feasible by setting up two asymmetric PCRs concurrently. The assay is sensitive, specific, simple to interpret, and takes less than 3 hours to complete.

Visual Format for Detection of Mycobacterium tuberculosis and M. bovis in Clinical Samples Using Molecular Beacons

PubMed Central

Kumar, Parameet; Nath, Kapili; Rath, Bimba; Sen, Manas K.; Vishalakshi, Potharuju; Chauhan, Devender S.; Katoch, Vishwa M.; Singh, Sarman; Tyagi, Sanjay; Sreenivas, Vishnubhatla; Prasad, Hanumanthappa K.

2009-01-01

A real-time polymerase chain reaction (PCR) assay for the direct identification of Mycobacterium tuberculosis and M. bovis using molecular beacons was developed. The assay was modified for use in regular thermal cyclers. Molecular beacons that were specific for M. tuberculosis (Tb-B) and M. bovis (Bo-B) were designed. The fluorescence of the target PCR product-molecular beacon probe complex was detected visually using a transilluminator. The results were then compared with those of conventional multiplex PCR (CM-PCR) assays and biochemical identification. The detection limit of Tb-B and Bo-B beacons was 500 fg and 50 fg by the visual format and real-time PCR assay, respectively, compared with 5 pg by CM-PCR assay. Pulmonary and extrapulmonary samples were examined. The agreement between culture and the two assays was very good in sputum samples and fair in extrapulmonary samples. The agreement between clinical diagnoses with the two assays was moderate in extrapulmonary samples. There was very good agreement between CM-PCR and visual format assays for all samples used in the study. Concordance in the identification of isolates by the visual, CM-PCR assay, and biochemical identification was seen. Hence, the use of molecular beacon detection of M. tuberculosis and M. bovis in clinical samples is feasible by setting up two asymmetric PCRs concurrently. The assay is sensitive, specific, simple to interpret, and takes less than 3 hours to complete. PMID:19661384

Self-consistent adjoint analysis for topology optimization of electromagnetic waves

NASA Astrophysics Data System (ADS)

Deng, Yongbo; Korvink, Jan G.

2018-05-01

In topology optimization of electromagnetic waves, the Gâteaux differentiability of the conjugate operator to the complex field variable results in the complexity of the adjoint sensitivity, which evolves the original real-valued design variable to be complex during the iterative solution procedure. Therefore, the self-inconsistency of the adjoint sensitivity is presented. To enforce the self-consistency, the real part operator has been used to extract the real part of the sensitivity to keep the real-value property of the design variable. However, this enforced self-consistency can cause the problem that the derived structural topology has unreasonable dependence on the phase of the incident wave. To solve this problem, this article focuses on the self-consistent adjoint analysis of the topology optimization problems for electromagnetic waves. This self-consistent adjoint analysis is implemented by splitting the complex variables of the wave equations into the corresponding real parts and imaginary parts, sequentially substituting the split complex variables into the wave equations with deriving the coupled equations equivalent to the original wave equations, where the infinite free space is truncated by the perfectly matched layers. Then, the topology optimization problems of electromagnetic waves are transformed into the forms defined on real functional spaces instead of complex functional spaces; the adjoint analysis of the topology optimization problems is implemented on real functional spaces with removing the variational of the conjugate operator; the self-consistent adjoint sensitivity is derived, and the phase-dependence problem is avoided for the derived structural topology. Several numerical examples are implemented to demonstrate the robustness of the derived self-consistent adjoint analysis.

Fast parallel approach for 2-D DHT-based real-valued discrete Gabor transform.

PubMed

Tao, Liang; Kwan, Hon Keung

2009-12-01

Two-dimensional fast Gabor transform algorithms are useful for real-time applications due to the high computational complexity of the traditional 2-D complex-valued discrete Gabor transform (CDGT). This paper presents two block time-recursive algorithms for 2-D DHT-based real-valued discrete Gabor transform (RDGT) and its inverse transform and develops a fast parallel approach for the implementation of the two algorithms. The computational complexity of the proposed parallel approach is analyzed and compared with that of the existing 2-D CDGT algorithms. The results indicate that the proposed parallel approach is attractive for real time image processing.

Evaluation of direct analysis in real time for the determination of highly polar pesticides in lettuce and celery using modified Quick Polar Pesticides Extraction method.

PubMed

Lara, Francisco J; Chan, Danny; Dickinson, Michael; Lloyd, Antony S; Adams, Stuart J

2017-05-05

Direct analysis in real time (DART) was evaluated for the determination of a number of highly polar pesticides using the Quick Polar Pesticides Extraction (QuPPe) method. DART was hyphenated to high resolution mass spectrometry (HRMS) in order to get the required selectivity that allows the determination of these compounds in complex samples such as lettuce and celery. Experimental parameters such as desorption temperature, scanning speed, and distances between the DART ion source and MS inlet were optimized. Two different mass analyzers (Orbitrap and QTOF) and two accessories for sample introduction (Dip-it ® tips and QuickStrip™ sample cards) were evaluated. An extra clean-up step using primary-secondary amine (PSA) was included in the QuPPe method to improve sensitivity. The main limitation found was in-source fragmentation, nevertheless QuPPe-DART-HRMS proved to be a fast and reliable tool with quantitative capabilities for at least seven compounds: amitrole, cyromazine, propamocarb, melamine, diethanolamine, triethanolamine and 1,2,4-triazole. The limits of detection ranged from 20 to 60μg/kg. Recoveries for fortified samples ranged from 71 to 115%, with relative standard deviations <18%. Copyright © 2017 Elsevier B.V. All rights reserved.

Ultrafast Screening and Quantitation of Pesticides in Food and Environmental Matrices by Solid-Phase Microextraction-Transmission Mode (SPME-TM) and Direct Analysis in Real Time (DART).

PubMed

Gómez-Ríos, Germán Augusto; Gionfriddo, Emanuela; Poole, Justen; Pawliszyn, Janusz

2017-07-05

The direct interface of microextraction technologies to mass spectrometry (MS) has unquestionably revolutionized the speed and efficacy at which complex matrices are analyzed. Solid Phase Micro Extraction-Transmission Mode (SPME-TM) is a technology conceived as an effective synergy between sample preparation and ambient ionization. Succinctly, the device consists of a mesh coated with polymeric particles that extracts analytes of interest present in a given sample matrix. This coated mesh acts as a transmission-mode substrate for Direct Analysis in Real Time (DART), allowing for rapid and efficient thermal desorption/ionization of analytes previously concentrated on the coating, and dramatically lowering the limits of detection attained by sole DART analysis. In this study, we present SPME-TM as a novel tool for the ultrafast enrichment of pesticides present in food and environmental matrices and their quantitative determination by MS via DART ionization. Limits of quantitation in the subnanogram per milliliter range can be attained, while total analysis time does not exceed 2 min per sample. In addition to target information obtained via tandem MS, retrospective studies of the same sample via high-resolution mass spectrometry (HRMS) were accomplished by thermally desorbing a different segment of the microextraction device.

Standardization of a TaqMan-based real-time PCR for the detection of Mycobacterium tuberculosis-complex in human sputum.

PubMed

Barletta, Francesca; Vandelannoote, Koen; Collantes, Jimena; Evans, Carlton A; Arévalo, Jorge; Rigouts, Leen

2014-10-01

Real-time polymerase chain reaction (qPCR) was optimized for detecting Mycobacterium tuberculosis in sputum. Sputum was collected from patients (N = 112) with suspected pulmonary tuberculosis, tested by smear microscopy, decontaminated, and split into equal aliquots that were cultured in Löwenstein-Jensen medium and tested by qPCR for the small mobile genetic element IS6110. The human ERV3 sequence was used as an internal control. 3 of 112 (3%) qPCR failed. For the remaining 109 samples, qPCR diagnosed tuberculosis in 79 of 84 patients with culture-proven tuberculosis, and sensitivity was greater than microscopy (94% versus 76%, respectively, P < 0.05). The qPCR sensitivity was similar (P = 0.9) for smear-positive (94%, 60 of 64) and smear-negative (95%, 19 of 20) samples. The qPCR was negative for 24 of 25 of the sputa with negative microscopy and culture (diagnostic specificity 96%). The qPCR had 99.5% sensitivity and specificity for 211 quality control samples including 84 non-tuberculosis mycobacteria. The qPCR cost ∼5US$ per sample and provided same-day results compared with 2-6 weeks for culture. © The American Society of Tropical Medicine and Hygiene.

The Origin of Complex Quantum Amplitudes

NASA Astrophysics Data System (ADS)

Goyal, Philip; Knuth, Kevin H.; Skilling, John

2009-12-01

Physics is real. Measurement produces real numbers. Yet quantum mechanics uses complex arithmetic, in which √-1 is necessary but mysteriously relates to nothing else. By applying the same sort of symmetry arguments that Cox [1, 2] used to justify probability calculus, we are now able to explain this puzzle. The dual device/object nature of observation requires us to describe the world in terms of pairs of real numbers about which we never have full knowledge. These pairs combine according to complex arithmetic, using Feynman's rules.

Identifying the starting point of a spreading process in complex networks.

PubMed

Comin, Cesar Henrique; Costa, Luciano da Fontoura

2011-11-01

When dealing with the dissemination of epidemics, one important question that can be asked is the location where the contamination began. In this paper, we analyze three spreading schemes and propose and validate an effective methodology for the identification of the source nodes. The method is based on the calculation of the centrality of the nodes on the sampled network, expressed here by degree, betweenness, closeness, and eigenvector centrality. We show that the source node tends to have the highest measurement values. The potential of the methodology is illustrated with respect to three theoretical complex network models as well as a real-world network, the email network of the University Rovira i Virgili.

Low complexity lossless compression of underwater sound recordings.

PubMed

Johnson, Mark; Partan, Jim; Hurst, Tom

2013-03-01

Autonomous listening devices are increasingly used to study vocal aquatic animals, and there is a constant need to record longer or with greater bandwidth, requiring efficient use of memory and battery power. Real-time compression of sound has the potential to extend recording durations and bandwidths at the expense of increased processing operations and therefore power consumption. Whereas lossy methods such as MP3 introduce undesirable artifacts, lossless compression algorithms (e.g., flac) guarantee exact data recovery. But these algorithms are relatively complex due to the wide variety of signals they are designed to compress. A simpler lossless algorithm is shown here to provide compression factors of three or more for underwater sound recordings over a range of noise environments. The compressor was evaluated using samples from drifting and animal-borne sound recorders with sampling rates of 16-240 kHz. It achieves >87% of the compression of more-complex methods but requires about 1/10 of the processing operations resulting in less than 1 mW power consumption at a sampling rate of 192 kHz on a low-power microprocessor. The potential to triple recording duration with a minor increase in power consumption and no loss in sound quality may be especially valuable for battery-limited tags and robotic vehicles.

Evaluation of physiologic complexity in time series using generalized sample entropy and surrogate data analysis

NASA Astrophysics Data System (ADS)

Eduardo Virgilio Silva, Luiz; Otavio Murta, Luiz

2012-12-01

Complexity in time series is an intriguing feature of living dynamical systems, with potential use for identification of system state. Although various methods have been proposed for measuring physiologic complexity, uncorrelated time series are often assigned high values of complexity, errouneously classifying them as a complex physiological signals. Here, we propose and discuss a method for complex system analysis based on generalized statistical formalism and surrogate time series. Sample entropy (SampEn) was rewritten inspired in Tsallis generalized entropy, as function of q parameter (qSampEn). qSDiff curves were calculated, which consist of differences between original and surrogate series qSampEn. We evaluated qSDiff for 125 real heart rate variability (HRV) dynamics, divided into groups of 70 healthy, 44 congestive heart failure (CHF), and 11 atrial fibrillation (AF) subjects, and for simulated series of stochastic and chaotic process. The evaluations showed that, for nonperiodic signals, qSDiff curves have a maximum point (qSDiffmax) for q ≠1. Values of q where the maximum point occurs and where qSDiff is zero were also evaluated. Only qSDiffmax values were capable of distinguish HRV groups (p-values 5.10×10-3, 1.11×10-7, and 5.50×10-7 for healthy vs. CHF, healthy vs. AF, and CHF vs. AF, respectively), consistently with the concept of physiologic complexity, and suggests a potential use for chaotic system analysis.

Synthesis of UiO-66-OH zirconium metal-organic framework and its application for selective extraction and trace determination of thorium in water samples by spectrophotometry

NASA Astrophysics Data System (ADS)

Moghaddam, Zahra Safaei; Kaykhaii, Massoud; Khajeh, Mostafa; Oveisi, Ali Reza

2018-04-01

In this study, a zirconium-based metal-organic framework (Zr-MOF), named UiO-66-OH, was synthesized by the solvo-thermal method and characterized by Fourier transform-infrared spectroscopy (FTIR), powder X-ray diffraction (PXRD), and scanning electron microscopy (SEM). This Zr-MOF was then employed as a sorbent for selective extraction and preconcentration of thorium ions after their complexation with 2-(2,4-dihydroxyphenyl)-3,5,7-trihydroxychromen-4-one (morin) from environmental water samples prior to its spectrophotometrical determination. The experimental parameters affecting extraction, such as pH of sample solution, amount of Zr-MOF, type and volume of eluting solvent, adsorption and desorption time, and concentration of complexing agent were evaluated and optimized. Under the optimized conditions, an enrichment factor of 250 was achieved. The limit of detection was calculated to be 0.35 μg·L- 1 with a linear range between 10 and 2000 μg·L- 1of thorium. The maximum sorption capacity of MOF toward thorium was found to be 47.5 mg·g- 1. The proposed procedure was successfully applied to the analysis of real water samples.

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.

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

A Real-Life Case Study of Audit Interactions--Resolving Messy, Complex Problems

ERIC Educational Resources Information Center

Beattie, Vivien; Fearnley, Stella; Hines, Tony

2012-01-01

Real-life accounting and auditing problems are often complex and messy, requiring the synthesis of technical knowledge in addition to the application of generic skills. To help students acquire the necessary skills to deal with these problems effectively, educators have called for the use of case-based methods. Cases based on real situations (such…

Gene expression variations during Drosophila metamorphosis in real and simulated gravity

NASA Astrophysics Data System (ADS)

Marco, R.; Leandro-García, L. J.; Benguría, A.; Herranz, R.; Zeballos, A.; Gassert, G.; van Loon, J. J.; Medina, F. J.

Establishing the extent and significance of the effects of the exposure to microgravity of complex living organisms is a critical piece of information if the long-term exploration of near-by planets involving human beings is going to take place in the Future As a first step in this direction we have started to look into the patterns of gene expression during Drosophila development in real and simulated microgravity using microarray analysis of mRNA isolated from samples exposed to different environmental conditions In these experiments we used Affymetrix chips version 1 0 containing probes for more than 14 000 genes almost the complete Drosophila genome 55 of which are tagged with some molecular or functional designation while 45 are still waiting to be identified in functional terms The real microgravity exposure was imposed on the samples during the crew exchanging Soyuz 8 Mission to the ISS in October 2003 when after 11 days in Microgravity the Spanish-born astronaut Pedro Duque returned in the Soyuz 7 capsule carrying the experiments prepared by our Team Due to the constraints in the current ISS experiments in these Missions we limited the stages explored in our experiment to the developmental processes occurring during Drosophila metamorphosis As the experimental conditions at the launch site Baikonour were fairly limited we prepared the experiment in Madrid Toulouse and transp o rted the samples at 15 C in a temperature controlled container to slow down the developmental process a

Hidden diversity within the lizard genus Liolaemus: Genetic vs morphological divergence in the L. rothi complex (Squamata:Liolaeminae).

PubMed

Olave, Melisa; Avila, Luciano J; Sites, Jack W; Morando, Mariana

2017-02-01

Currently, Liolaemus is the second most species-rich reptile genus in the world (257 species), and predictions of its real diversity suggest that it may be the most diverse genus. Originally, Liolaemus species were described as widely distributed and morphologically variable taxa, but extensive sampling in previously unexplored geographic areas, coupled with molecular and more extensive morphological studies, have discovered an unexpectedly high number of previously undetected species. Here, we study the level of molecular vs. morphological divergence within the L. rothi complex, combining a total of 14 loci (2 mitochondrial and 12 nuclear loci) for 97 individuals, as well as morphological data (nine morphometric and 15 color pattern variables), that represent all six described species of the L. rothi complex, plus two candidate species. We use the multi-coalescent species delimitation program iBPP and resolve strong differences in molecular divergence; and each species is inferred as an independent lineage supported by high posterior probabilities. However, morphological differences are not that clear, and our modeling of morphological characters suggests differential selection pressures implying some level of morphological stasis. We discuss the role of natural selection on phenotypic traits, which may be an important factor in "hiding" the real diversity of the genus. Copyright © 2016. Published by Elsevier Inc.

Vector method for strain estimation in phase-sensitive optical coherence elastography

NASA Astrophysics Data System (ADS)

Matveyev, A. L.; Matveev, L. A.; Sovetsky, A. A.; Gelikonov, G. V.; Moiseev, A. A.; Zaitsev, V. Y.

2018-06-01

A noise-tolerant approach to strain estimation in phase-sensitive optical coherence elastography, robust to decorrelation distortions, is discussed. The method is based on evaluation of interframe phase-variation gradient, but its main feature is that the phase is singled out at the very last step of the gradient estimation. All intermediate steps operate with complex-valued optical coherence tomography (OCT) signals represented as vectors in the complex plane (hence, we call this approach the ‘vector’ method). In comparison with such a popular method as least-square fitting of the phase-difference slope over a selected region (even in the improved variant with amplitude weighting for suppressing small-amplitude noisy pixels), the vector approach demonstrates superior tolerance to both additive noise in the receiving system and speckle-decorrelation caused by tissue straining. Another advantage of the vector approach is that it obviates the usual necessity of error-prone phase unwrapping. Here, special attention is paid to modifications of the vector method that make it especially suitable for processing deformations with significant lateral inhomogeneity, which often occur in real situations. The method’s advantages are demonstrated using both simulated and real OCT scans obtained during reshaping of a collagenous tissue sample irradiated by an IR laser beam producing complex spatially inhomogeneous deformations.

An examination of speech reception thresholds measured in a simulated reverberant cafeteria environment

PubMed Central

Best, Virginia; Keidser, Gitte; Buchholz, J(x004E7)rg M.; Freeston, Katrina

2016-01-01

Objective There is increasing demand in the hearing research community for the creation of laboratory environments that better simulate challenging real-world listening environments. The hope is that the use of such environments for testing will lead to more meaningful assessments of listening ability, and better predictions about the performance of hearing devices. Here we present one approach for simulating a complex acoustic environment in the laboratory, and investigate the effect of transplanting a speech test into such an environment. Design Speech reception thresholds were measured in a simulated reverberant cafeteria, and in a more typical anechoic laboratory environment containing background speech babble. Study Sample The participants were 46 listeners varying in age and hearing levels, including 25 hearing-aid wearers who were tested with and without their hearing aids. Results Reliable SRTs were obtained in the complex environment, but led to different estimates of performance and hearing aid benefit from those measured in the standard environment. Conclusions The findings provide a starting point for future efforts to increase the real-world relevance of laboratory-based speech tests. PMID:25853616

Resonant alteration of propagation in guiding structures with complex Robin parameter and its magnetic-field-induced restoration

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

Olendski, O., E-mail: oolendski@ksu.edu.sa

2011-06-15

Highlights: > Solutions of the wave equation are analyzed for the confined circular geometry with complex Robin boundary conditions. > Sharp extremum is found in the energy dependence on the imaginary part of the extrapolation length. > Nonzero real part of the Robin length or/and magnetic field wipe out the resonance. - Abstract: Solutions of the scalar Helmholtz wave equation are derived for the analysis of the transport and thermodynamic properties of the two-dimensional disk and three-dimensional infinitely long straight wire in the external uniform longitudinal magnetic field B under the assumption that the Robin boundary condition contains extrapolation lengthmore » {Lambda} with nonzero imaginary part {Lambda}{sub i}. As a result of this complexity, the self-adjointness of the Hamiltonian is lost, its eigenvalues E become complex too and the discrete bound states of the disk characteristic for the real {Lambda} turn into the corresponding quasibound states with their lifetime defined by the eigenenergies imaginary parts E{sub i}. Accordingly, the longitudinal flux undergoes an alteration as it flows along the wire with its attenuation/amplification being E{sub i}-dependent too. It is shown that, for zero magnetic field, the component E{sub i} as a function of the Robin imaginary part exhibits a pronounced sharp extremum with its magnitude being the largest for the zero real part {Lambda}{sub r} of the extrapolation length. Increasing magnitude of {Lambda}{sub r} quenches the E{sub i} - {Lambda}{sub i} resonance and at very large {Lambda}{sub r} the eigenenergies E approach the asymptotic real values independent of {Lambda}{sub i}. The extremum is also wiped out by the magnetic field when, for the large B, the energies tend to the Landau levels. Mathematical and physical interpretations of the obtained results are provided; in particular, it is shown that the finite lifetime of the disk quasibound states stems from the {Lambda}{sub i}-induced currents flowing through the sample boundary. Possible experimental tests of the calculated effect are discussed; namely, it is argued that it can be observed in superconductors by applying to them the external electric field E normal to the surface.« less

Complex networks as an emerging property of hierarchical preferential attachment.

PubMed

Hébert-Dufresne, Laurent; Laurence, Edward; Allard, Antoine; Young, Jean-Gabriel; Dubé, Louis J

2015-12-01

Real complex systems are not rigidly structured; no clear rules or blueprints exist for their construction. Yet, amidst their apparent randomness, complex structural properties universally emerge. We propose that an important class of complex systems can be modeled as an organization of many embedded levels (potentially infinite in number), all of them following the same universal growth principle known as preferential attachment. We give examples of such hierarchy in real systems, for instance, in the pyramid of production entities of the film industry. More importantly, we show how real complex networks can be interpreted as a projection of our model, from which their scale independence, their clustering, their hierarchy, their fractality, and their navigability naturally emerge. Our results suggest that complex networks, viewed as growing systems, can be quite simple, and that the apparent complexity of their structure is largely a reflection of their unobserved hierarchical nature.

Complex networks as an emerging property of hierarchical preferential attachment

NASA Astrophysics Data System (ADS)

Hébert-Dufresne, Laurent; Laurence, Edward; Allard, Antoine; Young, Jean-Gabriel; Dubé, Louis J.

2015-12-01

Real complex systems are not rigidly structured; no clear rules or blueprints exist for their construction. Yet, amidst their apparent randomness, complex structural properties universally emerge. We propose that an important class of complex systems can be modeled as an organization of many embedded levels (potentially infinite in number), all of them following the same universal growth principle known as preferential attachment. We give examples of such hierarchy in real systems, for instance, in the pyramid of production entities of the film industry. More importantly, we show how real complex networks can be interpreted as a projection of our model, from which their scale independence, their clustering, their hierarchy, their fractality, and their navigability naturally emerge. Our results suggest that complex networks, viewed as growing systems, can be quite simple, and that the apparent complexity of their structure is largely a reflection of their unobserved hierarchical nature.

Highly Sensitive Bacteriophage-Based Detection of Brucella abortus in Mixed Culture and Spiked Blood

PubMed Central

Sergueev, Kirill V.; Filippov, Andrey A.; Nikolich, Mikeljon P.

2017-01-01

For decades, bacteriophages (phages) have been used for Brucella species identification in the diagnosis and epidemiology of brucellosis. Traditional Brucella phage typing is a multi-day procedure including the isolation of a pure culture, a step that can take up to three weeks. In this study, we focused on the use of brucellaphages for sensitive detection of the pathogen in clinical and other complex samples, and developed an indirect method of Brucella detection using real-time quantitative PCR monitoring of brucellaphage DNA amplification via replication on live Brucella cells. This assay allowed the detection of single bacteria (down to 1 colony-forming unit per milliliter) within 72 h without DNA extraction and purification steps. The technique was equally efficient with Brucella abortus pure culture and with mixed cultures of B. abortus and α-proteobacterial near neighbors that can be misidentified as Brucella spp., Ochrobactrum anthropi and Afipia felis. The addition of a simple short sample preparation step enabled the indirect phage-based detection of B. abortus in spiked blood, with the same high sensitivity. This indirect phage-based detection assay enables the rapid and sensitive detection of live B. abortus in mixed cultures and in blood samples, and can potentially be applied for detection in other clinical samples and other complex sample types. PMID:28604602

Sample-Based Surface Coloring

PubMed Central

Bürger, Kai; Krüger, Jens; Westermann, Rüdiger

2011-01-01

In this paper, we present a sample-based approach for surface coloring, which is independent of the original surface resolution and representation. To achieve this, we introduce the Orthogonal Fragment Buffer (OFB)—an extension of the Layered Depth Cube—as a high-resolution view-independent surface representation. The OFB is a data structure that stores surface samples at a nearly uniform distribution over the surface, and it is specifically designed to support efficient random read/write access to these samples. The data access operations have a complexity that is logarithmic in the depth complexity of the surface. Thus, compared to data access operations in tree data structures like octrees, data-dependent memory access patterns are greatly reduced. Due to the particular sampling strategy that is employed to generate an OFB, it also maintains sample coherence, and thus, exhibits very good spatial access locality. Therefore, OFB-based surface coloring performs significantly faster than sample-based approaches using tree structures. In addition, since in an OFB, the surface samples are internally stored in uniform 2D grids, OFB-based surface coloring can efficiently be realized on the GPU to enable interactive coloring of high-resolution surfaces. On the OFB, we introduce novel algorithms for color painting using volumetric and surface-aligned brushes, and we present new approaches for particle-based color advection along surfaces in real time. Due to the intermediate surface representation we choose, our method can be used to color polygonal surfaces as well as any other type of surface that can be sampled. PMID:20616392

Complex Envelope Properties, Interpretation, Filtering, and Evaluation

DTIC Science & Technology

1991-02-01

BEHAVIOR The example of y(t) in (45) (when n# ± /2) illustrates the general rule that if a time function has a discontinuity of value D at time to, then...integration rule like trapezoidal, the "alias-free" interval in the time domain is approximately halved, as shown below. This does not necessarily mean that...approximated by the trapezoidal rule and the results added together. The two final approximations of interest come from sampling the results for causal real y(t

A method for real-time visual stimulus selection in the study of cortical object perception.

PubMed

Leeds, Daniel D; Tarr, Michael J

2016-06-01

The properties utilized by visual object perception in the mid- and high-level ventral visual pathway are poorly understood. To better establish and explore possible models of these properties, we adopt a data-driven approach in which we repeatedly interrogate neural units using functional Magnetic Resonance Imaging (fMRI) to establish each unit's image selectivity. This approach to imaging necessitates a search through a broad space of stimulus properties using a limited number of samples. To more quickly identify the complex visual features underlying human cortical object perception, we implemented a new functional magnetic resonance imaging protocol in which visual stimuli are selected in real-time based on BOLD responses to recently shown images. Two variations of this protocol were developed, one relying on natural object stimuli and a second based on synthetic object stimuli, both embedded in feature spaces based on the complex visual properties of the objects. During fMRI scanning, we continuously controlled stimulus selection in the context of a real-time search through these image spaces in order to maximize neural responses across pre-determined 1cm(3) rain regions. Elsewhere we have reported the patterns of cortical selectivity revealed by this approach (Leeds et al., 2014). In contrast, here our objective is to present more detailed methods and explore the technical and biological factors influencing the behavior of our real-time stimulus search. We observe that: 1) Searches converged more reliably when exploring a more precisely parameterized space of synthetic objects; 2) real-time estimation of cortical responses to stimuli is reasonably consistent; 3) search behavior was acceptably robust to delays in stimulus displays and subject motion effects. Overall, our results indicate that real-time fMRI methods may provide a valuable platform for continuing study of localized neural selectivity, both for visual object representation and beyond. Copyright © 2016 Elsevier Inc. All rights reserved.

A method for real-time visual stimulus selection in the study of cortical object perception

PubMed Central

Leeds, Daniel D.; Tarr, Michael J.

2016-01-01

The properties utilized by visual object perception in the mid- and high-level ventral visual pathway are poorly understood. To better establish and explore possible models of these properties, we adopt a data-driven approach in which we repeatedly interrogate neural units using functional Magnetic Resonance Imaging (fMRI) to establish each unit’s image selectivity. This approach to imaging necessitates a search through a broad space of stimulus properties using a limited number of samples. To more quickly identify the complex visual features underlying human cortical object perception, we implemented a new functional magnetic resonance imaging protocol in which visual stimuli are selected in real-time based on BOLD responses to recently shown images. Two variations of this protocol were developed, one relying on natural object stimuli and a second based on synthetic object stimuli, both embedded in feature spaces based on the complex visual properties of the objects. During fMRI scanning, we continuously controlled stimulus selection in the context of a real-time search through these image spaces in order to maximize neural responses across predetermined 1 cm3 brain regions. Elsewhere we have reported the patterns of cortical selectivity revealed by this approach (Leeds 2014). In contrast, here our objective is to present more detailed methods and explore the technical and biological factors influencing the behavior of our real-time stimulus search. We observe that: 1) Searches converged more reliably when exploring a more precisely parameterized space of synthetic objects; 2) Real-time estimation of cortical responses to stimuli are reasonably consistent; 3) Search behavior was acceptably robust to delays in stimulus displays and subject motion effects. Overall, our results indicate that real-time fMRI methods may provide a valuable platform for continuing study of localized neural selectivity, both for visual object representation and beyond. PMID:26973168

Sibling Curves and Complex Roots 2: Looking Ahead

ERIC Educational Resources Information Center

Harding, Ansie; Engelbrecht, Johann

2007-01-01

This paper, the second of a two part article, expands on an idea that appeared in literature in the 1950s to show that by restricting the domain to those complex numbers that map onto real numbers, representations of functions other than the ones in the real plane are obtained. In other words, the well-known curves in the real plane only depict…

Assessment of antibody library diversity through next generation sequencing and technical error compensation

PubMed Central

Lisi, Simonetta; Chirichella, Michele; Arisi, Ivan; Goracci, Martina; Cremisi, Federico; Cattaneo, Antonino

2017-01-01

Antibody libraries are important resources to derive antibodies to be used for a wide range of applications, from structural and functional studies to intracellular protein interference studies to developing new diagnostics and therapeutics. Whatever the goal, the key parameter for an antibody library is its complexity (also known as diversity), i.e. the number of distinct elements in the collection, which directly reflects the probability of finding in the library an antibody against a given antigen, of sufficiently high affinity. Quantitative evaluation of antibody library complexity and quality has been for a long time inadequately addressed, due to the high similarity and length of the sequences of the library. Complexity was usually inferred by the transformation efficiency and tested either by fingerprinting and/or sequencing of a few hundred random library elements. Inferring complexity from such a small sampling is, however, very rudimental and gives limited information about the real diversity, because complexity does not scale linearly with sample size. Next-generation sequencing (NGS) has opened new ways to tackle the antibody library complexity quality assessment. However, much remains to be done to fully exploit the potential of NGS for the quantitative analysis of antibody repertoires and to overcome current limitations. To obtain a more reliable antibody library complexity estimate here we show a new, PCR-free, NGS approach to sequence antibody libraries on Illumina platform, coupled to a new bioinformatic analysis and software (Diversity Estimator of Antibody Library, DEAL) that allows to reliably estimate the complexity, taking in consideration the sequencing error. PMID:28505201

Assessment of antibody library diversity through next generation sequencing and technical error compensation.

PubMed

Fantini, Marco; Pandolfini, Luca; Lisi, Simonetta; Chirichella, Michele; Arisi, Ivan; Terrigno, Marco; Goracci, Martina; Cremisi, Federico; Cattaneo, Antonino

2017-01-01

Antibody libraries are important resources to derive antibodies to be used for a wide range of applications, from structural and functional studies to intracellular protein interference studies to developing new diagnostics and therapeutics. Whatever the goal, the key parameter for an antibody library is its complexity (also known as diversity), i.e. the number of distinct elements in the collection, which directly reflects the probability of finding in the library an antibody against a given antigen, of sufficiently high affinity. Quantitative evaluation of antibody library complexity and quality has been for a long time inadequately addressed, due to the high similarity and length of the sequences of the library. Complexity was usually inferred by the transformation efficiency and tested either by fingerprinting and/or sequencing of a few hundred random library elements. Inferring complexity from such a small sampling is, however, very rudimental and gives limited information about the real diversity, because complexity does not scale linearly with sample size. Next-generation sequencing (NGS) has opened new ways to tackle the antibody library complexity quality assessment. However, much remains to be done to fully exploit the potential of NGS for the quantitative analysis of antibody repertoires and to overcome current limitations. To obtain a more reliable antibody library complexity estimate here we show a new, PCR-free, NGS approach to sequence antibody libraries on Illumina platform, coupled to a new bioinformatic analysis and software (Diversity Estimator of Antibody Library, DEAL) that allows to reliably estimate the complexity, taking in consideration the sequencing error.

The complex phase gradient method applied to leaky Lamb waves.

PubMed

Lenoir, O; Conoir, J M; Izbicki, J L

2002-10-01

The classical phase gradient method applied to the characterization of the angular resonances of an immersed elastic plate, i.e., the angular poles of its reflection coefficient R, was proved to be efficient when their real parts are close to the real zeros of R and their imaginary parts are not too large compared to their real parts. This method consists of plotting the partial reflection coefficient phase derivative with respect to the sine of the incidence angle, considered as real, versus incidence angle. In the vicinity of a resonance, this curve exhibits a Breit-Wigner shape, whose minimum is located at the pole real part and whose amplitude is the inverse of its imaginary part. However, when the imaginary part is large, this method is not sufficiently accurate compared to the exact calculation of the complex angular root. An improvement of this method consists of plotting, in 3D, in the complex angle plane and at a given frequency, the angular phase derivative with respect to the real part of the sine of the incidence angle, considered as complex. When the angular pole is reached, the 3D curve shows a clear-cut transition whose position is easily obtained.

Multiplex Real-Time PCR Assay Using TaqMan Probes for the Identification of Trypanosoma cruzi DTUs in Biological and Clinical Samples

PubMed Central

Cura, Carolina I.; Duffy, Tomas; Lucero, Raúl H.; Bisio, Margarita; Péneau, Julie; Jimenez-Coello, Matilde; Calabuig, Eva; Gimenez, María J.; Valencia Ayala, Edward; Kjos, Sonia A.; Santalla, José; Mahaney, Susan M.; Cayo, Nelly M.; Nagel, Claudia; Barcán, Laura; Málaga Machaca, Edith S.; Acosta Viana, Karla Y.; Brutus, Laurent; Ocampo, Susana B.; Aznar, Christine; Cuba Cuba, Cesar A.; Gürtler, Ricardo E.; Ramsey, Janine M.; Ribeiro, Isabela; VandeBerg, John L.; Yadon, Zaida E.; Osuna, Antonio; Schijman, Alejandro G.

2015-01-01

Background Trypanosoma cruzi has been classified into six Discrete Typing Units (DTUs), designated as TcI–TcVI. In order to effectively use this standardized nomenclature, a reproducible genotyping strategy is imperative. Several typing schemes have been developed with variable levels of complexity, selectivity and analytical sensitivity. Most of them can be only applied to cultured stocks. In this context, we aimed to develop a multiplex Real-Time PCR method to identify the six T. cruzi DTUs using TaqMan probes (MTq-PCR). Methods/Principal Findings The MTq-PCR has been evaluated in 39 cultured stocks and 307 biological samples from vectors, reservoirs and patients from different geographical regions and transmission cycles in comparison with a multi-locus conventional PCR algorithm. The MTq-PCR was inclusive for laboratory stocks and natural isolates and sensitive for direct typing of different biological samples from vectors, reservoirs and patients with acute, congenital infection or Chagas reactivation. The first round SL-IR MTq-PCR detected 1 fg DNA/reaction tube of TcI, TcII and TcIII and 1 pg DNA/reaction tube of TcIV, TcV and TcVI reference strains. The MTq-PCR was able to characterize DTUs in 83% of triatomine and 96% of reservoir samples that had been typed by conventional PCR methods. Regarding clinical samples, 100% of those derived from acute infected patients, 62.5% from congenitally infected children and 50% from patients with clinical reactivation could be genotyped. Sensitivity for direct typing of blood samples from chronic Chagas disease patients (32.8% from asymptomatic and 22.2% from symptomatic patients) and mixed infections was lower than that of the conventional PCR algorithm. Conclusions/Significance Typing is resolved after a single or a second round of Real-Time PCR, depending on the DTU. This format reduces carryover contamination and is amenable to quantification, automation and kit production. PMID:25993316

Multiplex Real-Time PCR Assay Using TaqMan Probes for the Identification of Trypanosoma cruzi DTUs in Biological and Clinical Samples.

PubMed

Cura, Carolina I; Duffy, Tomas; Lucero, Raúl H; Bisio, Margarita; Péneau, Julie; Jimenez-Coello, Matilde; Calabuig, Eva; Gimenez, María J; Valencia Ayala, Edward; Kjos, Sonia A; Santalla, José; Mahaney, Susan M; Cayo, Nelly M; Nagel, Claudia; Barcán, Laura; Málaga Machaca, Edith S; Acosta Viana, Karla Y; Brutus, Laurent; Ocampo, Susana B; Aznar, Christine; Cuba Cuba, Cesar A; Gürtler, Ricardo E; Ramsey, Janine M; Ribeiro, Isabela; VandeBerg, John L; Yadon, Zaida E; Osuna, Antonio; Schijman, Alejandro G

2015-05-01

Trypanosoma cruzi has been classified into six Discrete Typing Units (DTUs), designated as TcI-TcVI. In order to effectively use this standardized nomenclature, a reproducible genotyping strategy is imperative. Several typing schemes have been developed with variable levels of complexity, selectivity and analytical sensitivity. Most of them can be only applied to cultured stocks. In this context, we aimed to develop a multiplex Real-Time PCR method to identify the six T. cruzi DTUs using TaqMan probes (MTq-PCR). The MTq-PCR has been evaluated in 39 cultured stocks and 307 biological samples from vectors, reservoirs and patients from different geographical regions and transmission cycles in comparison with a multi-locus conventional PCR algorithm. The MTq-PCR was inclusive for laboratory stocks and natural isolates and sensitive for direct typing of different biological samples from vectors, reservoirs and patients with acute, congenital infection or Chagas reactivation. The first round SL-IR MTq-PCR detected 1 fg DNA/reaction tube of TcI, TcII and TcIII and 1 pg DNA/reaction tube of TcIV, TcV and TcVI reference strains. The MTq-PCR was able to characterize DTUs in 83% of triatomine and 96% of reservoir samples that had been typed by conventional PCR methods. Regarding clinical samples, 100% of those derived from acute infected patients, 62.5% from congenitally infected children and 50% from patients with clinical reactivation could be genotyped. Sensitivity for direct typing of blood samples from chronic Chagas disease patients (32.8% from asymptomatic and 22.2% from symptomatic patients) and mixed infections was lower than that of the conventional PCR algorithm. Typing is resolved after a single or a second round of Real-Time PCR, depending on the DTU. This format reduces carryover contamination and is amenable to quantification, automation and kit production.

A case for Sandia investment in complex adaptive systems science and technology.

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

Colbaugh, Richard; Tsao, Jeffrey Yeenien; Johnson, Curtis Martin

2012-05-01

This white paper makes a case for Sandia National Laboratories investments in complex adaptive systems science and technology (S&T) -- investments that could enable higher-value-added and more-robustly-engineered solutions to challenges of importance to Sandia's national security mission and to the nation. Complex adaptive systems are ubiquitous in Sandia's national security mission areas. We often ignore the adaptive complexity of these systems by narrowing our 'aperture of concern' to systems or subsystems with a limited range of function exposed to a limited range of environments over limited periods of time. But by widening our aperture of concern we could increase ourmore » impact considerably. To do so, the science and technology of complex adaptive systems must mature considerably. Despite an explosion of interest outside of Sandia, however, that science and technology is still in its youth. What has been missing is contact with real (rather than model) systems and real domain-area detail. With its center-of-gravity as an engineering laboratory, Sandia's has made considerable progress applying existing science and technology to real complex adaptive systems. It has focused much less, however, on advancing the science and technology itself. But its close contact with real systems and real domain-area detail represents a powerful strength with which to help complex adaptive systems science and technology mature. Sandia is thus both a prime beneficiary of, as well as potentially a prime contributor to, complex adaptive systems science and technology. Building a productive program in complex adaptive systems science and technology at Sandia will not be trivial, but a credible path can be envisioned: in the short run, continue to apply existing science and technology to real domain-area complex adaptive systems; in the medium run, jump-start the creation of new science and technology capability through Sandia's Laboratory Directed Research and Development program; and in the long run, inculcate an awareness at the Department of Energy of the importance of supporting complex adaptive systems science through its Office of Science.« less

Quantitative analysis of periodontal pathogens by ELISA and real-time polymerase chain reaction.

PubMed

Hamlet, Stephen M

2010-01-01

The development of analytical methods enabling the accurate identification and enumeration of bacterial species colonizing the oral cavity has led to the identification of a small number of bacterial pathogens that are major factors in the etiology of periodontal disease. Further, these methods also underpin more recent epidemiological analyses of the impact of periodontal disease on general health. Given the complex milieu of over 700 species of microorganisms known to exist within the complex biofilms found in the oral cavity, the identification and enumeration of oral periodontopathogens has not been an easy task. In recent years however, some of the intrinsic limitations of the more traditional microbiological analyses previously used have been overcome with the advent of immunological and molecular analytical methods. Of the plethora of methodologies reported in the literature, the enzyme-linked immunosorbent assay (ELISA), which combines the specificity of antibody with the sensitivity of simple enzyme assays and the polymerase chain reaction (PCR), has been widely utilized in both laboratory and clinical applications. Although conventional PCR does not allow quantitation of the target organism, real-time PCR (rtPCR) has the ability to detect amplicons as they accumulate in "real time" allowing subsequent quantitation. These methods enable the accurate quantitation of as few as 10(2) (using rtPCR) to 10(4) (using ELISA) periodontopathogens in dental plaque samples.

Comparison of Directigen Flu A+B with Real Time PCR in the Diagnosis of Influenza.

PubMed

Bosevska, Golubinka; Panovski, Nikola; Janceska, Elizabeta; Mikik, Vladimir; Topuzovska, Irena Kondova; Milenkovik, Zvonko

2015-01-01

Early diagnosis and treatment of patients with influenza is the reason why physicians need rapid high-sensitivity influenza diagnostic tests that require no complex lab equipment and can be performed and interpreted within 15 min. The Aim of this study was to compare the rapid Directigen Flu A+B test with real time PCR for detection of influenza viruses in the Republic of Macedonia. One-hundred-eight respiratory samples (combined nose and throat swabs) were routinely collected for detection of influenza virus during influenza seasons. Forty-one patients were pediatric cases and 59 were adult. Their mean age was 23 years. The patients were allocated into 6 age groups: 0-4 yrs, 5-9 yrs, 10-14 yrs, 15-19 yrs, 20-64 yrs and > 65 yrs. Each sample was tested with Directigen Flu A+B and CDC real time PCR kit for detection and typisation/subtypisation of influenza according to the lab diagnostic protocol. Directigen Flu A+B identified influenza A virus in 20 (18.5%) samples and influenza B virus in two 2 (1.9%) samples. The high specificity (100%) and PPV of Directigen Flu A+B we found in our study shows that the positive results do not need to be confirmed. The overall sensitivity of Directigen Flu A+B is 35.1% for influenza A virus and 33.0% for influenza B virus. The sensitivity for influenza A is higher among children hospitalized (45.0%) and outpatients (40.0%) versus adults. Directigen Flu A+B has relatively low sensitivity for detection of influenza viruses in combined nose and throat swabs. Negative results must be confirmed.

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 ...

Novel immunoassay formats for integrated microfluidic circuits: diffusion immunoassays (DIA)

NASA Astrophysics Data System (ADS)

Weigl, Bernhard H.; Hatch, Anson; Kamholz, Andrew E.; Yager, Paul

2000-03-01

Novel designs of integrated fluidic microchips allow separations, chemical reactions, and calibration-free analytical measurements to be performed directly in very small quantities of complex samples such as whole blood and contaminated environmental samples. This technology lends itself to applications such as clinical diagnostics, including tumor marker screening, and environmental sensing in remote locations. Lab-on-a-Chip based systems offer many *advantages over traditional analytical devices: They consume extremely low volumes of both samples and reagents. Each chip is inexpensive and small. The sampling-to-result time is extremely short. They perform all analytical functions, including sampling, sample pretreatment, separation, dilution, and mixing steps, chemical reactions, and detection in an integrated microfluidic circuit. Lab-on-a-Chip systems enable the design of small, portable, rugged, low-cost, easy to use, yet extremely versatile and capable diagnostic instruments. In addition, fluids flowing in microchannels exhibit unique characteristics ('microfluidics'), which allow the design of analytical devices and assay formats that would not function on a macroscale. Existing Lab-on-a-chip technologies work very well for highly predictable and homogeneous samples common in genetic testing and drug discovery processes. One of the biggest challenges for current Labs-on-a-chip, however, is to perform analysis in the presence of the complexity and heterogeneity of actual samples such as whole blood or contaminated environmental samples. Micronics has developed a variety of Lab-on-a-Chip assays that can overcome those shortcomings. We will now present various types of novel Lab- on-a-Chip-based immunoassays, including the so-called Diffusion Immunoassays (DIA) that are based on the competitive laminar diffusion of analyte molecules and tracer molecules into a region of the chip containing antibodies that target the analyte molecules. Advantages of this technique are a reduction in reagents, higher sensitivity, minimal preparation of complex samples such as blood, real-time calibration, and extremely rapid analysis.

A review on design of experiments and surrogate models in aircraft real-time and many-query aerodynamic analyses

NASA Astrophysics Data System (ADS)

Yondo, Raul; Andrés, Esther; Valero, Eusebio

2018-01-01

Full scale aerodynamic wind tunnel testing, numerical simulation of high dimensional (full-order) aerodynamic models or flight testing are some of the fundamental but complex steps in the various design phases of recent civil transport aircrafts. Current aircraft aerodynamic designs have increase in complexity (multidisciplinary, multi-objective or multi-fidelity) and need to address the challenges posed by the nonlinearity of the objective functions and constraints, uncertainty quantification in aerodynamic problems or the restrained computational budgets. With the aim to reduce the computational burden and generate low-cost but accurate models that mimic those full order models at different values of the design variables, Recent progresses have witnessed the introduction, in real-time and many-query analyses, of surrogate-based approaches as rapid and cheaper to simulate models. In this paper, a comprehensive and state-of-the art survey on common surrogate modeling techniques and surrogate-based optimization methods is given, with an emphasis on models selection and validation, dimensionality reduction, sensitivity analyses, constraints handling or infill and stopping criteria. Benefits, drawbacks and comparative discussions in applying those methods are described. Furthermore, the paper familiarizes the readers with surrogate models that have been successfully applied to the general field of fluid dynamics, but not yet in the aerospace industry. Additionally, the review revisits the most popular sampling strategies used in conducting physical and simulation-based experiments in aircraft aerodynamic design. Attractive or smart designs infrequently used in the field and discussions on advanced sampling methodologies are presented, to give a glance on the various efficient possibilities to a priori sample the parameter space. Closing remarks foster on future perspectives, challenges and shortcomings associated with the use of surrogate models by aircraft industrial aerodynamicists, despite their increased interest among the research communities.

An enhanced cluster analysis program with bootstrap significance testing for ecological community analysis

USGS Publications Warehouse

McKenna, J.E.

2003-01-01

The biosphere is filled with complex living patterns and important questions about biodiversity and community and ecosystem ecology are concerned with structure and function of multispecies systems that are responsible for those patterns. Cluster analysis identifies discrete groups within multivariate data and is an effective method of coping with these complexities, but often suffers from subjective identification of groups. The bootstrap testing method greatly improves objective significance determination for cluster analysis. The BOOTCLUS program makes cluster analysis that reliably identifies real patterns within a data set more accessible and easier to use than previously available programs. A variety of analysis options and rapid re-analysis provide a means to quickly evaluate several aspects of a data set. Interpretation is influenced by sampling design and a priori designation of samples into replicate groups, and ultimately relies on the researcher's knowledge of the organisms and their environment. However, the BOOTCLUS program provides reliable, objectively determined groupings of multivariate data.

Droplet Digital Enzyme-Linked Oligonucleotide Hybridization Assay for Absolute RNA Quantification.

PubMed

Guan, Weihua; Chen, Liben; Rane, Tushar D; Wang, Tza-Huei

2015-09-03

We present a continuous-flow droplet-based digital Enzyme-Linked Oligonucleotide Hybridization Assay (droplet digital ELOHA) for sensitive detection and absolute quantification of RNA molecules. Droplet digital ELOHA incorporates direct hybridization and single enzyme reaction via the formation of single probe-RNA-probe (enzyme) complex on magnetic beads. It enables RNA detection without reverse transcription and PCR amplification processes. The magnetic beads are subsequently encapsulated into a large number of picoliter-sized droplets with enzyme substrates in a continuous-flow device. This device is capable of generating droplets at high-throughput. It also integrates in-line enzymatic incubation and detection of fluorescent products. Our droplet digital ELOHA is able to accurately quantify (differentiate 40% difference) as few as ~600 RNA molecules in a 1 mL sample (equivalent to 1 aM or lower) without molecular replication. The absolute quantification ability of droplet digital ELOHA is demonstrated with the analysis of clinical Neisseria gonorrhoeae 16S rRNA to show its potential value in real complex samples.

Droplet Digital Enzyme-Linked Oligonucleotide Hybridization Assay for Absolute RNA Quantification

PubMed Central

Guan, Weihua; Chen, Liben; Rane, Tushar D.; Wang, Tza-Huei

2015-01-01

We present a continuous-flow droplet-based digital Enzyme-Linked Oligonucleotide Hybridization Assay (droplet digital ELOHA) for sensitive detection and absolute quantification of RNA molecules. Droplet digital ELOHA incorporates direct hybridization and single enzyme reaction via the formation of single probe-RNA-probe (enzyme) complex on magnetic beads. It enables RNA detection without reverse transcription and PCR amplification processes. The magnetic beads are subsequently encapsulated into a large number of picoliter-sized droplets with enzyme substrates in a continuous-flow device. This device is capable of generating droplets at high-throughput. It also integrates in-line enzymatic incubation and detection of fluorescent products. Our droplet digital ELOHA is able to accurately quantify (differentiate 40% difference) as few as ~600 RNA molecules in a 1 mL sample (equivalent to 1 aM or lower) without molecular replication. The absolute quantification ability of droplet digital ELOHA is demonstrated with the analysis of clinical Neisseria gonorrhoeae 16S rRNA to show its potential value in real complex samples. PMID:26333806

Droplet Digital Enzyme-Linked Oligonucleotide Hybridization Assay for Absolute RNA Quantification

NASA Astrophysics Data System (ADS)

Guan, Weihua; Chen, Liben; Rane, Tushar D.; Wang, Tza-Huei

2015-09-01

We present a continuous-flow droplet-based digital Enzyme-Linked Oligonucleotide Hybridization Assay (droplet digital ELOHA) for sensitive detection and absolute quantification of RNA molecules. Droplet digital ELOHA incorporates direct hybridization and single enzyme reaction via the formation of single probe-RNA-probe (enzyme) complex on magnetic beads. It enables RNA detection without reverse transcription and PCR amplification processes. The magnetic beads are subsequently encapsulated into a large number of picoliter-sized droplets with enzyme substrates in a continuous-flow device. This device is capable of generating droplets at high-throughput. It also integrates in-line enzymatic incubation and detection of fluorescent products. Our droplet digital ELOHA is able to accurately quantify (differentiate 40% difference) as few as ~600 RNA molecules in a 1 mL sample (equivalent to 1 aM or lower) without molecular replication. The absolute quantification ability of droplet digital ELOHA is demonstrated with the analysis of clinical Neisseria gonorrhoeae 16S rRNA to show its potential value in real complex samples.

Insights on Antioxidant Assays for Biological Samples Based on the Reduction of Copper Complexes—The Importance of Analytical Conditions

PubMed Central

Marques, Sara S.; Magalhães, Luís M.; Tóth, Ildikó V.; Segundo, Marcela A.

2014-01-01

Total antioxidant capacity assays are recognized as instrumental to establish antioxidant status of biological samples, however the varying experimental conditions result in conclusions that may not be transposable to other settings. After selection of the complexing agent, reagent addition order, buffer type and concentration, copper reducing assays were adapted to a high-throughput scheme and validated using model biological antioxidant compounds of ascorbic acid, Trolox (a soluble analogue of vitamin E), uric acid and glutathione. A critical comparison was made based on real samples including NIST-909c human serum certified sample, and five study samples. The validated method provided linear range up to 100 µM Trolox, (limit of detection 2.3 µM; limit of quantification 7.7 µM) with recovery results above 85% and precision <5%. The validated developed method with an increased sensitivity is a sound choice for assessment of TAC in serum samples. PMID:24968275

Improved FFT-based numerical inversion of Laplace transforms via fast Hartley transform algorithm

NASA Technical Reports Server (NTRS)

Hwang, Chyi; Lu, Ming-Jeng; Shieh, Leang S.

1991-01-01

The disadvantages of numerical inversion of the Laplace transform via the conventional fast Fourier transform (FFT) are identified and an improved method is presented to remedy them. The improved method is based on introducing a new integration step length Delta(omega) = pi/mT for trapezoidal-rule approximation of the Bromwich integral, in which a new parameter, m, is introduced for controlling the accuracy of the numerical integration. Naturally, this method leads to multiple sets of complex FFT computations. A new inversion formula is derived such that N equally spaced samples of the inverse Laplace transform function can be obtained by (m/2) + 1 sets of N-point complex FFT computations or by m sets of real fast Hartley transform (FHT) computations.

Microgravity validation of a novel system for RNA isolation and multiplex quantitative real time PCR analysis of gene expression on the International Space Station.

PubMed

Parra, Macarena; Jung, Jimmy; Boone, Travis D; Tran, Luan; Blaber, Elizabeth A; Brown, Mark; Chin, Matthew; Chinn, Tori; Cohen, Jacob; Doebler, Robert; Hoang, Dzung; Hyde, Elizabeth; Lera, Matthew; Luzod, Louie T; Mallinson, Mark; Marcu, Oana; Mohamedaly, Youssef; Ricco, Antonio J; Rubins, Kathleen; Sgarlato, Gregory D; Talavera, Rafael O; Tong, Peter; Uribe, Eddie; Williams, Jeffrey; Wu, Diana; Yousuf, Rukhsana; Richey, Charles S; Schonfeld, Julie; Almeida, Eduardo A C

2017-01-01

The International Space Station (ISS) National Laboratory is dedicated to studying the effects of space on life and physical systems, and to developing new science and technologies for space exploration. A key aspect of achieving these goals is to operate the ISS National Lab more like an Earth-based laboratory, conducting complex end-to-end experimentation, not limited to simple microgravity exposure. Towards that end NASA developed a novel suite of molecular biology laboratory tools, reagents, and methods, named WetLab-2, uniquely designed to operate in microgravity, and to process biological samples for real-time gene expression analysis on-orbit. This includes a novel fluidic RNA Sample Preparation Module and fluid transfer devices, all-in-one lyophilized PCR assays, centrifuge, and a real-time PCR thermal cycler. Here we describe the results from the WetLab-2 validation experiments conducted in microgravity during ISS increment 47/SPX-8. Specifically, quantitative PCR was performed on a concentration series of DNA calibration standards, and Reverse Transcriptase-quantitative PCR was conducted on RNA extracted and purified on-orbit from frozen Escherichia coli and mouse liver tissue. Cycle threshold (Ct) values and PCR efficiencies obtained on-orbit from DNA standards were similar to Earth (1 g) controls. Also, on-orbit multiplex analysis of gene expression from bacterial cells and mammalian tissue RNA samples was successfully conducted in about 3 h, with data transmitted within 2 h of experiment completion. Thermal cycling in microgravity resulted in the trapping of gas bubbles inside septa cap assay tubes, causing small but measurable increases in Ct curve noise and variability. Bubble formation was successfully suppressed in a rapid follow-up on-orbit experiment using standard caps to pressurize PCR tubes and reduce gas release during heating cycles. The WetLab-2 facility now provides a novel operational on-orbit research capability for molecular biology and demonstrates the feasibility of more complex wet bench experiments in the ISS National Lab environment.

Microgravity validation of a novel system for RNA isolation and multiplex quantitative real time PCR analysis of gene expression on the International Space Station

PubMed Central

Boone, Travis D.; Tran, Luan; Blaber, Elizabeth A.; Brown, Mark; Chin, Matthew; Chinn, Tori; Cohen, Jacob; Doebler, Robert; Hoang, Dzung; Hyde, Elizabeth; Lera, Matthew; Luzod, Louie T.; Mallinson, Mark; Marcu, Oana; Mohamedaly, Youssef; Ricco, Antonio J.; Rubins, Kathleen; Sgarlato, Gregory D.; Talavera, Rafael O.; Tong, Peter; Uribe, Eddie; Williams, Jeffrey; Wu, Diana; Yousuf, Rukhsana; Richey, Charles S.; Schonfeld, Julie

2017-01-01

The International Space Station (ISS) National Laboratory is dedicated to studying the effects of space on life and physical systems, and to developing new science and technologies for space exploration. A key aspect of achieving these goals is to operate the ISS National Lab more like an Earth-based laboratory, conducting complex end-to-end experimentation, not limited to simple microgravity exposure. Towards that end NASA developed a novel suite of molecular biology laboratory tools, reagents, and methods, named WetLab-2, uniquely designed to operate in microgravity, and to process biological samples for real-time gene expression analysis on-orbit. This includes a novel fluidic RNA Sample Preparation Module and fluid transfer devices, all-in-one lyophilized PCR assays, centrifuge, and a real-time PCR thermal cycler. Here we describe the results from the WetLab-2 validation experiments conducted in microgravity during ISS increment 47/SPX-8. Specifically, quantitative PCR was performed on a concentration series of DNA calibration standards, and Reverse Transcriptase-quantitative PCR was conducted on RNA extracted and purified on-orbit from frozen Escherichia coli and mouse liver tissue. Cycle threshold (Ct) values and PCR efficiencies obtained on-orbit from DNA standards were similar to Earth (1 g) controls. Also, on-orbit multiplex analysis of gene expression from bacterial cells and mammalian tissue RNA samples was successfully conducted in about 3 h, with data transmitted within 2 h of experiment completion. Thermal cycling in microgravity resulted in the trapping of gas bubbles inside septa cap assay tubes, causing small but measurable increases in Ct curve noise and variability. Bubble formation was successfully suppressed in a rapid follow-up on-orbit experiment using standard caps to pressurize PCR tubes and reduce gas release during heating cycles. The WetLab-2 facility now provides a novel operational on-orbit research capability for molecular biology and demonstrates the feasibility of more complex wet bench experiments in the ISS National Lab environment. PMID:28877184

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.

Performance of some biotic indices in the real variable world: a case study at different spatial scales in North-Western Mediterranean Sea.

PubMed

Tataranni, Mariella; Lardicci, Claudio

2010-01-01

The aim of this study was to analyse the variability of four different benthic biotic indices (AMBI, BENTIX, H', M-AMBI) in two marine coastal areas of the North-Western Mediterranean Sea. In each coastal area, 36 replicates were randomly selected according to a hierarchical sampling design, which allowed estimating the variance components of the indices associated with four different spatial scales (ranging from metres to kilometres). All the analyses were performed at two different sampling periods in order to evaluate if the observed trends were consistent over the time. The variance components of the four indices revealed complex trends and different patterns in the two sampling periods. These results highlighted that independently from the employed index, a rigorous and appropriate sampling design taking into account different scales should always be used in order to avoid erroneous classifications and to develop effective monitoring programs.

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.

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.

Effects of transcranial direct current stimulation (tDCS) on multiscale complexity of dual-task postural control in older adults.

PubMed

Zhou, Diange; Zhou, Junhong; Chen, Hu; Manor, Brad; Lin, Jianhao; Zhang, Jue

2015-08-01

Transcranial direct current stimulation (tDCS) targeting the prefrontal cortex reduces the size and speed of standing postural sway in younger adults, particularly when performing a cognitive dual task. Here, we hypothesized that tDCS would alter the complex dynamics of postural sway as quantified by multiscale entropy (MSE). Twenty healthy older adults completed two study visits. Center-of-pressure (COP) fluctuations were recorded during single-task (i.e., quiet standing) and dual-task (i.e., standing while performing serial subtractions) conditions, both before and after a 20-min session of real or sham tDCS. MSE was used to estimate COP complexity within each condition. The percentage change in complexity from single- to dual-task conditions (i.e., dual-task cost) was also calculated. Before tDCS, COP complexity was lower (p = 0.04) in the dual-task condition as compared to the single-task condition. Neither real nor sham tDCS altered complexity in the single-task condition. As compared to sham tDCS, real tDCS increased complexity in the dual-task condition (p = 0.02) and induced a trend toward improved serial subtraction performance (p = 0.09). Moreover, those subjects with lower dual-task COP complexity at baseline exhibited greater percentage increases in complexity following real tDCS (R = -0.39, p = 0.05). Real tDCS also reduced the dual-task cost to complexity (p = 0.02), while sham stimulation had no effect. A single session of tDCS targeting the prefrontal cortex increased standing postural sway complexity with concurrent non-postural cognitive task. This form of noninvasive brain stimulation may be a safe strategy to acutely improve postural control by enhancing the system's capacity to adapt to stressors.

Label-free nanoscale characterization of red blood cell structure and dynamics using single-shot transport of intensity equation

NASA Astrophysics Data System (ADS)

Poola, Praveen Kumar; John, Renu

2017-10-01

We report the results of characterization of red blood cell (RBC) structure and its dynamics with nanometric sensitivity using transport of intensity equation microscopy (TIEM). Conventional transport of intensity technique requires three intensity images and hence is not suitable for studying real-time dynamics of live biological samples. However, assuming the sample to be homogeneous, phase retrieval using transport of intensity equation has been demonstrated with single defocused measurement with x-rays. We adopt this technique for quantitative phase light microscopy of homogenous cells like RBCs. The main merits of this technique are its simplicity, cost-effectiveness, and ease of implementation on a conventional microscope. The phase information can be easily merged with regular bright-field and fluorescence images to provide multidimensional (three-dimensional spatial and temporal) information without any extra complexity in the setup. The phase measurement from the TIEM has been characterized using polymeric microbeads and the noise stability of the system has been analyzed. We explore the structure and real-time dynamics of RBCs and the subdomain membrane fluctuations using this technique.

Local kernel nonparametric discriminant analysis for adaptive extraction of complex structures

NASA Astrophysics Data System (ADS)

Li, Quanbao; Wei, Fajie; Zhou, Shenghan

2017-05-01

The linear discriminant analysis (LDA) is one of popular means for linear feature extraction. It usually performs well when the global data structure is consistent with the local data structure. Other frequently-used approaches of feature extraction usually require linear, independence, or large sample condition. However, in real world applications, these assumptions are not always satisfied or cannot be tested. In this paper, we introduce an adaptive method, local kernel nonparametric discriminant analysis (LKNDA), which integrates conventional discriminant analysis with nonparametric statistics. LKNDA is adept in identifying both complex nonlinear structures and the ad hoc rule. Six simulation cases demonstrate that LKNDA have both parametric and nonparametric algorithm advantages and higher classification accuracy. Quartic unilateral kernel function may provide better robustness of prediction than other functions. LKNDA gives an alternative solution for discriminant cases of complex nonlinear feature extraction or unknown feature extraction. At last, the application of LKNDA in the complex feature extraction of financial market activities is proposed.

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.

Cloud point extraction and diffuse reflectance-Fourier transform infrared spectroscopic determination of chromium(VI): A probe to adulteration in food stuffs.

PubMed

Tiwari, Swapnil; Deb, Manas Kanti; Sen, Bhupendra K

2017-04-15

A new cloud point extraction (CPE) method for the determination of hexavalent chromium i.e. Cr(VI) in food samples is established with subsequent diffuse reflectance-Fourier transform infrared (DRS-FTIR) analysis. The method demonstrates enrichment of Cr(VI) after its complexation with 1,5-diphenylcarbazide. The reddish-violet complex formed showed λ max at 540nm. Micellar phase separation at cloud point temperature of non-ionic surfactant, Triton X-100 occurred and complex was entrapped in surfactant and analyzed using DRS-FTIR. Under optimized conditions, the limit of detection (LOD) and quantification (LOQ) were 1.22 and 4.02μgmL -1 , respectively. Excellent linearity with correlation coefficient value of 0.94 was found for the concentration range of 1-100μgmL -1 . At 10μgmL -1 the standard deviation for 7 replicate measurements was found to be 0.11μgmL -1 . The method was successfully applied to commercially marketed food stuffs, and good recoveries (81-112%) were obtained by spiking the real samples. Copyright © 2016 Elsevier Ltd. All rights reserved.

3-D decoupled inversion of complex conductivity data in the real number domain

NASA Astrophysics Data System (ADS)

Johnson, Timothy C.; Thomle, Jonathan

2018-01-01

Complex conductivity imaging (also called induced polarization imaging or spectral induced polarization imaging when conducted at multiple frequencies) involves estimating the frequency-dependent complex electrical conductivity distribution of the subsurface. The superior diagnostic capabilities provided by complex conductivity spectra have driven advancements in mechanistic understanding of complex conductivity as well as modelling and inversion approaches over the past several decades. In this work, we demonstrate the theory and application for an approach to 3-D modelling and inversion of complex conductivity data in the real number domain. Beginning from first principles, we demonstrate how the equations for the real and imaginary components of the complex potential may be decoupled. This leads to a description of the real and imaginary source current terms, and a corresponding assessment of error arising from an assumption necessary to complete the decoupled modelling. We show that for most earth materials, which exhibit relatively small phases (e.g. less than 0.2 radians) in complex conductivity, these errors become insignificant. For higher phase materials, the errors may be quantified and corrected through an iterative procedure. We demonstrate the accuracy of numerical forward solutions by direct comparison to corresponding analytic solutions. We demonstrate the inversion using both synthetic and field examples with data collected over a waste infiltration trench, at frequencies ranging from 0.5 to 7.5 Hz.

Measurement of absolute frequency of continuous-wave terahertz radiation in real time using a free-running, dual-wavelength mode-locked, erbium-doped fibre laser

PubMed Central

Hu, Guoqing; Mizuguchi, Tatsuya; Zhao, Xin; Minamikawa, Takeo; Mizuno, Takahiko; Yang, Yuli; Li, Cui; Bai, Ming; Zheng, Zheng; Yasui, Takeshi

2017-01-01

A single, free-running, dual-wavelength mode-locked, erbium-doped fibre laser was exploited to measure the absolute frequency of continuous-wave terahertz (CW-THz) radiation in real time using dual THz combs of photo-carriers (dual PC-THz combs). Two independent mode-locked laser beams with different wavelengths and different repetition frequencies were generated from this laser and were used to generate dual PC-THz combs having different frequency spacings in photoconductive antennae. Based on the dual PC-THz combs, the absolute frequency of CW-THz radiation was determined with a relative precision of 1.2 × 10−9 and a relative accuracy of 1.4 × 10−9 at a sampling rate of 100 Hz. Real-time determination of the absolute frequency of CW-THz radiation varying over a few tens of GHz was also demonstrated. Use of a single dual-wavelength mode-locked fibre laser, in place of dual mode-locked lasers, greatly reduced the size, complexity, and cost of the measurement system while maintaining the real-time capability and high measurement precision. PMID:28186148

Accurate in situ measurement of complex refractive index and particle size in intralipid emulsions

NASA Astrophysics Data System (ADS)

Dong, Miao L.; Goyal, Kashika G.; Worth, Bradley W.; Makkar, Sorab S.; Calhoun, William R.; Bali, Lalit M.; Bali, Samir

2013-08-01

A first accurate measurement of the complex refractive index in an intralipid emulsion is demonstrated, and thereby the average scatterer particle size using standard Mie scattering calculations is extracted. Our method is based on measurement and modeling of the reflectance of a divergent laser beam from the sample surface. In the absence of any definitive reference data for the complex refractive index or particle size in highly turbid intralipid emulsions, we base our claim of accuracy on the fact that our work offers several critically important advantages over previously reported attempts. First, our measurements are in situ in the sense that they do not require any sample dilution, thus eliminating dilution errors. Second, our theoretical model does not employ any fitting parameters other than the two quantities we seek to determine, i.e., the real and imaginary parts of the refractive index, thus eliminating ambiguities arising from multiple extraneous fitting parameters. Third, we fit the entire reflectance-versus-incident-angle data curve instead of focusing on only the critical angle region, which is just a small subset of the data. Finally, despite our use of highly scattering opaque samples, our experiment uniquely satisfies a key assumption behind the Mie scattering formalism, namely, no multiple scattering occurs. Further proof of our method's validity is given by the fact that our measured particle size finds good agreement with the value obtained by dynamic light scattering.

Accurate in situ measurement of complex refractive index and particle size in intralipid emulsions.

PubMed

Dong, Miao L; Goyal, Kashika G; Worth, Bradley W; Makkar, Sorab S; Calhoun, William R; Bali, Lalit M; Bali, Samir

2013-08-01

A first accurate measurement of the complex refractive index in an intralipid emulsion is demonstrated, and thereby the average scatterer particle size using standard Mie scattering calculations is extracted. Our method is based on measurement and modeling of the reflectance of a divergent laser beam from the sample surface. In the absence of any definitive reference data for the complex refractive index or particle size in highly turbid intralipid emulsions, we base our claim of accuracy on the fact that our work offers several critically important advantages over previously reported attempts. First, our measurements are in situ in the sense that they do not require any sample dilution, thus eliminating dilution errors. Second, our theoretical model does not employ any fitting parameters other than the two quantities we seek to determine, i.e., the real and imaginary parts of the refractive index, thus eliminating ambiguities arising from multiple extraneous fitting parameters. Third, we fit the entire reflectance-versus-incident-angle data curve instead of focusing on only the critical angle region, which is just a small subset of the data. Finally, despite our use of highly scattering opaque samples, our experiment uniquely satisfies a key assumption behind the Mie scattering formalism, namely, no multiple scattering occurs. Further proof of our method's validity is given by the fact that our measured particle size finds good agreement with the value obtained by dynamic light scattering.

Sample Analysis at Mars Instrument Simulator

NASA Technical Reports Server (NTRS)

Benna, Mehdi; Nolan, Tom

2013-01-01

The Sample Analysis at Mars Instrument Simulator (SAMSIM) is a numerical model dedicated to plan and validate operations of the Sample Analysis at Mars (SAM) instrument on the surface of Mars. The SAM instrument suite, currently operating on the Mars Science Laboratory (MSL), is an analytical laboratory designed to investigate the chemical and isotopic composition of the atmosphere and volatiles extracted from solid samples. SAMSIM was developed using Matlab and Simulink libraries of MathWorks Inc. to provide MSL mission planners with accurate predictions of the instrument electrical, thermal, mechanical, and fluid responses to scripted commands. This tool is a first example of a multi-purpose, full-scale numerical modeling of a flight instrument with the purpose of supplementing or even eliminating entirely the need for a hardware engineer model during instrument development and operation. SAMSIM simulates the complex interactions that occur between the instrument Command and Data Handling unit (C&DH) and all subsystems during the execution of experiment sequences. A typical SAM experiment takes many hours to complete and involves hundreds of components. During the simulation, the electrical, mechanical, thermal, and gas dynamics states of each hardware component are accurately modeled and propagated within the simulation environment at faster than real time. This allows the simulation, in just a few minutes, of experiment sequences that takes many hours to execute on the real instrument. The SAMSIM model is divided into five distinct but interacting modules: software, mechanical, thermal, gas flow, and electrical modules. The software module simulates the instrument C&DH by executing a customized version of the instrument flight software in a Matlab environment. The inputs and outputs to this synthetic C&DH are mapped to virtual sensors and command lines that mimic in their structure and connectivity the layout of the instrument harnesses. This module executes, and thus validates, complex command scripts prior to their up-linking to the SAM instrument. As an output, this module generates synthetic data and message logs at a rate that is similar to the actual instrument.

Food for Thought: Cross-Classification and Category Organization in a Complex Real-World Domain.

ERIC Educational Resources Information Center

Ross, Brian H.; Murphy, Gregory L.

1999-01-01

Seven studies involving 256 undergraduates examined how people represent, access, and make inferences about the real-world category domain, foods. Results give a detailed picture of the use of cross-classification in a complex domain. (SLD)

End-User Applications of Real-Time Earthquake Information in Europe

NASA Astrophysics Data System (ADS)

Cua, G. B.; Gasparini, P.; Giardini, D.; Zschau, J.; Filangieri, A. R.; Reakt Wp7 Team

2011-12-01

The primary objective of European FP7 project REAKT (Strategies and Tools for Real-Time Earthquake Risk Reduction) is to improve the efficiency of real-time earthquake risk mitigation methods and their capability of protecting structures, infrastructures, and populations. REAKT aims to address the issues of real-time earthquake hazard and response from end-to-end, with efforts directed along the full spectrum of methodology development in earthquake forecasting, earthquake early warning, and real-time vulnerability systems, through optimal decision-making, and engagement and cooperation of scientists and end users for the establishment of best practices for use of real-time information. Twelve strategic test cases/end users throughout Europe have been selected. This diverse group of applications/end users includes civil protection authorities, railway systems, hospitals, schools, industrial complexes, nuclear plants, lifeline systems, national seismic networks, and critical structures. The scale of target applications covers a wide range, from two school complexes in Naples, to individual critical structures, such as the Rion Antirion bridge in Patras, and the Fatih Sultan Mehmet bridge in Istanbul, to large complexes, such as the SINES industrial complex in Portugal and the Thessaloniki port area, to distributed lifeline and transportation networks and nuclear plants. Some end-users are interested in in-depth feasibility studies for use of real-time information and development of rapid response plans, while others intend to install real-time instrumentation and develop customized automated control systems. From the onset, REAKT scientists and end-users will work together on concept development and initial implementation efforts using the data products and decision-making methodologies developed with the goal of improving end-user risk mitigation. The aim of this scientific/end-user partnership is to ensure that scientific efforts are applicable to operational, real-world problems.

Real time monitoring of accelerated chemical reactions by ultrasonication-assisted spray ionization mass spectrometry.

PubMed

Lin, Shu-Hsuan; Lo, Ta-Ju; Kuo, Fang-Yin; Chen, Yu-Chie

2014-01-01

Ultrasonication has been used to accelerate chemical reactions. It would be ideal if ultrasonication-assisted chemical reactions could be monitored by suitable detection tools such as mass spectrometry in real time. It would be helpful to clarify reaction intermediates/products and to have a better understanding of reaction mechanism. In this work, we developed a system for ultrasonication-assisted spray ionization mass spectrometry (UASI-MS) with an ~1.7 MHz ultrasonic transducer to monitor chemical reactions in real time. We demonstrated that simply depositing a sample solution on the MHz-based ultrasonic transducer, which was placed in front of the orifice of a mass spectrometer, the analyte signals can be readily detected by the mass spectrometer. Singly and multiply charged ions from small and large molecules, respectively, can be observed in the UASI mass spectra. Furthermore, the ultrasonic transducer used in the UASI setup accelerates the chemical reactions while being monitored via UASI-MS. The feasibility of using this approach for real-time acceleration/monitoring of chemical reactions was demonstrated. The reactions of Girard T reagent and hydroxylamine with steroids were used as the model reactions. Upon the deposition of reactant solutions on the ultrasonic transducer, the intermediate/product ions are readily generated and instantaneously monitored using MS within 1 s. Additionally, we also showed the possibility of using this reactive UASI-MS approach to assist the confirmation of trace steroids from complex urine samples by monitoring the generation of the product ions. Copyright © 2014 John Wiley & Sons, Ltd.

Purification of complex samples: Implementation of a modular and reconfigurable droplet-based microfluidic platform with cascaded deterministic lateral displacement separation modules

PubMed Central

Pudda, Catherine; Boizot, François; Verplanck, Nicolas; Revol-Cavalier, Frédéric; Berthier, Jean; Thuaire, Aurélie

2018-01-01

Particle separation in microfluidic devices is a common problematic for sample preparation in biology. Deterministic lateral displacement (DLD) is efficiently implemented as a size-based fractionation technique to separate two populations of particles around a specific size. However, real biological samples contain components of many different sizes and a single DLD separation step is not sufficient to purify these complex samples. When connecting several DLD modules in series, pressure balancing at the DLD outlets of each step becomes critical to ensure an optimal separation efficiency. A generic microfluidic platform is presented in this paper to optimize pressure balancing, when DLD separation is connected either to another DLD module or to a different microfluidic function. This is made possible by generating droplets at T-junctions connected to the DLD outlets. Droplets act as pressure controllers, which perform at the same time the encapsulation of DLD sorted particles and the balance of output pressures. The optimized pressures to apply on DLD modules and on T-junctions are determined by a general model that ensures the equilibrium of the entire platform. The proposed separation platform is completely modular and reconfigurable since the same predictive model applies to any cascaded DLD modules of the droplet-based cartridge. PMID:29768490

A Mathematical Motivation for Complex-Valued Convolutional Networks.

PubMed

Tygert, Mark; Bruna, Joan; Chintala, Soumith; LeCun, Yann; Piantino, Serkan; Szlam, Arthur

2016-05-01

A complex-valued convolutional network (convnet) implements the repeated application of the following composition of three operations, recursively applying the composition to an input vector of nonnegative real numbers: (1) convolution with complex-valued vectors, followed by (2) taking the absolute value of every entry of the resulting vectors, followed by (3) local averaging. For processing real-valued random vectors, complex-valued convnets can be viewed as data-driven multiscale windowed power spectra, data-driven multiscale windowed absolute spectra, data-driven multiwavelet absolute values, or (in their most general configuration) data-driven nonlinear multiwavelet packets. Indeed, complex-valued convnets can calculate multiscale windowed spectra when the convnet filters are windowed complex-valued exponentials. Standard real-valued convnets, using rectified linear units (ReLUs), sigmoidal (e.g., logistic or tanh) nonlinearities, or max pooling, for example, do not obviously exhibit the same exact correspondence with data-driven wavelets (whereas for complex-valued convnets, the correspondence is much more than just a vague analogy). Courtesy of the exact correspondence, the remarkably rich and rigorous body of mathematical analysis for wavelets applies directly to (complex-valued) convnets.

Real-time monitoring of clinical processes using complex event processing and transition systems.

PubMed

Meinecke, Sebastian

2014-01-01

Dependencies between tasks in clinical processes are often complex and error-prone. Our aim is to describe a new approach for the automatic derivation of clinical events identified via the behaviour of IT systems using Complex Event Processing. Furthermore we map these events on transition systems to monitor crucial clinical processes in real-time for preventing and detecting erroneous situations.

Modification and fixed-point analysis of a Kalman filter for orientation estimation based on 9D inertial measurement unit data.

PubMed

Brückner, Hans-Peter; Spindeldreier, Christian; Blume, Holger

2013-01-01

A common approach for high accuracy sensor fusion based on 9D inertial measurement unit data is Kalman filtering. State of the art floating-point filter algorithms differ in their computational complexity nevertheless, real-time operation on a low-power microcontroller at high sampling rates is not possible. This work presents algorithmic modifications to reduce the computational demands of a two-step minimum order Kalman filter. Furthermore, the required bit-width of a fixed-point filter version is explored. For evaluation real-world data captured using an Xsens MTx inertial sensor is used. Changes in computational latency and orientation estimation accuracy due to the proposed algorithmic modifications and fixed-point number representation are evaluated in detail on a variety of processing platforms enabling on-board processing on wearable sensor platforms.

Rational BRDF.

PubMed

Pacanowski, Romain; Salazar Celis, Oliver; Schlick, Christophe; Granier, Xavier; Poulin, Pierre; Cuyt, Annie

2012-11-01

Over the last two decades, much effort has been devoted to accurately measuring Bidirectional Reflectance Distribution Functions (BRDFs) of real-world materials and to use efficiently the resulting data for rendering. Because of their large size, it is difficult to use directly measured BRDFs for real-time applications, and fitting the most sophisticated analytical BRDF models is still a complex task. In this paper, we introduce Rational BRDF, a general-purpose and efficient representation for arbitrary BRDFs, based on Rational Functions (RFs). Using an adapted parametrization, we demonstrate how Rational BRDFs offer 1) a more compact and efficient representation using low-degree RFs, 2) an accurate fitting of measured materials with guaranteed control of the residual error, and 3) efficient importance sampling by applying the same fitting process to determine the inverse of the Cumulative Distribution Function (CDF) generated from the BRDF for use in Monte-Carlo rendering.

A new parallel plate shear cell for in situ real-space measurements of complex fluids under shear flow.

PubMed

Wu, Yu Ling; Brand, Joost H J; van Gemert, Josephus L A; Verkerk, Jaap; Wisman, Hans; van Blaaderen, Alfons; Imhof, Arnout

2007-10-01

We developed and tested a parallel plate shear cell that can be mounted on top of an inverted microscope to perform confocal real-space measurements on complex fluids under shear. To follow structural changes in time, a plane of zero velocity is created by letting the plates move in opposite directions. The location of this plane is varied by changing the relative velocities of the plates. The gap width is variable between 20 and 200 microm with parallelism better than 1 microm. Such a small gap width enables us to examine the total sample thickness using high numerical aperture objective lenses. The achieved shear rates cover the range of 0.02-10(3) s(-1). This shear cell can apply an oscillatory shear with adjustable amplitude and frequency. The maximum travel of each plate equals 1 cm, so that strains up to 500 can be applied. For most complex fluids, an oscillatory shear with such a large amplitude can be regarded as a continuous shear. We measured the flow profile of a suspension of silica colloids in this shear cell. It was linear except for a small deviation caused by sedimentation. To demonstrate the excellent performance and capabilities of this new setup we examined shear induced crystallization and melting of concentrated suspensions of 1 microm diameter silica colloids.

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

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.

Two-dimensional liquid chromatography consisting of twelve second-dimension columns for comprehensive analysis of intact proteins.

PubMed

Ren, Jiangtao; Beckner, Matthew A; Lynch, Kyle B; Chen, Huang; Zhu, Zaifang; Yang, Yu; Chen, Apeng; Qiao, Zhenzhen; Liu, Shaorong; Lu, Joann J

2018-05-15

A comprehensive two-dimensional liquid chromatography (LCxLC) system consisting of twelve columns in the second dimension was developed for comprehensive analysis of intact proteins in complex biological samples. The system consisted of an ion-exchange column in the first dimension and the twelve reverse-phase columns in the second dimension; all thirteen columns were monolithic and prepared inside 250 µm i.d. capillaries. These columns were assembled together through the use of three valves and an innovative configuration. The effluent from the first dimension was continuously fractionated and sequentially transferred into the twelve second-dimension columns, while the second-dimension separations were carried out in a series of batches (six columns per batch). This LCxLC system was tested first using standard proteins followed by real-world samples from E. coli. Baseline separation was observed for eleven standard proteins and hundreds of peaks were observed for the real-world sample analysis. Two-dimensional liquid chromatography, often considered as an effective tool for mapping proteins, is seen as laborious and time-consuming when configured offline. Our online LCxLC system with increased second-dimension columns promises to provide a solution to overcome these hindrances. Copyright © 2018 Elsevier B.V. All rights reserved.

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.

Direct Electrospray Ionization Mass Spectrometric Profiling of Real-World Samples via a Solid Sampling Probe

NASA Astrophysics Data System (ADS)

Yu, Zhan; Chen, Lee Chuin; Mandal, Mridul Kanti; Yoshimura, Kentaro; Takeda, Sen; Hiraoka, Kenzo

2013-10-01

This study presents a novel direct analysis strategy for rapid mass spectrometric profiling of biochemicals in real-world samples via a direct sampling probe (DSP) without sample pretreatments. Chemical modification is applied to a disposable stainless steel acupuncture needle to enhance its surface area and hydrophilicity. After insertion into real-world samples, biofluid can be attached on the DSP surface. With the presence of a high DC voltage and solvent vapor condensing on the tip of the DSP, analyte can be dissolved and electrosprayed. The simplicity in design, versatility in application aspects, and other advantages such as low cost and disposability make this new method a competitive tool for direct analysis of real-world samples.

How Good Are Statistical Models at Approximating Complex Fitness Landscapes?

PubMed Central

du Plessis, Louis; Leventhal, Gabriel E.; Bonhoeffer, Sebastian

2016-01-01

Fitness landscapes determine the course of adaptation by constraining and shaping evolutionary trajectories. Knowledge of the structure of a fitness landscape can thus predict evolutionary outcomes. Empirical fitness landscapes, however, have so far only offered limited insight into real-world questions, as the high dimensionality of sequence spaces makes it impossible to exhaustively measure the fitness of all variants of biologically meaningful sequences. We must therefore revert to statistical descriptions of fitness landscapes that are based on a sparse sample of fitness measurements. It remains unclear, however, how much data are required for such statistical descriptions to be useful. Here, we assess the ability of regression models accounting for single and pairwise mutations to correctly approximate a complex quasi-empirical fitness landscape. We compare approximations based on various sampling regimes of an RNA landscape and find that the sampling regime strongly influences the quality of the regression. On the one hand it is generally impossible to generate sufficient samples to achieve a good approximation of the complete fitness landscape, and on the other hand systematic sampling schemes can only provide a good description of the immediate neighborhood of a sequence of interest. Nevertheless, we obtain a remarkably good and unbiased fit to the local landscape when using sequences from a population that has evolved under strong selection. Thus, current statistical methods can provide a good approximation to the landscape of naturally evolving populations. PMID:27189564

Slaughterhouses Fungal Burden Assessment: A Contribution for the Pursuit of a Better Assessment Strategy

PubMed Central

Viegas, Carla; Faria, Tiago; dos Santos, Mateus; Carolino, Elisabete; Sabino, Raquel; Quintal Gomes, Anita; Viegas, Susana

2016-01-01

In slaughterhouses, the biological risk is present not only from the direct or indirect contact with animal matter, but also from the exposure to bioaerosols. Fungal contamination was already reported from the floors and walls of slaughterhouses. This study intends to assess fungal contamination by cultural and molecular methods in poultry, swine/bovine and large animal slaughterhouses. Air samples were collected through an impaction method, while surface samples were collected by the swabbing method and subjected to further macro- and micro-scopic observations. In addition, we collected air samples using the impinger method in order to perform real-time quantitative PCR (qPCR) amplification of genes from specific fungal species, namely A. flavus, A. fumigatus and A. ochraceus complexes. Poultry and swine/bovine slaughterhouses presented each two sampling sites that surpass the guideline of 150 CFU/m3. Scopulariopsis candida was the most frequently isolated (59.5%) in poultry slaughterhouse air; Cladosporium sp. (45.7%) in the swine/bovine slaughterhouse; and Penicillium sp. (80.8%) in the large animal slaughterhouse. Molecular tools successfully amplified DNA from the A. fumigatus complex in six sampling sites where the presence of this fungal species was not identified by conventional methods. This study besides suggesting the indicators that are representative of harmful fungal contamination, also indicates a strategy as a protocol to ensure a proper characterization of fungal occupational exposure. PMID:27005642

Development of liquid chromatography high resolution mass spectrometry strategies for the screening of complex organic matter: Application to astrophysical simulated materials.

PubMed

Eddhif, Balkis; Allavena, Audrey; Liu, Sylvie; Ribette, Thomas; Abou Mrad, Ninette; Chiavassa, Thierry; d'Hendecourt, Louis Le Sergeant; Sternberg, Robert; Danger, Gregoire; Geffroy-Rodier, Claude; Poinot, Pauline

2018-03-01

The present work aims at developing two LC-HRMS setups for the screening of organic matter in astrophysical samples. Their analytical development has been demonstrated on a 100-µg residue coming from the photo-thermo chemical processing of a cometary ice analog produced in laboratory. The first 1D-LC-HRMS setup combines a serially coupled columns configuration with HRMS detection. It has allowed to discriminate among different chemical families (amino acids, sugars, nucleobases and oligopeptides) in only one chromatographic run without neither a priori acid hydrolysis nor chemical derivatisation. The second setup is a dual-LC configuration which connects a series of trapping columns with analytical reverse-phase columns. By coupling on-line these two distinct LC units with a HRMS detection, high mass compounds (350

Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation.

PubMed

Cornuet, Jean-Marie; Santos, Filipe; Beaumont, Mark A; Robert, Christian P; Marin, Jean-Michel; Balding, David J; Guillemaud, Thomas; Estoup, Arnaud

2008-12-01

Genetic data obtained on population samples convey information about their evolutionary history. Inference methods can extract part of this information but they require sophisticated statistical techniques that have been made available to the biologist community (through computer programs) only for simple and standard situations typically involving a small number of samples. We propose here a computer program (DIY ABC) for inference based on approximate Bayesian computation (ABC), in which scenarios can be customized by the user to fit many complex situations involving any number of populations and samples. Such scenarios involve any combination of population divergences, admixtures and population size changes. DIY ABC can be used to compare competing scenarios, estimate parameters for one or more scenarios and compute bias and precision measures for a given scenario and known values of parameters (the current version applies to unlinked microsatellite data). This article describes key methods used in the program and provides its main features. The analysis of one simulated and one real dataset, both with complex evolutionary scenarios, illustrates the main possibilities of DIY ABC. The software DIY ABC is freely available at http://www.montpellier.inra.fr/CBGP/diyabc.

Label-Free Nanopore Biosensor for Rapid and Highly Sensitive Cocaine Detection in Complex Biological Fluids.

PubMed

Rauf, Sana; Zhang, Ling; Ali, Asghar; Liu, Yang; Li, Jinghong

2017-02-24

Detection of very low amounts of illicit drugs such as cocaine in clinical fluids like serum continues to be important for many areas in the fight against drug trafficking. Herein, we constructed a label-free nanopore biosensor for rapid and highly sensitive detection of cocaine in human serum and saliva samples based on target-induced strand release strategy. In this bioassay, an aptamer for cocaine was prehybridized with a short complementary DNA. Owing to cocaine specific binding with aptamer, the short DNA strand was displaced from aptamer and translocation of this output DNA through α-hemolysin nanopore generated distinct spike-like current blockages. When plotted in double-logarithmic scale, a linear relationship between target cocaine concentration and output DNA event frequency was obtained in a wide concentration range from 50 nM to 100 μM of cocaine, with the limit of detection down to 50 nM. In addition, this aptamer-based sensor method was successfully applied for cocaine detection in complex biological fluids like human saliva and serum samples with great selectivity. Simple preparation, low cost, rapid, label-free, and real sample detection are the motivating factors for practical application of the proposed biosensor.

A real-space approach to the X-ray phase problem

NASA Astrophysics Data System (ADS)

Liu, Xiangan

Over the past few decades, the phase problem of X-ray crystallography has been explored in reciprocal space in the so called direct methods . Here we investigate the problem using a real-space approach that bypasses the laborious procedure of frequent Fourier synthesis and peak picking. Starting from a completely random structure, we move the atoms around in real space to minimize a cost function. A Monte Carlo method named simulated annealing (SA) is employed to search the global minimum of the cost function which could be constructed in either real space or reciprocal space. In the hybrid minimal principle, we combine the dual space costs together. One part of the cost function monitors the probability distribution of the phase triplets, while the other is a real space cost function which represents the discrepancy between measured and calculated intensities. Compared to the single space cost functions, the dual space cost function has a greatly improved landscape and therefore could prevent the system from being trapped in metastable states. Thus, the structures of large molecules such as virginiamycin (C43H 49N7O10 · 3CH0OH), isoleucinomycin (C60H102N 6O18) and hexadecaisoleucinomycin (HEXIL) (C80H136 N8O24) can now be solved, whereas it would not be possible using the single cost function. When a molecule gets larger, the configurational space becomes larger, and the requirement of CPU time increases exponentially. The method of improved Monte Carlo sampling has demonstrated its capability to solve large molecular structures. The atoms are encouraged to sample the high density regions in space determined by an approximate density map which in turn is updated and modified by averaging and Fourier synthesis. This type of biased sampling has led to considerable reduction of the configurational space. It greatly improves the algorithm compared to the previous uniform sampling. Hence, for instance, 90% of computer run time could be cut in solving the complex structure of isoleucinomycin. Successful trial calculations include larger molecular structures such as HEXIL and a collagen-like peptide (PPG). Moving chemical fragment is proposed to reduce the degrees of freedom. Furthermore, stereochemical parameters are considered for geometric constraints and for a cost function related to chemical energy.

A novel differential pulse voltammetric (DPV) method for measuring the antioxidant capacity of polyphenols-reducing cupric neocuproine complex.

PubMed

Tufan, Ayşe Nur; Baki, Sefa; Güçlü, Kubilay; Özyürek, Mustafa; Apak, Reşat

2014-07-23

A novel differential pulse voltammetric (DPV) method is presented, using a chromogenic oxidizing reagent, cupric neocuproine complex (Cu(Nc)2(2+)), for the assessment of antioxidant capacity of polyphenolic compounds (i.e., flavonoids, simple phenolic acids, and hydroxycinnamic acids), ascorbic acid, and real samples for the first time. The electrochemical behavior of the Cu(Nc)2(2+) complex was studied by cyclic voltammetry at a glassy carbon (GC) electrode. The electroanalytical method was based on the reduction of Cu(Nc)2(2+) to Cu(Nc)2(+) by antioxidants and electrochemical detection of the remaining Cu(II)-Nc (unreacted complex), the difference being correlated to antioxidant capacity of the analytes. The calibration curves of individual compounds comprising polyphenolics and vitamin C were constructed, and their response sensitivities and linear concentration ranges were determined. The reagent on the GC electrode retained its reactivity toward antioxidants, and the measured trolox equivalent antioxidant capacity (TEAC) values of various antioxidants suggested that the reactivity of the Cu(II)-Nc reagent is comparable to that of the solution-based spectrophotometric cupric ion reducing antioxidant capacity (CUPRAC) assay. This electroanalytical method better tolerated sample turbidity and provided higher sensitivity (i.e., lower detection limits) in antioxidant determination than the spectrophotometric assay. The proposed method was successfully applied to the measurement of total antioxidant capacity (TAC) in some herbal tea samples such as green tea, sage, marjoram, and alchemilla. Results demonstrated that the proposed voltammetric method has precision and accuracy comparable to those of the spectrophotometric CUPRAC assay.

ARC-VM: An architecture real options complexity-based valuation methodology for military systems-of-systems acquisitions

NASA Astrophysics Data System (ADS)

Domercant, Jean Charles

The combination of today's national security environment and mandated acquisition policies makes it necessary for military systems to interoperate with each other to greater degrees. This growing interdependency results in complex Systems-of-Systems (SoS) that only continue to grow in complexity to meet evolving capability needs. Thus, timely and affordable acquisition becomes more difficult, especially in the face of mounting budgetary pressures. To counter this, architecting principles must be applied to SoS design. The research objective is to develop an Architecture Real Options Complexity-Based Valuation Methodology (ARC-VM) suitable for acquisition-level decision making, where there is a stated desire for more informed tradeoffs between cost, schedule, and performance during the early phases of design. First, a framework is introduced to measure architecture complexity as it directly relates to military SoS. Development of the framework draws upon a diverse set of disciplines, including Complexity Science, software architecting, measurement theory, and utility theory. Next, a Real Options based valuation strategy is developed using techniques established for financial stock options that have recently been adapted for use in business and engineering decisions. The derived complexity measure provides architects with an objective measure of complexity that focuses on relevant complex system attributes. These attributes are related to the organization and distribution of SoS functionality and the sharing and processing of resources. The use of Real Options provides the necessary conceptual and visual framework to quantifiably and traceably combine measured architecture complexity, time-valued performance levels, as well as programmatic risks and uncertainties. An example suppression of enemy air defenses (SEAD) capability demonstrates the development and usefulness of the resulting architecture complexity & Real Options based valuation methodology. Different portfolios of candidate system types are used to generate an array of architecture alternatives that are then evaluated using an engagement model. This performance data is combined with both measured architecture complexity and programmatic data to assign an acquisition value to each alternative. This proves useful when selecting alternatives most likely to meet current and future capability needs.

Simplified Pan-species Real-time PCR-based Detection of Plasmodium Spp. in Blood Smear.

PubMed

Hassanpour, Gholamreza; Mirhendi, Hossein; Mohebali, Mehdi; Raeisi, Ahmad; Zeraati, Hojjat; Keshavarz, Hossein

2016-01-01

We aimed to quicken and simplify the detection of Plasmodium in blood samples by developing and testing a pan- Plasmodium real-time PCR for accurate screening of individuals suspected of malaria. A single primer/probe set for pan-species Plasmodium -specific real time PCR targeting a conserved region of the small subunit 18S ribosomal DNA was designed and evaluated for rapid diagnosis and screening of malaria infections using dried blood smears. FTA cards were used for rapid and simple DNA extraction. The primers and probes showed a positive response with the DNA extracted from bloods infected with P. falciparum and P. vivax but not with DNA extracted from various smears from uninfected blood samples. Seven positive cases positive by both microscopy and nested PCR were found among 280 blood samples taken from in South and Southeast Iran. Five samples were identified as positive for P. vivax and two as positive for P. falciparum . All positive samples were positive by real-time PCR. Furthermore, all 38-blood samples positive by microscopy were positive by real-time PCR. No microscopy-negative samples were positive by real-time PCR. By using a simple FTA card for DNA extraction and by application of the real-time PCR developed in this study, sensitivity similar to nested-PCR and microscopy was achieved. This format simplifies the detection of Plasmodium in large numbers of samples.

Drawing at the Speed of Talk: doodling complex discussions in real-time to create animated ``Conversation Portraits''

NASA Astrophysics Data System (ADS)

Rosenberg, Flash

2012-02-01

What does your research look like as a drawing? Imagine the guy who delivered your pizza understanding the latest paper you delivered. Flash Rosenberg will describe how she ``live-draws'' discussions between prominent authors and scientists to create lucid animations. She will offer strategies for how to translate the impenetrable into the understandable, convert equations into sensations, and enable everyone to appreciate issues in physics as relevant, intriguing fun. View sample ``Conversation Portraits'' at http://vimeo.com/flashrosenberg/videos

Automated visual inspection for polished stone manufacture

NASA Astrophysics Data System (ADS)

Smith, Melvyn L.; Smith, Lyndon N.

2003-05-01

Increased globalisation of the ornamental stone market has lead to increased competition and more rigorous product quality requirements. As such, there are strong motivators to introduce new, more effective, inspection technologies that will help enable stone processors to reduce costs, improve quality and improve productivity. Natural stone surfaces may contain a mixture of complex two-dimensional (2D) patterns and three-dimensional (3D) features. The challenge in terms of automated inspection is to develop systems able to reliably identify 3D topographic defects, either naturally occurring or resulting from polishing, in the presence of concomitant complex 2D stochastic colour patterns. The resulting real-time analysis of the defects may be used in adaptive process control, in order to avoid the wasteful production of defective product. An innovative approach, using structured light and based upon an adaptation of the photometric stereo method, has been pioneered and developed at UWE to isolate and characterize mixed 2D and 3D surface features. The method is able to undertake tasks considered beyond the capabilities of existing surface inspection techniques. The approach has been successfully applied to real stone samples, and a selection of experimental results is presented.

Delayed vaccine virus replication in chickens vaccinated subcutaneously with an immune complex infectious bursal disease vaccine: Quantification of vaccine virus by real-time polymerase chain reaction

PubMed Central

2005-01-01

Abstract The distribution of the immune complex vaccine virus for infectious bursal disease (IBD) in tissue was examined and the viral loads of the organs were quantitatively compared. One-day-old specific pathogen free (SPF) and maternally immune broiler chickens were injected subcutaneously with the vaccine. Lymphoid and non-lymphoid tissues were collected at various time intervals during the experiment to test for infectious bursal disease virus (IBDV)-RNA by using reverse transcriptase-polymerase chain reaction (RT-PCR). Only the bursa of Fabricius was found to be positive with unusually long viral persistence in the broiler group. The positive bursa samples were further investigated by using real-time PCR coupled with a TaqMan probe. The highest amounts of the virus were detected at its first appearance in the bursa: on day 14 post vaccination (PV) in the SPF chickens and on day 17 and day 21 PV in the maternally immune broiler group. The virus then gradually cleared, most likely due to the parallel appearance of the active immune response indicated by seroconversion. PMID:15971678

Feature extraction using extrema sampling of discrete derivatives for spike sorting in implantable upper-limb neural prostheses.

PubMed

Zamani, Majid; Demosthenous, Andreas

2014-07-01

Next generation neural interfaces for upper-limb (and other) prostheses aim to develop implantable interfaces for one or more nerves, each interface having many neural signal channels that work reliably in the stump without harming the nerves. To achieve real-time multi-channel processing it is important to integrate spike sorting on-chip to overcome limitations in transmission bandwidth. This requires computationally efficient algorithms for feature extraction and clustering suitable for low-power hardware implementation. This paper describes a new feature extraction method for real-time spike sorting based on extrema analysis (namely positive peaks and negative peaks) of spike shapes and their discrete derivatives at different frequency bands. Employing simulation across different datasets, the accuracy and computational complexity of the proposed method are assessed and compared with other methods. The average classification accuracy of the proposed method in conjunction with online sorting (O-Sort) is 91.6%, outperforming all the other methods tested with the O-Sort clustering algorithm. The proposed method offers a better tradeoff between classification error and computational complexity, making it a particularly strong choice for on-chip spike sorting.

Kurtosis-Based Blind Source Extraction of Complex Non-Circular Signals with Application in EEG Artifact Removal in Real-Time

PubMed Central

Javidi, Soroush; Mandic, Danilo P.; Took, Clive Cheong; Cichocki, Andrzej

2011-01-01

A new class of complex domain blind source extraction algorithms suitable for the extraction of both circular and non-circular complex signals is proposed. This is achieved through sequential extraction based on the degree of kurtosis and in the presence of non-circular measurement noise. The existence and uniqueness analysis of the solution is followed by a study of fast converging variants of the algorithm. The performance is first assessed through simulations on well understood benchmark signals, followed by a case study on real-time artifact removal from EEG signals, verified using both qualitative and quantitative metrics. The results illustrate the power of the proposed approach in real-time blind extraction of general complex-valued sources. PMID:22319461

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

Complex dielectric properties of anhydrous polycrystalline glucose in the terahertz region

NASA Astrophysics Data System (ADS)

Sun, P.; Liu, W.; Zou, Y.; Jia, Qiong Z.; Li, Jia Y.

2015-03-01

We utilized terahertz time-domain spectroscopy (THz-TDS) to investigate the complex dielectric properties of solid polycrystalline material of anhydrous glucose (D-(+)-glucose with purity >99.9%). THz transmission spectra of samples were measured from 0.2 to 2.2 THz. The samples were prepared into tablets with thicknesses of 0.362, 0.447, 0.504, 0.522 and 0.626 mm, respectively. The imaginary part of the complex dielectric function of polycrystalline glucose showed that there were multiple characteristic absorption peaks at 1.232, 1.445, 1.522, 1.608, 1.811 and 1.987 THz, respectively. Moreover, for a given characteristic absorption peak, the real part of the complex dielectric function showed anomalous dispersion within the full width half maximum (FWHM) of the absorption peak. Both finite difference time-domain (FDTD) numerical simulations and experimental results showed that the complex dielectric function of anhydrous polycrystalline glucose fits well with the Lorentz dielectric mode. The plasma oscillation frequency was below the frequency of the light waves suggesting that the light waves passed through the polycrystalline glucose tablets. Calculations based on density functional theory (DFT) showed that the characteristic absorption peaks of polycrystalline glucose originated mainly from collective intermolecular vibrations such as hydrogen bonds and crystal phonon modes. The THz radiation can excite the vibrational or rotational energy levels of the biological macromolecules. This leads to changes in their spatial configuration or interactions. This study showed that THz-TDS has potential applications in biological and pharmaceutical research and food industry.

An innate immune system-mimicking, real-time biosensing of infectious bacteria.

PubMed

Seo, Sung-Min; Jeon, Jin-Woo; Kim, Tae-Yong; Paek, Se-Hwan

2015-09-07

An animal cell-based biosensor was investigated to monitor bacterial contamination in an unattended manner by mimicking the innate immune response. The cells (RAW 264.7 cell line) were first attached onto the solid surfaces of a 96-well microtiter plate and co-incubated in the culture medium with a sample that might contain bacterial contaminants. As Toll-like receptors were present on the cell membrane surfaces, they acted as a sentinel by binding to pathogen-associated molecular patterns (PAMPs) of any contaminant. Such biological recognition initiates signal transmission along various pathways to produce different proinflammatory mediators, one of which, tumor necrosis factor-α (TNF-α) was measured using an immunosensor. To demonstrate automated bacterium monitoring, a capture antibody specific for TNF-α was immobilized on an optical fiber sensor tip and then used to measure complex formation in a label-free sensor system (e.g., Octet Red). The sensor response time depended significantly on the degree of agitation of the culture medium, controlling the biological recognition and further autocrine/paracrine signaling by cytokines. The response, particularly under non-agitated conditions, was also influenced by the medium volume, revealing a local gradient change of the cytokine concentration and also acidity, caused by bacterial growth near the bottom surfaces. A biosensor system retaining 50 μL medium and not employing agitation could be used for the early detection of bacterial contamination. This novel biosensing model was applied to the real-time monitoring of different bacteria, Shigella sonnei, Staphylococcus aureus, and Listeria monocytogenes. They (<100 CFU mL(-1)) could be detected automatically within the working time. Such analysis was carried out without any manual handling regardless of the bacterial species, suggesting the concept of non-targeted bacterial real-time monitoring. This technique was further applied to real sample testing (e.g., with milk) to exemplify, for example, the food quality control process without using any additional sample pretreatment such as magnetic concentration.

Real time viability detection of bacterial spores

DOEpatents

Vanderberg, Laura A.; Herdendorf, Timothy J.; Obiso, Richard J.

2003-07-29

This invention relates to a process for detecting the presence of viable bacterial spores in a sample and to a spore detection system, the process including placing a sample in a germination medium for a period of time sufficient for commitment of any present viable bacterial spores to occur, mixing the sample with a solution of a lanthanide capable of forming a fluorescent complex with dipicolinic acid, and, measuring the sample for the presence of dipicolinic acid, and the system including a germination chamber having inlets from a sample chamber, a germinant chamber and a bleach chamber, the germination chamber further including an outlet through a filtering means, the outlet connected to a detection chamber, the detection chamber having an inlet from a fluorescence promoting metal chamber and the detection chamber including a spectral excitation source and a means of measuring emission spectra from a sample, the detection chamber further connected to a waste chamber. A germination reaction mixture useful for promoting commitment of any viable bacterial spores in a sample including a combination of L-alanine, L-asparagine and D-glucose is also described.

Sample preparation techniques for the determination of trace residues and contaminants in foods.

PubMed

Ridgway, Kathy; Lalljie, Sam P D; Smith, Roger M

2007-06-15

The determination of trace residues and contaminants in complex matrices, such as food, often requires extensive sample extraction and preparation prior to instrumental analysis. Sample preparation is often the bottleneck in analysis and there is a need to minimise the number of steps to reduce both time and sources of error. There is also a move towards more environmentally friendly techniques, which use less solvent and smaller sample sizes. Smaller sample size becomes important when dealing with real life problems, such as consumer complaints and alleged chemical contamination. Optimal sample preparation can reduce analysis time, sources of error, enhance sensitivity and enable unequivocal identification, confirmation and quantification. This review considers all aspects of sample preparation, covering general extraction techniques, such as Soxhlet and pressurised liquid extraction, microextraction techniques such as liquid phase microextraction (LPME) and more selective techniques, such as solid phase extraction (SPE), solid phase microextraction (SPME) and stir bar sorptive extraction (SBSE). The applicability of each technique in food analysis, particularly for the determination of trace organic contaminants in foods is discussed.

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

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.

Novel One-Tube-One-Step Real-Time Methodology for Rapid Transcriptomic Biomarker Detection: Signal Amplification by Ternary Initiation Complexes.

PubMed

Fujita, Hiroto; Kataoka, Yuka; Tobita, Seiji; Kuwahara, Masayasu; Sugimoto, Naoki

2016-07-19

We have developed a novel RNA detection method, termed signal amplification by ternary initiation complexes (SATIC), in which an analyte sample is simply mixed with the relevant reagents and allowed to stand for a short time under isothermal conditions (37 °C). The advantage of the technique is that there is no requirement for (i) heat annealing, (ii) thermal cycling during the reaction, (iii) a reverse transcription step, or (iv) enzymatic or mechanical fragmentation of the target RNA. SATIC involves the formation of a ternary initiation complex between the target RNA, a circular DNA template, and a DNA primer, followed by rolling circle amplification (RCA) to generate multiple copies of G-quadruplex (G4) on a long DNA strand like beads on a string. The G4s can be specifically fluorescence-stained with N(3)-hydroxyethyl thioflavin T (ThT-HE), which emits weakly with single- and double-stranded RNA/DNA but strongly with parallel G4s. An improved dual SATIC system, which involves the formation of two different ternary initiation complexes in the RCA process, exhibited a wide quantitative detection range of 1-5000 pM. Furthermore, this enabled visual observation-based RNA detection, which is more rapid and convenient than conventional isothermal methods, such as reverse transcription-loop-mediated isothermal amplification, signal mediated amplification of RNA technology, and RNA-primed rolling circle amplification. Thus, SATIC methodology may serve as an on-site and real-time measurement technique for transcriptomic biomarkers for various diseases.

The problem of complex eigensystems in the semianalytical solution for advancement of time in solute transport simulations: a new method using real arithmetic

USGS Publications Warehouse

Umari, Amjad M.J.; Gorelick, Steven M.

1986-01-01

In the numerical modeling of groundwater solute transport, explicit solutions may be obtained for the concentration field at any future time without computing concentrations at intermediate times. The spatial variables are discretized and time is left continuous in the governing differential equation. These semianalytical solutions have been presented in the literature and involve the eigensystem of a coefficient matrix. This eigensystem may be complex (i.e., have imaginary components) due to the asymmetry created by the advection term in the governing advection-dispersion equation. Previous investigators have either used complex arithmetic to represent a complex eigensystem or chosen large dispersivity values for which the imaginary components of the complex eigenvalues may be ignored without significant error. It is shown here that the error due to ignoring the imaginary components of complex eigenvalues is large for small dispersivity values. A new algorithm that represents the complex eigensystem by converting it to a real eigensystem is presented. The method requires only real arithmetic.

Evaluation of partial coherence correction in X-ray ptychography

DOE PAGES

Burdet, Nicolas; Shi, Xiaowen; Parks, Daniel; ...

2015-02-23

Coherent X-ray Diffraction Imaging (CDI) and X-ray ptychography both heavily rely on the high degree of spatial coherence of the X-ray illumination for sufficient experimental data quality for reconstruction convergence. Nevertheless, the majority of the available synchrotron undulator sources have a limited degree of partial coherence, leading to reduced data quality and a lower speckle contrast in the coherent diffraction patterns. It is still an open question whether experimentalists should compromise the coherence properties of an X-ray source in exchange for a higher flux density at a sample, especially when some materials of scientific interest are relatively weak scatterers. Amore » previous study has suggested that in CDI, the best strategy for the study of strong phase objects is to maintain a high degree of coherence of the illuminating X-rays because of the broadening of solution space resulting from the strong phase structures. In this article, we demonstrate the first systematic analysis of the effectiveness of partial coherence correction in ptychography as a function of the coherence properties, degree of complexity of illumination (degree of phase diversity of the probe) and sample phase complexity. We have also performed analysis of how well ptychographic algorithms refine X-ray probe and complex coherence functions when those variables are unknown at the start of reconstructions, for noise-free simulated data, in the case of both real-valued and highly-complex objects.« less

Molecular Diagnosis of Invasive Aspergillosis and Detection of Azole Resistance by a Newly Commercialized PCR Kit

PubMed Central

Gabriel, Frédéric; Gaboyard, Manuel; Lagardere, Gaëlle; Audebert, Lucile; Quesne, Gilles; Godichaud, Sandrine; Verweij, Paul E.; Accoceberry, Isabelle

2017-01-01

ABSTRACT Aspergillus fumigatus is the main species responsible for aspergillosis in humans. The diagnosis of aspergillosis remains difficult, and the rapid emergence of azole resistance in A. fumigatus is worrisome. The aim of this study was to validate the new MycoGENIE A. fumigatus real-time PCR kit and to evaluate its performance on clinical samples for the detection of A. fumigatus and its azole resistance. This multiplex assay detects DNA from the A. fumigatus species complex by targeting the multicopy 28S rRNA gene and specific TR34 and L98H mutations in the single-copy-number cyp51A gene of A. fumigatus. The specificity of cyp51A mutation detection was assessed by testing DNA samples from 25 wild-type or mutated clinical A. fumigatus isolates. Clinical validation was performed on 88 respiratory samples obtained from 62 patients and on 69 serum samples obtained from 16 patients with proven or probable aspergillosis and 13 patients without aspergillosis. The limit of detection was <1 copy for the Aspergillus 28S rRNA gene and 6 copies for the cyp51A gene harboring the TR34 and L98H alterations. No cross-reactivity was detected with various fungi and bacteria. All isolates harboring the TR34 and L98H mutations were accurately detected by quantitative PCR (qPCR) analysis. With respiratory samples, qPCR results showed a sensitivity and specificity of 92.9% and 90.1%, respectively, while with serum samples, the sensitivity and specificity were 100% and 84.6%, respectively. Our study demonstrated that this new real-time PCR kit enables sensitive and rapid detection of A. fumigatus DNA and azole resistance due to TR34 and L98H mutations in clinical samples. PMID:28814586

Classification of subsurface objects using singular values derived from signal frames

DOEpatents

Chambers, David H; Paglieroni, David W

2014-05-06

The classification system represents a detected object with a feature vector derived from the return signals acquired by an array of N transceivers operating in multistatic mode. The classification system generates the feature vector by transforming the real-valued return signals into complex-valued spectra, using, for example, a Fast Fourier Transform. The classification system then generates a feature vector of singular values for each user-designated spectral sub-band by applying a singular value decomposition (SVD) to the N.times.N square complex-valued matrix formed from sub-band samples associated with all possible transmitter-receiver pairs. The resulting feature vector of singular values may be transformed into a feature vector of singular value likelihoods and then subjected to a multi-category linear or neural network classifier for object classification.

Selective and sensitive speciation analysis of Cr(VI) and Cr(III), at sub-μgL-1 levels in water samples by electrothermal atomic absorption spectrometry after electromembrane extraction.

PubMed

Tahmasebi, Zeinab; Davarani, Saied Saeed Hosseiny

2016-12-01

In this work, electromembrane extraction in combination with electrothermal atomic absorption spectrometry (ET-AAS) was investigated for speciation, preconcentration and quantification of Cr(VI) and Cr(III) in water samples through the selective complexation of Cr(VI) with 1,5-diphenylcarbazide (DPC) as a complexing agent. DPC reduces Cr(VI) to Cr(III) ions and then Cr(III) species are extracted based on electrokinetic migration of their cationic complex (Cr(III)-DPC) toward the negative electrode placed in the hollow fiber. Also, once oxidized to Cr(VI), Cr(III) ions in initial sample were determined by this procedure. The influence of extraction parameters such as pH, type of organic solvent, chelating agent concentration, stirring rate, extraction time and applied voltage were evaluated following a one-at-a-time optimization approach. Under optimized conditions, the extracted analyte was quantified by ETAAS, with an acceptable linearity in the range of 0.05-5ngmL -1 (R 2 value=0.996), and a repeatability (%RSD) between 3.7% and 12.2% (n=4) for 5.0 and 1.0ngmL -1 of Cr(VI), respectively. Also, we obtained an enrichment factor of 110 that corresponded to the recovery of 66%. The detection limit (S/N ratio of 3:1) was 0.02ngmL -1 . Finally, this new method was successfully employed to determine Cr(III) and Cr(VI) species in real water samples. Copyright © 2016. Published by Elsevier B.V.

A nonlinear dynamic age-structured model of e-commerce in spain: Stability analysis of the equilibrium by delay and stochastic perturbations

NASA Astrophysics Data System (ADS)

Burgos, C.; Cortés, J.-C.; Shaikhet, L.; Villanueva, R.-J.

2018-11-01

First, we propose a deterministic age-structured epidemiological model to study the diffusion of e-commerce in Spain. Afterwards, we determine the parameters (death, birth and growth rates) of the underlying demographic model as well as the parameters (transmission of the use of e-commerce rates) of the proposed epidemiological model that best fit real data retrieved from the Spanish National Statistical Institute. Motivated by the two following facts: first the dynamics of acquiring the use of a new technology as e-commerce is mainly driven by the feedback after interacting with our peers (family, friends, mates, mass media, etc.), hence having a certain delay, and second the inherent uncertainty of sampled real data and the social complexity of the phenomena under analysis, we introduce aftereffect and stochastic perturbations in the initial deterministic model. This leads to a delayed stochastic model for e-commerce. We then investigate sufficient conditions in order to guarantee the stability in probability of the equilibrium point of the dynamic e-commerce delayed stochastic model. Our theoretical findings are numerically illustrated using real data.

An approximate Riemann solver for real gas parabolized Navier-Stokes equations

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

Urbano, Annafederica, E-mail: annafederica.urbano@uniroma1.it; Nasuti, Francesco, E-mail: francesco.nasuti@uniroma1.it

2013-01-15

Under specific assumptions, parabolized Navier-Stokes equations are a suitable mean to study channel flows. A special case is that of high pressure flow of real gases in cooling channels where large crosswise gradients of thermophysical properties occur. To solve the parabolized Navier-Stokes equations by a space marching approach, the hyperbolicity of the system of governing equations is obtained, even for very low Mach number flow, by recasting equations such that the streamwise pressure gradient is considered as a source term. For this system of equations an approximate Roe's Riemann solver is developed as the core of a Godunov type finitemore » volume algorithm. The properties of the approximated Riemann solver, which is a modification of Roe's Riemann solver for the parabolized Navier-Stokes equations, are presented and discussed with emphasis given to its original features introduced to handle fluids governed by a generic real gas EoS. Sample solutions are obtained for low Mach number high compressible flows of transcritical methane, heated in straight long channels, to prove the solver ability to describe flows dominated by complex thermodynamic phenomena.« less

Quantum theory in real Hilbert space: How the complex Hilbert space structure emerges from Poincaré symmetry

NASA Astrophysics Data System (ADS)

Moretti, Valter; Oppio, Marco

As earlier conjectured by several authors and much later established by Solèr (relying on partial results by Piron, Maeda-Maeda and other authors), from the lattice theory point of view, Quantum Mechanics may be formulated in real, complex or quaternionic Hilbert spaces only. Stückelberg provided some physical, but not mathematically rigorous, reasons for ruling out the real Hilbert space formulation, assuming that any formulation should encompass a statement of Heisenberg principle. Focusing on this issue from another — in our opinion, deeper — viewpoint, we argue that there is a general fundamental reason why elementary quantum systems are not described in real Hilbert spaces. It is their basic symmetry group. In the first part of the paper, we consider an elementary relativistic system within Wigner’s approach defined as a locally-faithful irreducible strongly-continuous unitary representation of the Poincaré group in a real Hilbert space. We prove that, if the squared-mass operator is non-negative, the system admits a natural, Poincaré invariant and unique up to sign, complex structure which commutes with the whole algebra of observables generated by the representation itself. This complex structure leads to a physically equivalent reformulation of the theory in a complex Hilbert space. Within this complex formulation, differently from what happens in the real one, all selfadjoint operators represent observables in accordance with Solèr’s thesis, and the standard quantum version of Noether theorem may be formulated. In the second part of this work, we focus on the physical hypotheses adopted to define a quantum elementary relativistic system relaxing them on the one hand, and making our model physically more general on the other hand. We use a physically more accurate notion of irreducibility regarding the algebra of observables only, we describe the symmetries in terms of automorphisms of the restricted lattice of elementary propositions of the quantum system and we adopt a notion of continuity referred to the states viewed as probability measures on the elementary propositions. Also in this case, the final result proves that there exists a unique (up to sign) Poincaré invariant complex structure making the theory complex and completely fitting into Solèr’s picture. This complex structure reveals a nice interplay of Poincaré symmetry and the classification of the commutant of irreducible real von Neumann algebras.

Real-time simulation of the nonlinear visco-elastic deformations of soft tissues.

PubMed

Basafa, Ehsan; Farahmand, Farzam

2011-05-01

Mass-spring-damper (MSD) models are often used for real-time surgery simulation due to their fast response and fairly realistic deformation replication. An improved real time simulation model of soft tissue deformation due to a laparoscopic surgical indenter was developed and tested. The mechanical realization of conventional MSD models was improved using nonlinear springs and nodal dampers, while their high computational efficiency was maintained using an adapted implicit integration algorithm. New practical algorithms for model parameter tuning, collision detection, and simulation were incorporated. The model was able to replicate complex biological soft tissue mechanical properties under large deformations, i.e., the nonlinear and viscoelastic behaviors. The simulated response of the model after tuning of its parameters to the experimental data of a deer liver sample, closely tracked the reference data with high correlation and maximum relative differences of less than 5 and 10%, for the tuning and testing data sets respectively. Finally, implementation of the proposed model and algorithms in a graphical environment resulted in a real-time simulation with update rates of 150 Hz for interactive deformation and haptic manipulation, and 30 Hz for visual rendering. The proposed real time simulation model of soft tissue deformation due to a laparoscopic surgical indenter was efficient, realistic, and accurate in ex vivo testing. This model is a suitable candidate for testing in vivo during laparoscopic surgery.

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.

Simplified Pan-species Real-time PCR-based Detection of Plasmodium Spp. in Blood Smear

PubMed Central

HASSANPOUR, Gholamreza; MIRHENDI, Hossein; MOHEBALI, Mehdi; RAEISI, Ahmad; ZERAATI, Hojjat; KESHAVARZ, Hossein

2016-01-01

Background: We aimed to quicken and simplify the detection of Plasmodium in blood samples by developing and testing a pan-Plasmodium real-time PCR for accurate screening of individuals suspected of malaria. Methods: A single primer/probe set for pan-species Plasmodium-specific real time PCR targeting a conserved region of the small subunit 18S ribosomal DNA was designed and evaluated for rapid diagnosis and screening of malaria infections using dried blood smears. FTA cards were used for rapid and simple DNA extraction. Results: The primers and probes showed a positive response with the DNA extracted from bloods infected with P. falciparum and P. vivax but not with DNA extracted from various smears from uninfected blood samples. Seven positive cases positive by both microscopy and nested PCR were found among 280 blood samples taken from in South and Southeast Iran. Five samples were identified as positive for P. vivax and two as positive for P. falciparum. All positive samples were positive by real-time PCR. Furthermore, all 38-blood samples positive by microscopy were positive by real-time PCR. No microscopy-negative samples were positive by real-time PCR. Conclusion: By using a simple FTA card for DNA extraction and by application of the real-time PCR developed in this study, sensitivity similar to nested-PCR and microscopy was achieved. This format simplifies the detection of Plasmodium in large numbers of samples. PMID:28127357

Phase Imaging: A Compressive Sensing Approach

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

Schneider, Sebastian; Stevens, Andrew; Browning, Nigel D.

Since Wolfgang Pauli posed the question in 1933, whether the probability densities |Ψ(r)|² (real-space image) and |Ψ(q)|² (reciprocal space image) uniquely determine the wave function Ψ(r) [1], the so called Pauli Problem sparked numerous methods in all fields of microscopy [2, 3]. Reconstructing the complete wave function Ψ(r) = a(r)e-iφ(r) with the amplitude a(r) and the phase φ(r) from the recorded intensity enables the possibility to directly study the electric and magnetic properties of the sample through the phase. In transmission electron microscopy (TEM), electron holography is by far the most established method for phase reconstruction [4]. Requiring a highmore » stability of the microscope, next to the installation of a biprism in the TEM, holography cannot be applied to any microscope straightforwardly. Recently, a phase retrieval approach was proposed using conventional TEM electron diffractive imaging (EDI). Using the SAD aperture as reciprocal-space constraint, a localized sample structure can be reconstructed from its diffraction pattern and a real-space image using the hybrid input-output algorithm [5]. We present an alternative approach using compressive phase-retrieval [6]. Our approach does not require a real-space image. Instead, random complimentary pairs of checkerboard masks are cut into a 200 nm Pt foil covering a conventional TEM aperture (cf. Figure 1). Used as SAD aperture, subsequently diffraction patterns are recorded from the same sample area. Hereby every mask blocks different parts of gold particles on a carbon support (cf. Figure 2). The compressive sensing problem has the following formulation. First, we note that the complex-valued reciprocal-space wave-function is the Fourier transform of the (also complex-valued) real-space wave-function, Ψ(q) = F[Ψ(r)], and subsequently the diffraction pattern image is given by |Ψ(q)|2 = |F[Ψ(r)]|2. We want to find Ψ(r) given a few differently coded diffraction pattern measurements yn = |F[HnΨ(r)]|2, where the matrices Hn encode the mask structure of the aperture. This is a nonlinear inverse problem, but has been shown to be solvable even in the underdetermined case [6]. Since each diffraction pattern yn contains diffraction information from selected regions of the same sample, the differences in each pattern contain local phase information, which can be combined to form a full estimate of the real-space wave-function[7]. References: [1] W. Pauli in “Die allgemeinen Prinzipien der Wellenmechanik“, ed. H Geiger and W Scheel, (Julius Springer, Berlin). [2] A. Tonomura, Rev. Mod. Phys. 59 (1987), p. 639. [3] J. Miao et al, Nature 400 (1999), p. 342. [4] H. Lichte et al, Annu. Rev. Mater. Res. 37 (2007), p. 539. [5] J. Yamasaki et al, Appl. Phys. Lett. 101 (2012), 234105. [6] P Schniter and S Rangan. Signal Proc., IEEE Trans. on. 64(4), (2015), pp. 1043. [7] Supported by the Chemical Imaging, Signature Discovery, and Analytics in Motion initiatives at PNNL. PNNL is operated by Battelle Memorial Inst. for the US DOE; contract DE-AC05-76RL01830.« less

A General Framework for Thermodynamically Consistent Parameterization and Efficient Sampling of Enzymatic Reactions

PubMed Central

Saa, Pedro; Nielsen, Lars K.

2015-01-01

Kinetic models provide the means to understand and predict the dynamic behaviour of enzymes upon different perturbations. Despite their obvious advantages, classical parameterizations require large amounts of data to fit their parameters. Particularly, enzymes displaying complex reaction and regulatory (allosteric) mechanisms require a great number of parameters and are therefore often represented by approximate formulae, thereby facilitating the fitting but ignoring many real kinetic behaviours. Here, we show that full exploration of the plausible kinetic space for any enzyme can be achieved using sampling strategies provided a thermodynamically feasible parameterization is used. To this end, we developed a General Reaction Assembly and Sampling Platform (GRASP) capable of consistently parameterizing and sampling accurate kinetic models using minimal reference data. The former integrates the generalized MWC model and the elementary reaction formalism. By formulating the appropriate thermodynamic constraints, our framework enables parameterization of any oligomeric enzyme kinetics without sacrificing complexity or using simplifying assumptions. This thermodynamically safe parameterization relies on the definition of a reference state upon which feasible parameter sets can be efficiently sampled. Uniform sampling of the kinetics space enabled dissecting enzyme catalysis and revealing the impact of thermodynamics on reaction kinetics. Our analysis distinguished three reaction elasticity regions for common biochemical reactions: a steep linear region (0> ΔGr >-2 kJ/mol), a transition region (-2> ΔGr >-20 kJ/mol) and a constant elasticity region (ΔGr <-20 kJ/mol). We also applied this framework to model more complex kinetic behaviours such as the monomeric cooperativity of the mammalian glucokinase and the ultrasensitive response of the phosphoenolpyruvate carboxylase of Escherichia coli. In both cases, our approach described appropriately not only the kinetic behaviour of these enzymes, but it also provided insights about the particular features underpinning the observed kinetics. Overall, this framework will enable systematic parameterization and sampling of enzymatic reactions. PMID:25874556

Wide-field surface plasmon microscopy of nano- and microparticles: features, benchmarking, limitations, and bioanalytical applications

NASA Astrophysics Data System (ADS)

Nizamov, Shavkat; Scherbahn, Vitali; Mirsky, Vladimir M.

2017-05-01

Detection of nano- and micro-particles is an important task for chemical analytics, food industry, biotechnology, environmental monitoring and many other fields of science and industry. For this purpose, a method based on the detection and analysis of minute signals in surface plasmon resonance images due to adsorption of single nanopartciles was developed. This new technology allows one a real-time detection of interaction of single nano- and micro-particles with sensor surface. Adsorption of each nanoparticle leads to characteristic diffraction image whose intensity depends on the size and chemical composition of the particle. The adsorption rate characterizes volume concentration of nano- and micro-particles. Large monitored surface area of sensor enables a high dynamic range of counting and to a correspondingly high dynamic range in concentration scale. Depending on the type of particles and experimental conditions, the detection limit for aqueous samples can be below 1000 particles per microliter. For application of method in complex media, nanoparticle images are discriminated from image perturbations due to matrix components. First, the characteristic SPRM images of nanoparticles (templates) are collected in aqueous suspensions or spiked real samples. Then, the detection of nanoparticles in complex media using template matching is performed. The detection of various NPs in consumer products like cosmetics, mineral water, juices, and wines was shown at sub-ppb level. The method can be applied for ultrasensitive detection and analysis of nano- and micro-particles of biological (bacteria, viruses, endosomes), biotechnological (liposomes, protein nanoparticles for drug delivery) or technical origin.

Idiosyncratic responding during movie-watching predicted by age differences in attentional control

PubMed Central

Campbell, Karen L.; Shafto, Meredith A.; Wright, Paul; Tsvetanov, Kamen A.; Geerligs, Linda; Cusack, Rhodri; Tyler, Lorraine K.; Brayne, Carol; Bullmore, Ed; Calder, Andrew; Cusack, Rhodri; Dalgleish, Tim; Duncan, John; Henson, Rik; Matthews, Fiona; Marslen-Wilson, William; Rowe, James; Shafto, Meredith; Campbell, Karen; Cheung, Teresa; Davis, Simon; Geerligs, Linda; Kievit, Rogier; McCarrey, Anna; Price, Darren; Taylor, Jason; Tsvetanov, Kamen; Williams, Nitin; Bates, Lauren; Emery, Tina; Erzinçlioglu, Sharon; Gadie, Andrew; Gerbase, Sofia; Georgieva, Stanimira; Hanley, Claire; Parkin, Beth; Troy, David; Allen, Jodie; Amery, Gillian; Amunts, Liana; Barcroft, Anne; Castle, Amanda; Dias, Cheryl; Dowrick, Jonathan; Fair, Melissa; Fisher, Hayley; Goulding, Anna; Grewal, Adarsh; Hale, Geoff; Hilton, Andrew; Johnson, Frances; Johnston, Patricia; Kavanagh-Williamson, Thea; Kwasniewska, Magdalena; McMinn, Alison; Norman, Kim; Penrose, Jessica; Roby, Fiona; Rowland, Diane; Sargeant, John; Squire, Maggie; Stevens, Beth; Stoddart, Aldabra; Stone, Cheryl; Thompson, Tracy; Yazlik, Ozlem; Dixon, Marie; Barnes, Dan; Hillman, Jaya; Mitchell, Joanne; Villis, Laura; Tyler, Lorraine K.

2015-01-01

Much is known about how age affects the brain during tightly controlled, though largely contrived, experiments, but do these effects extrapolate to everyday life? Naturalistic stimuli, such as movies, closely mimic the real world and provide a window onto the brain's ability to respond in a timely and measured fashion to complex, everyday events. Young adults respond to these stimuli in a highly synchronized fashion, but it remains to be seen how age affects neural responsiveness during naturalistic viewing. To this end, we scanned a large (N = 218), population-based sample from the Cambridge Centre for Ageing and Neuroscience (Cam-CAN) during movie-watching. Intersubject synchronization declined with age, such that older adults' response to the movie was more idiosyncratic. This decreased synchrony related to cognitive measures sensitive to attentional control. Our findings suggest that neural responsivity changes with age, which likely has important implications for real-world event comprehension and memory. PMID:26359527

Visible to near-infrared refractive properties of freshly-excised human-liver tissues: marking hepatic malignancies

PubMed Central

Giannios, Panagiotis; Toutouzas, Konstantinos G.; Matiatou, Maria; Stasinos, Konstantinos; Konstadoulakis, Manousos M.; Zografos, George C.; Moutzouris, Konstantinos

2016-01-01

The refractive index is an optical constant that plays a significant role in the description of light-matter interactions. When it comes to biological media, refraction is understudied despite recent advances in the field of bio-optics. In the present article, we report on the measurement of the refractive properties of freshly excised healthy and cancerous human liver samples, by use of a prism-coupling technique covering the visible and near-infrared spectral range. Novel data on the wavelength-dependent complex refractive index of human liver tissues are presented. The magnitude of the real and imaginary part of the refractive index is correlated with hepatic pathology. Notably, the real index contrast is pointed out as a marker of discrimination between normal liver tissue and hepatic metastases. In view of the current progress in optical biosensor technologies, our findings may be exploited for the development of novel surgical and endoscopic tools. PMID:27297034

Multivariate analysis of standoff laser-induced breakdown spectroscopy spectra for classification of explosive-containing residues

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

De Lucia, Frank C. Jr.; Gottfried, Jennifer L.; Munson, Chase A.

2008-11-01

A technique being evaluated for standoff explosives detection is laser-induced breakdown spectroscopy (LIBS). LIBS is a real-time sensor technology that uses components that can be configured into a ruggedized standoff instrument. The U.S. Army Research Laboratory has been coupling standoff LIBS spectra with chemometrics for several years now in order to discriminate between explosives and nonexplosives. We have investigated the use of partial least squares discriminant analysis (PLS-DA) for explosives detection. We have extended our study of PLS-DA to more complex sample types, including binary mixtures, different types of explosives, and samples not included in the model. We demonstrate themore » importance of building the PLS-DA model by iteratively testing it against sample test sets. Independent test sets are used to test the robustness of the final model.« less

Comparison effects and dielectric properties of different dose methylene-blue-doped hydrogels.

PubMed

Yalçın, O; Coşkun, R; Okutan, M; Öztürk, M

2013-08-01

The dielectric properties of methylene blue (MB)-doped hydrogels were investigated by impedance spectroscopy. The real part (ε') and the imaginary part (ε") of the complex dielectric constant and the energy loss tangent/dissipation factor (tan δ) were measured in the frequency range of 10 Hz to 100 MHz at room temperature for pH 5.5 value. Frequency variations of the resistance, the reactance, and the impedance of the samples have also been investigated. The dielectric permittivity of the MB-doped hydrogels is sensitive to ionic conduction and electrode polarization in low frequency. Furthermore, the dielectric behavior in high-frequency parts was attributed to the Brownian motion of the hydrogen bonds. The ionic conduction for MB-doped samples was prevented for Cole-Cole plots, while the Cole-Cole plots for pure sample show equivalent electrical circuit. The alternative current (ac) conductivity increases with the increasing MB concentration and the frequency.

Learning Bayesian Networks from Correlated Data

NASA Astrophysics Data System (ADS)

Bae, Harold; Monti, Stefano; Montano, Monty; Steinberg, Martin H.; Perls, Thomas T.; Sebastiani, Paola

2016-05-01

Bayesian networks are probabilistic models that represent complex distributions in a modular way and have become very popular in many fields. There are many methods to build Bayesian networks from a random sample of independent and identically distributed observations. However, many observational studies are designed using some form of clustered sampling that introduces correlations between observations within the same cluster and ignoring this correlation typically inflates the rate of false positive associations. We describe a novel parameterization of Bayesian networks that uses random effects to model the correlation within sample units and can be used for structure and parameter learning from correlated data without inflating the Type I error rate. We compare different learning metrics using simulations and illustrate the method in two real examples: an analysis of genetic and non-genetic factors associated with human longevity from a family-based study, and an example of risk factors for complications of sickle cell anemia from a longitudinal study with repeated measures.

Microfluidics-based integrated airborne pathogen detection systems

NASA Astrophysics Data System (ADS)

Northrup, M. Allen; Alleman-Sposito, Jennifer; Austin, Todd; Devitt, Amy; Fong, Donna; Lin, Phil; Nakao, Brian; Pourahmadi, Farzad; Vinas, Mary; Yuan, Bob

2006-09-01

Microfluidic Systems is focused on building microfluidic platforms that interface front-end mesofluidics to handle real world sample volumes for optimal sensitivity coupled to microfluidic circuitry to process small liquid volumes for complex reagent metering, mixing, and biochemical analysis, particularly for pathogens. MFSI is the prime contractor on two programs for the US Department of Homeland Security: BAND (Bioagent Autonomous Networked Detector) and IBADS (Instantaneous Bio-Aerosol Detection System). The goal of BAND is to develop an autonomous system for monitoring the air for known biological agents. This consists of air collection, sample lysis, sample purification, detection of DNA, RNA, and toxins, and a networked interface to report the results. For IBADS, MFSI is developing the confirmatory device which must verify the presence of a pathogen with 5 minutes of an air collector/trigger sounding an alarm. Instrument designs and biological assay results from both BAND and IBADS will be presented.

Time dependent semiclassical tunneling through one dimensional barriers using only real valued trajectories

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

Herman, Michael F.

2015-10-28

The time independent semiclassical treatment of barrier tunneling has been understood for a very long time. Several semiclassical approaches to time dependent tunneling through barriers have also been presented. These typically involve trajectories for which the position variable is a complex function of time. In this paper, a method is presented that uses only real valued trajectories, thus avoiding the complications that can arise when complex trajectories are employed. This is accomplished by expressing the time dependent wave packet as an integration over momentum. The action function in the exponent in this expression is expanded to second order in themore » momentum. The expansion is around the momentum, p{sub 0{sup *}}, at which the derivative of the real part of the action is zero. The resulting Gaussian integral is then taken. The stationary phase approximation requires that the derivative of the full action is zero at the expansion point, and this leads to a complex initial momentum and complex tunneling trajectories. The “pseudo-stationary phase” approximation employed in this work results in real values for the initial momentum and real valued trajectories. The transmission probabilities obtained are found to be in good agreement with exact quantum results.« less

Profiling and classification of French propolis by combined multivariate data analysis of planar chromatograms and scanning direct analysis in real time mass spectra.

PubMed

Chasset, Thibaut; Häbe, Tim T; Ristivojevic, Petar; Morlock, Gertrud E

2016-09-23

Quality control of propolis is challenging, as it is a complex natural mixture of compounds, and thus, very difficult to analyze and standardize. Shown on the example of 30 French propolis samples, a strategy for an improved quality control was demonstrated in which high-performance thin-layer chromatography (HPTLC) fingerprints were evaluated in combination with selected mass signals obtained by desorption-based scanning mass spectrometry (MS). The French propolis sample extracts were separated by a newly developed reversed phase (RP)-HPTLC method. The fingerprints obtained by two different detection modes, i.e. after (1) derivatization and fluorescence detection (FLD) at UV 366nm and (2) scanning direct analysis in real time (DART)-MS, were analyzed by multivariate data analysis. Thus, RP-HPTLC-FLD and RP-HPTLC-DART-MS fingerprints were explored and the best classification was obtained using both methods in combination with pattern recognition techniques, such as principal component analysis. All investigated French propolis samples were divided in two types and characteristic patterns were observed. Phenolic compounds such as caffeic acid, p-coumaric acid, chrysin, pinobanksin, pinobanksin-3-acetate, galangin, kaempferol, tectochrysin and pinocembrin were identified as characteristic marker compounds of French propolis samples. This study expanded the research on the European poplar type of propolis and confirmed the presence of two botanically different types of propolis, known as the blue and orange types. Copyright © 2016 Elsevier B.V. All rights reserved.

Wastewater Biosolid Composting Optimization Based on UV-VNIR Spectroscopy Monitoring

PubMed Central

Temporal-Lara, Beatriz; Melendez-Pastor, Ignacio; Gómez, Ignacio; Navarro-Pedreño, Jose

2016-01-01

Conventional wastewater treatment generates large amounts of organic matter–rich sludge that requires adequate treatment to avoid public health and environmental problems. The mixture of wastewater sludge and some bulking agents produces a biosolid to be composted at adequate composting facilities. The composting process is chemically and microbiologically complex and requires an adequate aeration of the biosolid (e.g., with a turner machine) for proper maturation of the compost. Adequate (near) real-time monitoring of the compost maturity process is highly difficult and the operation of composting facilities is not as automatized as other industrial processes. Spectroscopic analysis of compost samples has been successfully employed for compost maturity assessment but the preparation of the solid compost samples is difficult and time-consuming. This manuscript presents a methodology based on a combination of a less time-consuming compost sample preparation and ultraviolet, visible and short-wave near-infrared spectroscopy. Spectroscopic measurements were performed with liquid compost extract instead of solid compost samples. Partial least square (PLS) models were developed to quantify chemical fractions commonly employed for compost maturity assessment. Effective regression models were obtained for total organic matter (residual predictive deviation—RPD = 2.68), humification ratio (RPD = 2.23), total exchangeable carbon (RPD = 2.07) and total organic carbon (RPD = 1.66) with a modular and cost-effective visible and near infrared (VNIR) spectroradiometer. This combination of a less time-consuming compost sample preparation with a versatile sensor system provides an easy-to-implement, efficient and cost-effective protocol for compost maturity assessment and near-real-time monitoring. PMID:27854280

Wastewater Biosolid Composting Optimization Based on UV-VNIR Spectroscopy Monitoring.

PubMed

Temporal-Lara, Beatriz; Melendez-Pastor, Ignacio; Gómez, Ignacio; Navarro-Pedreño, Jose

2016-11-15

Conventional wastewater treatment generates large amounts of organic matter-rich sludge that requires adequate treatment to avoid public health and environmental problems. The mixture of wastewater sludge and some bulking agents produces a biosolid to be composted at adequate composting facilities. The composting process is chemically and microbiologically complex and requires an adequate aeration of the biosolid (e.g., with a turner machine) for proper maturation of the compost. Adequate (near) real-time monitoring of the compost maturity process is highly difficult and the operation of composting facilities is not as automatized as other industrial processes. Spectroscopic analysis of compost samples has been successfully employed for compost maturity assessment but the preparation of the solid compost samples is difficult and time-consuming. This manuscript presents a methodology based on a combination of a less time-consuming compost sample preparation and ultraviolet, visible and short-wave near-infrared spectroscopy. Spectroscopic measurements were performed with liquid compost extract instead of solid compost samples. Partial least square (PLS) models were developed to quantify chemical fractions commonly employed for compost maturity assessment. Effective regression models were obtained for total organic matter (residual predictive deviation-RPD = 2.68), humification ratio (RPD = 2.23), total exchangeable carbon (RPD = 2.07) and total organic carbon (RPD = 1.66) with a modular and cost-effective visible and near infrared (VNIR) spectroradiometer. This combination of a less time-consuming compost sample preparation with a versatile sensor system provides an easy-to-implement, efficient and cost-effective protocol for compost maturity assessment and near-real-time monitoring.

Failure to Replicate a Genetic Association May Provide Important Clues About Genetic Architecture

PubMed Central

Greene, Casey S.; Penrod, Nadia M.; Williams, Scott M.; Moore, Jason H.

2009-01-01

Replication has become the gold standard for assessing statistical results from genome-wide association studies. Unfortunately this replication requirement may cause real genetic effects to be missed. A real result can fail to replicate for numerous reasons including inadequate sample size or variability in phenotype definitions across independent samples. In genome-wide association studies the allele frequencies of polymorphisms may differ due to sampling error or population differences. We hypothesize that some statistically significant independent genetic effects may fail to replicate in an independent dataset when allele frequencies differ and the functional polymorphism interacts with one or more other functional polymorphisms. To test this hypothesis, we designed a simulation study in which case-control status was determined by two interacting polymorphisms with heritabilities ranging from 0.025 to 0.4 with replication sample sizes ranging from 400 to 1600 individuals. We show that the power to replicate the statistically significant independent main effect of one polymorphism can drop dramatically with a change of allele frequency of less than 0.1 at a second interacting polymorphism. We also show that differences in allele frequency can result in a reversal of allelic effects where a protective allele becomes a risk factor in replication studies. These results suggest that failure to replicate an independent genetic effect may provide important clues about the complexity of the underlying genetic architecture. We recommend that polymorphisms that fail to replicate be checked for interactions with other polymorphisms, particularly when samples are collected from groups with distinct ethnic backgrounds or different geographic regions. PMID:19503614

Fabrication of diverse pH-sensitive functional mesoporous silica for selective removal or depletion of highly abundant proteins from biological samples.

PubMed

Wang, Jiaojiao; Lan, Jingfeng; Li, Huihui; Liu, Xiaoyan; Zhang, Haixia

2017-01-01

In proteomic studies, poor detection of low abundant proteins is a major problem due to the presence of highly abundant proteins. Therefore, the specific removal or depletion of highly abundant proteins prior to analysis is necessary. In response to this problem, a series of pH-sensitive functional mesoporous silica materials composed of 2-(diethylamino)ethyl methacrylate and methacrylic acid units were designed and synthesized via atom transfer radical polymerization. These functional mesoporous silica materials were characterized and their ability for adsorption and separation of proteins was evaluated. Possessing a pH-sensitive feature, the synthesized functional materials showed selective adsorption of some proteins in aqueous or buffer solutions at certain pH values. The specific removal of a particular protein from a mixed protein solution was subsequently studied. The analytical results confirmed that all the target proteins (bovine serum albumin, ovalbumin, and lysozyme) can be removed by the proposed materials from a five-protein mixture in a single operation. Finally, the practical application of this approach was also evaluated by the selective removal of certain proteins from real biological samples. The results revealed that the maximum removal efficiencies of ovalbumin and lysozyme from egg white sample were obtained as 99% and 92%, respectively, while the maximum removal efficiency of human serum albumin from human serum sample was about 80% by the proposed method. It suggested that this treatment process reduced the complexity of real biological samples and facilitated the identification of hidden proteins in chromatograms. Copyright © 2016 Elsevier B.V. All rights reserved.

High-resolution correlation

NASA Astrophysics Data System (ADS)

Nelson, D. J.

2007-09-01

In the basic correlation process a sequence of time-lag-indexed correlation coefficients are computed as the inner or dot product of segments of two signals. The time-lag(s) for which the magnitude of the correlation coefficient sequence is maximized is the estimated relative time delay of the two signals. For discrete sampled signals, the delay estimated in this manner is quantized with the same relative accuracy as the clock used in sampling the signals. In addition, the correlation coefficients are real if the input signals are real. There have been many methods proposed to estimate signal delay to more accuracy than the sample interval of the digitizer clock, with some success. These methods include interpolation of the correlation coefficients, estimation of the signal delay from the group delay function, and beam forming techniques, such as the MUSIC algorithm. For spectral estimation, techniques based on phase differentiation have been popular, but these techniques have apparently not been applied to the correlation problem . We propose a phase based delay estimation method (PBDEM) based on the phase of the correlation function that provides a significant improvement of the accuracy of time delay estimation. In the process, the standard correlation function is first calculated. A time lag error function is then calculated from the correlation phase and is used to interpolate the correlation function. The signal delay is shown to be accurately estimated as the zero crossing of the correlation phase near the index of the peak correlation magnitude. This process is nearly as fast as the conventional correlation function on which it is based. For real valued signals, a simple modification is provided, which results in the same correlation accuracy as is obtained for complex valued signals.

Measuring the complexity of design in real-time imaging software

NASA Astrophysics Data System (ADS)

Sangwan, Raghvinder S.; Vercellone-Smith, Pamela; Laplante, Phillip A.

2007-02-01

Due to the intricacies in the algorithms involved, the design of imaging software is considered to be more complex than non-image processing software (Sangwan et al, 2005). A recent investigation (Larsson and Laplante, 2006) examined the complexity of several image processing and non-image processing software packages along a wide variety of metrics, including those postulated by McCabe (1976), Chidamber and Kemerer (1994), and Martin (2003). This work found that it was not always possible to quantitatively compare the complexity between imaging applications and nonimage processing systems. Newer research and an accompanying tool (Structure 101, 2006), however, provides a greatly simplified approach to measuring software complexity. Therefore it may be possible to definitively quantify the complexity differences between imaging and non-imaging software, between imaging and real-time imaging software, and between software programs of the same application type. In this paper, we review prior results and describe the methodology for measuring complexity in imaging systems. We then apply a new complexity measurement methodology to several sets of imaging and non-imaging code in order to compare the complexity differences between the two types of applications. The benefit of such quantification is far reaching, for example, leading to more easily measured performance improvement and quality in real-time imaging code.

On some genetic consequences of social structure, mating systems, dispersal, and sampling

PubMed Central

Parreira, Bárbara R.; Chikhi, Lounès

2015-01-01

Many species are spatially and socially organized, with complex social organizations and dispersal patterns that are increasingly documented. Social species typically consist of small age-structured units, where a limited number of individuals monopolize reproduction and exhibit complex mating strategies. Here, we model social groups as age-structured units and investigate the genetic consequences of social structure under distinct mating strategies commonly found in mammals. Our results show that sociality maximizes genotypic diversity, which contradicts the belief that social groups are necessarily subject to strong genetic drift and at high risk of inbreeding depression. Social structure generates an excess of genotypic diversity. This is commonly observed in ecological studies but rarely reported in population genetic studies that ignore social structure. This heterozygosity excess, when detected, is often interpreted as a consequence of inbreeding avoidance mechanisms, but we show that it can occur even in the absence of such mechanisms. Many seemly contradictory results from ecology and population genetics can be reconciled by genetic models that include the complexities of social species. We find that such discrepancies can be explained by the intrinsic properties of social groups and by the sampling strategies of real populations. In particular, the number of social groups and the nature of the individuals that compose samples (e.g., nonreproductive and reproductive individuals) are key factors in generating outbreeding signatures. Sociality is an important component of population structure that needs to be revisited by ecologists and population geneticists alike. PMID:26080393

Real-time analysis of dual-display phage immobilization and autoantibody screening using quartz crystal microbalance with dissipation monitoring.

PubMed

Rajaram, Kaushik; Losada-Pérez, Patricia; Vermeeren, Veronique; Hosseinkhani, Baharak; Wagner, Patrick; Somers, Veerle; Michiels, Luc

2015-01-01

Over the last three decades, phage display technology has been used for the display of target-specific biomarkers, peptides, antibodies, etc. Phage display-based assays are mostly limited to the phage ELISA, which is notorious for its high background signal and laborious methodology. These problems have been recently overcome by designing a dual-display phage with two different end functionalities, namely, streptavidin (STV)-binding protein at one end and a rheumatoid arthritis-specific autoantigenic target at the other end. Using this dual-display phage, a much higher sensitivity in screening specificities of autoantibodies in complex serum sample has been detected compared to single-display phage system on phage ELISA. Herein, we aimed to develop a novel, rapid, and sensitive dual-display phage to detect autoantibodies presence in serum samples using quartz crystal microbalance with dissipation monitoring as a sensing platform. The vertical functionalization of the phage over the STV-modified surfaces resulted in clear frequency and dissipation shifts revealing a well-defined viscoelastic signature. Screening for autoantibodies using antihuman IgG-modified surfaces and the dual-display phage with STV magnetic bead complexes allowed to isolate the target entities from complex mixtures and to achieve a large response as compared to negative control samples. This novel dual-display strategy can be a potential alternative to the time consuming phage ELISA protocols for the qualitative analysis of serum autoantibodies and can be taken as a departure point to ultimately achieve a point of care diagnostic system.

Thermo Physics Facilities Branch Brochure ARC Jet Complex Fact Sheets, Hypervelocity Free-Flight Aerodynamic Facility Fact Sheets, Ames Vertical Gun Range Fact Sheets

NASA Technical Reports Server (NTRS)

Fretter, E. F. (Editor); Kuhns, Jay (Editor); Nuez, Jay (Editor)

2003-01-01

The Ames Arc Jet Complex has a rich heritage of over 40 years in Thermal Protection System (TPS) development for every NASA Space Transportation and Planetary program, including Apollo, Space Shuttle, Viking, Pioneer-Venus, Galileo, Mars Pathfinder,Stardust, NASP,X-33,X-34,SHARP-B1 and B2,X-37 and Mars Exploration Rovers. With this early TPS history came a long heritage in the development of the arc jet facilities. These are used to simulate the aerodynamic heating that occurs on the nose cap, wing leading edges and on other areas of the spacecraft requiring thermal protection. TPS samples have been run in the arc jets from a few minutes to over an hour,from one exposure to multiple exposures of the same sample, in order t o understand the TPS materials response to a hot gas flow environment (representative of real hyperthermal environments experienced in flight). The Ames Arc l e t Complex is a key enabler for customers involved in the three major areas of TPS development: selection, validation, and qualification. The arc jet data are critical for validating TPS thermal models, heat shield designs and repairs, and ultimately for flight qualification.

Effect of toughened epoxy resin on partial discharge at solid-solid interface

NASA Astrophysics Data System (ADS)

Li, Manping; Wu, Kai; Zhang, Zhao; Cheng, Yonghong

2017-02-01

A series of solid-solid interfaces, consisting of ceramic-epoxy resin interface samples with a tip-plate electrode, were investigated by performing partial discharge tests and real-time electrical tree observations. A toughening agent was added to the epoxy resin at different ratios for comparison. The impact strength, differential scanning calorimetry (DSC) and dielectric properties of the cured compositions and ceramic were tested. The electric field strength at the tip was calculated based on Maxwell’s theory. The test results show that the addition of a toughener can improve the impact strength of epoxy resin but it decreases the partial discharge inception voltage (PDIV) of the interface sample. At the same time, toughening leads to complex branches of the electrical tree. The simulation result suggests that this reduction of the PDIV cannot be explained by a change of permittivity due to the addition of a toughening agent. The microstructural change caused by toughening was considered to be the key factor for lower PDIV and complex electrical tree branches. Supported by China Academy of Engineering Physics (Project 2014B05005).

Extractive Atmospheric Pressure Photoionization (EAPPI) Mass Spectrometry: Rapid Analysis of Chemicals in Complex Matrices.

PubMed

Liu, Chengyuan; Yang, Jiuzhong; Wang, Jian; Hu, Yonghua; Zhao, Wan; Zhou, Zhongyue; Qi, Fei; Pan, Yang

2016-10-01

Extractive atmospheric pressure photoionization (EAPPI) mass spectrometry was designed for rapid qualitative and quantitative analysis of chemicals in complex matrices. In this method, an ultrasonic nebulization system was applied to sample extraction, nebulization, and vaporization. Mixed with a gaseous dopant, vaporized analytes were ionized through ambient photon-induced ion-molecule reactions, and were mass-analyzed by a high resolution time-of-flight mass spectrometer (TOF-MS). After careful optimization and testing with pure sample solution, EAPPI was successfully applied to the fast screening of capsules, soil, natural products, and viscous compounds. Analysis was completed within a few seconds without the need for preseparation. Moreover, the quantification capability of EAPPI for matrices was evaluated by analyzing six polycyclic aromatic hydrocarbons (PAHs) in soil. The correlation coefficients (R (2) ) for standard curves of all six PAHs were above 0.99, and the detection limits were in the range of 0.16-0.34 ng/mg. In addition, EAPPI could also be used to monitor organic chemical reactions in real time. Graphical Abstract ᅟ.

Application of novel Ni(II) complex and ZrO2 nanoparticle as mediators for electrocatalytic determination of N-acetylcysteine in drug samples.

PubMed

Karimi-Maleh, Hassan; Salehi, Mehdi; Faghani, Fatemeh

2017-10-01

The electrooxidation of N-acetylcysteine (N-AC) was studied by a novel Ni(II) complex modified ZrO 2 nanoparticle carbon paste electrode [Ni(II)/ZrO 2 /NPs/CPE] using voltammetric methods. The results showed that Ni(II)/ZrO 2 /NPs/CPE had high electrocatalytic activity for the electrooxidation of N-AC in aqueous buffer solution (pH = 7.0). The electrocatalytic oxidation peak currents increase linearly with N-AC concentrations over the concentration ranges of 0.05-600μM using square wave voltammetric methods. The detection limit for N-AC was equal to 0.009μM. The catalytic reaction rate constant, k h , was calculated (7.01 × 10 2  M -1  s -1 ) using the chronoamperometry method. Finally, Ni(II)/ZrO 2 /NPs/CPE was also examined as an ultrasensitive electrochemical sensor for the determination of N-AC in real samples such as tablet and urine. Copyright © 2017. Published by Elsevier B.V.

A New Method to Develop Human Dental Pulp Cells and Platelet-rich Fibrin Complex.

PubMed

He, Xuan; Chen, Wen-Xia; Ban, Guifei; Wei, Wei; Zhou, Jun; Chen, Wen-Jin; Li, Xian-Yu

2016-11-01

Platelet-rich fibrin (PRF) has been used as a scaffold material in various tissue regeneration studies. In the previous methods to combine seed cells with PRF, the structure of PRF was damaged, and the manipulation time in vitro was also increased. The objective of this in vitro study was to explore an appropriate method to develop a PRF-human dental pulp cell (hDPC) complex to maintain PRF structure integrity and to find out the most efficient part of PRF. The PRF-hDPC complex was developed at 3 different time points during PRF preparation: (1) the before centrifugation (BC) group, the hDPC suspension was added to the venous blood before blood centrifugation; (2) the immediately after centrifugation (IAC) group, the hDPC suspension was added immediately after blood centrifugation; (3) the after centrifugation (AC) group, the hDPC suspension was added 10 minutes after blood centrifugation; and (4) the control group, PRF without hDPC suspension. The prepared PRF-hDPC complexes were cultured for 7 days. The samples were fixed for histologic, immunohistochemistry, and scanning electron microscopic evaluation. Real-time polymerase chain reaction was performed to evaluate messenger RNA expression of alkaline phosphatase and dentin sialophosphoprotein. Enzyme-linked immunosorbent assay quantification for growth factors was performed within the different parts of the PRF. Histologic, immunohistochemistry, and scanning electron microscopic results revealed that hDPCs were only found in the BC group and exhibited favorable proliferation. Real-time polymerase chain reaction revealed that alkaline phosphatase and dentin sialophosphoprotein expression increased in the cultured PRF-hDPC complex. The lower part of the PRF released the maximum quantity of growth factors. Our new method to develop a PRF-hDPCs complex maintained PRF structure integrity. The hDPCs were distributed in the buffy coat, which might be the most efficient part of PRF. Copyright © 2016 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

A reagentless real-time method for the multiparameter analysis of nanoparticles as a potential 'trigger' device

NASA Astrophysics Data System (ADS)

Carr, Bob; Knowles, John; Warren, Jeremy

2008-10-01

We describe the continuing development of a laser-based, light scattering detector system capable of detecting and analysing liquid-borne nanoparticles. Using a finely focussed and specially configured laser beam to illuminate a suspension of nanoparticles in a small (250ul) sample and videoing the Brownian motion of each and every particle in the detection zone should allow individual but simultaneous detection and measurement of particle size, scattered light intensity, electrophoretic mobility and, where applicable, shape asymmetry. This real-time, multi-parameter analysis capability offers the prospect of reagentlessly differentiating between different particle types within a complex sample of potentially high and variable background. Employing relatively low powered (50-100mW) laser diode modules and low resolution CCD arrays, each component could be run off battery power, allowing distributed/remote or personal deployment. Voltages needed for electrophoresis measurement s would be similarly low (e.g. 20V, low current) and 30second videos (exported at mobile/cell phone download speeds) analysed remotely. The potential of such low-cost technology as a field-deployable grid of remote, battery powered and reagentless, multi-parameter sensors for use as trigger devices is discussed.

Observation of the magnetic flux and three-dimensional structure of skyrmion lattices by electron holography.

PubMed

Park, Hyun Soon; Yu, Xiuzhen; Aizawa, Shinji; Tanigaki, Toshiaki; Akashi, Tetsuya; Takahashi, Yoshio; Matsuda, Tsuyoshi; Kanazawa, Naoya; Onose, Yoshinori; Shindo, Daisuke; Tonomura, Akira; Tokura, Yoshinori

2014-05-01

Skyrmions are nanoscale spin textures that are viewed as promising candidates as information carriers in future spintronic devices. Skyrmions have been observed using neutron scattering and microscopy techniques. Real-space imaging using electrons is a straightforward way to interpret spin configurations by detecting the phase shifts due to electromagnetic fields. Here, we report the first observation by electron holography of the magnetic flux and the three-dimensional spin configuration of a skyrmion lattice in Fe(0.5)Co(0.5)Si thin samples. The magnetic flux inside and outside a skyrmion was directly visualized and the handedness of the magnetic flux flow was found to be dependent on the direction of the applied magnetic field. The electron phase shifts φ in the helical and skyrmion phases were determined using samples with a stepped thickness t (from 55 nm to 510 nm), revealing a linear relationship (φ = 0.00173 t). The phase measurements were used to estimate the three-dimensional structures of both the helical and skyrmion phases, demonstrating that electron holography is a useful tool for studying complex magnetic structures and for three-dimensional, real-space mapping of magnetic fields.

MACRO: a combined microchip-PCR and microarray system for high-throughput monitoring of genetically modified organisms.

PubMed

Shao, Ning; Jiang, Shi-Meng; Zhang, Miao; Wang, Jing; Guo, Shu-Juan; Li, Yang; Jiang, He-Wei; Liu, Cheng-Xi; Zhang, Da-Bing; Yang, Li-Tao; Tao, Sheng-Ce

2014-01-21

The monitoring of genetically modified organisms (GMOs) is a primary step of GMO regulation. However, there is presently a lack of effective and high-throughput methodologies for specifically and sensitively monitoring most of the commercialized GMOs. Herein, we developed a multiplex amplification on a chip with readout on an oligo microarray (MACRO) system specifically for convenient GMO monitoring. This system is composed of a microchip for multiplex amplification and an oligo microarray for the readout of multiple amplicons, containing a total of 91 targets (18 universal elements, 20 exogenous genes, 45 events, and 8 endogenous reference genes) that covers 97.1% of all GM events that have been commercialized up to 2012. We demonstrate that the specificity of MACRO is ~100%, with a limit of detection (LOD) that is suitable for real-world applications. Moreover, the results obtained of simulated complex samples and blind samples with MACRO were 100% consistent with expectations and the results of independently performed real-time PCRs, respectively. Thus, we believe MACRO is the first system that can be applied for effectively monitoring the majority of the commercialized GMOs in a single test.

Apparently low reproducibility of true differential expression discoveries in microarray studies.

PubMed

Zhang, Min; Yao, Chen; Guo, Zheng; Zou, Jinfeng; Zhang, Lin; Xiao, Hui; Wang, Dong; Yang, Da; Gong, Xue; Zhu, Jing; Li, Yanhui; Li, Xia

2008-09-15

Differentially expressed gene (DEG) lists detected from different microarray studies for a same disease are often highly inconsistent. Even in technical replicate tests using identical samples, DEG detection still shows very low reproducibility. It is often believed that current small microarray studies will largely introduce false discoveries. Based on a statistical model, we show that even in technical replicate tests using identical samples, it is highly likely that the selected DEG lists will be very inconsistent in the presence of small measurement variations. Therefore, the apparently low reproducibility of DEG detection from current technical replicate tests does not indicate low quality of microarray technology. We also demonstrate that heterogeneous biological variations existing in real cancer data will further reduce the overall reproducibility of DEG detection. Nevertheless, in small subsamples from both simulated and real data, the actual false discovery rate (FDR) for each DEG list tends to be low, suggesting that each separately determined list may comprise mostly true DEGs. Rather than simply counting the overlaps of the discovery lists from different studies for a complex disease, novel metrics are needed for evaluating the reproducibility of discoveries characterized with correlated molecular changes. Supplementaty information: Supplementary data are available at Bioinformatics online.

Method for Hot Real-Time Sampling of Pyrolysis Vapors

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

Pomeroy, Marc D

Biomass Pyrolysis has been an increasing topic of research, in particular as a replacement for crude oil. This process utilizes moderate temperatures to thermally deconstruct the biomass which is then condensed into a mixture of liquid oxygenates to be used as fuel precursors. Pyrolysis oils contain more than 400 compounds, up to 60 percent of which do not re-volatilize for subsequent chemical analysis. Vapor chemical composition is also complicated as additional condensation reactions occur during the condensation and collection of the product. Due to the complexity of the pyrolysis oil, and a desire to catalytically upgrade the vapor composition beforemore » condensation, online real-time analytical techniques such as Molecular Beam Mass Spectrometry (MBMS) are of great use. However, in order to properly sample hot pyrolysis vapors, many challenges must be overcome. Sampling must occur within a narrow range of temperatures to reduce product composition changes from overheating or partial condensation or plugging of lines from condensed products. Residence times must be kept at a minimum to reduce further reaction chemistries. Pyrolysis vapors also form aerosols that are carried far downstream and can pass through filters resulting in build-up in downstream locations. The co-produced bio-char and ash from the pyrolysis process can lead to plugging of the sample lines, and must be filtered out at temperature, even with the use of cyclonic separators. A practical approach for considerations and sampling system design, as well as lessons learned are integrated into the hot analytical sampling system of the National Renewable Energy Laboratory's (NREL) Thermochemical Process Development Unit (TCPDU) to provide industrially relevant demonstrations of thermochemical transformations of biomass feedstocks at the pilot scale.« less

Advanced functional materials in solid phase extraction for ICP-MS determination of trace elements and their species - A review.

PubMed

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

2017-06-22

For the determination of trace elements and their species in various real samples by inductively coupled plasma mass spectrometry (ICP-MS), solid phase extraction (SPE) is a commonly used sample pretreatment technique to remove complex matrix, pre-concentrate target analytes and make the samples suitable for subsequent sample introduction and measurements. The sensitivity, selectivity/anti-interference ability, sample throughput and application potential of the methodology of SPE-ICP-MS are greatly dependent on SPE adsorbents. This article presents a general overview of the use of advanced functional materials (AFMs) in SPE for ICP-MS determination of trace elements and their species in the past decade. Herein the AFMs refer to the materials featuring with high adsorption capacity, good selectivity, fast adsorption/desorption dynamics and satisfying special requirements in real sample analysis, including nanometer-sized materials, porous materials, ion imprinting polymers, restricted access materials and magnetic materials. Carbon/silica/metal/metal oxide nanometer-sized adsorbents with high surface area and plenty of adsorption sites exhibit high adsorption capacity, and porous adsorbents would provide more adsorption sites and faster adsorption dynamics. The selectivity of the materials for target elements/species can be improved by using physical/chemical modification, ion imprinting and restricted accessed technique. Magnetic adsorbents in conventional batch operation offer unique magnetic response and high surface area-volume ratio which provide a very easy phase separation, greater extraction capacity and efficiency over conventional adsorbents, and chip-based magnetic SPE provides a versatile platform for special requirement (e.g. cell analysis). The performance of these adsorbents for the determination of trace elements and their species in different matrices by ICP-MS is discussed in detail, along with perspectives and possible challenges in the future development. Copyright © 2017 Elsevier B.V. All rights reserved.

Digital double random amplitude image encryption method based on the symmetry property of the parametric discrete Fourier transform

NASA Astrophysics Data System (ADS)

Bekkouche, Toufik; Bouguezel, Saad

2018-03-01

We propose a real-to-real image encryption method. It is a double random amplitude encryption method based on the parametric discrete Fourier transform coupled with chaotic maps to perform the scrambling. The main idea behind this method is the introduction of a complex-to-real conversion by exploiting the inherent symmetry property of the transform in the case of real-valued sequences. This conversion allows the encrypted image to be real-valued instead of being a complex-valued image as in all existing double random phase encryption methods. The advantage is to store or transmit only one image instead of two images (real and imaginary parts). Computer simulation results and comparisons with the existing double random amplitude encryption methods are provided for peak signal-to-noise ratio, correlation coefficient, histogram analysis, and key sensitivity.

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.

Investigation of Legionella Contamination in Bath Water Samples by Culture, Amoebic Co-Culture, and Real-Time Quantitative PCR Methods.

PubMed

Edagawa, Akiko; Kimura, Akio; Kawabuchi-Kurata, Takako; Adachi, Shinichi; Furuhata, Katsunori; Miyamoto, Hiroshi

2015-10-19

We investigated Legionella contamination in bath water samples, collected from 68 bathing facilities in Japan, by culture, culture with amoebic co-culture, real-time quantitative PCR (qPCR), and real-time qPCR with amoebic co-culture. Using the conventional culture method, Legionella pneumophila was detected in 11 samples (11/68, 16.2%). Contrary to our expectation, the culture method with the amoebic co-culture technique did not increase the detection rate of Legionella (4/68, 5.9%). In contrast, a combination of the amoebic co-culture technique followed by qPCR successfully increased the detection rate (57/68, 83.8%) compared with real-time qPCR alone (46/68, 67.6%). Using real-time qPCR after culture with amoebic co-culture, more than 10-fold higher bacterial numbers were observed in 30 samples (30/68, 44.1%) compared with the same samples without co-culture. On the other hand, higher bacterial numbers were not observed after propagation by amoebae in 32 samples (32/68, 47.1%). Legionella was not detected in the remaining six samples (6/68, 8.8%), irrespective of the method. These results suggest that application of the amoebic co-culture technique prior to real-time qPCR may be useful for the sensitive detection of Legionella from bath water samples. Furthermore, a combination of amoebic co-culture and real-time qPCR might be useful to detect viable and virulent Legionella because their ability to invade and multiply within free-living amoebae is considered to correlate with their pathogenicity for humans. This is the first report evaluating the efficacy of the amoebic co-culture technique for detecting Legionella in bath water samples.

Investigation of Legionella Contamination in Bath Water Samples by Culture, Amoebic Co-Culture, and Real-Time Quantitative PCR Methods

PubMed Central

Edagawa, Akiko; Kimura, Akio; Kawabuchi-Kurata, Takako; Adachi, Shinichi; Furuhata, Katsunori; Miyamoto, Hiroshi

2015-01-01

We investigated Legionella contamination in bath water samples, collected from 68 bathing facilities in Japan, by culture, culture with amoebic co-culture, real-time quantitative PCR (qPCR), and real-time qPCR with amoebic co-culture. Using the conventional culture method, Legionella pneumophila was detected in 11 samples (11/68, 16.2%). Contrary to our expectation, the culture method with the amoebic co-culture technique did not increase the detection rate of Legionella (4/68, 5.9%). In contrast, a combination of the amoebic co-culture technique followed by qPCR successfully increased the detection rate (57/68, 83.8%) compared with real-time qPCR alone (46/68, 67.6%). Using real-time qPCR after culture with amoebic co-culture, more than 10-fold higher bacterial numbers were observed in 30 samples (30/68, 44.1%) compared with the same samples without co-culture. On the other hand, higher bacterial numbers were not observed after propagation by amoebae in 32 samples (32/68, 47.1%). Legionella was not detected in the remaining six samples (6/68, 8.8%), irrespective of the method. These results suggest that application of the amoebic co-culture technique prior to real-time qPCR may be useful for the sensitive detection of Legionella from bath water samples. Furthermore, a combination of amoebic co-culture and real-time qPCR might be useful to detect viable and virulent Legionella because their ability to invade and multiply within free-living amoebae is considered to correlate with their pathogenicity for humans. This is the first report evaluating the efficacy of the amoebic co-culture technique for detecting Legionella in bath water samples. PMID:26492259

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.

Proposed imaging of the ultrafast electronic motion in samples using x-ray phase contrast.

PubMed

Dixit, Gopal; Slowik, Jan Malte; Santra, Robin

2013-03-29

Tracing the motion of electrons has enormous relevance to understanding ubiquitous phenomena in ultrafast science, such as the dynamical evolution of the electron density during complex chemical and biological processes. Scattering of ultrashort x-ray pulses from an electronic wave packet would appear to be the most obvious approach to image the electronic motion in real time and real space with the notion that such scattering patterns, in the far-field regime, encode the instantaneous electron density of the wave packet. However, recent results by Dixit et al. [Proc. Natl. Acad. Sci. U.S.A. 109, 11636 (2012)] have put this notion into question and have shown that the scattering in the far-field regime probes spatiotemporal density-density correlations. Here, we propose a possible way to image the instantaneous electron density of the wave packet via ultrafast x-ray phase contrast imaging. Moreover, we show that inelastic scattering processes, which plague ultrafast scattering in the far-field regime, do not contribute in ultrafast x-ray phase contrast imaging as a consequence of an interference effect. We illustrate our general findings by means of a wave packet that lies in the time and energy range of the dynamics of valence electrons in complex molecular and biological systems. This present work offers a potential to image not only instantaneous snapshots of nonstationary electron dynamics, but also the laplacian of these snapshots which provide information about the complex bonding and topology of the charge distributions in the systems.

Proposed Imaging of the Ultrafast Electronic Motion in Samples using X-Ray Phase Contrast

NASA Astrophysics Data System (ADS)

Dixit, Gopal; Slowik, Jan Malte; Santra, Robin

2013-03-01

Tracing the motion of electrons has enormous relevance to understanding ubiquitous phenomena in ultrafast science, such as the dynamical evolution of the electron density during complex chemical and biological processes. Scattering of ultrashort x-ray pulses from an electronic wave packet would appear to be the most obvious approach to image the electronic motion in real time and real space with the notion that such scattering patterns, in the far-field regime, encode the instantaneous electron density of the wave packet. However, recent results by Dixit et al. [Proc. Natl. Acad. Sci. U.S.A. 109, 11 636 (2012)] have put this notion into question and have shown that the scattering in the far-field regime probes spatiotemporal density-density correlations. Here, we propose a possible way to image the instantaneous electron density of the wave packet via ultrafast x-ray phase contrast imaging. Moreover, we show that inelastic scattering processes, which plague ultrafast scattering in the far-field regime, do not contribute in ultrafast x-ray phase contrast imaging as a consequence of an interference effect. We illustrate our general findings by means of a wave packet that lies in the time and energy range of the dynamics of valence electrons in complex molecular and biological systems. This present work offers a potential to image not only instantaneous snapshots of nonstationary electron dynamics, but also the Laplacian of these snapshots which provide information about the complex bonding and topology of the charge distributions in the systems.

Real-time PCR strategy for the identification of Trypanosoma cruzi discrete typing units directly in chronically infected human blood.

PubMed

Muñoz-San Martín, Catalina; Apt, Werner; Zulantay, Inés

2017-04-01

The protozoan Trypanosoma cruzi is the causative agent of Chagas disease, a major public health problem in Latin America. This parasite has a complex population structure comprised by six or seven major evolutionary lineages (discrete typing units or DTUs) TcI-TcVI and TcBat, some of which have apparently resulted from ancient hybridization events. Because of the existence of significant biological differences between these lineages, strain characterization methods have been essential to study T. cruzi in its different vectors and hosts. However, available methods can be laborious and costly, limited in resolution or sensitivity. In this study, a new genotyping strategy by real-time PCR to identify each of the six DTUs in clinical blood samples have been developed and evaluated. Two nuclear (SL-IR and 18S rDNA) and two mitochondrial genes (COII and ND1) were selected to develop original primers. The method was evaluated with eight genomic DNA of T. cruzi populations belonging to the six DTUs, one genomic DNA of Trypanosoma rangeli, and 53 blood samples from individuals with chronic Chagas disease. The assays had an analytical sensitivity of 1-25fg of DNA per reaction tube depending on the DTU analyzed. The selectivity of trials with 20fg/μL of genomic DNA identified each DTU, excluding non-targets DTUs in every test. The method was able to characterize 67.9% of the chronically infected clinical samples with high detection of TcII followed by TcI. With the proposed original genotyping methodology, each DTU was established with high sensitivity after a single real-time PCR assay. This novel protocol reduces carryover contamination, enables detection of each DTU independently and in the future, the quantification of each DTU in clinical blood samples. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

Second-order data obtained by beta-cyclodextrin complexes: a novel approach for multicomponent analysis with three-way multivariate calibration methods.

PubMed

Khani, Rouhollah; Ghasemi, Jahan B; Shemirani, Farzaneh

2014-10-01

This research reports the first application of β-cyclodextrin (β-CD) complexes as a new method for generation of three way data, combined with second-order calibration methods for quantification of a binary mixture of caffeic (CA) and vanillic (VA) acids, as model compounds in fruit juices samples. At first, the basic experimental parameters affecting the formation of inclusion complexes between target analytes and β-CD were investigated and optimized. Then under the optimum conditions, parallel factor analysis (PARAFAC) and bilinear least squares/residual bilinearization (BLLS/RBL) were applied for deconvolution of trilinear data to get spectral and concentration profiles of CA and VA as a function of β-CD concentrations. Due to severe concentration profile overlapping between CA and VA in β-CD concentration dimension, PARAFAC could not be successfully applied to the studied samples. So, BLLS/RBL performed better than PARAFAC. The resolution of the model compounds was possible due to differences in the spectral absorbance changes of the β-CD complexes signals of the investigated analytes, opening a new approach for second-order data generation. The proposed method was validated by comparison with a reference method based on high-performance liquid chromatography photodiode array detection (HPLC-PDA), and no significant differences were found between the reference values and the ones obtained with the proposed method. Such a chemometrics-based protocol may be a very promising tool for more analytical applications in real samples monitoring, due to its advantages of simplicity, rapidity, accuracy, sufficient spectral resolution and concentration prediction even in the presence of unknown interferents. Copyright © 2014 Elsevier B.V. All rights reserved.

Real-time bilinear rotation decoupling in absorptive mode J-spectroscopy: Detecting low-intensity metabolite peak close to high-intensity metabolite peak with convenience.

PubMed

Verma, Ajay; Baishya, Bikash

2016-05-01

"Pure shift" NMR spectra display singlet peak per chemical site. Thus, high resolution is offered at the cost of valuable J-coupling information. In the present work, real-time BIRD (BIlinear Rotation Decoupling) is applied to the absorptive-mode 2D J-spectroscopy to provide pure shift spectrum in the direct dimension and J-coupling information in the indirect dimension. Quite often in metabolomics, proton NMR spectra from complex bio-fluids display tremendous signal overlap. Although conventional J-spectroscopy in principle overcomes this problem by separating the multiplet information from chemical shift information, however, only magnitude mode of the experiment is practical, sacrificing much of the potential high resolution that could be achieved. Few J-spectroscopy methods have been reported so far that produce high-resolution pure shift spectrum along with J-coupling information for crowded spectral regions. In the present work, high-quality J-resolved spectrum from important metabolomic mixture such as tissue extract from rat cortex is demonstrated. Many low-intensity metabolite peaks which are obscured by the broad dispersive tails from high-intensity metabolite peaks in regular magnitude mode J-spectrum can be clearly identified in real-time BIRD J-resolved spectrum. The general practice of removing such spectral overlap is tedious and time-consuming as it involves repeated sample preparation to change the pH of the tissue extract sample and subsequent spectra recording. Copyright © 2016 Elsevier Inc. All rights reserved.

Research on photodiode detector-based spatial transient light detection and processing system

NASA Astrophysics Data System (ADS)

Liu, Meiying; Wang, Hu; Liu, Yang; Zhao, Hui; Nan, Meng

2016-10-01

In order to realize real-time signal identification and processing of spatial transient light, the features and the energy of the captured target light signal are first described and quantitatively calculated. Considering that the transient light signal has random occurrence, a short duration and an evident beginning and ending, a photodiode detector based spatial transient light detection and processing system is proposed and designed in this paper. This system has a large field of view and is used to realize non-imaging energy detection of random, transient and weak point target under complex background of spatial environment. Weak signal extraction under strong background is difficult. In this paper, considering that the background signal changes slowly and the target signal changes quickly, filter is adopted for signal's background subtraction. A variable speed sampling is realized by the way of sampling data points with a gradually increased interval. The two dilemmas that real-time processing of large amount of data and power consumption required by the large amount of data needed to be stored are solved. The test results with self-made simulative signal demonstrate the effectiveness of the design scheme. The practical system could be operated reliably. The detection and processing of the target signal under the strong sunlight background was realized. The results indicate that the system can realize real-time detection of target signal's characteristic waveform and monitor the system working parameters. The prototype design could be used in a variety of engineering applications.

Multiway real-time PCR gene expression profiling in yeast Saccharomyces cerevisiae reveals altered transcriptional response of ADH-genes to glucose stimuli.

PubMed

Ståhlberg, Anders; Elbing, Karin; Andrade-Garda, José Manuel; Sjögreen, Björn; Forootan, Amin; Kubista, Mikael

2008-04-16

The large sensitivity, high reproducibility and essentially unlimited dynamic range of real-time PCR to measure gene expression in complex samples provides the opportunity for powerful multivariate and multiway studies of biological phenomena. In multiway studies samples are characterized by their expression profiles to monitor changes over time, effect of treatment, drug dosage etc. Here we perform a multiway study of the temporal response of four yeast Saccharomyces cerevisiae strains with different glucose uptake rates upon altered metabolic conditions. We measured the expression of 18 genes as function of time after addition of glucose to four strains of yeast grown in ethanol. The data are analyzed by matrix-augmented PCA, which is a generalization of PCA for 3-way data, and the results are confirmed by hierarchical clustering and clustering by Kohonen self-organizing map. Our approach identifies gene groups that respond similarly to the change of nutrient, and genes that behave differently in mutant strains. Of particular interest is our finding that ADH4 and ADH6 show a behavior typical of glucose-induced genes, while ADH3 and ADH5 are repressed after glucose addition. Multiway real-time PCR gene expression profiling is a powerful technique which can be utilized to characterize functions of new genes by, for example, comparing their temporal response after perturbation in different genetic variants of the studied subject. The technique also identifies genes that show perturbed expression in specific strains.

Multiway real-time PCR gene expression profiling in yeast Saccharomyces cerevisiae reveals altered transcriptional response of ADH-genes to glucose stimuli

PubMed Central

Ståhlberg, Anders; Elbing, Karin; Andrade-Garda, José Manuel; Sjögreen, Björn; Forootan, Amin; Kubista, Mikael

2008-01-01

Background The large sensitivity, high reproducibility and essentially unlimited dynamic range of real-time PCR to measure gene expression in complex samples provides the opportunity for powerful multivariate and multiway studies of biological phenomena. In multiway studies samples are characterized by their expression profiles to monitor changes over time, effect of treatment, drug dosage etc. Here we perform a multiway study of the temporal response of four yeast Saccharomyces cerevisiae strains with different glucose uptake rates upon altered metabolic conditions. Results We measured the expression of 18 genes as function of time after addition of glucose to four strains of yeast grown in ethanol. The data are analyzed by matrix-augmented PCA, which is a generalization of PCA for 3-way data, and the results are confirmed by hierarchical clustering and clustering by Kohonen self-organizing map. Our approach identifies gene groups that respond similarly to the change of nutrient, and genes that behave differently in mutant strains. Of particular interest is our finding that ADH4 and ADH6 show a behavior typical of glucose-induced genes, while ADH3 and ADH5 are repressed after glucose addition. Conclusion Multiway real-time PCR gene expression profiling is a powerful technique which can be utilized to characterize functions of new genes by, for example, comparing their temporal response after perturbation in different genetic variants of the studied subject. The technique also identifies genes that show perturbed expression in specific strains. PMID:18412983

Real-time bilinear rotation decoupling in absorptive mode J-spectroscopy: Detecting low-intensity metabolite peak close to high-intensity metabolite peak with convenience

NASA Astrophysics Data System (ADS)

Verma, Ajay; Baishya, Bikash

2016-05-01

;Pure shift; NMR spectra display singlet peak per chemical site. Thus, high resolution is offered at the cost of valuable J-coupling information. In the present work, real-time BIRD (BIlinear Rotation Decoupling) is applied to the absorptive-mode 2D J-spectroscopy to provide pure shift spectrum in the direct dimension and J-coupling information in the indirect dimension. Quite often in metabolomics, proton NMR spectra from complex bio-fluids display tremendous signal overlap. Although conventional J-spectroscopy in principle overcomes this problem by separating the multiplet information from chemical shift information, however, only magnitude mode of the experiment is practical, sacrificing much of the potential high resolution that could be achieved. Few J-spectroscopy methods have been reported so far that produce high-resolution pure shift spectrum along with J-coupling information for crowded spectral regions. In the present work, high-quality J-resolved spectrum from important metabolomic mixture such as tissue extract from rat cortex is demonstrated. Many low-intensity metabolite peaks which are obscured by the broad dispersive tails from high-intensity metabolite peaks in regular magnitude mode J-spectrum can be clearly identified in real-time BIRD J-resolved spectrum. The general practice of removing such spectral overlap is tedious and time-consuming as it involves repeated sample preparation to change the pH of the tissue extract sample and subsequent spectra recording.

The geometric nature of weights in real complex networks

NASA Astrophysics Data System (ADS)

Allard, Antoine; Serrano, M. Ángeles; García-Pérez, Guillermo; Boguñá, Marián

2017-01-01

The topology of many real complex networks has been conjectured to be embedded in hidden metric spaces, where distances between nodes encode their likelihood of being connected. Besides of providing a natural geometrical interpretation of their complex topologies, this hypothesis yields the recipe for sustainable Internet's routing protocols, sheds light on the hierarchical organization of biochemical pathways in cells, and allows for a rich characterization of the evolution of international trade. Here we present empirical evidence that this geometric interpretation also applies to the weighted organization of real complex networks. We introduce a very general and versatile model and use it to quantify the level of coupling between their topology, their weights and an underlying metric space. Our model accurately reproduces both their topology and their weights, and our results suggest that the formation of connections and the assignment of their magnitude are ruled by different processes.

Community detection in complex networks by using membrane algorithm

NASA Astrophysics Data System (ADS)

Liu, Chuang; Fan, Linan; Liu, Zhou; Dai, Xiang; Xu, Jiamei; Chang, Baoren

Community detection in complex networks is a key problem of network analysis. In this paper, a new membrane algorithm is proposed to solve the community detection in complex networks. The proposed algorithm is based on membrane systems, which consists of objects, reaction rules, and a membrane structure. Each object represents a candidate partition of a complex network, and the quality of objects is evaluated according to network modularity. The reaction rules include evolutionary rules and communication rules. Evolutionary rules are responsible for improving the quality of objects, which employ the differential evolutionary algorithm to evolve objects. Communication rules implement the information exchanged among membranes. Finally, the proposed algorithm is evaluated on synthetic, real-world networks with real partitions known and the large-scaled networks with real partitions unknown. The experimental results indicate the superior performance of the proposed algorithm in comparison with other experimental algorithms.

Simultaneous quantification of Aroclor mixtures in soil samples by gas chromatography/mass spectrometry with solid phase microextraction using partial least-squares regression.

PubMed

Zhang, Mengliang; Harrington, Peter de B

2015-01-01

Multivariate partial least-squares (PLS) method was applied to the quantification of two complex polychlorinated biphenyls (PCBs) commercial mixtures, Aroclor 1254 and 1260, in a soil matrix. PCBs in soil samples were extracted by headspace solid phase microextraction (SPME) and determined by gas chromatography/mass spectrometry (GC/MS). Decachlorinated biphenyl (deca-CB) was used as internal standard. After the baseline correction was applied, four data representations including extracted ion chromatograms (EIC) for Aroclor 1254, EIC for Aroclor 1260, EIC for both Aroclors and two-way data sets were constructed for PLS-1 and PLS-2 calibrations and evaluated with respect to quantitative prediction accuracy. The PLS model was optimized with respect to the number of latent variables using cross validation of the calibration data set. The validation of the method was performed with certified soil samples and real field soil samples and the predicted concentrations for both Aroclors using EIC data sets agreed with the certified values. The linear range of the method was from 10μgkg(-1) to 1000μgkg(-1) for both Aroclor 1254 and 1260 in soil matrices and the detection limit was 4μgkg(-1) for Aroclor 1254 and 6μgkg(-1) for Aroclor 1260. This holistic approach for the determination of mixtures of complex samples has broad application to environmental forensics and modeling. Copyright © 2014 Elsevier Ltd. All rights reserved.

A relay identification fluorescence probe for Fe3 + and phosphate anion and its applications

NASA Astrophysics Data System (ADS)

Tang, Xu; Wang, Yun; Han, Juan; Ni, Liang; Wang, Lei; Li, Longhua; Zhang, Huiqin; Li, Cheng; Li, Jing; Li, Haoran

2018-02-01

A simple relay identification fluorescence probe for Fe3 + and phosphate anion with ;on-off-on; switching was designed and synthesized based on the phenylthiazole and biphenylcarbonitrile. Probe 1 displayed highly selective and sensitive recognition to Fe3 + in HEPES aqueous buffer (EtOH/H2O = 2:8, v/v, pH = 7.4) solutions. The optimized structures and HOMO and LUMO of probe 1 and [1-Fe3 +] complex were obtained by the density functional theory (DFT) calculations with B3LYP as the exchange and correlation functional using a suite of Gaussian 09 programs. The [1-Fe3 +] complex solution also showed a high selectivity toward PO43 -. The lower limits of detection of probe 1 to Fe3 + and [1-Fe3 +] complex to PO43 - were estimated to 1.09 × 10- 7 M and 1.86 × 10- 7 M. Besides, the probe 1 also was used to detected the target ions in real water sample and living cells successfully.

Development and Validation of an Extractive Spectrophotometric Method for Miconazole Nitrate Assay in Pharmaceutical Formulations.

PubMed

Eticha, Tadele; Kahsay, Getu; Hailu, Teklebrhan; Gebretsadikan, Tesfamichael; Asefa, Fitsum; Gebretsadik, Hailekiros; Thangabalan, Boovizhikannan

2018-01-01

A simple extractive spectrophotometric technique has been developed and validated for the determination of miconazole nitrate in pure and pharmaceutical formulations. The method is based on the formation of a chloroform-soluble ion-pair complex between the drug and bromocresol green (BCG) dye in an acidic medium. The complex showed absorption maxima at 422 nm, and the system obeys Beer's law in the concentration range of 1-30  µ g/mL with molar absorptivity of 2.285 × 10 4  L/mol/cm. The composition of the complex was studied by Job's method of continuous variation, and the results revealed that the mole ratio of drug : BCG is 1 : 1. Full factorial design was used to optimize the effect of variable factors, and the method was validated based on the ICH guidelines. The method was applied for the determination of miconazole nitrate in real samples.

Characterizing air quality data from complex network perspective.

PubMed

Fan, Xinghua; Wang, Li; Xu, Huihui; Li, Shasha; Tian, Lixin

2016-02-01

Air quality depends mainly on changes in emission of pollutants and their precursors. Understanding its characteristics is the key to predicting and controlling air quality. In this study, complex networks were built to analyze topological characteristics of air quality data by correlation coefficient method. Firstly, PM2.5 (particulate matter with aerodynamic diameter less than 2.5 μm) indexes of eight monitoring sites in Beijing were selected as samples from January 2013 to December 2014. Secondly, the C-C method was applied to determine the structure of phase space. Points in the reconstructed phase space were considered to be nodes of the network mapped. Then, edges were determined by nodes having the correlation greater than a critical threshold. Three properties of the constructed networks, degree distribution, clustering coefficient, and modularity, were used to determine the optimal value of the critical threshold. Finally, by analyzing and comparing topological properties, we pointed out that similarities and difference in the constructed complex networks revealed influence factors and their different roles on real air quality system.

DNAzyme sensors for detection of metal ions in the environment and imaging them in living cells

PubMed Central

McGhee, Claire E.; Loh, Kang Yong

2017-01-01

The on-site and real-time detection of metal ions is important for environmental monitoring and for understanding the impact of metal ions on human health. However, developing sensors selective for a wide range of metal ions that can work in the complex matrices of untreated samples and cells presents significant challenges. To meet these challenges, DNAzymes, an emerging class of metal ion-dependent enzymes selective for almost any metal ion, have been functionalized with fluorophores, nanoparticles and other imaging agents and incorporated into sensors for the detection of metal ions in environmental samples and for imaging the metal ions in living cells. Herein, we highlight the recent developments of DNAzyme-based fluorescent, colorimetric, SERS, electrochemical and electrochemiluminscent sensors for metal ions for these applications. PMID:28458112

From Theory to Practice: A Path through Imperfection--Lessons from Evaluation of Policy Oriented Environmental Health Research in Belgium

ERIC Educational Resources Information Center

Keune, Hans; Morrens, Bert; Loots, Ilse; Springael, Johan

2011-01-01

Background: Dealing with complex issues per definition bears the burden of imperfection. Whatever comforting theoretical concepts may promise, real life complexity will take its messy toll once travelling from conceptual ambition to real life practice. We specifically reflect on the social scientific contribution to these inter- and…

Graphical Solution of the Monic Quadratic Equation with Complex Coefficients

ERIC Educational Resources Information Center

Laine, A. D.

2015-01-01

There are many geometrical approaches to the solution of the quadratic equation with real coefficients. In this article it is shown that the monic quadratic equation with complex coefficients can also be solved graphically, by the intersection of two hyperbolas; one hyperbola being derived from the real part of the quadratic equation and one from…

Sky-High I's

ERIC Educational Resources Information Center

Berry, Andrew J.

2004-01-01

When discussing the topic of elementary complex variables, students are often mystified by the fact that ii is real. After seeing a proof of this statement, a standard question is "well, what about iii or iiii etc., are these real or complex?" In this paper the meaning of the infinite power-tower iii...is considered both from the "bottom-up" and…

Real topological entropy versus metric entropy for birational measure-preserving transformations

NASA Astrophysics Data System (ADS)

Abarenkova, N.; Anglès d'Auriac, J.-Ch.; Boukraa, S.; Maillard, J.-M.

2000-10-01

We consider a family of birational measure-preserving transformations of two complex variables, depending on one parameter for which simple rational expressions for the dynamical zeta function have been conjectured, together with an equality between the topological entropy and the logarithm of the Arnold complexity (divided by the number of iterations). Similar results have been obtained for the adaptation of these two concepts to dynamical systems of real variables, yielding to introduce a “real topological entropy” and a “real Arnold complexity”. We try to compare, here, the Kolmogorov-Sinai metric entropy and this real Arnold complexity, or real topological entropy, on this particular example of a one-parameter dependent birational transformation of two variables. More precisely, we analyze, using an infinite precision calculation, the Lyapunov characteristic exponents for various values of the parameter of the birational transformation, in order to compare these results with the ones for the real Arnold complexity. We find a quite surprising result: for this very birational example, and, in fact, for a large set of birational measure-preserving mappings generated by involutions, the Lyapunov characteristic exponents seem to be equal to zero or, at least, extremely small, for all the orbits we have considered, and for all values of the parameter. Birational measure-preserving transformations, generated by involutions, could thus allow to better understand the difference between the topological description and the probabilistic description of discrete dynamical systems. Many birational measure-preserving transformations, generated by involutions, seem to provide examples of discrete dynamical systems which can be topologically chaotic while they are metrically almost quasi-periodic. Heuristically, this can be understood as a consequence of the fact that their orbits seem to form some kind of “transcendental foliation” of the two-dimensional space of variables.

On complex matrices with simple spectrum that are unitarily similar to real matrices

NASA Astrophysics Data System (ADS)

Ikramov, Khakim D.

2011-04-01

Suppose that one should verify whether a given complex n × n matrix can be converted into a real matrix by a unitary similarity transformation. Sufficient conditions for this property to hold were found in an earlier publication of this author. These conditions are relaxed in the following way: as before, the spectrum is required to be simple, but pairs of complex conjugate eigenvalues λ ,bar λ are now allowed. However, the eigenvectors corresponding to such eigenvalues must not be orthogonal.

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.

A system for measuring complex dielectric properties of thin films at submillimeter wavelengths using an open hemispherical cavity and a vector network analyzer.

PubMed

Rahman, Rezwanur; Taylor, P C; Scales, John A

2013-08-01

Quasi-optical (QO) methods of dielectric spectroscopy are well established in the millimeter and submillimeter frequency bands. These methods exploit standing wave structure in the sample produced by a transmitted Gaussian beam to achieve accurate, low-noise measurement of the complex permittivity of the sample [e.g., J. A. Scales and M. Batzle, Appl. Phys. Lett. 88, 062906 (2006); R. N. Clarke and C. B. Rosenberg, J. Phys. E 15, 9 (1982); T. M. Hirovnen, P. Vainikainen, A. Lozowski, and A. V. Raisanen, IEEE Trans. Instrum. Meas. 45, 780 (1996)]. In effect the sample itself becomes a low-Q cavity. On the other hand, for optically thin samples (films of thickness much less than a wavelength) or extremely low loss samples (loss tangents below 10(-5)) the QO approach tends to break down due to loss of signal. In such a case it is useful to put the sample in a high-Q cavity and measure the perturbation of the cavity modes. Provided that the average mode frequency divided by the shift in mode frequency is less than the Q (quality factor) of the mode, then the perturbation should be resolvable. Cavity perturbation techniques are not new, but there are technological difficulties in working in the millimeter/submillimeter wave region. In this paper we will show applications of cavity perturbation to the dielectric characterization of semi-conductor thin films of the type used in the manufacture of photovoltaics in the 100 and 350 GHz range. We measured the complex optical constants of hot-wire chemical deposition grown 1-μm thick amorphous silicon (a-Si:H) film on borosilicate glass substrate. The real part of the refractive index and dielectric constant of the glass-substrate varies from frequency-independent to linearly frequency-dependent. We also see power-law behavior of the frequency-dependent optical conductivity from 316 GHz (9.48 cm(-1)) down to 104 GHz (3.12 cm(-1)).

Complex matrix multiplication operations with data pre-conditioning in a high performance computing architecture

DOEpatents

Eichenberger, Alexandre E; Gschwind, Michael K; Gunnels, John A

2014-02-11

Mechanisms for performing a complex matrix multiplication operation are provided. A vector load operation is performed to load a first vector operand of the complex matrix multiplication operation to a first target vector register. The first vector operand comprises a real and imaginary part of a first complex vector value. A complex load and splat operation is performed to load a second complex vector value of a second vector operand and replicate the second complex vector value within a second target vector register. The second complex vector value has a real and imaginary part. A cross multiply add operation is performed on elements of the first target vector register and elements of the second target vector register to generate a partial product of the complex matrix multiplication operation. The partial product is accumulated with other partial products and a resulting accumulated partial product is stored in a result vector register.

Self-potential and Complex Conductivity Monitoring of In Situ Hydrocarbon Remediation in Microbial Fuel Cell

NASA Astrophysics Data System (ADS)

Zhang, C.; Revil, A.; Ren, Z.; Karaoulis, M.; Mendonca, C. A.

2013-12-01

Petroleum hydrocarbon contamination of soil and groundwater in both non-aqueous phase liquid and dissolved forms generated from spills and leaks is a wide spread environmental issue. Traditional cleanup of hydrocarbon contamination in soils and ground water using physical, chemical, and biological remedial techniques is often expensive and ineffective. Recent studies show that the microbial fuel cell (MFC) can simultaneously enhance biodegradation of hydrocarbons in soil and groundwater and yield electricity. Non-invasive geophysical techniques such as self-potential (SP) and complex conductivity (induced polarization) have shown the potential to detect and characterize the nature of electron transport mechanism of in situ bioremediation of organic contamination plumes. In this study, we deployed both SP and complex conductivity in lab scale MFCs to monitor time-laps geophysical response of degradation of hydrocarbons by MFC. Two different sizes of MFC reactors were used in this study (DI=15 cm cylinder reactor and 94.5cm x 43.5 cm rectangle reactor), and the initial hydrocarbon concentration is 15 g diesel/kg soil. SP and complex conductivity measurements were measured using non-polarizing Ag/AgCl electrodes. Sensitivity study was also performed using COMSOL Multiphysics to test different electrode configurations. The SP measurements showed stronger anomalies adjacent to the MFC than locations afar, and both real and imaginary parts of complex conductivity are greater in areas close to MFC than areas further away and control samples without MFC. The joint use of SP and complex conductivity could in situ evaluate the dynamic changes of electrochemical parameters during this bioremediation process at spatiotemporal scales unachievable with traditional sampling methods. The joint inversion of these two methods to evaluate the efficiency of MFC enhanced hydrocarbon remediation in the subsurface.

Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation

PubMed Central

Cornuet, Jean-Marie; Santos, Filipe; Beaumont, Mark A.; Robert, Christian P.; Marin, Jean-Michel; Balding, David J.; Guillemaud, Thomas; Estoup, Arnaud

2008-01-01

Summary: Genetic data obtained on population samples convey information about their evolutionary history. Inference methods can extract part of this information but they require sophisticated statistical techniques that have been made available to the biologist community (through computer programs) only for simple and standard situations typically involving a small number of samples. We propose here a computer program (DIY ABC) for inference based on approximate Bayesian computation (ABC), in which scenarios can be customized by the user to fit many complex situations involving any number of populations and samples. Such scenarios involve any combination of population divergences, admixtures and population size changes. DIY ABC can be used to compare competing scenarios, estimate parameters for one or more scenarios and compute bias and precision measures for a given scenario and known values of parameters (the current version applies to unlinked microsatellite data). This article describes key methods used in the program and provides its main features. The analysis of one simulated and one real dataset, both with complex evolutionary scenarios, illustrates the main possibilities of DIY ABC. Availability: The software DIY ABC is freely available at http://www.montpellier.inra.fr/CBGP/diyabc. Contact: j.cornuet@imperial.ac.uk Supplementary information: Supplementary data are also available at http://www.montpellier.inra.fr/CBGP/diyabc PMID:18842597

A dispersive liquid--liquid microextraction methodology for copper (II) in environmental samples prior to determination using microsample injection flame atomic absorption spectrometry.

PubMed

Alothman, Zeid A; Habila, Mohamed; Yilmaz, Erkan; Soylak, Mustafa

2013-01-01

A simple, environmentally friendly, and efficient dispersive liquid-liquid microextraction method combined with microsample injection flame atomic absorption spectrometry was developed for the separation and preconcentration of Cu(II). 2-(5-Bromo-2-pyridylazo)-5-(diethylamino)phenol (5-Br-PADAP) was used to form a hydrophobic complex of Cu(II) ions in the aqueous phase before extraction. To extract the Cu(II)-5-Br-PADAP complex from the aqueous phase to the organic phase, 2.0 mL of acetone as a disperser solvent and 200 microL of chloroform as an extraction solvent were used. The influences of important analytical parameters, such as the pH, types and volumes of the extraction and disperser solvents, amount of chelating agent, sample volume, and matrix effects, on the microextraction procedure were evaluated and optimized. Using the optimal conditions, the LOD, LOQ, preconcentration factor, and RSD were determined to be 1.4 microg/L, 4.7 microg/L, 120, and 6.5%, respectively. The accuracy of the proposed method was investigated using standard addition/recovery tests. The analysis of certified reference materials produced satisfactory analytical results. The developed method was applied for the determination of Cu in real samples.

[Preparation and applications of a supported liquid-liquid extraction column with a composite diatomite material].

PubMed

Bao, Jianmin; Ma, Zhishuang; Sun, Ying; Wang, Yongzun; Li, Youxin

2012-08-01

A rapid and special supported liquid-liquid extraction (SLE) column was developed with a composite diatomite material. The SLE column was evaluated by high performance liquid chromatography (HPLC) with acidic, neutral and alkaline compounds dissolved in water. Furthermore, some real complex samples were also analyzed by HPLC with the SLE method. The recoveries of benzoic acid (acidic), p-nitroaniline (alkaline) and 4-hydroxy-benzoic methyl ester (neutral) treated by the SLE column were 90.6%, 98.1% and 97.7%. However, the recoveries of the three compounds treated by traditional liquid-liquid extraction (LLE) method were 71.9%, 81.9% and 83.9%. The results showed that the SLE technique had higher recoveries than the traditional LLE method. The spiked recoveries of the complex samples, such as benzoic acid in Sprite and dexamethasone acetate, chlorphenamine maleate, indomethacin in bovine serum, were between 80% and 110% and the relative standard deviations (RSDs) were less than 15%. For biological specimen, the results could be accepted. Meantime, many disadvantages associated with traditional LLE method, such as emulsion formation, didn't occur using SLE column. The SLE column technique is a good sample preparation method with many advantages, such as rapid, simple, robust, easily automated, high recovery and high-throughput, which would be widely used in the future.

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.

Direct detection of Mycobacterium tuberculosis complex in bovine and bubaline tissues through nested-PCR.

PubMed

Araújo, Cristina P; Osório, Ana Luiza A R; Jorge, Klaudia S G; Ramos, Carlos A N; Souza Filho, Antonio F; Vidal, Carlos E S; Vargas, Agueda P C; Roxo, Eliana; Rocha, Adalgiza S; Suffys, Philip N; Fonseca, Antônio A; Silva, Marcio R; Barbosa Neto, José D; Cerqueira, Valíria D; Araújo, Flábio R

2014-01-01

Post-mortem bacterial culture and specific biochemical tests are currently performed to characterize the etiologic agent of bovine tuberculosis. Cultures take up to 90 days to develop. A diagnosis by molecular tests such as PCR can provide fast and reliable results while significantly decreasing the time of confirmation. In the present study, a nested-PCR system, targeting rv2807, with conventional PCR followed by real-time PCR, was developed to detect Mycobacterium tuberculosis complex (MTC) organisms directly from bovine and bubaline tissue homogenates. The sensitivity and specificity of the reactions were assessed with DNA samples extracted from tuberculous and non-tuberculous mycobacteria, as well as other Actinomycetales species and DNA samples extracted directly from bovine and bubaline tissue homogenates. Regarding the analytical sensitivity, DNA of the M. bovis AN5 strain was detected up to 1.5 pg by nested-PCR, whereas DNA of M. tuberculosis H37Rv strain was detected up to 6.1 pg. The nested-PCR system showed 100% analytical specificity for MTC when tested with DNA of reference strains of non-tuberculous mycobacteria and closely-related Actinomycetales. A clinical sensitivity level of 76.7% was detected with tissues samples positive for MTC by means of the culture and conventional PCR. A clinical specificity of 100% was detected with DNA from tissue samples of cattle with negative results in the comparative intradermal tuberculin test. These cattle exhibited no visible lesions and were negative in the culture for MTC. The use of the nested-PCR assay to detect M. tuberculosis complex in tissue homogenates provided a rapid diagnosis of bovine and bubaline tuberculosis.

Direct detection of Mycobacterium tuberculosis complex in bovine and bubaline tissues through nested-PCR

PubMed Central

Araújo, Cristina P.; Osório, Ana Luiza A.R.; Jorge, Klaudia S.G.; Ramos, Carlos A.N.; Souza Filho, Antonio F.; Vidal, Carlos E.S.; Vargas, Agueda P.C.; Roxo, Eliana; Rocha, Adalgiza S.; Suffys, Philip N.; Fonseca, Antônio A.; Silva, Marcio R.; Barbosa Neto, José D.; Cerqueira, Valíria D.; Araújo, Flábio R.

2014-01-01

Post-mortem bacterial culture and specific biochemical tests are currently performed to characterize the etiologic agent of bovine tuberculosis. Cultures take up to 90 days to develop. A diagnosis by molecular tests such as PCR can provide fast and reliable results while significantly decreasing the time of confirmation. In the present study, a nested-PCR system, targeting rv2807, with conventional PCR followed by real-time PCR, was developed to detect Mycobacterium tuberculosis complex (MTC) organisms directly from bovine and bubaline tissue homogenates. The sensitivity and specificity of the reactions were assessed with DNA samples extracted from tuberculous and non-tuberculous mycobacteria, as well as other Actinomycetales species and DNA samples extracted directly from bovine and bubaline tissue homogenates. Regarding the analytical sensitivity, DNA of the M. bovis AN5 strain was detected up to 1.5 pg by nested-PCR, whereas DNA of M. tuberculosis H37Rv strain was detected up to 6.1 pg. The nested-PCR system showed 100% analytical specificity for MTC when tested with DNA of reference strains of non-tuberculous mycobacteria and closely-related Actinomycetales. A clinical sensitivity level of 76.7% was detected with tissues samples positive for MTC by means of the culture and conventional PCR. A clinical specificity of 100% was detected with DNA from tissue samples of cattle with negative results in the comparative intradermal tuberculin test. These cattle exhibited no visible lesions and were negative in the culture for MTC. The use of the nested-PCR assay to detect M. tuberculosis complex in tissue homogenates provided a rapid diagnosis of bovine and bubaline tuberculosis. PMID:25242951

On the break down of reality at superluminal velocities, Quantum entanglement and Singularities (Complex Universe)

NASA Astrophysics Data System (ADS)

Estakhr, Ahmad Reza

2017-09-01

In the real world nothing can move faster than the speed of light. But what convinces you that our world is all real? I realized that reality break down at superluminal velocities (By studying the physics of tachyonic neutrinos), Quantum entanglement and Singularities of Black Holes, I realized that infact our world is complex and has two parts, one part of the world is real (the part that nothing can move faster than the speed of light) but the other part of the world is imaginary. z = a + ib Einstein was wrong because he thought our world is completely real (Of course he was not alone in this belief almost all physicists believe that our world is completely real) Eventually his false interpretation of reality censored imaginary part of the universe. Einstein's Second Postulate of special theory of relativity was a misleading guide to the true nature of reality. He `expected' the true nature of reality will follow to his (false) postulate, But the true nature of reality is unlike what anyone ever `expected'!. Einstein twist facts to suit his theory of relativity instead of theories to suit facts!. This is a dramatic revisions to our conception of the theory of relativity, Reality is complex but We always perceive its real part.

Real-time and interactive virtual Doppler ultrasound

NASA Astrophysics Data System (ADS)

Hirji, Samira; Downey, Donal B.; Holdsworth, David W.; Steinman, David A.

2005-04-01

This paper describes our "virtual" Doppler ultrasound (DUS) system, in which colour DUS (CDUS) images and DUS spectrograms are generated on-the-fly and displayed in real-time in response to position and orientation cues provided by a magnetically tracked handheld probe. As the presence of complex flow often confounds the interpretation of Doppler ultrasound data, this system will serve to be a fundamental tool for training sonographers and gaining insight into the relationship between ambiguous DUS images and complex blood flow dynamics. Recently, we demonstrated that DUS spectra could be realistically simulated in real-time, by coupling a semi-empirical model of the DUS physics to a 3-D computational fluid dynamics (CFD) model of a clinically relevant flow field. Our system is an evolution of this approach where a motion-tracking device is used to continuously update the origin and orientation of a slice passing through a CFD model of a stenosed carotid bifurcation. After calibrating our CFD model onto a physical representation of a human neck, virtual CDUS images from an instantaneous slice are then displayed at a rate of approximately 15 Hz by simulating, on-the-fly, an array of DUS spectra and colour coding the resulting spectral mean velocity using a traditional Doppler colour scale. Mimicking a clinical examination, the operator can freeze the CDUS image on-screen, and a spectrogram corresponding to the selected sample volume location is rendered at a higher frame rate of at least 30 Hz. All this is achieved using an inexpensive desktop workstation and commodity graphics card.

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.

Interlaboratory study of DNA extraction from multiple ground samples, multiplex real-time PCR, and multiplex qualitative PCR for individual kernel detection system of genetically modified maize.

PubMed

Akiyama, Hiroshi; Sakata, Kozue; Makiyma, Daiki; Nakamura, Kosuke; Teshima, Reiko; Nakashima, Akie; Ogawa, Asako; Yamagishi, Toru; Futo, Satoshi; Oguchi, Taichi; Mano, Junichi; Kitta, Kazumi

2011-01-01

In many countries, the labeling of grains, feed, and foodstuff is mandatory if the genetically modified (GM) organism content exceeds a certain level of approved GM varieties. We previously developed an individual kernel detection system consisting of grinding individual kernels, DNA extraction from the individually ground kernels, GM detection using multiplex real-time PCR, and GM event detection using multiplex qualitative PCR to analyze the precise commingling level and varieties of GM maize in real sample grains. We performed the interlaboratory study of the DNA extraction with multiple ground samples, multiplex real-time PCR detection, and multiplex qualitative PCR detection to evaluate its applicability, practicality, and ruggedness for the individual kernel detection system of GM maize. DNA extraction with multiple ground samples, multiplex real-time PCR, and multiplex qualitative PCR were evaluated by five laboratories in Japan, and all results from these laboratories were consistent with the expected results in terms of the commingling level and event analysis. Thus, the DNA extraction with multiple ground samples, multiplex real-time PCR, and multiplex qualitative PCR for the individual kernel detection system is applicable and practicable in a laboratory to regulate the commingling level of GM maize grain for GM samples, including stacked GM maize.

Development of a one-run real-time PCR detection system for pathogens associated with bovine respiratory disease complex.

PubMed

Kishimoto, Mai; Tsuchiaka, Shinobu; Rahpaya, Sayed Samim; Hasebe, Ayako; Otsu, Keiko; Sugimura, Satoshi; Kobayashi, Suguru; Komatsu, Natsumi; Nagai, Makoto; Omatsu, Tsutomu; Naoi, Yuki; Sano, Kaori; Okazaki-Terashima, Sachiko; Oba, Mami; Katayama, Yukie; Sato, Reiichiro; Asai, Tetsuo; Mizutani, Tetsuya

2017-03-18

Bovine respiratory disease complex (BRDC) is frequently found in cattle worldwide. The etiology of BRDC is complicated by infections with multiple pathogens, making identification of the causal pathogen difficult. Here, we developed a detection system by applying TaqMan real-time PCR (Dembo respiratory-PCR) to screen a broad range of microbes associated with BRDC in a single run. We selected 16 bovine respiratory pathogens (bovine viral diarrhea virus, bovine coronavirus, bovine parainfluenza virus 3, bovine respiratory syncytial virus, influenza D virus, bovine rhinitis A virus, bovine rhinitis B virus, bovine herpesvirus 1, bovine adenovirus 3, bovine adenovirus 7, Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, Trueperella pyogenes, Mycoplasma bovis and Ureaplasma diversum) as detection targets and designed novel specific primer-probe sets for nine of them. The assay performance was assessed using standard curves from synthesized DNA. In addition, the sensitivity of the assay was evaluated by spiking solutions extracted from nasal swabs that were negative by Dembo respiratory-PCR for nucleic acids of pathogens or synthesized DNA. All primer-probe sets showed high sensitivity. In this study, a total of 40 nasal swab samples from cattle on six farms were tested by Dembo respiratory-PCR. Dembo respiratory-PCR can be applied as a screening system with wide detection targets.

Trace detection of organic compounds in complex sample matrixes by single photon ionization ion trap mass spectrometry: real-time detection of security-relevant compounds and online analysis of the coffee-roasting process.

PubMed

Schramm, Elisabeth; Kürten, Andreas; Hölzer, Jasper; Mitschke, Stefan; Mühlberger, Fabian; Sklorz, Martin; Wieser, Jochen; Ulrich, Andreas; Pütz, Michael; Schulte-Ladbeck, Rasmus; Schultze, Rainer; Curtius, Joachim; Borrmann, Stephan; Zimmermann, Ralf

2009-06-01

An in-house-built ion trap mass spectrometer combined with a soft ionization source has been set up and tested. As ionization source, an electron beam pumped vacuum UV (VUV) excimer lamp (EBEL) was used for single-photon ionization. It was shown that soft ionization allows the reduction of fragmentation of the target analytes and the suppression of most matrix components. Therefore, the combination of photon ionization with the tandem mass spectrometry (MS/MS) capability of an ion trap yields a powerful tool for molecular ion peak detection and identification of organic trace compounds in complex matrixes. This setup was successfully tested for two different applications. The first one is the detection of security-relevant substances like explosives, narcotics, and chemical warfare agents. One test substance from each of these groups was chosen and detected successfully with single photon ionization ion trap mass spectrometry (SPI-ITMS) MS/MS measurements. Additionally, first tests were performed, demonstrating that this method is not influenced by matrix compounds. The second field of application is the detection of process gases. Here, exhaust gas from coffee roasting was analyzed in real time, and some of its compounds were identified using MS/MS studies.

Rehabilitation of executive functioning in patients with frontal lobe brain damage with goal management training.

PubMed

Levine, Brian; Schweizer, Tom A; O'Connor, Charlene; Turner, Gary; Gillingham, Susan; Stuss, Donald T; Manly, Tom; Robertson, Ian H

2011-01-01

Executive functioning deficits due to brain disease affecting frontal lobe functions cause significant real-life disability, yet solid evidence in support of executive functioning interventions is lacking. Goal Management Training (GMT), an executive functioning intervention that draws upon theories concerning goal processing and sustained attention, has received empirical support in studies of patients with traumatic brain injury, normal aging, and case studies. GMT promotes a mindful approach to complex real-life tasks that pose problems for patients with executive functioning deficits, with a main goal of periodically stopping ongoing behavior to monitor and adjust goals. In this controlled trial, an expanded version of GMT was compared to an alternative intervention, Brain Health Workshop that was matched to GMT on non-specific characteristics that can affect intervention outcome. Participants included 19 individuals in the chronic phase of recovery from brain disease (predominantly stroke) affecting frontal lobe function. Outcome data indicated specific effects of GMT on the Sustained Attention to Response Task as well as the Tower Test, a visuospatial problem-solving measure that reflected far transfer of training effects. There were no significant effects on self-report questionnaires, likely owing to the complexity of these measures in this heterogeneous patient sample. Overall, these data support the efficacy of GMT in the rehabilitation of executive functioning deficits.

A critical analysis of single-frequency LCR databridge impedance measurements of human skin.

PubMed

White, Erick A; Orazem, Mark E; Bunge, Annette L

2011-06-01

Testing whether the barrier of skin samples has sufficient integrity for meaningful measurements of in-vitro chemical permeability is usually required when data are generated for regulatory purposes. Recently, skin integrity has been assessed using LCR databridge measurements, which are reported as resistances determined in either series (SER) or parallel (PAR) modes at a single frequency, typically 100 or 1000Hz. Measurements made at different combinations of mode and frequency are known to differ, although the skin literature reveals confusion over the meaning of these differences and the impact on the interpretation of integrity test results. Here, the theoretical meanings of resistance and capacitance measurements in PAR and SER mode are described and confirmed experimentally. SER-mode resistances are equal to the real part of the complex impedance; whereas, PAR-mode resistances are the inverse of the real part of the admittance. Capacitance measurements reported in SER and PAR modes are similar manipulations of the imaginary parts of the complex impedance and admittance. A large body of data from human cadaver skin is used to show that the PAR-mode resistance and SER-mode capacitance measured at 100Hz are sensitive to skin resistivity, which is the electrical measurement most closely related to skin integrity. Copyright © 2011 Elsevier Ltd. All rights reserved.

Implementation of a portable device for real-time ECG signal analysis.

PubMed

Jeon, Taegyun; Kim, Byoungho; Jeon, Moongu; Lee, Byung-Geun

2014-12-10

Cardiac disease is one of the main causes of catastrophic mortality. Therefore, detecting the symptoms of cardiac disease as early as possible is important for increasing the patient's survival. In this study, a compact and effective architecture for detecting atrial fibrillation (AFib) and myocardial ischemia is proposed. We developed a portable device using this architecture, which allows real-time electrocardiogram (ECG) signal acquisition and analysis for cardiac diseases. A noisy ECG signal was preprocessed by an analog front-end consisting of analog filters and amplifiers before it was converted into digital data. The analog front-end was minimized to reduce the size of the device and power consumption by implementing some of its functions with digital filters realized in software. With the ECG data, we detected QRS complexes based on wavelet analysis and feature extraction for morphological shape and regularity using an ARM processor. A classifier for cardiac disease was constructed based on features extracted from a training dataset using support vector machines. The classifier then categorized the ECG data into normal beats, AFib, and myocardial ischemia. A portable ECG device was implemented, and successfully acquired and processed ECG signals. The performance of this device was also verified by comparing the processed ECG data with high-quality ECG data from a public cardiac database. Because of reduced computational complexity, the ARM processor was able to process up to a thousand samples per second, and this allowed real-time acquisition and diagnosis of heart disease. Experimental results for detection of heart disease showed that the device classified AFib and ischemia with a sensitivity of 95.1% and a specificity of 95.9%. Current home care and telemedicine systems have a separate device and diagnostic service system, which results in additional time and cost. Our proposed portable ECG device provides captured ECG data and suspected waveform to identify sporadic and chronic events of heart diseases. This device has been built and evaluated for high quality of signals, low computational complexity, and accurate detection.

Sound stream segregation: a neuromorphic approach to solve the “cocktail party problem” in real-time

PubMed Central

Thakur, Chetan Singh; Wang, Runchun M.; Afshar, Saeed; Hamilton, Tara J.; Tapson, Jonathan C.; Shamma, Shihab A.; van Schaik, André

2015-01-01

The human auditory system has the ability to segregate complex auditory scenes into a foreground component and a background, allowing us to listen to specific speech sounds from a mixture of sounds. Selective attention plays a crucial role in this process, colloquially known as the “cocktail party effect.” It has not been possible to build a machine that can emulate this human ability in real-time. Here, we have developed a framework for the implementation of a neuromorphic sound segregation algorithm in a Field Programmable Gate Array (FPGA). This algorithm is based on the principles of temporal coherence and uses an attention signal to separate a target sound stream from background noise. Temporal coherence implies that auditory features belonging to the same sound source are coherently modulated and evoke highly correlated neural response patterns. The basis for this form of sound segregation is that responses from pairs of channels that are strongly positively correlated belong to the same stream, while channels that are uncorrelated or anti-correlated belong to different streams. In our framework, we have used a neuromorphic cochlea as a frontend sound analyser to extract spatial information of the sound input, which then passes through band pass filters that extract the sound envelope at various modulation rates. Further stages include feature extraction and mask generation, which is finally used to reconstruct the targeted sound. Using sample tonal and speech mixtures, we show that our FPGA architecture is able to segregate sound sources in real-time. The accuracy of segregation is indicated by the high signal-to-noise ratio (SNR) of the segregated stream (90, 77, and 55 dB for simple tone, complex tone, and speech, respectively) as compared to the SNR of the mixture waveform (0 dB). This system may be easily extended for the segregation of complex speech signals, and may thus find various applications in electronic devices such as for sound segregation and speech recognition. PMID:26388721

Sound stream segregation: a neuromorphic approach to solve the "cocktail party problem" in real-time.

PubMed

Thakur, Chetan Singh; Wang, Runchun M; Afshar, Saeed; Hamilton, Tara J; Tapson, Jonathan C; Shamma, Shihab A; van Schaik, André

2015-01-01

The human auditory system has the ability to segregate complex auditory scenes into a foreground component and a background, allowing us to listen to specific speech sounds from a mixture of sounds. Selective attention plays a crucial role in this process, colloquially known as the "cocktail party effect." It has not been possible to build a machine that can emulate this human ability in real-time. Here, we have developed a framework for the implementation of a neuromorphic sound segregation algorithm in a Field Programmable Gate Array (FPGA). This algorithm is based on the principles of temporal coherence and uses an attention signal to separate a target sound stream from background noise. Temporal coherence implies that auditory features belonging to the same sound source are coherently modulated and evoke highly correlated neural response patterns. The basis for this form of sound segregation is that responses from pairs of channels that are strongly positively correlated belong to the same stream, while channels that are uncorrelated or anti-correlated belong to different streams. In our framework, we have used a neuromorphic cochlea as a frontend sound analyser to extract spatial information of the sound input, which then passes through band pass filters that extract the sound envelope at various modulation rates. Further stages include feature extraction and mask generation, which is finally used to reconstruct the targeted sound. Using sample tonal and speech mixtures, we show that our FPGA architecture is able to segregate sound sources in real-time. The accuracy of segregation is indicated by the high signal-to-noise ratio (SNR) of the segregated stream (90, 77, and 55 dB for simple tone, complex tone, and speech, respectively) as compared to the SNR of the mixture waveform (0 dB). This system may be easily extended for the segregation of complex speech signals, and may thus find various applications in electronic devices such as for sound segregation and speech recognition.

Exploration of complex visual feature spaces for object perception

PubMed Central

Leeds, Daniel D.; Pyles, John A.; Tarr, Michael J.

2014-01-01

The mid- and high-level visual properties supporting object perception in the ventral visual pathway are poorly understood. In the absence of well-specified theory, many groups have adopted a data-driven approach in which they progressively interrogate neural units to establish each unit's selectivity. Such methods are challenging in that they require search through a wide space of feature models and stimuli using a limited number of samples. To more rapidly identify higher-level features underlying human cortical object perception, we implemented a novel functional magnetic resonance imaging method in which visual stimuli are selected in real-time based on BOLD responses to recently shown stimuli. This work was inspired by earlier primate physiology work, in which neural selectivity for mid-level features in IT was characterized using a simple parametric approach (Hung et al., 2012). To extend such work to human neuroimaging, we used natural and synthetic object stimuli embedded in feature spaces constructed on the basis of the complex visual properties of the objects themselves. During fMRI scanning, we employed a real-time search method to control continuous stimulus selection within each image space. This search was designed to maximize neural responses across a pre-determined 1 cm3 brain region within ventral cortex. To assess the value of this method for understanding object encoding, we examined both the behavior of the method itself and the complex visual properties the method identified as reliably activating selected brain regions. We observed: (1) Regions selective for both holistic and component object features and for a variety of surface properties; (2) Object stimulus pairs near one another in feature space that produce responses at the opposite extremes of the measured activity range. Together, these results suggest that real-time fMRI methods may yield more widely informative measures of selectivity within the broad classes of visual features associated with cortical object representation. PMID:25309408

Exact sampling of graphs with prescribed degree correlations

NASA Astrophysics Data System (ADS)

Bassler, Kevin E.; Del Genio, Charo I.; Erdős, Péter L.; Miklós, István; Toroczkai, Zoltán

2015-08-01

Many real-world networks exhibit correlations between the node degrees. For instance, in social networks nodes tend to connect to nodes of similar degree and conversely, in biological and technological networks, high-degree nodes tend to be linked with low-degree nodes. Degree correlations also affect the dynamics of processes supported by a network structure, such as the spread of opinions or epidemics. The proper modelling of these systems, i.e., without uncontrolled biases, requires the sampling of networks with a specified set of constraints. We present a solution to the sampling problem when the constraints imposed are the degree correlations. In particular, we develop an exact method to construct and sample graphs with a specified joint-degree matrix, which is a matrix providing the number of edges between all the sets of nodes of a given degree, for all degrees, thus completely specifying all pairwise degree correlations, and additionally, the degree sequence itself. Our algorithm always produces independent samples without backtracking. The complexity of the graph construction algorithm is {O}({NM}) where N is the number of nodes and M is the number of edges.

Nanocolloidal gold-based immuno-dip strip assay for rapid detection of Sudan red I in food samples.

PubMed

Wang, Jia; Wang, Zhanhui; Liu, Jing; Li, Hao; Li, Qing X; Li, Ji; Xu, Ting

2013-02-15

A semiquantitative dip strip assay was developed using nanocolloidal gold-labelled monoclonal antibody (Mab) 8A10 for the rapid detection of Sudan red I in food samples. A protein-Sudan red I conjugate was coated on a nitro cellulose membrane strip in a defined test line. In flow of the complex of nanocolloidal gold labelled-Mab and Sudan red I along the strip, intensive red colour that was formed in the test line reflected the Sudan red I concentration. The test required 10 min and had a visual limit of detection of 10 ng/g Sudan red I in tomato sauce and chilli powder samples. The results of the strip assay agreed well with those of a high performance liquid chromatography method for both spiked and real commercial samples. The strip was stable for at least 2 months at 4°C. The strip assay offers the potential as a useful rapid and simple method for screening of Sudan red I in food samples. Copyright © 2012 Elsevier Ltd. All rights reserved.

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.

DNA barcoding and real-time PCR detection of Bactrocera xanthodes (Tephritidae: Diptera) complex.

PubMed

Li, D; Waite, D W; Gunawardana, D N; McCarthy, B; Anderson, D; Flynn, A; George, S

2018-05-06

Immature fruit fly stages of the family Tephritidae are commonly intercepted on breadfruit from Pacific countries at the New Zealand border but are unable to be identified to the species level using morphological characters. Subsequent molecular identification showed that they belong to Bactrocera xanthodes, which is part of a species complex that includes Bactrocera paraxanthodes, Bactrocera neoxanthodes and an undescribed species. To establish a more reliable molecular identification system for B. xanthodes, a reference database of DNA barcode sequences for the 5'-fragment of COI gene region was constructed for B. xanthodes from Fiji, Samoa and Tonga. To better understand the species complex, B. neoxanthodes from Vanuatu and B. paraxanthodes from New Caledonia were also barcoded. Using the results of this analysis, real-time TaqMan polymerase chain reaction (PCR) assays for the detection of B. xanthodes complex and for the three individual species of the complex were developed and validated. The assay showed high specificity for the target species, with no cross-reaction observed for closely related organisms. Each of the real-time PCR assays is sensitive, detecting the target sequences at concentrations as low as ten copies µl-1 and can be used as either singleplex or multiplex formats. This real-time PCR assay for B. xanthodes has been successfully applied at the borders in New Zealand, leading to the rapid identification of intercepted Tephritidae eggs and larvae. The developed assays will be useful biosecurity tools for rapid detection of species in the B. xanthodes complex worldwide.

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.

Efficient sampling of complex network with modified random walk strategies

NASA Astrophysics Data System (ADS)

Xie, Yunya; Chang, Shuhua; Zhang, Zhipeng; Zhang, Mi; Yang, Lei

2018-02-01

We present two novel random walk strategies, choosing seed node (CSN) random walk and no-retracing (NR) random walk. Different from the classical random walk sampling, the CSN and NR strategies focus on the influences of the seed node choice and path overlap, respectively. Three random walk samplings are applied in the Erdös-Rényi (ER), Barabási-Albert (BA), Watts-Strogatz (WS), and the weighted USAir networks, respectively. Then, the major properties of sampled subnets, such as sampling efficiency, degree distributions, average degree and average clustering coefficient, are studied. The similar conclusions can be reached with these three random walk strategies. Firstly, the networks with small scales and simple structures are conducive to the sampling. Secondly, the average degree and the average clustering coefficient of the sampled subnet tend to the corresponding values of original networks with limited steps. And thirdly, all the degree distributions of the subnets are slightly biased to the high degree side. However, the NR strategy performs better for the average clustering coefficient of the subnet. In the real weighted USAir networks, some obvious characters like the larger clustering coefficient and the fluctuation of degree distribution are reproduced well by these random walk strategies.

GPU-Meta-Storms: computing the structure similarities among massive amount of microbial community samples using GPU.

PubMed

Su, Xiaoquan; Wang, Xuetao; Jing, Gongchao; Ning, Kang

2014-04-01

The number of microbial community samples is increasing with exponential speed. Data-mining among microbial community samples could facilitate the discovery of valuable biological information that is still hidden in the massive data. However, current methods for the comparison among microbial communities are limited by their ability to process large amount of samples each with complex community structure. We have developed an optimized GPU-based software, GPU-Meta-Storms, to efficiently measure the quantitative phylogenetic similarity among massive amount of microbial community samples. Our results have shown that GPU-Meta-Storms would be able to compute the pair-wise similarity scores for 10 240 samples within 20 min, which gained a speed-up of >17 000 times compared with single-core CPU, and >2600 times compared with 16-core CPU. Therefore, the high-performance of GPU-Meta-Storms could facilitate in-depth data mining among massive microbial community samples, and make the real-time analysis and monitoring of temporal or conditional changes for microbial communities possible. GPU-Meta-Storms is implemented by CUDA (Compute Unified Device Architecture) and C++. Source code is available at http://www.computationalbioenergy.org/meta-storms.html.

Lateral Flow Immunoassays for Ebola Virus Disease Detection in Liberia.

PubMed

Phan, Jill C; Pettitt, James; George, Josiah S; Fakoli, Lawrence S; Taweh, Fahn M; Bateman, Stacey L; Bennett, Richard S; Norris, Sarah L; Spinnler, David A; Pimentel, Guillermo; Sahr, Phillip K; Bolay, Fatorma K; Schoepp, Randal J

2016-10-15

Lateral flow immunoassays (LFIs) are point-of-care diagnostic assays that are designed for single use outside a formal laboratory, with in-home pregnancy tests the best-known example of these tests. Although the LFI has some limitations over more-complex immunoassay procedures, such as reduced sensitivity and the potential for false-positive results when using complex sample matrices, the assay has the benefits of a rapid time to result and ease of use. These benefits make it an attractive option for obtaining rapid results in an austere environment. In an outbreak of any magnitude, a field-based rapid diagnostic assay would allow proper patient transport and for safe burials to be conducted without the delay caused by transport of samples between remote villages and testing facilities. Use of such point-of-care instruments in the ongoing Ebola virus disease (EVD) outbreak in West Africa would have distinct advantages in control and prevention of local outbreaks, but proper understanding of the technology and interpretation of results are important. In this study, a LFI, originally developed by the Naval Medical Research Center for Ebola virus environmental testing, was evaluated for its ability to detect the virus in clinical samples in Liberia. Clinical blood and plasma samples and post mortem oral swabs submitted to the Liberian Institute for Biomedical Research, the National Public Health Reference Laboratory for EVD testing, were tested and compared to results of real-time reverse transcription-polymerase chain reaction (rRT-PCR), using assays targeting Ebola virus glycoprotein and nucleoprotein. The LFI findings correlated well with those of the real-time RT-PCR assays used as benchmarks. Rapid antigen-detection tests such as LFIs are attractive alternatives to traditional immunoassays but have reduced sensitivity and specificity, resulting in increases in false-positive and false-negative results. An understanding of the strengths, weaknesses, and limitations of a particular assay lets the diagnostician choose the correct situation to use the correct assay and properly interpret the results. Published by Oxford University Press for the Infectious Diseases Society of America 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Decoding 2D-PAGE complex maps: relevance to proteomics.

PubMed

Pietrogrande, Maria Chiara; Marchetti, Nicola; Dondi, Francesco; Righetti, Pier Giorgio

2006-03-20

This review describes two mathematical approaches useful for decoding the complex signal of 2D-PAGE maps of protein mixtures. These methods are helpful for interpreting the large amount of data of each 2D-PAGE map by extracting all the analytical information hidden therein by spot overlapping. Here the basic theory and application to 2D-PAGE maps are reviewed: the means for extracting information from the experimental data and their relevance to proteomics are discussed. One method is based on the quantitative theory of statistical model of peak overlapping (SMO) using the spot experimental data (intensity and spatial coordinates). The second method is based on the study of the 2D-autocovariance function (2D-ACVF) computed on the experimental digitised map. They are two independent methods that are able to extract equal and complementary information from the 2D-PAGE map. Both methods permit to obtain fundamental information on the sample complexity and the separation performance and to single out ordered patterns present in spot positions: the availability of two independent procedures to compute the same separation parameters is a powerful tool to estimate the reliability of the obtained results. The SMO procedure is an unique tool to quantitatively estimate the degree of spot overlapping present in the map, while the 2D-ACVF method is particularly powerful in simply singling out the presence of order in the spot position from the complexity of the whole 2D map, i.e., spot trains. The procedures were validated by extensive numerical computation on computer-generated maps describing experimental 2D-PAGE gels of protein mixtures. Their applicability to real samples was tested on reference maps obtained from literature sources. The review describes the most relevant information for proteomics: sample complexity, separation performance, overlapping extent, identification of spot trains related to post-translational modifications (PTMs).

Conjugate gradient type methods for linear systems with complex symmetric coefficient matrices

NASA Technical Reports Server (NTRS)

Freund, Roland

1989-01-01

We consider conjugate gradient type methods for the solution of large sparse linear system Ax equals b with complex symmetric coefficient matrices A equals A(T). Such linear systems arise in important applications, such as the numerical solution of the complex Helmholtz equation. Furthermore, most complex non-Hermitian linear systems which occur in practice are actually complex symmetric. We investigate conjugate gradient type iterations which are based on a variant of the nonsymmetric Lanczos algorithm for complex symmetric matrices. We propose a new approach with iterates defined by a quasi-minimal residual property. The resulting algorithm presents several advantages over the standard biconjugate gradient method. We also include some remarks on the obvious approach to general complex linear systems by solving equivalent real linear systems for the real and imaginary parts of x. Finally, numerical experiments for linear systems arising from the complex Helmholtz equation are reported.

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

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.

Enhanced detection of tuberculous mycobacteria in animal tissues using a semi-nested probe-based real-time PCR.

PubMed

Costa, Pedro; Ferreira, Ana S; Amaro, Ana; Albuquerque, Teresa; Botelho, Ana; Couto, Isabel; Cunha, Mónica V; Viveiros, Miguel; Inácio, João

2013-01-01

Bovine tuberculosis has been tackled for decades by costly eradication programs in most developed countries, involving the laboratory testing of tissue samples from allegedly infected animals for detection of Mycobacterium tuberculosis complex (MTC) members, namely Mycobacterium bovis. Definitive diagnosis is usually achieved by bacteriological culture, which may take up to 6-12 weeks, during which the suspect animal carcass and herd are under sanitary arrest. In this work, a user-friendly DNA extraction protocol adapted for tissues was coupled with an IS6110-targeted semi-nested duplex real-time PCR assay to enhance the direct detection of MTC bacteria in animal specimens, reducing the time to achieve a diagnosis and, thus, potentially limiting the herd restriction period. The duplex use of a novel β-actin gene targeted probe, with complementary targets in most mammals, allowed the assessment of amplification inhibitors in the tissue samples. The assay was evaluated with a group of 128 fresh tissue specimens collected from bovines, wild boars, deer and foxes. Mycobacterium bovis was cultured from 57 of these samples. Overall, the full test performance corresponds to a diagnostic sensitivity and specificity of 98.2% (CIP95% 89.4-99.9%) and 88.7% (CIP95% 78.5-94.7%), respectively. An observed kappa coefficient was estimated in 0.859 (CI P95% 0.771-0.948) for the overall agreement between the semi-nested PCR assay and the bacteriological culture. Considering only bovine samples (n = 69), the diagnostic sensitivity and specificity were estimated in 100% (CIP95% 84.0-100%) and 97.7% (CIP95% 86.2-99.9%), respectively. Eight negative culture samples exhibiting TB-like lesions were detected by the semi-nested real-time PCR, thus emphasizing the increased potential of this molecular approach to detect MTC-infected animal tissues. This novel IS6110-targeted assay allows the fast detection of tuberculous mycobacteria in animal specimens with very high sensitivity and specificity, being amenable and cost effective for use in the routine veterinary diagnostic laboratory with further automation possibilities.

Task complexity modulates pilot electroencephalographic activity during real flights.

PubMed

Di Stasi, Leandro L; Diaz-Piedra, Carolina; Suárez, Juan; McCamy, Michael B; Martinez-Conde, Susana; Roca-Dorda, Joaquín; Catena, Andrés

2015-07-01

Most research connecting task performance and neural activity to date has been conducted in laboratory conditions. Thus, field studies remain scarce, especially in extreme conditions such as during real flights. Here, we investigated the effects of flight procedures of varied complexity on the in-flight EEG activity of military helicopter pilots. Flight procedural complexity modulated the EEG power spectrum: highly demanding procedures (i.e., takeoff and landing) were associated with higher EEG power in the higher frequency bands, whereas less demanding procedures (i.e., flight exercises) were associated with lower EEG power over the same frequency bands. These results suggest that EEG recordings may help to evaluate an operator's cognitive performance in challenging real-life scenarios, and thus could aid in the prevention of catastrophic events. © 2015 Society for Psychophysiological Research.

Fast 2D NMR Spectroscopy for In vivo Monitoring of Bacterial Metabolism in Complex Mixtures.

PubMed

Dass, Rupashree; Grudzia Ż, Katarzyna; Ishikawa, Takao; Nowakowski, Michał; Dȩbowska, Renata; Kazimierczuk, Krzysztof

2017-01-01

The biological toolbox is full of techniques developed originally for analytical chemistry. Among them, spectroscopic experiments are very important source of atomic-level structural information. Nuclear magnetic resonance (NMR) spectroscopy, although very advanced in chemical and biophysical applications, has been used in microbiology only in a limited manner. So far, mostly one-dimensional 1 H experiments have been reported in studies of bacterial metabolism monitored in situ . However, low spectral resolution and limited information on molecular topology limits the usability of these methods. These problems are particularly evident in the case of complex mixtures, where spectral peaks originating from many compounds overlap and make the interpretation of changes in a spectrum difficult or even impossible. Often a suite of two-dimensional (2D) NMR experiments is used to improve resolution and extract structural information from internuclear correlations. However, for dynamically changing sample, like bacterial culture, the time-consuming sampling of so-called indirect time dimensions in 2D experiments is inefficient. Here, we propose the technique known from analytical chemistry and structural biology of proteins, i.e., time-resolved non-uniform sampling. The method allows application of 2D (and multi-D) experiments in the case of quickly varying samples. The indirect dimension here is sparsely sampled resulting in significant reduction of experimental time. Compared to conventional approach based on a series of 1D measurements, this method provides extraordinary resolution and is a real-time approach to process monitoring. In this study, we demonstrate the usability of the method on a sample of Escherichia coli culture affected by ampicillin and on a sample of Propionibacterium acnes , an acne causing bacterium, mixed with a dose of face tonic, which is a complicated, multi-component mixture providing complex NMR spectrum. Through our experiments we determine the exact concentration and time at which the anti-bacterial agents affect the bacterial metabolism. We show, that it is worth to extend the NMR toolbox for microbiology by including techniques of 2D z-TOCSY, for total "fingerprinting" of a sample and 2D 13 C-edited HSQC to monitor changes in concentration of metabolites in selected metabolic pathways.

Integrating complex business processes for knowledge-driven clinical decision support systems.

PubMed

Kamaleswaran, Rishikesan; McGregor, Carolyn

2012-01-01

This paper presents in detail the component of the Complex Business Process for Stream Processing framework that is responsible for integrating complex business processes to enable knowledge-driven Clinical Decision Support System (CDSS) recommendations. CDSSs aid the clinician in supporting the care of patients by providing accurate data analysis and evidence-based recommendations. However, the incorporation of a dynamic knowledge-management system that supports the definition and enactment of complex business processes and real-time data streams has not been researched. In this paper we discuss the process web service as an innovative method of providing contextual information to a real-time data stream processing CDSS.

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.

Next Generation Real-Time Systems: Investigating the Potential of Partial-Solution Tasks.

DTIC Science & Technology

1994-12-01

insufficient for dealing with the complexities of next-generation real - time systems . New methods of intelligent control must be developed for guaranteeing...on-time task completion for real - time systems that are faced with unpredictable and dynamically changing requirements. Implementing real-time...tasks by experimentally measuring the change in performance of 11 simulated real - time systems when converted from all-or-nothing tasks to partial

Purification of cardiac myocytes from human heart biopsies for gene expression analysis.

PubMed

Kosloski, L M; Bales, I K; Allen, K B; Walker, B L; Borkon, A M; Stuart, R S; Pak, A F; Wacker, M J

2009-09-01

The collection of gene expression data from human heart biopsies is important for understanding the cellular mechanisms of arrhythmias and diseases such as cardiac hypertrophy and heart failure. Many clinical and basic research laboratories conduct gene expression analysis using RNA from whole cardiac biopsies. This allows for the analysis of global changes in gene expression in areas of the heart, while eliminating the need for more complex and technically difficult single-cell isolation procedures (such as flow cytometry, laser capture microdissection, etc.) that require expensive equipment and specialized training. The abundance of fibroblasts and other cell types in whole biopsies, however, can complicate gene expression analysis and the interpretation of results. Therefore, we have designed a technique to quickly and easily purify cardiac myocytes from whole cardiac biopsies for RNA extraction. Human heart tissue samples were collected, and our purification method was compared with the standard nonpurification method. Cell imaging using acridine orange staining of the purified sample demonstrated that >98% of total RNA was contained within identifiable cardiac myocytes. Real-time RT-PCR was performed comparing nonpurified and purified samples for the expression of troponin T (myocyte marker), vimentin (fibroblast marker), and alpha-smooth muscle actin (smooth muscle marker). Troponin T expression was significantly increased, and vimentin and alpha-smooth muscle actin were significantly decreased in the purified sample (n = 8; P < 0.05). Extracted RNA was analyzed during each step of the purification, and no significant degradation occurred. These results demonstrate that this isolation method yields a more purified cardiac myocyte RNA sample suitable for downstream applications, such as real-time RT-PCR, and allows for more accurate gene expression changes in cardiac myocytes from heart biopsies.

Simultaneous in situ derivatization and ultrasound-assisted dispersive magnetic solid phase extraction for thiamine determination by spectrofluorimetry.

PubMed

Tarigh, Ghazale Daneshvar; Shemirani, Farzaneh

2014-06-01

A simple and rapid method for the simultaneous in situ derivatizaion, preconcentration and extraction of thiamine (vitamin B1) as a model analyte was developed by a novel quantitative method, namely ultrasound-assisted dispersive magnetic solid phase extraction spectrofluorimetry (USA-DMSPE-FL) from different real samples. This method consists of sample preparation, in situ derivatization, exhaustive extraction and clean up by a single process. High extraction efficiency and in situ derivatization in a short period of time is the main advantages of this procedure. For this purpose, the reusable magnetic multi-wall carbon nanotube (MMWCNT) nanocomposite was used as an adsorbent for preconcentration and determination of thiamine. Thiamine was, simultaneously, in situ derivatized as thiochrome by potassium hexacyanoferrate (III) and adsorbed on MMWCNT in an ultrasonic water bath. The MMWCNTs were then collected using an external magnetic field. Subsequently, the extracted thiochrome was washed from the surface of the adsorbent and determined by spectrofluorimetry. The developed method, which has been analytically characterized under its optimal operating conditions, allows the detection of the analyte in the samples with method detection limits of 0.37 µg L(-1). The repeatability of the method, expressed as the relative standard deviation (RSD, n=6), varies between 2.0% and 4.8% in different real samples, while the enhancement factor is 197. The proposed procedure has been applied for the determination of thiamine in biological (serum and urine), pharmaceutical (multivitamin tablet and B complex syrup) and foodstuff samples (cereal, wheat flour, banana and honey) with the good recoveries in the range from 90% to 105%. Copyright © 2014 Elsevier B.V. All rights reserved.

A new tunable dispersive liquid-liquid micro extraction method developed for the simultaneous preconcentration of lead and cadmium from lakes water: a multivariate study

NASA Astrophysics Data System (ADS)

Bilal, Muhammad; Kazi, Tasneem Gul; Afridi, Hassan Imran; Ali, Jamshed; Baig, Jameel Ahmed; Arain, Mohammad Balal; Khan, Mustafa

2017-08-01

A green tunable dispersive liquid-liquid micro extraction (TDLLME) technique was established for the simultaneous enrichment of lead (Pb) and cadmium (Cd) from different lakes water before analysis by flame atomic absorption spectrometry (FAAS). A solvent known as tunable polarity solvent (TPS), mixture of 1,8-diazabicyclo-[5.4.0]-undec-7-ene (DBU) and 1-decanol, has been employed as extractant in aqueous medium. In first step this mixture can be made polar by slowly bubbling the antisolvent trigger (CO2) through the solution, which makes a monophasic solution. During this step hydrophobic complexes of the metals with 8-hydroxy quinoline (8-HQ) were extracted by TPS. Then the mixture was switched back to hydrophobic one by heating and/or bubbling nitrogen, turning the mixture into two phases again. In second phase the metals were leached out from the complexes entrapped in TPS, by treating with a solution of nitric acid and exposing the mixture to CO2, which switched the mixture into single phase. Then N2 purging and/or heating again turned the mixture into two phases. The acidic aqueous phase containing the metals was introduced to FAAS for analysis, whereas TPS was recycled for next experiment. Different parameters, affecting the efficiency the technique, were optimized by multivariate approach. The method was applied to certified reference material of water and to a real sample spiked with standards of known concentration, to confirm its validity and accuracy. LOD obtained for Pb and Cd were 0.560 and 0.056 μg L- 1 respectively. The developed method was applied successfully to the real water samples of two lakes of Sindh, Pakistan.

Kaposi's Sarcoma-Associated Herpesvirus MicroRNA Single-Nucleotide Polymorphisms Identified in Clinical Samples Can Affect MicroRNA Processing, Level of Expression, and Silencing Activity

PubMed Central

Han, Soo-Jin; Marshall, Vickie; Barsov, Eugene; Quiñones, Octavio; Ray, Alex; Labo, Nazzarena; Trivett, Matthew; Ott, David; Renne, Rolf

2013-01-01

Kaposi's sarcoma-associated herpesvirus (KSHV) encodes 12 pre-microRNAs that can produce 25 KSHV mature microRNAs. We previously reported single-nucleotide polymorphisms (SNPs) in KSHV-encoded pre-microRNA and mature microRNA sequences from clinical samples (V. Marshall et al., J. Infect. Dis., 195:645–659, 2007). To determine whether microRNA SNPs affect pre-microRNA processing and, ultimately, mature microRNA expression levels, we performed a detailed comparative analysis of (i) mature microRNA expression levels, (ii) in vitro Drosha/Dicer processing, and (iii) RNA-induced silencing complex-dependent targeting of wild-type (wt) and variant microRNA genes. Expression of pairs of wt and variant pre-microRNAs from retroviral vectors and measurement of KSHV mature microRNA expression by real-time reverse transcription-PCR (RT-PCR) revealed differential expression levels that correlated with the presence of specific sequence polymorphisms. Measurement of KSHV mature microRNA expression in a panel of primary effusion lymphoma cell lines by real-time RT-PCR recapitulated some observed expression differences but suggested a more complex relationship between sequence differences and expression of mature microRNA. Furthermore, in vitro maturation assays demonstrated significant SNP-associated changes in Drosha/DGCR8 and/or Dicer processing. These data demonstrate that SNPs within KSHV-encoded pre-microRNAs are associated with differential microRNA expression levels. Given the multiple reports on the involvement of microRNAs in cancer, the biological significance of these phenotypic and genotypic variants merits further studies in patients with KSHV-associated malignancies. PMID:24006441

Algorithmic complexity of real financial markets

NASA Astrophysics Data System (ADS)

Mansilla, R.

2001-12-01

A new approach to the understanding of complex behavior of financial markets index using tools from thermodynamics and statistical physics is developed. Physical complexity, a quantity rooted in the Kolmogorov-Chaitin theory is applied to binary sequences built up from real time series of financial markets indexes. The study is based on NASDAQ and Mexican IPC data. Different behaviors of this quantity are shown when applied to the intervals of series placed before crashes and to intervals when no financial turbulence is observed. The connection between our results and the efficient market hypothesis is discussed.

Carded Tow Real-Time Color Assessment: A Spectral Camera-Based System.

PubMed

Furferi, Rocco; Governi, Lapo; Volpe, Yary; Carfagni, Monica

2016-08-31

One of the most important parameters to be controlled during the production of textile yarns obtained by mixing pre-colored fibers, is the color correspondence between the manufactured yarn and a given reference, usually provided by a designer or a customer. Obtaining yarns from raw pre-colored fibers is a complex manufacturing process entailing a number of steps such as laboratory sampling, color recipe corrections, blowing, carding and spinning. Carding process is the one devoted to transform a "fuzzy mass" of tufted fibers into a regular mass of untwisted fibers, named "tow". During this process, unfortunately, the correspondence between the color of the tow and the target one cannot be assured, thus leading to yarns whose color differs from the one used for reference. To solve this issue, the main aim of this work is to provide a system able to perform a spectral camera-based real-time measurement of a carded tow, to assess its color correspondence with a reference carded fabric and, at the same time, to monitor the overall quality of the tow during the carding process. Tested against a number of differently colored carded fabrics, the proposed system proved its effectiveness in reliably assessing color correspondence in real-time.

Integrated Aeroservoelastic Optimization: Status and Direction

NASA Technical Reports Server (NTRS)

Livne, Eli

1999-01-01

The interactions of lightweight flexible airframe structures, steady and unsteady aerodynamics, and wide-bandwidth active controls on modern airplanes lead to considerable multidisciplinary design challenges. More than 25 years of mathematical and numerical methods' development, numerous basic research studies, simulations and wind-tunnel tests of simple models, wind-tunnel tests of complex models of real airplanes, as well as flight tests of actively controlled airplanes, have all contributed to the accumulation of a substantial body of knowledge in the area of aeroservoelasticity. A number of analysis codes, with the capabilities to model real airplane systems under the assumptions of linearity, have been developed. Many tests have been conducted, and results were correlated with analytical predictions. A selective sample of references covering aeroservoelastic testing programs from the 1960s to the early 1980s, as well as more recent wind-tunnel test programs of real or realistic configurations, are included in the References section of this paper. An examination of references 20-29 will reveal that in the course of development (or later modification), of almost every modern airplane with a high authority active control system, there arose a need to face aeroservoelastic problems and aeroservoelastic design challenges.

Reflection and Refraction of Light in Absorbing Media

NASA Astrophysics Data System (ADS)

Katsumata, Koichi; Sasaki, Shosuke

2018-05-01

The results of a rigorous calculation of optical phenomena in absorbing media based on Maxwell's equations are reported. In the case of an absorbing dielectric, we assume a complex dielectric constant. We find an expression for the angle of refraction as a function of the incident angle and the real and imaginary parts of the complex dielectric constant, all of which are real. The amplitudes of the reflected and transmitted waves are calculated on the same footing. These amplitudes are shown to be complex, from which we deduce the magnitude and phase change of the reflection and transmission coefficients. The same argument applies to an absorbing magnetic material if we replace the complex dielectric constant by a complex magnetic permeability.

Delivering real-time status and arrival information to commuter rail passengers at complex stations

DOT National Transportation Integrated Search

2003-08-01

Software was developed for calculating real-time train status in an Automated Train Information Display System (ATIDS) at NJ Transit. Interfaces were developed for passing schedules and real-time train position and routing data from a rail traffic co...

Fast microextraction of phthalate acid esters from beverage, environmental water and perfume samples by magnetic multi-walled carbon nanotubes.

PubMed

Luo, Yan-Bo; Yu, Qiong-Wei; Yuan, Bi-Feng; Feng, Yu-Qi

2012-02-15

In this work, magnetic carbon nanotubes (CNTs) were prepared by mixing the magnetic particles and multi-walled carbon nanotubes dispersed solutions. Due to their excellent adsorption capability towards hydrophobic compounds, the magnetic CNTs were used as adsorbent of magnetic solid-phase extraction (MSPE) to extract phthalate acid esters (PAEs), which are widely used in many consumable products with potential carcinogenic properties. By coupling MSPE with gas chromatography/mass spectrometry (GC/MS), a rapid, sensitive and cost-effective method for the analysis of PAEs was established. Our results showed that the limits of detection (LODs) of 16 PAEs ranged from 4.9 to 38 ng L(-1), which are much lower compared to the previously reported methods. And good linearities of the detection method were obtained with correlation coefficients (R(2)) between 0.9821 and 0.9993. In addition, a satisfying reproducibility was achieved by evaluating the intra- and inter-day precisions with relative standard deviations (RSDs) less than 11.7% and 14.6%, respectively. Finally, the established MSPE-GC/MS method was successfully applied to the determination of PAEs from bottled beverages, tap water and perfume samples. The recoveries of the 16 PAEs from the real samples ranged from 64.6% to 125.6% with the RSDs less than 16.5%. Taken together, the MSPE-GC/MS method developed in current study provides a new option for the detection of PAEs from real samples with complex matrices. Copyright © 2012 Elsevier B.V. All rights reserved.

Zirconium(IV) functionalized magnetic nanocomposites for extraction of organophosphorus pesticides from environmental water samples.

PubMed

Jiang, Li; Huang, Tengjun; Feng, Shun; Wang, Jide

2016-07-22

The widespread use of organophosphate pesticides (OPPs) in agriculture leads to residue accumulation in the environment which is dangerous to human health and disrupts the ecological balance. In this work, one nanocomposite immobilized zirconium (Zr, IV) was prepared and used as the affinity probes to quickly and selectively extract organophosphorus pesticides (OPPs) from water samples. The Fe3O4-ethylenediamine tetraacetic acid (EDTA)@Zr(IV) nanocomposites (NPs) were prepared by simply mixing Zr(IV) ions with Fe3O4-EDTA NPs synthesized by one-pot chemical co-precipitation method. The immobilized Zr(IV) ions were further utilized to capture OPPs based on their high affinity for the phosphate moiety in OPPs. Coupled with GC-MS, four OPPs were used as models to demonstrate the feasibility of this approach. Under the optimum conditions, the limits of detection for target OPPs were in the range of 0.10-10.30ngmL(-1) with relative standard deviations (RSDs) of 0.61-4.40% (n=3), respectively. The linear ranges were over three orders of magnitudes (correlation coefficients, R(2)>0.9995). The Fe3O4-EDTA@Zr(IV) NPs were successfully applied to extract OPPs samples with recoveries of 86.95-112.60% and RSDs of 1.20-10.42% (n=3) from two spiked real water. By the proposed method, the matrix interference could be effectively eliminated. We hope our finding can provide a promising alternative for the fast extraction of OPPs from complex real samples. Copyright © 2016 Elsevier B.V. All rights reserved.

Development and evaluation of real-time loop-mediated isothermal amplification assay for rapid detection of cystic echinococcosis.

PubMed

Ahmed, Mohamed E; Eldigail, Mawahib H; Elamin, Fatima M; Ali, Ibtisam A; Grobusch, Martin P; Aradaib, Imadeldin E

2016-09-13

Cystic echinococcosis (CE) or hydatidosis, caused by the larval stage of Echinococcus granulosus (EG)-complex, is a neglected parasitic disease of public health importance. The disease is endemic in many African and Mediterranean countries including the Sudan. The objective of the present study was to develop and evaluate a real-time loop-mediated isothermal amplification (LAMP) assay for simple and rapid detection of CE in humans and domestic live stock in Sudan. A set of six LAMP primers, designed from the mitochondrial NADH-1 gene of EG cattle strain of genotype 5 (G5), was used as a target for LAMP assay. The assay was performed at a constant temperature (63 °C), with a real-time follow-up using a LightCycler and fluorochrome dye. Following amplification cycles in a simple water bath, LAMP products were observed for color change by naked eye and were visualized under UV light source using agarose gel electrophoresis. The real-time LAMP assay identified a variety of hydatid cysts strains recovered in the Sudan, including Echinococcus canadenses (G6) and Echinococcus ortleppi (G5). Real-time LAMP positive results were detected by the presence of an amplification curve, whereas negative results were indicated by absence of fluorescence detection. Positive LAMP results appeared as a bluish-colored reaction as observed by naked eye, whereas negative LAMP results were observed as purple-colored reaction. The sensitivity studies indicated that the LAMP assay detected as little as a 10 fg of parasite DNA. There was 100 % agreement between results of the LAMP assay and our previously described nested PCR when testing 10-fold serial dilution of DNA extracted from EG-complex hydatid cyst. However, there was no cross-reactivity with other parasites including cysticercus bovis, Fasciola gigantica, and Schistosoma bovis and nucleic acid free samples. The developed LAMP assay would be expected to prove highly significant in epidemiological surveys of CE in developing countries or areas of resource-poor settings for both ease of use and cost.

Development and comparative evaluation of SYBR Green I-based one-step real-time RT-PCR assay for detection and quantification of West Nile virus in human patients.

PubMed

Kumar, Jyoti S; Saxena, Divyasha; Parida, Manmohan

2014-01-01

The recent outbreaks of West Nile Virus (WNV) in the Northeastern American continents and other regions of the world have made it essential to develop an efficient protocol for surveillance of WN virus. Nucleic acid based techniques like, RT-PCR have the advantage of sensitivity, specificity and rapidity. A one step single tube Env gene specific real-time RT-PCR was developed for early and reliable clinical diagnosis of WNV infection in clinical samples. The applicability of this assay for clinical diagnosis was validated with 105 suspected acute-phase serum and plasma samples from the recent epidemic of mysterious fever in Tamil Nadu, India in 2009-10. The comparative evaluation revealed the higher sensitivity of real-time RT-PCR assay by picking up 4 additional samples with low copy number of template in comparison to conventional RT-PCR. All the real-time positive samples further confirmed by CDC reported TaqMan real-time RT-PCR and quantitative real-time RT-PCR assays for the simultaneous detection of WNV lineage 1 and 2 strains. The quantitation of the viral load samples was done using a standard curve. These findings demonstrated that the assay has the potential usefulness for clinical diagnosis due to detection and quantification of WNV in acute-phase patient serum samples. Copyright © 2014 Elsevier Ltd. All rights reserved.

Remote laboratories for optical metrology: from the lab to the cloud

NASA Astrophysics Data System (ADS)

Osten, W.; Wilke, M.; Pedrini, G.

2012-10-01

The idea of remote and virtual metrology has been reported already in 2000 with a conceptual illustration by use of comparative digital holography, aimed at the comparison of two nominally identical but physically different objects, e.g., master and sample, in industrial inspection processes. However, the concept of remote and virtual metrology can be extended far beyond this. For example, it does not only allow for the transmission of static holograms over the Internet, but also provides an opportunity to communicate with and eventually control the physical set-up of a remote metrology system. Furthermore, the metrology system can be modeled in the environment of a 3D virtual reality using CAD or similar technology, providing a more intuitive interface to the physical setup within the virtual world. An engineer or scientist who would like to access the remote real world system can log on to the virtual system, moving and manipulating the setup through an avatar and take the desired measurements. The real metrology system responds to the interaction between the avatar and the 3D virtual representation, providing a more intuitive interface to the physical setup within the virtual world. The measurement data are stored and interpreted automatically for appropriate display within the virtual world, providing the necessary feedback to the experimenter. Such a system opens up many novel opportunities in industrial inspection such as the remote master-sample-comparison and the virtual assembling of parts that are fabricated at different places. Moreover, a multitude of new techniques can be envisaged. To them belong modern ways for documenting, efficient methods for metadata storage, the possibility for remote reviewing of experimental results, the adding of real experiments to publications by providing remote access to the metadata and to the experimental setup via Internet, the presentation of complex experiments in classrooms and lecture halls, the sharing of expensive and complex infrastructure within international collaborations, the implementation of new ways for the remote test of new devices, for their maintenance and service, and many more. The paper describes the idea of remote laboratories and illustrates the potential of the approach on selected examples with special attention to optical metrology.

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.

Real-Time linux dynamic clamp: a fast and flexible way to construct virtual ion channels in living cells.

PubMed

Dorval, A D; Christini, D J; White, J A

2001-10-01

We describe a system for real-time control of biological and other experiments. This device, based around the Real-Time Linux operating system, was tested specifically in the context of dynamic clamping, a demanding real-time task in which a computational system mimics the effects of nonlinear membrane conductances in living cells. The system is fast enough to represent dozens of nonlinear conductances in real time at clock rates well above 10 kHz. Conductances can be represented in deterministic form, or more accurately as discrete collections of stochastically gating ion channels. Tests were performed using a variety of complex models of nonlinear membrane mechanisms in excitable cells, including simulations of spatially extended excitable structures, and multiple interacting cells. Only in extreme cases does the computational load interfere with high-speed "hard" real-time processing (i.e., real-time processing that never falters). Freely available on the worldwide web, this experimental control system combines good performance. immense flexibility, low cost, and reasonable ease of use. It is easily adapted to any task involving real-time control, and excels in particular for applications requiring complex control algorithms that must operate at speeds over 1 kHz.

Fish tracking by combining motion based segmentation and particle filtering

NASA Astrophysics Data System (ADS)

Bichot, E.; Mascarilla, L.; Courtellemont, P.

2006-01-01

In this paper, we suggest a new importance sampling scheme to improve a particle filtering based tracking process. This scheme relies on exploitation of motion segmentation. More precisely, we propagate hypotheses from particle filtering to blobs of similar motion to target. Hence, search is driven toward regions of interest in the state space and prediction is more accurate. We also propose to exploit segmentation to update target model. Once the moving target has been identified, a representative model is learnt from its spatial support. We refer to this model in the correction step of the tracking process. The importance sampling scheme and the strategy to update target model improve the performance of particle filtering in complex situations of occlusions compared to a simple Bootstrap approach as shown by our experiments on real fish tank sequences.

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

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.

Dynamical singularities for complex initial conditions and the motion at a real separatrix.

PubMed

Shnerb, Tamar; Kay, K G

2006-04-01

This work investigates singularities occurring at finite real times in the classical dynamics of one-dimensional double-well systems with complex initial conditions. The objective is to understand the relationship between these singularities and the behavior of the systems for real initial conditions. An analytical treatment establishes that the dynamics of a quartic double well system possesses a doubly infinite sequence of singularities. These are associated with initial conditions that converge to those for the real separatrix as the singularity time becomes infinite. This confluence of singularities is shown to lead to the unstable behavior that characterizes the real motion at the separatrix. Numerical calculations confirm the existence of a large number of singularities converging to the separatrix for this and two additional double-well systems. The approach of singularities to the real axis is of particular interest since such behavior has been related to the formation of chaos in nonintegrable systems. The properties of the singular trajectories which cause this convergence to the separatrix are identified. The hyperbolic fixed point corresponding to the potential energy maximum, responsible for the characteristic motion at a separatrix, also plays a critical role in the formation of the complex singularities by delaying trajectories and then deflecting them into asymptotic regions of space from where they are directly repelled to infinity in a finite time.

Real-time Feynman path integral with Picard–Lefschetz theory and its applications to quantum tunneling

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

Tanizaki, Yuya, E-mail: yuya.tanizaki@riken.jp; Theoretical Research Division, Nishina Center, RIKEN, Wako 351-0198; Koike, Takayuki, E-mail: tkoike@ms.u-tokyo.ac.jp

Picard–Lefschetz theory is applied to path integrals of quantum mechanics, in order to compute real-time dynamics directly. After discussing basic properties of real-time path integrals on Lefschetz thimbles, we demonstrate its computational method in a concrete way by solving three simple examples of quantum mechanics. It is applied to quantum mechanics of a double-well potential, and quantum tunneling is discussed. We identify all of the complex saddle points of the classical action, and their properties are discussed in detail. However a big theoretical difficulty turns out to appear in rewriting the original path integral into a sum of path integralsmore » on Lefschetz thimbles. We discuss generality of that problem and mention its importance. Real-time tunneling processes are shown to be described by those complex saddle points, and thus semi-classical description of real-time quantum tunneling becomes possible on solid ground if we could solve that problem. - Highlights: • Real-time path integral is studied based on Picard–Lefschetz theory. • Lucid demonstration is given through simple examples of quantum mechanics. • This technique is applied to quantum mechanics of the double-well potential. • Difficulty for practical applications is revealed, and we discuss its generality. • Quantum tunneling is shown to be closely related to complex classical solutions.« less

Spectral refractive index assessment of turbid samples by combining spatial frequency near-infrared spectroscopy with Kramers-Kronig analysis

NASA Astrophysics Data System (ADS)

Meitav, Omri; Shaul, Oren; Abookasis, David

2018-03-01

A practical algorithm for estimating the wavelength-dependent refractive index (RI) of a turbid sample in the spatial frequency domain with the aid of Kramers-Kronig (KK) relations is presented. In it, phase-shifted sinusoidal patterns (structured illumination) are serially projected at a high spatial frequency onto the sample surface (mouse scalp) at different near-infrared wavelengths while a camera mounted normally to the sample surface captures the reflected diffuse light. In the offline analysis pipeline, recorded images at each wavelength are converted to spatial absorption maps by logarithmic function, and once the absorption coefficient information is obtained, the imaginary part (k) of the complex RI (CRI), based on Maxell's equations, can be calculated. Using the data represented by k, the real part of the CRI (n) is then resolved by KK analysis. The wavelength dependence of n ( λ ) is then fitted separately using four standard dispersion models: Cornu, Cauchy, Conrady, and Sellmeier. In addition, three-dimensional surface-profile distribution of n is provided based on phase profilometry principles and a phase-unwrapping-based phase-derivative-variance algorithm. Experimental results demonstrate the capability of the proposed idea for sample's determination of a biological sample's RI value.

Indirect competitive immunoassay for the detection of fungicide Thiabendazole in whole orange samples by Surface Plasmon Resonance.

PubMed

Estevez, M-Carmen; Belenguer, Jose; Gomez-Montes, Silvia; Miralles, Javier; Escuela, Alfonso M; Montoya, Angel; Lechuga, Laura M

2012-12-07

A highly sensitive and specific SPR-based competitive immunoassay for the detection of Thiabendazole (TBZ) has been developed. An indirect format where a TBZ-protein conjugate is immobilized onto gold surfaces has been selected. Under the optimal conditions, a LOD of 0.67 nM (0.13 μg L(-1)) and an IC(50) of 3.2 nM (0.64 μg L(-1)) have been achieved which are comparable to the values obtained by conventional ELISA. Analysis of real samples has been attempted by first evaluating the influence of complex matrix samples coming from whole oranges and secondly measuring samples containing TBZ previously evaluated by chromatographic methods. A methanolic extraction procedure followed by a simple dilution in assay buffer has proven to be sufficient to measure orange samples using the developed immunoassay with an excellent recovery percentage. The sensitivity and the feasibility of measuring whole orange samples demonstrate the effectiveness and robustness of the SPR biosensor, which can be useful for the determination of TBZ in food at concentrations below the Maximum Residue Levels (MRLs) established by the European legislation.

A Practical Measure for the Complexity of Evolving Seismicity Patterns

NASA Astrophysics Data System (ADS)

Goltz, C.

2005-12-01

Earthquakes are a "complex" phenomenon. There is, however, no clear definition of what complexity actually is. Yet, it is important to distinguish between what is merely complicated and what is complex in the sense that simple rules can give rise to very rich behaviour. Seismicity is certainly a complicated phenomenon (difficult to understand) but simple models such as cellular automata indicate that earthquakes are truly complex. From the observational point of view, there exists the problem of quantification of complexity in real world seismicity patterns. Such a measurement is desirable, not only for fundamental understanding but also for monitoring and possibly for forecasting. Maybe the most workable definitions of complexity exist in informatics, summarised under the topic of algorithmic complexity. Here, after introducing the concepts, I apply such a measure of complexity to temporally evolving real-world seismicity patterns. Finally, I discuss the usefulness of the approach and regard the results in view of the occurrence of large earthquakes.

The presence of opportunistic pathogens, Legionella spp., L. pneumophila and Mycobacterium avium complex, in South Australian reuse water distribution pipelines.

PubMed

Whiley, H; Keegan, A; Fallowfield, H; Bentham, R

2015-06-01

Water reuse has become increasingly important for sustainable water management. Currently, its application is primarily constrained by the potential health risks. Presently there is limited knowledge regarding the presence and fate of opportunistic pathogens along reuse water distribution pipelines. In this study opportunistic human pathogens Legionella spp., L. pneumophila and Mycobacterium avium complex were detected using real-time polymerase chain reaction along two South Australian reuse water distribution pipelines at maximum concentrations of 10⁵, 10³ and 10⁵ copies/mL, respectively. During the summer period of sampling the concentration of all three organisms significantly increased (P < 0.05) along the pipeline, suggesting multiplication and hence viability. No seasonality in the decrease in chlorine residual along the pipelines was observed. This suggests that the combination of reduced chlorine residual and increased water temperature promoted the presence of these opportunistic pathogens.

Leidenfrost Phenomenon-assisted Thermal Desorption (LPTD) and Its Application to Open Ion Sources at Atmospheric Pressure Mass Spectrometry

NASA Astrophysics Data System (ADS)

Saha, Subhrakanti; Chen, Lee Chuin; Mandal, Mridul Kanti; Hiraoka, Kenzo

2013-03-01

This work describes the development and application of a new thermal desorption technique that makes use of the Leidenfrost phenomenon in open ion sources at atmospheric pressure for direct mass spectrometric detection of ultratrace levels of illicit, therapeutic, and stimulant drugs, toxicants, and peptides (molecular weight above 1 kDa) in their unaltered state from complex real world samples without or with minor sample pretreatment. A low temperature dielectric barrier discharge ion source was used throughout the experiments and the analytical figures of merit of this technique were investigated. Further, this desorption technique coupled with other ionization sources such as electrospray ionization (ESI) and dc corona discharge atmospheric pressure chemical ionization (APCI) in open atmosphere was also investigated. The use of the high-resolution `Exactive Orbitrap' mass spectrometer provided unambiguous identification of trace levels of the targeted compounds from complex mixtures and background noise; the limits of detection for various small organic molecules and peptides treated with this technique were at the level of parts per trillion and 10-9 M, respectively. The high sensitivity of the present technique is attributed to the spontaneous enrichment of analyte molecules during the slow evaporation of the solvent, as well as to the sequential desorption of molecules from complex mixtures based on their volatilities. This newly developed desorption technique is simple and fast, while molecular ions are observed as the major ions.

X-ray absorption spectroscopy to watch catalysis by metalloenzymes: status and perspectives discussed for the water-splitting manganese complex of photosynthesis.

PubMed

Dau, Holger; Haumann, Michael

2003-01-01

Understanding structure-function relations is one of the main interests in the molecular biosciences. X-ray absorption spectroscopy of biological samples (BioXAS) has gained the status of a useful tool for characterization of the structure of protein-bound metal centers with respect to the electronic structure (oxidation states, orbital occupancies) and atomic structure (arrangement of ligand atoms). Owing to progress in the performance characteristics of synchrotron radiation sources and of experimental stations dedicated to the study of (ultra-dilute) biological samples, it is now possible to carry out new types of BioXAS experiments, which have been impracticable in the past. Of particular interest are approaches to follow biological catalysis at metal sites by characterization of functionally relevant structural changes. In this Article, the first steps towards the use of BioXAS to 'watch' biological catalysis are reviewed for the water-splitting reactions occurring at the manganese complex of photosynthesis. The following aspects are considered: the role of BioXAS in life sciences; methodological aspects of BioXAS; catalysis at the Mn complex of photosynthesis; combination of EXAFS and crystallographic information; the freeze-quench technique to capture semi-stable states; time-resolved BioXAS using a freeze-quench approach; room-temperature experiments and 'real-time' BioXAS; tasks and perspectives.

Multiple-image authentication with a cascaded multilevel architecture based on amplitude field random sampling and phase information multiplexing.

PubMed

Fan, Desheng; Meng, Xiangfeng; Wang, Yurong; Yang, Xiulun; Pan, Xuemei; Peng, Xiang; He, Wenqi; Dong, Guoyan; Chen, Hongyi

2015-04-10

A multiple-image authentication method with a cascaded multilevel architecture in the Fresnel domain is proposed, in which a synthetic encoded complex amplitude is first fabricated, and its real amplitude component is generated by iterative amplitude encoding, random sampling, and space multiplexing for the low-level certification images, while the phase component of the synthetic encoded complex amplitude is constructed by iterative phase information encoding and multiplexing for the high-level certification images. Then the synthetic encoded complex amplitude is iteratively encoded into two phase-type ciphertexts located in two different transform planes. During high-level authentication, when the two phase-type ciphertexts and the high-level decryption key are presented to the system and then the Fresnel transform is carried out, a meaningful image with good quality and a high correlation coefficient with the original certification image can be recovered in the output plane. Similar to the procedure of high-level authentication, in the case of low-level authentication with the aid of a low-level decryption key, no significant or meaningful information is retrieved, but it can result in a remarkable peak output in the nonlinear correlation coefficient of the output image and the corresponding original certification image. Therefore, the method realizes different levels of accessibility to the original certification image for different authority levels with the same cascaded multilevel architecture.

MULTI-K: accurate classification of microarray subtypes using ensemble k-means clustering

PubMed Central

Kim, Eun-Youn; Kim, Seon-Young; Ashlock, Daniel; Nam, Dougu

2009-01-01

Background Uncovering subtypes of disease from microarray samples has important clinical implications such as survival time and sensitivity of individual patients to specific therapies. Unsupervised clustering methods have been used to classify this type of data. However, most existing methods focus on clusters with compact shapes and do not reflect the geometric complexity of the high dimensional microarray clusters, which limits their performance. Results We present a cluster-number-based ensemble clustering algorithm, called MULTI-K, for microarray sample classification, which demonstrates remarkable accuracy. The method amalgamates multiple k-means runs by varying the number of clusters and identifies clusters that manifest the most robust co-memberships of elements. In addition to the original algorithm, we newly devised the entropy-plot to control the separation of singletons or small clusters. MULTI-K, unlike the simple k-means or other widely used methods, was able to capture clusters with complex and high-dimensional structures accurately. MULTI-K outperformed other methods including a recently developed ensemble clustering algorithm in tests with five simulated and eight real gene-expression data sets. Conclusion The geometric complexity of clusters should be taken into account for accurate classification of microarray data, and ensemble clustering applied to the number of clusters tackles the problem very well. The C++ code and the data sets tested are available from the authors. PMID:19698124

Molecularly imprinted polymer coupled with dispersive liquid-liquid microextraction and injector port silylation: a novel approach for the determination of 3-phenoxybenzoic acid in complex biological samples using gas chromatography-tandem mass spectrometry.

PubMed

Mudiam, Mohana Krishna Reddy; Chauhan, Abhishek; Jain, Rajeev; Dhuriya, Yogesh Kumar; Saxena, Prem Narain; Khanna, Vinay Kumar

2014-01-15

A novel analytical approach based on molecularly imprinted solid phase extraction (MISPE) coupled with dispersive liquid-liquid microextraction (DLLME), and injector port silylation (IPS) has been developed for the selective preconcentration, derivatization and analysis of 3-phenoxybenzoic acid (3-PBA) using gas chromatography-tandem mass spectrometry (GC-MS/MS) in complex biological samples such as rat blood and liver. Factors affecting the synthesis of MIP were evaluated and the best monomer and cross-linker were selected based on binding affinity studies. Various parameters of MISPE, DLLME and IPS were optimized for the selective preconcentration and derivatization of 3-PBA. The developed method offers a good linearity over the calibration range of 0.02-2.5ngmg(-1) and 7.5-2000ngmL(-1) for liver and blood respectively. Under optimized conditions, the recovery of 3-PBA in liver and blood samples were found to be in the range of 83-91%. The detection limit was found to be 0.0045ngmg(-1) and 1.82ngmL(-1) in liver and blood respectively. SRM transition of 271→227 and 271→197 has been selected as quantifier and qualifier transition for 3-PBA derivative. Intra and inter-day precision for five replicates in a day and for five, successive days was found to be less than 8%. The method developed was successfully applied to real samples, i.e. rat blood and tissue for quantitative evaluation of 3-PBA. The analytical approach developed is rapid, economic, simple, eco-friendly and possess immense utility for the analysis of analytes with polar functional groups in complex biological samples by GC-MS/MS. Copyright © 2013 Elsevier B.V. All rights reserved.

Rapid and accurate identification of Mycobacterium tuberculosis complex and common non-tuberculous mycobacteria by multiplex real-time PCR targeting different housekeeping genes.

PubMed

Nasr Esfahani, Bahram; Rezaei Yazdi, Hadi; Moghim, Sharareh; Ghasemian Safaei, Hajieh; Zarkesh Esfahani, Hamid

2012-11-01

Rapid and accurate identification of mycobacteria isolates from primary culture is important due to timely and appropriate antibiotic therapy. Conventional methods for identification of Mycobacterium species based on biochemical tests needs several weeks and may remain inconclusive. In this study, a novel multiplex real-time PCR was developed for rapid identification of Mycobacterium genus, Mycobacterium tuberculosis complex (MTC) and the most common non-tuberculosis mycobacteria species including M. abscessus, M. fortuitum, M. avium complex, M. kansasii, and the M. gordonae in three reaction tubes but under same PCR condition. Genetic targets for primer designing included the 16S rDNA gene, the dnaJ gene, the gyrB gene and internal transcribed spacer (ITS). Multiplex real-time PCR was setup with reference Mycobacterium strains and was subsequently tested with 66 clinical isolates. Results of multiplex real-time PCR were analyzed with melting curves and melting temperature (T (m)) of Mycobacterium genus, MTC, and each of non-tuberculosis Mycobacterium species were determined. Multiplex real-time PCR results were compared with amplification and sequencing of 16S-23S rDNA ITS for identification of Mycobacterium species. Sensitivity and specificity of designed primers were each 100 % for MTC, M. abscessus, M. fortuitum, M. avium complex, M. kansasii, and M. gordonae. Sensitivity and specificity of designed primer for genus Mycobacterium was 96 and 100 %, respectively. According to the obtained results, we conclude that this multiplex real-time PCR with melting curve analysis and these novel primers can be used for rapid and accurate identification of genus Mycobacterium, MTC, and the most common non-tuberculosis Mycobacterium species.

Molecular Diagnosis of Invasive Aspergillosis and Detection of Azole Resistance by a Newly Commercialized PCR Kit.

PubMed

Dannaoui, Eric; Gabriel, Frédéric; Gaboyard, Manuel; Lagardere, Gaëlle; Audebert, Lucile; Quesne, Gilles; Godichaud, Sandrine; Verweij, Paul E; Accoceberry, Isabelle; Bougnoux, Marie-Elisabeth

2017-11-01

Aspergillus fumigatus is the main species responsible for aspergillosis in humans. The diagnosis of aspergillosis remains difficult, and the rapid emergence of azole resistance in A. fumigatus is worrisome. The aim of this study was to validate the new MycoGENIE A. fumigatus real-time PCR kit and to evaluate its performance on clinical samples for the detection of A. fumigatus and its azole resistance. This multiplex assay detects DNA from the A. fumigatus species complex by targeting the multicopy 28S rRNA gene and specific TR 34 and L98H mutations in the single-copy-number cyp51A gene of A. fumigatus The specificity of cyp51A mutation detection was assessed by testing DNA samples from 25 wild-type or mutated clinical A. fumigatus isolates. Clinical validation was performed on 88 respiratory samples obtained from 62 patients and on 69 serum samples obtained from 16 patients with proven or probable aspergillosis and 13 patients without aspergillosis. The limit of detection was <1 copy for the Aspergillus 28S rRNA gene and 6 copies for the cyp51A gene harboring the TR 34 and L98H alterations. No cross-reactivity was detected with various fungi and bacteria. All isolates harboring the TR 34 and L98H mutations were accurately detected by quantitative PCR (qPCR) analysis. With respiratory samples, qPCR results showed a sensitivity and specificity of 92.9% and 90.1%, respectively, while with serum samples, the sensitivity and specificity were 100% and 84.6%, respectively. Our study demonstrated that this new real-time PCR kit enables sensitive and rapid detection of A. fumigatus DNA and azole resistance due to TR 34 and L98H mutations in clinical samples. Copyright © 2017 American Society for Microbiology.

Genetic Characterization of Serotypes A and Asia-1 Foot-and-mouth Disease Viruses in Balochistan, Pakistan, in 2011.

PubMed

Ullah, A; Jamal, S M; Romey, A; Gorna, K; Kakar, M A; Abbas, F; Ahmad, J; Zientara, S; Bakkali Kassimi, L

2017-10-01

This study reports characterization of foot-and-mouth disease virus (FMDV) in samples collected from Balochistan, Pakistan. FMDV was detected by pan-FMDV real-time RT-PCR in 31 samples (epithelial and oral swabs) collected in 2011 from clinical suspect cases. Of these, 29 samples were serotyped by serotype-specific real-time RT-PCR assays and were confirmed by sequencing the VP1 coding region. Sixteen samples were found positive for serotype A and eight for serotype Asia-1, whereas five samples were found positive for both serotypes A and Asia-1. Two serotype A positive samples were found positive for two different strains of serotype A FMDV each. Phylogenetic analyses of serotype A FMDVs showed circulation of at least three different sublineages within the A-Iran05 lineage. These included two earlier reported sublineages, A-Iran05 HER -10 and A-Iran05 FAR -11 , and a new sublineage, designated here as A-Iran05 BAL -11 . This shows that viruses belonging to the A-Iran05 lineage are continuously evolving in the region. Viruses belonging to the A-Iran05 FAR -11 sublineage showed close identity with the viruses circulating in 2009 in Pakistan and Afghanistan. However, viruses belonging to the A-Iran05 HER -10 detected in Balochistan, Pakistan, showed close identity with the viruses circulating in Kyrgyzstan, Iran and Kazakhstan in 2011 and 2012, showing that viruses responsible for outbreak in these countries have a common origin. Serotype Asia-1 FMDVs reported in this study all belonged to the earlier reported Group-VII (Sindh-08), which is currently a dominant strain in the West Eurasian region. Detection of two different serotypes of FMDV or/and two different strains of the same serotype in one animal/sample shows complexity in occurrence of FMD in the region. © 2016 Blackwell Verlag GmbH.

Change deafness for real spatialized environmental scenes.

PubMed

Gaston, Jeremy; Dickerson, Kelly; Hipp, Daniel; Gerhardstein, Peter

2017-01-01

The everyday auditory environment is complex and dynamic; often, multiple sounds co-occur and compete for a listener's cognitive resources. 'Change deafness', framed as the auditory analog to the well-documented phenomenon of 'change blindness', describes the finding that changes presented within complex environments are often missed. The present study examines a number of stimulus factors that may influence change deafness under real-world listening conditions. Specifically, an AX (same-different) discrimination task was used to examine the effects of both spatial separation over a loudspeaker array and the type of change (sound source additions and removals) on discrimination of changes embedded in complex backgrounds. Results using signal detection theory and accuracy analyses indicated that, under most conditions, errors were significantly reduced for spatially distributed relative to non-spatial scenes. A second goal of the present study was to evaluate a possible link between memory for scene contents and change discrimination. Memory was evaluated by presenting a cued recall test following each trial of the discrimination task. Results using signal detection theory and accuracy analyses indicated that recall ability was similar in terms of accuracy, but there were reductions in sensitivity compared to previous reports. Finally, the present study used a large and representative sample of outdoor, urban, and environmental sounds, presented in unique combinations of nearly 1000 trials per participant. This enabled the exploration of the relationship between change perception and the perceptual similarity between change targets and background scene sounds. These (post hoc) analyses suggest both a categorical and a stimulus-level relationship between scene similarity and the magnitude of change errors.

Complex Functions with GeoGebra

ERIC Educational Resources Information Center

Breda, Ana Maria D'azevedo; Dos Santos, José Manuel Dos Santos

2016-01-01

Complex functions, generally feature some interesting peculiarities, seen as extensions of real functions. The visualization of complex functions properties usually requires the simultaneous visualization of two-dimensional spaces. The multiple Windows of GeoGebra, combined with its ability of algebraic computation with complex numbers, allow the…

Real-time, haptics-enabled simulator for probing ex vivo liver tissue.

PubMed

Lister, Kevin; Gao, Zhan; Desai, Jaydev P

2009-01-01

The advent of complex surgical procedures has driven the need for realistic surgical training simulators. Comprehensive simulators that provide realistic visual and haptic feedback during surgical tasks are required to familiarize surgeons with the procedures they are to perform. Complex organ geometry inherent to biological tissues and intricate material properties drive the need for finite element methods to assure accurate tissue displacement and force calculations. Advances in real-time finite element methods have not reached the state where they are applicable to soft tissue surgical simulation. Therefore a real-time, haptics-enabled simulator for probing of soft tissue has been developed which utilizes preprocessed finite element data (derived from accurate constitutive model of the soft-tissue obtained from carefully collected experimental data) to accurately replicate the probing task in real-time.

Field Extension of Real Values of Physical Observables in Classical Theory can Help Attain Quantum Results

NASA Astrophysics Data System (ADS)

Wang, Hai; Kumar, Asutosh; Cho, Minhyung; Wu, Junde

2018-04-01

Physical quantities are assumed to take real values, which stems from the fact that an usual measuring instrument that measures a physical observable always yields a real number. Here we consider the question of what would happen if physical observables are allowed to assume complex values. In this paper, we show that by allowing observables in the Bell inequality to take complex values, a classical physical theory can actually get the same upper bound of the Bell expression as quantum theory. Also, by extending the real field to the quaternionic field, we can puzzle out the GHZ problem using local hidden variable model. Furthermore, we try to build a new type of hidden-variable theory of a single qubit based on the result.

Software Tools for Formal Specification and Verification of Distributed Real-Time Systems.

DTIC Science & Technology

1997-09-30

set of software tools for specification and verification of distributed real time systems using formal methods. The task of this SBIR Phase II effort...to be used by designers of real - time systems for early detection of errors. The mathematical complexity of formal specification and verification has

Determining Individual Grains' Magnetic Moments by Micromagnetic Tomography

NASA Astrophysics Data System (ADS)

de Groot, L. V.; Fabian, K.; Béguin, A.; Reith, P.; Rastogi, A.; Barnhoorn, A.; Hilgenkamp, H.

2017-12-01

Methods to derive paleodirections or paleointensities from rocks currently rely on measurements of bulk samples (typically 10 cc). These samples contain many millions of magnetic remanence carrying grains, their statistical assemblage gives rise to a net magnetic moment for the entire sample. The magnetic properties of these grains, however, differ because of their sizes, shapes, and chemical composition. When dealing with lavas this complex magnetic behavior often hampers paleointensity experiments; while occasionally a reliable paleodirection is obscured. If we would be able to isolate the contribution of each magnetic grain in a sample to the bulk magnetic moment of that sample, a wealth of opportunities for highly detailed magnetic analysis would be opened, possibly leading to an entirely new approach in retrieving paleomagnetic signals from complex mineralogies. Here we take the first practical steps towards this goal by developing a new technique: 'micromagnetic tomography'. Firstly, the distribution and volume of the remanence carrying grains in the sample must be assessed; this is done using a MicroCT scanner capable of detecting grains 1 micron. Secondly, the magnetic stray field perpendicular to the surface of a thin sample is measured using a high-resolution DC SQUID microscope. A mathematical inversion of these measurements yields the isolated direction and magnitude of the magnetic moment of individual grains in the sample. As the measured strength of the magnetic field decreases with the third power as function of distance to the exerting grain (as a result of decay in three dimensions), grains in the top 30-40 microns of our synthetic sample with a relatively low dispersion of grains in a matrix can be assessed reliably. We will discuss the potential of our new inversion scheme, and current challenges we need to overcome for both the scanning SQUID and MicroCT techniques before we can analyse 'real' volcanic samples with our technique.

Some Comments on the Use of de Moivre's Theorem to Solve Quadratic Equations with Real or Complex Coefficients

ERIC Educational Resources Information Center

Bardell, Nicholas S.

2014-01-01

This paper describes how a simple application of de Moivre's theorem may be used to not only find the roots of a quadratic equation with real or generally complex coefficients but also to pinpoint their location in the Argand plane. This approach is much simpler than the comprehensive analysis presented by Bardell (2012, 2014), but it does not…

A heuristic method for simulating open-data of arbitrary complexity that can be used to compare and evaluate machine learning methods.

PubMed

Moore, Jason H; Shestov, Maksim; Schmitt, Peter; Olson, Randal S

2018-01-01

A central challenge of developing and evaluating artificial intelligence and machine learning methods for regression and classification is access to data that illuminates the strengths and weaknesses of different methods. Open data plays an important role in this process by making it easy for computational researchers to easily access real data for this purpose. Genomics has in some examples taken a leading role in the open data effort starting with DNA microarrays. While real data from experimental and observational studies is necessary for developing computational methods it is not sufficient. This is because it is not possible to know what the ground truth is in real data. This must be accompanied by simulated data where that balance between signal and noise is known and can be directly evaluated. Unfortunately, there is a lack of methods and software for simulating data with the kind of complexity found in real biological and biomedical systems. We present here the Heuristic Identification of Biological Architectures for simulating Complex Hierarchical Interactions (HIBACHI) method and prototype software for simulating complex biological and biomedical data. Further, we introduce new methods for developing simulation models that generate data that specifically allows discrimination between different machine learning methods.

Fast determination of royal jelly freshness by a chromogenic reaction.

PubMed

Zheng, Huo-Qing; Wei, Wen-Ting; Wu, Li-Ming; Hu, Fu-Liang; Dietemann, Vincent

2012-06-01

Royal jelly is one of the most important products of honeybees. Given its role in development of bee brood into fertile individuals of the royal caste it is also used in health products for human consumption. Royal jelly spoils and loses its health-promoting properties depending on storage duration and conditions. To ensure product quality before selling, it is therefore necessary to assess royal jelly freshness. Many indexes of freshness have been suggested, but they all lack reliability or require complex and time-consuming analyses. Here we describe a method to detect royal jelly freshness based on a chromogenic reaction between royal jelly and HCl. We demonstrate that analyses based on color parameters allow for the discrimination of royal jelly samples based on the duration of their storage. Color parameters of royal jelly stored at -18 and 4 °C for 28 d remained comparable to that of fresh samples, which supports the reliability of the method. The method of freshness determination described is practical, cheap, and fast and can thus be used in real-time when trading royal jelly. The method developed can be used to assess royal jelly freshness. It is practical, cheap, and fast and can thus be used in real-time when trading royal jelly. © 2012 Institute of Food Technologists®

Inhomogeneous point-process entropy: An instantaneous measure of complexity in discrete systems

NASA Astrophysics Data System (ADS)

Valenza, Gaetano; Citi, Luca; Scilingo, Enzo Pasquale; Barbieri, Riccardo

2014-05-01

Measures of entropy have been widely used to characterize complexity, particularly in physiological dynamical systems modeled in discrete time. Current approaches associate these measures to finite single values within an observation window, thus not being able to characterize the system evolution at each moment in time. Here, we propose a new definition of approximate and sample entropy based on the inhomogeneous point-process theory. The discrete time series is modeled through probability density functions, which characterize and predict the time until the next event occurs as a function of the past history. Laguerre expansions of the Wiener-Volterra autoregressive terms account for the long-term nonlinear information. As the proposed measures of entropy are instantaneously defined through probability functions, the novel indices are able to provide instantaneous tracking of the system complexity. The new measures are tested on synthetic data, as well as on real data gathered from heartbeat dynamics of healthy subjects and patients with cardiac heart failure and gait recordings from short walks of young and elderly subjects. Results show that instantaneous complexity is able to effectively track the system dynamics and is not affected by statistical noise properties.

A Multifunctional Bimetallic Molecular Device for Ultrasensitive Detection, Naked-Eye Recognition, and Elimination of Cyanide Ions.

PubMed

Chow, Cheuk-Fai; Ho, Pui-Yu; Wong, Wing-Leung; Gong, Cheng-Bin

2015-09-07

A new bimetallic Fe(II) -Cu(II) complex was synthesized, characterized, and applied as a selective and sensitive sensor for cyanide detection in water. This complex is the first multifunctional device that can simultaneously detect cyanide ions in real water samples, amplify the colorimetric signal upon detection for naked-eye recognition at the parts-per-million (ppb) level, and convert the toxic cyanide ion into the much safer cyanate ion in situ. The mechanism of the bimetallic complex for high-selectivity recognition and signaling toward cyanide ions was investigated through a series of binding kinetics of the complex with different analytes, including CN(-) , SO4 (2-) , HCO3 (-) , HPO4 (2-) , N3 (-) , CH3 COO(-) , NCS(-) , NO3 (-) , and Cl(-) ions. In addition, the use of the indicator/catalyst displacement assay (ICDA) is demonstrated in the present system in which one metal center acts as a receptor and inhibitor and is bridged to another metal center that is responsible for signal transduction and catalysis, thus showing a versatile approach to the design of new multifunctional devices. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Development Status of the WetLab-2 Project: New Tools for On-orbit Real-time Quantitative Gene Expression.

NASA Technical Reports Server (NTRS)

Jung, Jimmy; Parra, Macarena P.; Almeida, Eduardo; Boone, Travis; Chinn, Tori; Ricco, Antonio; Souza, Kenneth; Hyde, Liz; Rukhsana, Yousuf; Richey, C. Scott

2013-01-01

The primary objective of NASA Ames Research Centers WetLab-2 Project is to place on the ISS a research platform to facilitate gene expression analysis via quantitative real-time PCR (qRT-PCR) of biological specimens grown or cultured on orbit. The WetLab-2 equipment will be capable of processing multiple sample types ranging from microbial cultures to animal tissues dissected on-orbit. In addition to the logistical benefits of in-situ sample processing and analysis, conducting qRT-PCR on-orbit eliminates the confounding effects on gene expression of reentry stresses and shock acting on live cells and organisms. The system can also validate terrestrial analyses of samples returned from ISS by providing quantitative on-orbit gene expression benchmarking prior to sample return. The ability to get on orbit data will provide investigators with the opportunity to adjust experimental parameters for subsequent trials based on the real-time data analysis without need for sample return and re-flight. Finally, WetLab-2 can be used for analysis of air, surface, water, and clinical samples to monitor environmental contaminants and crew health. The verification flight of the instrument is scheduled to launch on SpaceX-5 in Aug. 2014.Progress to date: The WetLab-2 project completed a thorough study of commercially available qRT-PCR systems and performed a downselect based on both scientific and engineering requirements. The selected instrument, the Cepheid SmartCycler, has advantages including modular design (16 independent PCR modules), low power consumption, and rapid ramp times. The SmartCycler has multiplex capabilities, assaying up to four genes of interest in each of the 16 modules. The WetLab-2 team is currently working with Cepheid to modify the unit for housing within an EXPRESS rack locker on the ISS. This will enable the downlink of data to the ground and provide uplink capabilities for programming, commanding, monitoring, and instrument maintenance. The project is currently designing a module that will lyse the cells and extract RNA of sufficient quality for use in qRT-PCR reactions while using a housekeeping gene to normalize RNA concentration and integrity. Current testing focuses on two promising commercial products and chemistries that allow for RNA extraction with minimal complexity and crew time.

Ultrasonic-energy enhance the ionic liquid-based dual microextraction to preconcentrate the lead in ground and stored rain water samples as compared to conventional shaking method.

PubMed

Nizamani, Sooraj; Kazi, Tasneem G; Afridi, Hassan I

2018-01-01

An efficient preconcentration technique based on ultrasonic-assisted ionic liquid-based dual microextraction (UA-ILDµE) method has been developed to preconcentrate the lead (Pb +2 ) in ground and stored rain water. In the current proposed method, Pb +2 was complexed with a chelating agent (dithizone), whereas an ionic liquid (1-butyl-3-methylimidazolium hexafluorophosphate) was used for extraction purpose. The ultrasonic irradiation and electrical shaking system were applied to enhance the dispersion and extraction of Pb +2 complex in aqueous samples. For second phase, dual microextraction (DµE phase), the enriched Pb +2 complex in ionic liquid, extracted back into the acidic aqueous solution and finally determined by flame atomic absorption spectrometry. Some major analytical parameters that influenced the extraction efficiency of developed method, such as pH, concentration of ligand, volume of ionic liquid and samples, time of shaking in thermostatic electrical shaker and ultrasonic bath, effect of back extracting HNO 3 volume, matrix effect, centrifugation time and rate were optimized. At the sample volume of 25mL, the calculated preconcentration factor was 62.2. The limit of detection of proposed procedure for Pb +2 ions was found to be 0.54μgL -1 . The validation of developed method was performed by the analysis of certified sample of water SRM 1643e and standard addition method in a real water sample. The extraction recovery of Pb +2 was enhanced≥2% with shaking time of 80s in ultrasonic bath as compared to used thermostatic electrical shaker, where for optimum recovery up to 10min was required. The developed procedure was successfully used for the enrichment of Pb +2 in ground and stored rain water (surface water) samples of an endemic region of Pakistan. The resulted data indicated that the ground water samples were highly contaminated with Pb +2 , while some of the surface water samples were also have higher values of Pb +2 than permissible limit of WHO. The concentration of Pb +2 in surface and ground water samples was found in the range of 17.5-24.5 and 25.6-99.1μgL - 1 respectively. Copyright © 2017 Elsevier B.V. All rights reserved.

Molecular detection of Giardia duodenalis and Cryptosporidium spp. in canine faecal samples contaminating public areas in Northern Italy.

PubMed

Simonato, Giulia; Frangipane di Regalbono, Antonio; Cassini, Rudi; Traversa, Donato; Tessarin, Cinzia; Di Cesare, Angela; Pietrobelli, Mario

2017-12-01

Giardia duodenalis and Cryptosporidium spp. are common intestinal pathogens of humans and animals. Dogs may be infected by zoonotic isolates of G. duodenalis and Cryptosporidium spp. that, consequently, have high interest under public health perspective. This study estimated the occurrence of these protozoa in canine faeces polluting public areas of Padua municipality (Northern Italy), towards a potential evaluation of health risks for dogs and humans. A total of 705 canine stools was collected in green (n = 270) and urban (n = 435) areas and processed by duplex real-time PCR and real-time PCR SYBR® Green I for the detection of both protozoa. Positive samples were submitted to specific nested PCRs (i.e. β-giardin/SSU-rRNA genes for Giardia; SSU-rRNA gene for Cryptosporidium) to obtain detailed information on the isolates retrieved.Giardia and Cryptosporidium prevalence were 28.9% and 1.7%, respectively. Twenty-one Giardia-positive samples were successfully identified as dog-specific assemblages C and D, and 1 as the human-specific assemblage B. One isolate was identified as Cryptosporidium canis, while the other 11 were confirmed to belong to the Cryptosporidium parvum species complex. Contrariwise to the Cryptosporidium low prevalence, the wide distribution of Giardia suggests a high risk of infection for dogs attending public areas. Although data indicate a limited risk for human health, it is necessary to improve general education to reduce canine faecal pollution towards a widespread awareness of health risks.

Developing smartphone apps for behavioural studies: The AlcoRisk app case study.

PubMed

Smith, Anthony; de Salas, Kristy; Lewis, Ian; Schüz, Benjamin

2017-08-01

Smartphone apps have emerged as valuable research tools to sample human behaviours at their time of occurrence within natural environments. Human behaviour sampling methods, such as Ecological Momentary Assessment (EMA), aim to facilitate research that is situated in ecologically valid real world environments rather than laboratory environments. Researchers have trialled a range of EMA smartphone apps to sample human behaviours such as dieting, physical activity and smoking. Software development processes for EMA smartphones apps, however, are not widely documented with little guidance provided for the integration of complex multidisciplinary behavioural and technical fields. In this paper, the AlcoRisk app for studying alcohol consumption and risk taking tendencies is presented alongside a software development process that integrates these multidisciplinary fields. The software development process consists of three stages including requirements analysis, feature and interface design followed by app implementation. Results from a preliminary feasibility study support the efficacy of the AlcoRisk app's software development process. Copyright © 2017 Elsevier Inc. All rights reserved.

Noninvasive Diagnosis of Coronary Artery Disease Using 12-Lead High-Frequency Electrocardiograms

NASA Technical Reports Server (NTRS)

Schlegel, Todd T.; Arenare, Brian

2006-01-01

A noninvasive, sensitive method of diagnosing certain pathological conditions of the human heart involves computational processing of digitized electrocardiographic (ECG) signals acquired from a patient at all 12 conventional ECG electrode positions. In the processing, attention is focused on low-amplitude, high-frequency components of those portions of the ECG signals known in the art as QRS complexes. The unique contribution of this method lies in the utilization of signal features and combinations of signal features from various combinations of electrode positions, not reported previously, that have been found to be helpful in diagnosing coronary artery disease and such related pathological conditions as myocardial ischemia, myocardial infarction, and congestive heart failure. The electronic hardware and software used to acquire the QRS complexes and perform some preliminary analyses of their high-frequency components were summarized in Real-Time, High-Frequency QRS Electrocardiograph (MSC- 23154), NASA Tech Briefs, Vol. 27, No. 7 (July 2003), pp. 26-28. To recapitulate, signals from standard electrocardiograph electrodes are preamplified, then digitized at a sampling rate of 1,000 Hz, then analyzed by the software that detects R waves and QRS complexes and analyzes them from several perspectives. The software includes provisions for averaging signals over multiple beats and for special-purpose nonrecursive digital filters with specific low- and high-frequency cutoffs. These filters, applied to the averaged signal, effect a band-pass operation in the frequency range from 150 to 250 Hz. The output of the bandpass filter is the desired high-frequency QRS signal. Further processing is then performed in real time to obtain the beat-to-beat root mean square (RMS) voltage amplitude of the filtered signal, certain variations of the RMS voltage, and such standard measures as the heart rate and R-R interval at any given time. A key signal feature analyzed in the present method is the presence versus the absence of reduced-amplitude zones (RAZs). In terms that must be simplified for the sake of brevity, an RAZ comprises several cycles of a high-frequency QRS signal during which the amplitude of the high-frequency oscillation in a portion of the signal is abnormally low (see figure). A given signal sample exhibiting an interval of reduced amplitude may or may not be classified as an RAZ, depending on quantitative criteria regarding peaks and troughs within the reduced-amplitude portion of the high-frequency QRS signal. This analysis is performed in all 12 leads in real time.

A Multi-Pumping Flow System for In Situ Measurements of Dissolved Manganese in Aquatic Systems

PubMed Central

Meyer, David; Prien, Ralf D.; Dellwig, Olaf; Waniek, Joanna J.; Schuffenhauer, Ingo; Donath, Jan; Krüger, Siegfried; Pallentin, Malte; Schulz-Bull, Detlef E.

2016-01-01

A METals In Situ analyzer (METIS) has been used to determine dissolved manganese (II) concentrations in the subhalocline waters of the Gotland Deep (central Baltic Sea). High-resolution in situ measurements of total dissolved Mn were obtained in near real-time by spectrophotometry using 1-(2-pyridylazo)-2-naphthol (PAN). PAN is a complexing agent of dissolved Mn and forms a wine-red complex with a maximum absorbance at a wavelength of 562 nm. Results are presented together with ancillary temperature, salinity, and dissolved O2 data. Lab calibration of the analyzer was performed in a pressure testing tank. A detection limit of 77 nM was obtained. For validation purposes, discrete water samples were taken by using a pump-CTD system. Dissolved Mn in these samples was determined by an independent laboratory based method (inductively coupled plasma–optical emission spectrometry, ICP-OES). Mn measurements from both METIS and ICP-OES analysis were in good agreement. The results showed that the in situ analysis of dissolved Mn is a powerful technique reducing dependencies on heavy and expensive equipment (pump-CTD system, ICP-OES) and is also cost and time effective. PMID:27916898

A Versatile Integrated Ambient Ionization Source Platform.

PubMed

Ai, Wanpeng; Nie, Honggang; Song, Shiyao; Liu, Xiaoyun; Bai, Yu; Liu, Huwei

2018-04-30

The pursuit of high-throughput sample analysis from complex matrix demands development of multiple ionization techniques with complementary specialties. A versatile integrated ambient ionization source (iAmIS) platform is proposed in this work, based on the idea of integrating multiple functions, enhancing the efficiency of current ionization techniques, extending the applications, and decreasing the cost of the instrument. The design of the iAmIS platform combines flowing atmospheric pressure afterglow (FAPA) source/direct analysis in real time (DART), dielectric barrier discharge ionization (DBDI)/low-temperature plasma (LTP), desorption electrospray ionization (DESI), and laser desorption (LD) technique. All individual and combined ionization modes can be easily attained by modulating parameters. In particular, the FAPA/DART&DESI mode can realize the detection of polar and nonpolar compounds at the same time with two different ionization mechanisms: proton transfer and charge transfer. The introduction of LD contributes to the mass spectrometry imaging and the surface-assisted laser desorption (SALDI) under ambient condition. Compared with other individual or multi-mode ion source, the iAmIS platform provides the flexibility of choosing different ionization modes, broadens the scope of the analyte detection, and facilitates the analysis of complex samples. Graphical abstract ᅟ.

Development of a solenoid pumped in situ zinc analyzer for environmental monitoring

USGS Publications Warehouse

Chapin, T.P.; Wanty, R.B.

2005-01-01

A battery powered submersible chemical analyzer, the Zn-DigiScan (Zn Digital Submersible Chemical Analyzer), has been developed for near real-time, in situ monitoring of zinc in aquatic systems. Microprocessor controlled solenoid pumps propel sample and carrier through an anion exchange column to separate zinc from interferences, add colorimetric reagents, and propel the reaction complex through a simple photometric detector. The Zn-DigiScan is capable of self-calibration with periodic injections of standards and blanks. The detection limit with this approach was 30 ??g L-1. Precision was 5-10% relative standard deviation (R.S.D.) below 100 ??g L-1, improving to 1% R.S.D. at 1000 ??g L-1. The linear range extended from 30 to 3000 ??g L-1. In situ field results were in agreement with samples analyzed by inductively coupled plasma mass spectrometry (ICPMS). This pump technology is quite versatile and colorimetric methods with complex online manipulations such as column reduction, preconcentration, and dilution can be performed with the DigiScan. However, long-term field deployments in shallow high altitude streams were hampered by air bubble formation in the photometric detector. ?? 2005 Elsevier B.V. All rights reserved.

Mapping of epistatic quantitative trait loci in four-way crosses.

PubMed

He, Xiao-Hong; Qin, Hongde; Hu, Zhongli; Zhang, Tianzhen; Zhang, Yuan-Ming

2011-01-01

Four-way crosses (4WC) involving four different inbred lines often appear in plant and animal commercial breeding programs. Direct mapping of quantitative trait loci (QTL) in these commercial populations is both economical and practical. However, the existing statistical methods for mapping QTL in a 4WC population are built on the single-QTL genetic model. This simple genetic model fails to take into account QTL interactions, which play an important role in the genetic architecture of complex traits. In this paper, therefore, we attempted to develop a statistical method to detect epistatic QTL in 4WC population. Conditional probabilities of QTL genotypes, computed by the multi-point single locus method, were used to sample the genotypes of all putative QTL in the entire genome. The sampled genotypes were used to construct the design matrix for QTL effects. All QTL effects, including main and epistatic effects, were simultaneously estimated by the penalized maximum likelihood method. The proposed method was confirmed by a series of Monte Carlo simulation studies and real data analysis of cotton. The new method will provide novel tools for the genetic dissection of complex traits, construction of QTL networks, and analysis of heterosis.

A Versatile Integrated Ambient Ionization Source Platform

NASA Astrophysics Data System (ADS)

Ai, Wanpeng; Nie, Honggang; Song, Shiyao; Liu, Xiaoyun; Bai, Yu; Liu, Huwei

2018-04-01

The pursuit of high-throughput sample analysis from complex matrix demands development of multiple ionization techniques with complementary specialties. A versatile integrated ambient ionization source (iAmIS) platform is proposed in this work, based on the idea of integrating multiple functions, enhancing the efficiency of current ionization techniques, extending the applications, and decreasing the cost of the instrument. The design of the iAmIS platform combines flowing atmospheric pressure afterglow (FAPA) source/direct analysis in real time (DART), dielectric barrier discharge ionization (DBDI)/low-temperature plasma (LTP), desorption electrospray ionization (DESI), and laser desorption (LD) technique. All individual and combined ionization modes can be easily attained by modulating parameters. In particular, the FAPA/DART&DESI mode can realize the detection of polar and nonpolar compounds at the same time with two different ionization mechanisms: proton transfer and charge transfer. The introduction of LD contributes to the mass spectrometry imaging and the surface-assisted laser desorption (SALDI) under ambient condition. Compared with other individual or multi-mode ion source, the iAmIS platform provides the flexibility of choosing different ionization modes, broadens the scope of the analyte detection, and facilitates the analysis of complex samples. [Figure not available: see fulltext.

Composition analysis by scanning femtosecond laser ultraprobing (CASFLU).

DOEpatents

Ishikawa, Muriel Y.; Wood, Lowell L.; Campbell, E. Michael; Stuart, Brent C.; Perry, Michael D.

2002-01-01

The composition analysis by scanning femtosecond ultraprobing (CASFLU) technology scans a focused train of extremely short-duration, very intense laser pulses across a sample. The partially-ionized plasma ablated by each pulse is spectrometrically analyzed in real time, determining the ablated material's composition. The steering of the scanned beam thus is computer directed to either continue ablative material-removal at the same site or to successively remove nearby material for the same type of composition analysis. This invention has utility in high-speed chemical-elemental, molecular-fragment and isotopic analyses of the microstructure composition of complex objects, e.g., the oxygen isotopic compositions of large populations of single osteons in bone.

Microwave properties of ice from The Great Lakes

NASA Technical Reports Server (NTRS)

Vickers, R. S.

1975-01-01

The increasing use of radar systems as remote sensors of ice thickness has revealed a lack of basic data on the microwave properties of fresh-water ice. A program, in which the complex dielectric constant was measured for a series of ice samples taken from the Great Lakes, is described. The measurements were taken at temperatures of -5, -10, and -15 C. It is noted that the ice has considerable internal layered structure, and the effects of the layering are examined. Values of 3.0 to 3.2 are reported for the real part of the dielectric constant, with an error bar of + or - 0.01.

Influence Function Learning in Information Diffusion Networks.

PubMed

Du, Nan; Liang, Yingyu; Balcan, Maria-Florina; Song, Le

2014-06-01

Can we learn the influence of a set of people in a social network from cascades of information diffusion? This question is often addressed by a two-stage approach: first learn a diffusion model, and then calculate the influence based on the learned model. Thus, the success of this approach relies heavily on the correctness of the diffusion model which is hard to verify for real world data. In this paper, we exploit the insight that the influence functions in many diffusion models are coverage functions, and propose a novel parameterization of such functions using a convex combination of random basis functions. Moreover, we propose an efficient maximum likelihood based algorithm to learn such functions directly from cascade data, and hence bypass the need to specify a particular diffusion model in advance. We provide both theoretical and empirical analysis for our approach, showing that the proposed approach can provably learn the influence function with low sample complexity, be robust to the unknown diffusion models, and significantly outperform existing approaches in both synthetic and real world data.

Idiosyncratic responding during movie-watching predicted by age differences in attentional control.

PubMed

Campbell, Karen L; Shafto, Meredith A; Wright, Paul; Tsvetanov, Kamen A; Geerligs, Linda; Cusack, Rhodri; Tyler, Lorraine K

2015-11-01

Much is known about how age affects the brain during tightly controlled, though largely contrived, experiments, but do these effects extrapolate to everyday life? Naturalistic stimuli, such as movies, closely mimic the real world and provide a window onto the brain's ability to respond in a timely and measured fashion to complex, everyday events. Young adults respond to these stimuli in a highly synchronized fashion, but it remains to be seen how age affects neural responsiveness during naturalistic viewing. To this end, we scanned a large (N = 218), population-based sample from the Cambridge Centre for Ageing and Neuroscience (Cam-CAN) during movie-watching. Intersubject synchronization declined with age, such that older adults' response to the movie was more idiosyncratic. This decreased synchrony related to cognitive measures sensitive to attentional control. Our findings suggest that neural responsivity changes with age, which likely has important implications for real-world event comprehension and memory. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Fourier ptychographic reconstruction using Poisson maximum likelihood and truncated Wirtinger gradient.

PubMed

Bian, Liheng; Suo, Jinli; Chung, Jaebum; Ou, Xiaoze; Yang, Changhuei; Chen, Feng; Dai, Qionghai

2016-06-10

Fourier ptychographic microscopy (FPM) is a novel computational coherent imaging technique for high space-bandwidth product imaging. Mathematically, Fourier ptychographic (FP) reconstruction can be implemented as a phase retrieval optimization process, in which we only obtain low resolution intensity images corresponding to the sub-bands of the sample's high resolution (HR) spatial spectrum, and aim to retrieve the complex HR spectrum. In real setups, the measurements always suffer from various degenerations such as Gaussian noise, Poisson noise, speckle noise and pupil location error, which would largely degrade the reconstruction. To efficiently address these degenerations, we propose a novel FP reconstruction method under a gradient descent optimization framework in this paper. The technique utilizes Poisson maximum likelihood for better signal modeling, and truncated Wirtinger gradient for effective error removal. Results on both simulated data and real data captured using our laser-illuminated FPM setup show that the proposed method outperforms other state-of-the-art algorithms. Also, we have released our source code for non-commercial use.

Verification of the numerical model of insert-type joint of scaffolding in relation to experimental research

NASA Astrophysics Data System (ADS)

Pieńko, Michał; Błazik-Borowa, Ewa

2018-01-01

This paper presents the problem of comparing the results of computer simulations with the results of laboratory tests. The subject of the study was the insert-type joint of scaffolding loaded with a bending moment. The research was carried out on the real elements of the scaffolding. Due to the complexity of the connection different friction coefficients and depths of wedge insertion were taken into account in the analysis. The aim of conducting the series of analyses was to determine the sensitivity of the model to the mentioned characteristics. Since laboratory tests were carried out on the real samples, there were no preparations of surface involved in the load transfer. This approach caused many problems with the clear definition of the nature of work of individual node elements during the load. The analysis consist of two stages: the stage in which the connection is defined (the wedge is inserted into the rosette), and the loading stage (the node is loaded by the bending moment).

Gaussian process regression for sensor networks under localization uncertainty

USGS Publications Warehouse

Jadaliha, M.; Xu, Yunfei; Choi, Jongeun; Johnson, N.S.; Li, Weiming

2013-01-01

In this paper, we formulate Gaussian process regression with observations under the localization uncertainty due to the resource-constrained sensor networks. In our formulation, effects of observations, measurement noise, localization uncertainty, and prior distributions are all correctly incorporated in the posterior predictive statistics. The analytically intractable posterior predictive statistics are proposed to be approximated by two techniques, viz., Monte Carlo sampling and Laplace's method. Such approximation techniques have been carefully tailored to our problems and their approximation error and complexity are analyzed. Simulation study demonstrates that the proposed approaches perform much better than approaches without considering the localization uncertainty properly. Finally, we have applied the proposed approaches on the experimentally collected real data from a dye concentration field over a section of a river and a temperature field of an outdoor swimming pool to provide proof of concept tests and evaluate the proposed schemes in real situations. In both simulation and experimental results, the proposed methods outperform the quick-and-dirty solutions often used in practice.

Effects of statistical learning on the acquisition of grammatical categories through Qur'anic memorization: A natural experiment.

PubMed

Zuhurudeen, Fathima Manaar; Huang, Yi Ting

2016-03-01

Empirical evidence for statistical learning comes from artificial language tasks, but it is unclear how these effects scale up outside of the lab. The current study turns to a real-world test case of statistical learning where native English speakers encounter the syntactic regularities of Arabic through memorization of the Qur'an. This unique input provides extended exposure to the complexity of a natural language, with minimal semantic cues. Memorizers were asked to distinguish unfamiliar nouns and verbs based on their co-occurrence with familiar pronouns in an Arabic language sample. Their performance was compared to that of classroom learners who had explicit knowledge of pronoun meanings and grammatical functions. Grammatical judgments were more accurate in memorizers compared to non-memorizers. No effects of classroom experience were found. These results demonstrate that real-world exposure to the statistical properties of a natural language facilitates the acquisition of grammatical categories. Copyright © 2015 Elsevier B.V. All rights reserved.

Dependable Real-Time Systems

DTIC Science & Technology

1991-09-30

0196 or 413 545-0720 PI E-mail Address: krithi@nirvan.cs.umass.edu, stankovic(ocs.umass.edu Grant or Contract Title: Dependable Real - Time Systems Grant...Dependable Real - Time Systems " Grant or Contract Number: N00014-85-k-0398 L " Reporting Period: 1 Oct 87 - 30 Sep 91 , 2. Summary of Accomplishments ’ 2.1 Our...in developing a sound approach to scheduling tasks in complex real - time systems , (2) developed a real-time operating system kernel, a preliminary

Development and Validation of a Real-Time PCR Assay for Rapid Detection of Candida auris from Surveillance Samples

PubMed Central

Leach, L.; Zhu, Y.

2017-01-01

ABSTRACT Candida auris is an emerging multidrug-resistant yeast causing invasive health care-associated infection with high mortality worldwide. Rapid identification of C. auris is of primary importance for the implementation of public health measures to control the spread of infection. To achieve these goals, we developed and validated a TaqMan-based real-time PCR assay targeting the internal transcribed spacer 2 (ITS2) region of the ribosomal gene. The assay was highly specific, reproducible, and sensitive, with the detection limit of 1 C. auris CFU/PCR. The performance of the C. auris real-time PCR assay was evaluated by using 623 surveillance samples, including 365 patient swabs and 258 environmental sponges. Real-time PCR yielded positive results from 49 swab and 58 sponge samples, with 89% and 100% clinical sensitivity with regard to their respective culture-positive results. The real-time PCR also detected C. auris DNA from 1% and 12% of swab and sponge samples with culture-negative results, indicating the presence of dead or culture-impaired C. auris. The real-time PCR yielded results within 4 h of sample processing, compared to 4 to 14 days for culture, reducing turnaround time significantly. The new real-time PCR assay allows for accurate and rapid screening of C. auris and can increase effective control and prevention of this emerging multidrug-resistant fungal pathogen in health care facilities. PMID:29187562

Development and Validation of a Real-Time PCR Assay for Rapid Detection of Candida auris from Surveillance Samples.

PubMed

Leach, L; Zhu, Y; Chaturvedi, S

2018-02-01

Candida auris is an emerging multidrug-resistant yeast causing invasive health care-associated infection with high mortality worldwide. Rapid identification of C. auris is of primary importance for the implementation of public health measures to control the spread of infection. To achieve these goals, we developed and validated a TaqMan-based real-time PCR assay targeting the internal transcribed spacer 2 ( ITS 2) region of the ribosomal gene. The assay was highly specific, reproducible, and sensitive, with the detection limit of 1 C. auris CFU/PCR. The performance of the C. auris real-time PCR assay was evaluated by using 623 surveillance samples, including 365 patient swabs and 258 environmental sponges. Real-time PCR yielded positive results from 49 swab and 58 sponge samples, with 89% and 100% clinical sensitivity with regard to their respective culture-positive results. The real-time PCR also detected C. auris DNA from 1% and 12% of swab and sponge samples with culture-negative results, indicating the presence of dead or culture-impaired C. auris The real-time PCR yielded results within 4 h of sample processing, compared to 4 to 14 days for culture, reducing turnaround time significantly. The new real-time PCR assay allows for accurate and rapid screening of C. auris and can increase effective control and prevention of this emerging multidrug-resistant fungal pathogen in health care facilities. Copyright © 2018 Leach et al.

Characteristics of real futures trading networks

NASA Astrophysics Data System (ADS)

Wang, Junjie; Zhou, Shuigeng; Guan, Jihong

2011-01-01

Futures trading is the core of futures business, and it is considered as one of the typical complex systems. To investigate the complexity of futures trading, we employ the analytical method of complex networks. First, we use real trading records from the Shanghai Futures Exchange to construct futures trading networks, in which nodes are trading participants, and two nodes have a common edge if the two corresponding investors appear simultaneously in at least one trading record as a purchaser and a seller, respectively. Then, we conduct a comprehensive statistical analysis on the constructed futures trading networks. Empirical results show that the futures trading networks exhibit features such as scale-free behavior with interesting odd-even-degree divergence in low-degree regions, small-world effect, hierarchical organization, power-law betweenness distribution, disassortative mixing, and shrinkage of both the average path length and the diameter as network size increases. To the best of our knowledge, this is the first work that uses real data to study futures trading networks, and we argue that the research results can shed light on the nature of real futures business.

Evaluation of the Illumigene Malaria LAMP: A Robust Molecular Diagnostic Tool for Malaria Parasites

PubMed Central

Lucchi, Naomi W.; Gaye, Marie; Diallo, Mammadou Alpha; Goldman, Ira F.; Ljolje, Dragan; Deme, Awa Bineta; Badiane, Aida; Ndiaye, Yaye Die; Barnwell, John W.; Udhayakumar, Venkatachalam; Ndiaye, Daouda

2016-01-01

Isothermal nucleic acid amplification assays such as the loop mediated isothermal amplification (LAMP), are well suited for field use as they do not require thermal cyclers to amplify the DNA. To further facilitate the use of LAMP assays in remote settings, simpler sample preparation methods and lyophilized reagents are required. The performance of a commercial malaria LAMP assay (Illumigene Malaria LAMP) was evaluated using two sample preparation workflows (simple filtration prep (SFP)) and gravity-driven filtration prep (GFP)) and pre-dispensed lyophilized reagents. Laboratory and clinical samples were tested in a field laboratory in Senegal and the results independently confirmed in a reference laboratory in the U.S.A. The Illumigene Malaria LAMP assay was easily implemented in the clinical laboratory and gave similar results to a real-time PCR reference test with limits of detection of ≤2.0 parasites/μl depending on the sample preparation method used. This assay reliably detected Plasmodium sp. parasites in a simple low-tech format, providing a much needed alternative to the more complex molecular tests for malaria diagnosis. PMID:27827432

Eigenvalue sensitivity of sampled time systems operating in closed loop

NASA Astrophysics Data System (ADS)

Bernal, Dionisio

2018-05-01

The use of feedback to create closed-loop eigenstructures with high sensitivity has received some attention in the Structural Health Monitoring field. Although practical implementation is necessarily digital, and thus in sampled time, work thus far has center on the continuous time framework, both in design and in checking performance. It is shown in this paper that the performance in discrete time, at typical sampling rates, can differ notably from that anticipated in the continuous time formulation and that discrepancies can be particularly large on the real part of the eigenvalue sensitivities; a consequence being important error on the (linear estimate) of the level of damage at which closed-loop stability is lost. As one anticipates, explicit consideration of the sampling rate poses no special difficulties in the closed-loop eigenstructure design and the relevant expressions are developed in the paper, including a formula for the efficient evaluation of the derivative of the matrix exponential based on the theory of complex perturbations. The paper presents an easily reproduced numerical example showing the level of error that can result when the discrete time implementation of the controller is not considered.

Study of the Effect on Ionic Conductivity and Structral Morphology of the SR Doped Lanthanum Gallate Solid Electrolyte

NASA Astrophysics Data System (ADS)

Sood, Kapil; Singh, K.; Pandey, O. P.

2013-07-01

In the present study, lanthanum gallate and Sr-doped lanthanum gallate samples were prepared by conventional solid state reaction method. The phase conformation has been performed by using X-ray diffraction (XRD) study. The elemental composition has been confirmed using energy dispersive spectroscopy (EDS) analysis. Ac conductivity of the samples has been measured in the frequency range 0.1-106 Hz and from 50-800 °C. The impedance plots among real and complex impedances at particular temperature have been discussed. The behavior shows the effect of bulk and grain boundary effects of the doped sample. The impedance plots with frequency have been analyzed. The plots have been well fitted to equivalent circuit model. The conductivity shows the Arrhenius type of behavior. The activation energy has been calculated from the plots and represents that the conductivity through the material is mainly ionic. The structural morphology of the samples has been investigated using scanning electron microscope (SEM). The micrograph shows that the porosity and grain size both decreases with Sr-doping.

[A capillary blood flow velocity detection system based on linear array charge-coupled devices].

PubMed

Zhou, Houming; Wang, Ruofeng; Dang, Qi; Yang, Li; Wang, Xiang

2017-12-01

In order to detect the flow characteristics of blood samples in the capillary, this paper introduces a blood flow velocity measurement system based on field-programmable gate array (FPGA), linear charge-coupled devices (CCD) and personal computer (PC) software structure. Based on the analysis of the TCD1703C and AD9826 device data sheets, Verilog HDL hardware description language was used to design and simulate the driver. Image signal acquisition and the extraction of the real-time edge information of the blood sample were carried out synchronously in the FPGA. Then a series of discrete displacement were performed in a differential operation to scan each of the blood samples displacement, so that the sample flow rate could be obtained. Finally, the feasibility of the blood flow velocity detection system was verified by simulation and debugging. After drawing the flow velocity curve and analyzing the velocity characteristics, the significance of measuring blood flow velocity is analyzed. The results show that the measurement of the system is less time-consuming and less complex than other flow rate monitoring schemes.

Converting optical scanning holograms of real objects to binary Fourier holograms using an iterative direct binary search algorithm.

PubMed

Leportier, Thibault; Park, Min Chul; Kim, You Seok; Kim, Taegeun

2015-02-09

In this paper, we present a three-dimensional holographic imaging system. The proposed approach records a complex hologram of a real object using optical scanning holography, converts the complex form to binary data, and then reconstructs the recorded hologram using a spatial light modulator (SLM). The conversion from the recorded hologram to a binary hologram is achieved using a direct binary search algorithm. We present experimental results that verify the efficacy of our approach. To the best of our knowledge, this is the first time that a hologram of a real object has been reconstructed using a binary SLM.

Mathematical concepts for modeling human behavior in complex man-machine systems

NASA Technical Reports Server (NTRS)

Johannsen, G.; Rouse, W. B.

1979-01-01

Many human behavior (e.g., manual control) models have been found to be inadequate for describing processes in certain real complex man-machine systems. An attempt is made to find a way to overcome this problem by examining the range of applicability of existing mathematical models with respect to the hierarchy of human activities in real complex tasks. Automobile driving is chosen as a baseline scenario, and a hierarchy of human activities is derived by analyzing this task in general terms. A structural description leads to a block diagram and a time-sharing computer analogy.

Error Estimates for Approximate Solutions of the Riccati Equation with Real or Complex Potentials

NASA Astrophysics Data System (ADS)

Finster, Felix; Smoller, Joel

2010-09-01

A method is presented for obtaining rigorous error estimates for approximate solutions of the Riccati equation, with real or complex potentials. Our main tool is to derive invariant region estimates for complex solutions of the Riccati equation. We explain the general strategy for applying these estimates and illustrate the method in typical examples, where the approximate solutions are obtained by gluing together WKB and Airy solutions of corresponding one-dimensional Schrödinger equations. Our method is motivated by, and has applications to, the analysis of linear wave equations in the geometry of a rotating black hole.

All ASD complex and real 4-dimensional Einstein spaces with Λ≠0 admitting a nonnull Killing vector

NASA Astrophysics Data System (ADS)

Chudecki, Adam

2016-12-01

Anti-self-dual (ASD) 4-dimensional complex Einstein spaces with nonzero cosmological constant Λ equipped with a nonnull Killing vector are considered. It is shown that any conformally nonflat metric of such spaces can be always brought to a special form and the Einstein field equations can be reduced to the Boyer-Finley-Plebański equation (Toda field equation). Some alternative forms of the metric are discussed. All possible real slices (neutral, Euclidean and Lorentzian) of ASD complex Einstein spaces with Λ≠0 admitting a nonnull Killing vector are found.

Single-photon test of hyper-complex quantum theories using a metamaterial.

PubMed

Procopio, Lorenzo M; Rozema, Lee A; Wong, Zi Jing; Hamel, Deny R; O'Brien, Kevin; Zhang, Xiang; Dakić, Borivoje; Walther, Philip

2017-04-21

In standard quantum mechanics, complex numbers are used to describe the wavefunction. Although this has so far proven sufficient to predict experimental results, there is no theoretical reason to choose them over real numbers or generalizations of complex numbers, that is, hyper-complex numbers. Experiments performed to date have proven that real numbers are insufficient, but the need for hyper-complex numbers remains an open question. Here we experimentally probe hyper-complex quantum theories, studying one of their deviations from complex quantum theory: the non-commutativity of phases. We do so by passing single photons through a Sagnac interferometer containing both a metamaterial with a negative refractive index, and a positive phase shifter. To accomplish this we engineered a fishnet metamaterial to have a negative refractive index at 780 nm. We show that the metamaterial phase commutes with other phases with high precision, allowing us to place limits on a particular prediction of hyper-complex quantum theories.

Single-photon test of hyper-complex quantum theories using a metamaterial

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

Procopio, Lorenzo M.; Rozema, Lee A.; Wong, Zi Jing

In standard quantum mechanics, complex numbers are used to describe the wavefunction. Although this has so far proven sufficient to predict experimental results, there is no theoretical reason to choose them over real numbers or generalizations of complex numbers, that is, hyper-complex numbers. Experiments performed to date have proven that real numbers are insufficient, but the need for hyper-complex numbers remains an open question. Here we experimentally probe hyper-complex quantum theories, studying one of their deviations from complex quantum theory: the non-commutativity of phases. We do so by passing single photons through a Sagnac interferometer containing both a metamaterial withmore » a negative refractive index, and a positive phase shifter. In order to accomplish this we engineered a fishnet metamaterial to have a negative refractive index at 780 nm. Here, we show that the metamaterial phase commutes with other phases with high precision, allowing us to place limits on a particular prediction of hyper-complex quantum theories.« less

Single-photon test of hyper-complex quantum theories using a metamaterial

DOE PAGES

Procopio, Lorenzo M.; Rozema, Lee A.; Wong, Zi Jing; ...

2017-04-21

In standard quantum mechanics, complex numbers are used to describe the wavefunction. Although this has so far proven sufficient to predict experimental results, there is no theoretical reason to choose them over real numbers or generalizations of complex numbers, that is, hyper-complex numbers. Experiments performed to date have proven that real numbers are insufficient, but the need for hyper-complex numbers remains an open question. Here we experimentally probe hyper-complex quantum theories, studying one of their deviations from complex quantum theory: the non-commutativity of phases. We do so by passing single photons through a Sagnac interferometer containing both a metamaterial withmore » a negative refractive index, and a positive phase shifter. In order to accomplish this we engineered a fishnet metamaterial to have a negative refractive index at 780 nm. Here, we show that the metamaterial phase commutes with other phases with high precision, allowing us to place limits on a particular prediction of hyper-complex quantum theories.« less

Single-photon test of hyper-complex quantum theories using a metamaterial

PubMed Central

Procopio, Lorenzo M.; Rozema, Lee A.; Wong, Zi Jing; Hamel, Deny R.; O'Brien, Kevin; Zhang, Xiang; Dakić, Borivoje; Walther, Philip

2017-01-01

In standard quantum mechanics, complex numbers are used to describe the wavefunction. Although this has so far proven sufficient to predict experimental results, there is no theoretical reason to choose them over real numbers or generalizations of complex numbers, that is, hyper-complex numbers. Experiments performed to date have proven that real numbers are insufficient, but the need for hyper-complex numbers remains an open question. Here we experimentally probe hyper-complex quantum theories, studying one of their deviations from complex quantum theory: the non-commutativity of phases. We do so by passing single photons through a Sagnac interferometer containing both a metamaterial with a negative refractive index, and a positive phase shifter. To accomplish this we engineered a fishnet metamaterial to have a negative refractive index at 780 nm. We show that the metamaterial phase commutes with other phases with high precision, allowing us to place limits on a particular prediction of hyper-complex quantum theories. PMID:28429711

CROSS-DISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: The Fractal Dimensions of Complex Networks

NASA Astrophysics Data System (ADS)

Guo, Long; Cai, XU

2009-08-01

It is shown that many real complex networks share distinctive features, such as the small-world effect and the heterogeneous property of connectivity of vertices, which are different from random networks and regular lattices. Although these features capture the important characteristics of complex networks, their applicability depends on the style of networks. To unravel the universal characteristics many complex networks have in common, we study the fractal dimensions of complex networks using the method introduced by Shanker. We find that the average 'density' (ρ(r)) of complex networks follows a better power-law function as a function of distance r with the exponent df, which is defined as the fractal dimension, in some real complex networks. Furthermore, we study the relation between df and the shortcuts Nadd in small-world networks and the size N in regular lattices. Our present work provides a new perspective to understand the dependence of the fractal dimension df on the complex network structure.

Real Space Imaging of Nanoparticle Assembly at Liquid-Liquid Interfaces with Nanoscale Resolution.

PubMed

Costa, Luca; Li-Destri, Giovanni; Thomson, Neil H; Konovalov, Oleg; Pontoni, Diego

2016-09-14

Bottom up self-assembly of functional materials at liquid-liquid interfaces has recently emerged as method to design and produce novel two-dimensional (2D) nanostructured membranes and devices with tailored properties. Liquid-liquid interfaces can be seen as a "factory floor" for nanoparticle (NP) self-assembly, because NPs are driven there by a reduction of interfacial energy. Such 2D assembly can be characterized by reciprocal space techniques, namely X-ray and neutron scattering or reflectivity. These techniques have drawbacks, however, as the structural information is averaged over the finite size of the radiation beam and nonperiodic isolated assemblies in 3D or defects may not be easily detected. Real-space in situ imaging methods are more appropriate in this context, but they often suffer from limited resolution and underperform or fail when applied to challenging liquid-liquid interfaces. Here, we study the surfactant-induced assembly of SiO2 nanoparticle monolayers at a water-oil interface using in situ atomic force microscopy (AFM) achieving nanoscale resolved imaging capabilities. Hitherto, AFM imaging has been restricted to solid-liquid interfaces because applications to liquid interfaces have been hindered by their softness and intrinsic dynamics, requiring accurate sample preparation methods and nonconventional AFM operational schemes. Comparing both AFM and grazing incidence X-ray small angle scattering data, we unambiguously demonstrate correlation between real and reciprocal space structure determination showing that the average interfacial NP density is found to vary with surfactant concentration. Additionally, the interaction between the tip and the interface can be exploited to locally determine the acting interfacial interactions. This work opens up the way to studying complex nanostructure formation and phase behavior in a range of liquid-liquid and complex liquid interfaces.

Linking hydrolytic activities to variables influencing a submerged membrane bioreactor (MBR) treating urban wastewater under real operating conditions.

PubMed

Gómez-Silván, C; Arévalo, J; Pérez, J; González-López, J; Rodelas, B

2013-01-01

The seasonal variation of the hydrolytic activities acid and alkaline phosphatase, α-glucosidase and protease, was studied in both the aerated and anoxic phases of a full-scale membrane bioreactor (MBR) (total operational volume = 28.2 m(3)), operated in pre-denitrification mode and fed real urban wastewater. Non-metric multidimensional scaling (MDS) and BIO-ENV analysis were used to study the distribution of enzyme activities in different seasons of the year (spring, summer and autumn) and unveil their relationships with changes in variables influencing the system (composition of influent wastewater, activated sludge temperature and biomass concentration in the bioreactors). The activities of all the tested hydrolases were remarkably dynamic, and each enzyme showed complex and diverse patterns of variation. Except in the summer season, the variables included in this study gave a good explanation of those patterns and displayed high and consistent correlations with them; however, markedly different correlation trends were found in each season, indicating dissimilar adaptation responses of the community to the influence of changing conditions. A consistent and highly negative correlation between protease and α-glucosidase was revealed in all the experiments. The variables included in this study showed contrary influences on these activities, suggesting an alternation of the major groups of carbon-degrading hydrolases in connection to changes in temperature and the availability and composition of nutrients in the different seasons. Sampling over a long period of time was required to adequately lay down the links between hydrolytic activities and the variables influencing the MBR system. These results highlight the complexity of the regulation of substrate degradation by the mixed microbial sludge communities under real operating conditions. Copyright © 2012 Elsevier Ltd. All rights reserved.

Detection of Giardia intestinalis in water samples collected from natural water reservoirs and wells in northern and north-eastern Poland using LAMP, real-time PCR and nested PCR.

PubMed

Lass, Anna; Szostakowska, Beata; Korzeniewski, Krzysztof; Karanis, Panagiotis

2017-10-01

Giardia intestinalis is a protozoan parasite, transmitted to humans and animals by the faecal-oral route, mainly through contaminated water and food. Knowledge about the distribution of this parasite in surface water in Poland is fragmentary and incomplete. Accordingly, 36 environmental water samples taken from surface water reservoirs and wells were collected in Pomerania and Warmia-Masuria provinces, Poland. The 50 L samples were filtered and subsequently analysed with three molecular detection methods: loop-mediated isothermal amplification (LAMP), real-time polymerase chain reaction (real-time PCR) and nested PCR. Of the samples examined, Giardia DNA was found in 15 (42%) samples with the use of LAMP; in 12 (33%) of these samples, Giardia DNA from this parasite was also detected using real-time PCR; and in 9 (25%) using nested PCR. Sequencing of selected positive samples confirmed that the PCR products were fragments of the Giardia intestinalis small subunit rRNA gene. Genotyping using multiplex real-time PCR indicated the presence of assemblages A and B, with the latter predominating. The results indicate that surface water in Poland, as well as water taken from surface wells, may be a source of Giardia strains which are potentially pathogenic for humans. It was also demonstrated that LAMP assay is more sensitive than the other two molecular assays.

[Determination of Trace Lead in Water by UV-Visible Diffuse Reflectance Spectroscopy Combined with Surfactant and Membrane Filtration-Enrichment].

PubMed

Zhang, Xiao-fang; Zhu, Bi-lin; Li, Wei; Wang, Lei; Zhang, Lei; Wu, Ting; Du, Yi-ping

2015-07-01

In this paper, a method of determination of trace lead in water by UV-Visible diffuse reflectance spectroscopy combined with surfactant and membrane filtration enrichment was proposed. In the NH3 x H2O-NH4Cl buffer solution with pH 8.5, the lead(II) ion would react with dithizone to form the red complex under vigorous stirring, which is hydrophobic and can be enriched by the mixed cellulose ester membrane. In addition, the nonionic surfactant Polyoxyethylene lauryl ether (Brij-30) was added into the solution to improve the enrichment efficiency, then visible diffuse reflectance spectra of the membrane were measured directly after the membrane were naturally dried. We also optimized the reaction conditions which may affect the complexation reaction process, such as type of surfactants, the concentration of the surfactant, the reaction acidity, the concentration of dithizone as well as the reaction time. The research results show that under the optimum conditions, a good linear correlation between absorbance at 485 nm and concentration of lead in the range of 5.0-100.0 microg x L(-1) was obtained with a squared correlation coefficient (R2) of 0.9906, and the detection limit was estimated accordingly to be 2.88 microg x L(-1). To determine real water sample, the interference from some potential coexisting ions was also studied at the optimal conditions when the concentration of lead (II) ion standard solution was fixed to 20 microg x L(-1). The results indicate that the following ions cannot interfere in the determination of lead with the proposed method: 500 times of the K+, Na+, Ca2+, Mg2+, NH4+, NO3-, Cl-, CH3COO-, SO4(2-); 10 times of the Al3+ (using 10% NaF as a masking reagent to avoid the interference); 10 times of the Fe3+ (using 10% NaF and 10% sodium potassium tartrate as masking reagents); 10 times of Hg2+ or Zn2+ (using 10% NaSCN and 10% potassium sodium tartrate as masking reagents); the same amount of Cd2+, Cu2+. The proposed method was applied to the determnation of lead (II) in bottled water as a real sample. The determination results show good agreements between the proposed method and graphite furnace atomic absorption spectrometry (GFAAS) method. The recoveries in case of spiked real samples were between 95.4% and 104.5%, and the standard deviations (SD) were between 0.5 micro x L(-1) and 1.5 microg x L(-1), which indicate that the method developed in the present work with advantages of accuracy, simpleness, sensitiveness are of potential application for the determination of trace lead in water samples.

Measuring the Level of Complexity of Scientific Inquiries: The LCSI Index

ERIC Educational Resources Information Center

Eilam, Efrat

2015-01-01

The study developed and applied an index for measuring the level of complexity of full authentic scientific inquiry. Complexity is a fundamental attribute of real life scientific research. The level of complexity is an overall reflection of complex cognitive and metacognitive processes which are required for navigating the authentic inquiry…

Attempt to generalize fractional-order electric elements to complex-order ones

NASA Astrophysics Data System (ADS)

Si, Gangquan; Diao, Lijie; Zhu, Jianwei; Lei, Yuhang; Zhang, Yanbin

2017-06-01

The complex derivative {D}α +/- {{j}β }, with α, β \\in R+ is a generalization of the concept of integer derivative, where α=1, β=0. Fractional-order electric elements and circuits are becoming more and more attractive. In this paper, the complex-order electric elements concept is proposed for the first time, and the complex-order elements are modeled and analyzed. Some interesting phenomena are found that the real part of the order affects the phase of output signal, and the imaginary part affects the amplitude for both the complex-order capacitor and complex-order memristor. More interesting is that the complex-order capacitor can do well at the time of fitting electrochemistry impedance spectra. The complex-order memristor is also analyzed. The area inside the hysteresis loops increases with the increasing of the imaginary part of the order and decreases with the increasing of the real part. Some complex case of complex-order memristors hysteresis loops are analyzed at last, whose loop has touching points beyond the origin of the coordinate system.

Screen Space Ambient Occlusion Based Multiple Importance Sampling for Real-Time Rendering

NASA Astrophysics Data System (ADS)

Zerari, Abd El Mouméne; Babahenini, Mohamed Chaouki

2018-03-01

We propose a new approximation technique for accelerating the Global Illumination algorithm for real-time rendering. The proposed approach is based on the Screen-Space Ambient Occlusion (SSAO) method, which approximates the global illumination for large, fully dynamic scenes at interactive frame rates. Current algorithms that are based on the SSAO method suffer from difficulties due to the large number of samples that are required. In this paper, we propose an improvement to the SSAO technique by integrating it with a Multiple Importance Sampling technique that combines a stratified sampling method with an importance sampling method, with the objective of reducing the number of samples. Experimental evaluation demonstrates that our technique can produce high-quality images in real time and is significantly faster than traditional techniques.

Enzyme-coupled nanoparticles-assisted laser desorption ionization mass spectrometry for searching for low-mass inhibitors of enzymes in complex mixtures.

PubMed

Salwiński, Aleksander; Da Silva, David; Delépée, Raphaël; Maunit, Benoît

2014-04-01

In this report, enzyme-coupled magnetic nanoparticles (EMPs) were shown to be an effective affinity-based tool for finding specific interactions between enzymatic targets and the low-mass molecules in complex mixtures using classic MALDI-TOF apparatus. EMPs used in this work act as nonorganic matrix enabling ionization of small molecules without any interference in the low-mass range (enzyme-coupled nanoparticles-assisted laser desorption ionization MS, ENALDI MS) and simultaneously carry the superficial specific binding sites to capture inhibitors present in a studied mixture. We evaluated ENALDI approach in two complementary variations: 'ion fading' (IF-ENALDI), based on superficial adsorption of inhibitors and 'ion hunting' (IH-ENALDI), based on selective pre-concentration of inhibitors. IF-ENALDI was applied for two sets of enzyme-inhibitor pairs: tyrosinase-glabridin and trypsin-leupeptin and for the real plant sample: Sparrmannia discolor leaf and stem methanol extract. The efficacy of IH-ENALDI was shown for the pair of trypsin-leupeptin. Both ENALDI approaches pose an alternative for bioassay-guided fractionation, the common method for finding inhibitors in the complex mixtures.

Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing

PubMed Central

Tsai, Yu-Chih; Deming, Clayton; Segre, Julia A.; Kong, Heidi H.; Korlach, Jonas

2016-01-01

ABSTRACT Deep metagenomic shotgun sequencing has emerged as a powerful tool to interrogate composition and function of complex microbial communities. Computational approaches to assemble genome fragments have been demonstrated to be an effective tool for de novo reconstruction of genomes from these communities. However, the resultant “genomes” are typically fragmented and incomplete due to the limited ability of short-read sequence data to assemble complex or low-coverage regions. Here, we use single-molecule, real-time (SMRT) sequencing to reconstruct a high-quality, closed genome of a previously uncharacterized Corynebacterium simulans and its companion bacteriophage from a skin metagenomic sample. Considerable improvement in assembly quality occurs in hybrid approaches incorporating short-read data, with even relatively small amounts of long-read data being sufficient to improve metagenome reconstruction. Using short-read data to evaluate strain variation of this C. simulans in its skin community at single-nucleotide resolution, we observed a dominant C. simulans strain with moderate allelic heterozygosity throughout the population. We demonstrate the utility of SMRT sequencing and hybrid approaches in metagenome quantitation, reconstruction, and annotation. PMID:26861018

Characterize kinematic rupture history of large earthquakes with Multiple Haskell sources

NASA Astrophysics Data System (ADS)

Jia, Z.; Zhan, Z.

2017-12-01

Earthquakes are often regarded as continuous rupture along a single fault, but the occurrence of complex large events involving multiple faults and dynamic triggering challenges this view. Such rupture complexities cause difficulties in existing finite fault inversion algorithms, because they rely on specific parameterizations and regularizations to obtain physically meaningful solutions. Furthermore, it is difficult to assess reliability and uncertainty of obtained rupture models. Here we develop a Multi-Haskell Source (MHS) method to estimate rupture process of large earthquakes as a series of sub-events of varying location, timing and directivity. Each sub-event is characterized by a Haskell rupture model with uniform dislocation and constant unilateral rupture velocity. This flexible yet simple source parameterization allows us to constrain first-order rupture complexity of large earthquakes robustly. Additionally, relatively few parameters in the inverse problem yields improved uncertainty analysis based on Markov chain Monte Carlo sampling in a Bayesian framework. Synthetic tests and application of MHS method on real earthquakes show that our method can capture major features of large earthquake rupture process, and provide information for more detailed rupture history analysis.

A micromachined silicon parallel acoustic delay line (PADL) array for real-time photoacoustic tomography (PAT)

NASA Astrophysics Data System (ADS)

Cho, Young Y.; Chang, Cheng-Chung; Wang, Lihong V.; Zou, Jun

2015-03-01

To achieve real-time photoacoustic tomography (PAT), massive transducer arrays and data acquisition (DAQ) electronics are needed to receive the PA signals simultaneously, which results in complex and high-cost ultrasound receiver systems. To address this issue, we have developed a new PA data acquisition approach using acoustic time delay. Optical fibers were used as parallel acoustic delay lines (PADLs) to create different time delays in multiple channels of PA signals. This makes the PA signals reach a single-element transducer at different times. As a result, they can be properly received by single-channel DAQ electronics. However, due to their small diameter and fragility, using optical fiber as acoustic delay lines poses a number of challenges in the design, construction and packaging of the PADLs, thereby limiting their performances and use in real imaging applications. In this paper, we report the development of new silicon PADLs, which are directly made from silicon wafers using advanced micromachining technologies. The silicon PADLs have very low acoustic attenuation and distortion. A linear array of 16 silicon PADLs were assembled into a handheld package with one common input port and one common output port. To demonstrate its real-time PAT capability, the silicon PADL array (with its output port interfaced with a single-element transducer) was used to receive 16 channels of PA signals simultaneously from a tissue-mimicking optical phantom sample. The reconstructed PA image matches well with the imaging target. Therefore, the silicon PADL array can provide a 16× reduction in the ultrasound DAQ channels for real-time PAT.

Advancing Porous Silicon Biosensor Technology for Use in Clinical Diagnostics

NASA Astrophysics Data System (ADS)

Bonanno, Lisa Marie

Inexpensive and robust analytical techniques for detecting molecular recognition events are in great demand in healthcare, food safety, and environmental monitoring. Despite vast research in this area, challanges remain to develop practical biomolecular platforms that, meet the rigorous demands of real-world applications. This includes maintaining low-cost devices that are sensitive and specific in complex test specimens, are stable after storage, have short assay time, and possess minimal complexity of instrumentation for readout. Nanostructured porous silicon (PSi) material has been identified as an ideal candidate towards achieving these goals and the past decade has seen diverse proof-of-principle studies developing optical-based sensing techniques. In Part 1 of this thesis, the impact of surface chemistry and PSi morphology on detection sensitivity of target molecules is investigated. Initial proof-of-concept that PSi devices facilitate detection of protein in whole blood is demonstrated. This work highlights the importance of material stability and blocking chemistry for sensor use in real world biological samples. In addition, the intrinisic filtering capability of the 3-D PSi morphology is shown as an advantage in complex solutions, such as whole blood. Ultimately, this initial work identified a need to improve detection sensitivity of the PSI biosensor technique to facilitate clinical diagnostic use over relevant target concentration ranges. The second part of this thesis, builds upon sensitivity challenges that are highlighted in the first part of the thesis and development of a surface-bound competitive inhibition immunoassay facilitated improved detection sensitivity of small molecular weight targets (opiates) over a relevant clinical concentration range. In addition, optimization of assay protocol addressed issues of maintaining stability of sensors after storage. Performance of the developed assay (specificity and sensitivity) was then validated in a blind clinical study that screened real patient urine samples (n=70) for opiates in collaboration with Strong Memorial Hospital Clinical Toxicology Laboratory. PSI sensor results showed improved clinical specificity over current commercial opiate immunoassay techniques and therefore, identified potential for a reduction in false-negative and false-positive screening results. Here, we demonstrate for the first time, successful clinical capability of a PSi sensor to detect opiates as a model target in real-world patient samples. The final part of this thesis explores novel sensor designs to leverage the tunable optical properties of PSi photonic devices and facilitate colorimetric readout of molecular recognition events by the unaided eye. Such a design is ideal for uncomplicated diagnostic screening at point-of-care as no instrumentation is needed for result readout. The photonic PSi transducers were integrated with target analyte-responsive hydrogels (TRAP-gels) that upon exposure to a target solution would swell and dissolute, inducing material property changes that were optically detected by the incorporated PSi transducer. This strategy extends target detection throughout the 3-ll internal volume of the PSi, improving upon current techniques that limit detection to the surface area (2-ll) of PSi. Work to acheive this approach involved design of TRAP-gel networks, polymer synthesis and characterization techniques, and optical characterization of the hybrid hydrogel-PSi material sensor. Successful implementation of a hybrid sensor design was exhibited for a. model chemical target (reducing agent), in which visual colorimetric change from red to green was observed for above-threshold exposure to the chemical target. In addition, initial proof-of-concept of an opiate responsive TRAP-gel is also demonstrated where cross-links are formed between antibody-antigen interactions and exposure to opiates induces bulk gel dissolution.

Performance characteristics of the new Abbott Real Time MTB assay for detection of Mycobacterium tuberculosis complex in respiratory specimens.

PubMed

Vinuesa, Víctor; Navarro, David; Poujois, Sandrine; Zaragoza, Susana; Borrás, Rafael

2016-03-01

The performance of the Abbott Real Time MTB assay for detection of Mycobacterium tuberculosis complex in respiratory specimens was evaluated using a standard culture as the reference. The overall concordance between both methods was 0.95. The assay displayed an excellent sensitivity (100% for smear-positive/92.3% for smear-negative specimens) and specificity (100%). Copyright © 2015 Elsevier Inc. All rights reserved.

Vectors a Fortran 90 module for 3-dimensional vector and dyadic arithmetic

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

Brock, B.C.

1998-02-01

A major advance contained in the new Fortran 90 language standard is the ability to define new data types and the operators associated with them. Writing computer code to implement computations with real and complex three-dimensional vectors and dyadics is greatly simplified if the equations can be implemented directly, without the need to code the vector arithmetic explicitly. The Fortran 90 module described here defines new data types for real and complex 3-dimensional vectors and dyadics, along with the common operations needed to work with these objects. Routines to allow convenient initialization and output of the new types are alsomore » included. In keeping with the philosophy of data abstraction, the details of the implementation of the data types are maintained private, and the functions and operators are made generic to simplify the combining of real, complex, single- and double-precision vectors and dyadics.« less

The way to uncover community structure with core and diversity

NASA Astrophysics Data System (ADS)

Chang, Y. F.; Han, S. K.; Wang, X. D.

2018-07-01

Communities are ubiquitous in nature and society. Individuals that share common properties often self-organize to form communities. Avoiding the shortages of computation complexity, pre-given information and unstable results in different run, in this paper, we propose a simple and efficient method to deepen our understanding of the emergence and diversity of communities in complex systems. By introducing the rational random selection, our method reveals the hidden deterministic and normal diverse community states of community structure. To demonstrate this method, we test it with real-world systems. The results show that our method could not only detect community structure with high sensitivity and reliability, but also provide instructional information about the hidden deterministic community world and the real normal diverse community world by giving out the core-community, the real-community, the tide and the diversity. Thizs is of paramount importance in understanding, predicting, and controlling a variety of collective behaviors in complex systems.

Best Practices for Real Property Management

DTIC Science & Technology

2016-04-21

organizations and are experienced in creating reliable and actionable solutions to complex management issues guided by proven best business practices...DEFENSE BUSINESS BOARD For the Secretary of Defense Best Practices for Real Property Management DBB...FY16-02 Recommendations on the best practices for management of Department of Defense real property assets Defense Business

Performance evaluation of the Aptima® HCV Quant Dx assay for hepatitis C virus (HCV) RNA detection and quantification in comparison to the Abbott RealTime HCV assay.

PubMed

Garbuglia, Anna Rosa; Bibbò, Angela; Sciamanna, Roberta; Pisciotta, Marina; Capobianchi, Maria Rosaria

2017-07-01

The Aptima HCV Quant Dx assay (Aptima) is a real-time transcription-mediated amplification assay CE-approved for the diagnosis and monitoring of hepatitis C virus (HCV) infection. Aptima's analytical performance was compared to the Abbott RealTime HCV assay (RealTime) in a clinical routine setting. Overall 295 clinical plasma samples (117 prospective/fresh; 178 retrospective/frozen) from HCV-infected patients were tested in Aptima and RealTime to determine concordance on qualitative and quantitative results. Linearity and precision at low viral loads (VLs; 0.8-3.3LogIU/mL) was tested using dilutions of the 5th WHO standard, in 10 and 20 replicates in the two assays, respectively. The ability to measure different HCV genotypes and accuracy were analyzed using the Seracare EQA panel. Inter-assay agreement for qualitative results (prospective samples) was 88% (kappa=0.78). For the 127 samples with quantitative results in both assays, Aptima yielded on average slightly higher values (by 0.24LogIU/mL; Bland-Altman method) than RealTime. Concordance between assay results was excellent (R=0.98). At low VLs (0.8-3.3LogIU/mL), Aptima demonstrated good linearity and precision, similar to RealTime. Aptima detected and accurately quantified all main HCV genotypes. Aptima demonstrated excellent precision, linearity, and accuracy in all genotypes tested. Good concordance was observed between Aptima and RealTime assays in clinical samples. The performance of the Aptima assay, on the fully automated Panther platform, makes it an excellent candidate for the detection and monitoring of HCV RNA in plasma and serum samples. Copyright © 2017 Elsevier B.V. All rights reserved.

Real-time PCR detection of Plasmodium directly from whole blood and filter paper samples

PubMed Central

2011-01-01

Background Real-time PCR is a sensitive and specific method for the analysis of Plasmodium DNA. However, prior purification of genomic DNA from blood is necessary since PCR inhibitors and quenching of fluorophores from blood prevent efficient amplification and detection of PCR products. Methods Reagents designed to specifically overcome PCR inhibition and quenching of fluorescence were evaluated for real-time PCR amplification of Plasmodium DNA directly from blood. Whole blood from clinical samples and dried blood spots collected in the field in Colombia were tested. Results Amplification and fluorescence detection by real-time PCR were optimal with 40× SYBR® Green dye and 5% blood volume in the PCR reaction. Plasmodium DNA was detected directly from both whole blood and dried blood spots from clinical samples. The sensitivity and specificity ranged from 93-100% compared with PCR performed on purified Plasmodium DNA. Conclusions The methodology described facilitates high-throughput testing of blood samples collected in the field by fluorescence-based real-time PCR. This method can be applied to a broad range of clinical studies with the advantages of immediate sample testing, lower experimental costs and time-savings. PMID:21851640

Evaluation of propidium monoazide real-time PCR for enumeration of probiotic lactobacilli microencapsulated in calcium alginate beads.

PubMed

Oketič, K; Matijašić, B Bogovič; Obermajer, T; Radulović, Z; Lević, S; Mirković, N; Nedović, V

2015-01-01

The aim of the study was to evaluate real-time PCR coupled with propidium monoazide (PMA) treatment for enumeration of microencapsulated probiotic lactobacilli microencapsulated in calcium alginate beads. Lactobacillus gasseri K7 (CCM 7710) and Lactobacillus delbrueckii subsp. bulgaricus (CCM 7712) were analysed by plate counting and PMA real-time PCR during storage at 4 °C for 90 days. PMA was effective in preventing PCR amplification of the target sequences of DNA released from heat-compromised bacteria. The values obtained by real-time PCR of non-treated samples were in general higher than those obtained by real-time PCR of PMA-treated samples or by plate counting, indicating the presence of sub-lethally injured cells. This study shows that plate count could not be completely replaced by culture independent method PMA real-time PCR for enumeration of probiotics, but may rather complement the well-established plate counting, providing useful information about the ratio of compromised bacteria in the samples.

TaqMan real-time polymerase chain reaction for detection of Ophidiomyces ophiodiicola, the fungus associated with snake fungal disease.

PubMed

Bohuski, Elizabeth; Lorch, Jeffrey M; Griffin, Kathryn M; Blehert, David S

2015-04-15

Fungal skin infections associated with Ophidiomyces ophiodiicola, a member of the Chrysosporium anamorph of Nannizziopsis vriesii (CANV) complex, have been linked to an increasing number of cases of snake fungal disease (SFD) in captive snakes around the world and in wild snake populations in eastern North America. The emergence of SFD in both captive and wild situations has led to an increased need for tools to better diagnose and study the disease. We developed two TaqMan real-time polymerase chain reaction (PCR) assays to rapidly detect O. ophiodiicola in clinical samples. One assay targets the internal transcribed spacer region (ITS) of the fungal genome while the other targets the more variable intergenic spacer region (IGS). The PCR assays were qualified using skin samples collected from 50 snakes for which O. ophiodiicola had been previously detected by culture, 20 snakes with gross skin lesions suggestive of SFD but which were culture-negative for O. ophiodiicola, and 16 snakes with no clinical signs of infection. Both assays performed equivalently and proved to be more sensitive than traditional culture methods, detecting O. ophiodiicola in 98% of the culture-positive samples and in 40% of the culture-negative snakes that had clinical signs of SFD. In addition, the assays did not cross-react with a panel of 28 fungal species that are closely related to O. ophiodiicola or that commonly occur on the skin of snakes. The assays did, however, indicate that some asymptomatic snakes (~6%) may harbor low levels of the fungus, and that PCR should be paired with histology when a definitive diagnosis is required. These assays represent the first published methods to detect O. ophiodiicola by real-time PCR. The ITS assay has great utility for assisting with SFD diagnoses whereas the IGS assay offers a valuable tool for research-based applications.

Rehabilitation of Executive Functioning in Patients with Frontal Lobe Brain Damage with Goal Management Training

PubMed Central

Levine, Brian; Schweizer, Tom A.; O'Connor, Charlene; Turner, Gary; Gillingham, Susan; Stuss, Donald T.; Manly, Tom; Robertson, Ian H.

2011-01-01

Executive functioning deficits due to brain disease affecting frontal lobe functions cause significant real-life disability, yet solid evidence in support of executive functioning interventions is lacking. Goal Management Training (GMT), an executive functioning intervention that draws upon theories concerning goal processing and sustained attention, has received empirical support in studies of patients with traumatic brain injury, normal aging, and case studies. GMT promotes a mindful approach to complex real-life tasks that pose problems for patients with executive functioning deficits, with a main goal of periodically stopping ongoing behavior to monitor and adjust goals. In this controlled trial, an expanded version of GMT was compared to an alternative intervention, Brain Health Workshop that was matched to GMT on non-specific characteristics that can affect intervention outcome. Participants included 19 individuals in the chronic phase of recovery from brain disease (predominantly stroke) affecting frontal lobe function. Outcome data indicated specific effects of GMT on the Sustained Attention to Response Task as well as the Tower Test, a visuospatial problem-solving measure that reflected far transfer of training effects. There were no significant effects on self-report questionnaires, likely owing to the complexity of these measures in this heterogeneous patient sample. Overall, these data support the efficacy of GMT in the rehabilitation of executive functioning deficits. PMID:21369362

Control of complex components with Smart Flexible Phased Arrays.

PubMed

Casula, O; Poidevin, C; Cattiaux, G; Dumas, Ph

2006-12-22

The inspection is mainly performed in contact with ultrasonic wedge transducers; However, the shape cannot fit the changing geometries of components (butt weld, nozzle, elbow). The variable thickness of the coupling layer, between the wedge and the local surface, leads to beam distortions and losses of sensitivity. Previous studies have shown that these two phenomena contribute to reduce the inspection performances leading to shadow area, split beam.... Flexible phased arrays have been developed to fit the complex profile and improve such controls. The radiating surface is composed with independent piezoelectric elements mechanically assembled and a profilometer, embedded in the transducer, measures the local distortion. The computed shape is used by an algorithm to compute in real-time the adapted delay laws compensating the distortions of 2D or 3D profiles. Those delay laws are transferred to the real-time UT acquisition system, which applies them to the piezoelectric elements. This self-adaptive process preserves, during the scanning, the features of the focused beam (orientation and focal depth) in the specimen. To validate the concept of the Smart Flexible Phased Array Transducer, prototypes have been integrated to detect flaws machined in mock-ups with realistic irregular 2D and 3D shapes. Inspections have been carried out on samples showing the enhancement performances of the "Smart Flexible Phased Array" and validating the mechanical and acoustical behaviors of these probes.

HyperForest: A high performance multi-processor architecture for real-time intelligent systems

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

Garcia, P. Jr.; Rebeil, J.P.; Pollard, H.

1997-04-01

Intelligent Systems are characterized by the intensive use of computer power. The computer revolution of the last few years is what has made possible the development of the first generation of Intelligent Systems. Software for second generation Intelligent Systems will be more complex and will require more powerful computing engines in order to meet real-time constraints imposed by new robots, sensors, and applications. A multiprocessor architecture was developed that merges the advantages of message-passing and shared-memory structures: expendability and real-time compliance. The HyperForest architecture will provide an expandable real-time computing platform for computationally intensive Intelligent Systems and open the doorsmore » for the application of these systems to more complex tasks in environmental restoration and cleanup projects, flexible manufacturing systems, and DOE`s own production and disassembly activities.« less

Comparison of Nested Polymerase Chain Reaction and Real-Time Polymerase Chain Reaction with Parasitological Methods for Detection of Strongyloides stercoralis in Human Fecal Samples

PubMed Central

Sharifdini, Meysam; Mirhendi, Hossein; Ashrafi, Keyhan; Hosseini, Mostafa; Mohebali, Mehdi; Khodadadi, Hossein; Kia, Eshrat Beigom

2015-01-01

This study was performed to evaluate nested polymerase chain reaction (PCR) and real-time PCR methods for detection of Strongyloides stercoralis in fecal samples compared with parasitological methods. A total of 466 stool samples were examined by conventional parasitological methods (formalin ether concentration [FEC] and agar plate culture [APC]). DNA was extracted using an in-house method, and mitochondrial cytochrome c oxidase subunit 1 and 18S ribosomal genes were amplified by nested PCR and real-time PCR, respectively. Among 466 samples, 12.7% and 18.2% were found infected with S. stercoralis by FEC and APC, respectively. DNA of S. stercoralis was detected in 18.9% and 25.1% of samples by real-time PCR and nested PCR, respectively. Considering parasitological methods as the diagnostic gold standard, the sensitivity and specificity of nested PCR were 100% and 91.6%, respectively, and that of real-time PCR were 84.7% and 95.8%, respectively. However, considering sequence analyzes of the selected nested PCR products, the specificity of nested PCR is increased. In general, molecular methods were superior to parasitological methods. They were more sensitive and more reliable in detection of S. stercoralis in comparison with parasitological methods. Between the two molecular methods, the sensitivity of nested PCR was higher than real-time PCR. PMID:26350449

Graph distance for complex networks

NASA Astrophysics Data System (ADS)

Shimada, Yutaka; Hirata, Yoshito; Ikeguchi, Tohru; Aihara, Kazuyuki

2016-10-01

Networks are widely used as a tool for describing diverse real complex systems and have been successfully applied to many fields. The distance between networks is one of the most fundamental concepts for properly classifying real networks, detecting temporal changes in network structures, and effectively predicting their temporal evolution. However, this distance has rarely been discussed in the theory of complex networks. Here, we propose a graph distance between networks based on a Laplacian matrix that reflects the structural and dynamical properties of networked dynamical systems. Our results indicate that the Laplacian-based graph distance effectively quantifies the structural difference between complex networks. We further show that our approach successfully elucidates the temporal properties underlying temporal networks observed in the context of face-to-face human interactions.

Self-paced model learning for robust visual tracking

NASA Astrophysics Data System (ADS)

Huang, Wenhui; Gu, Jason; Ma, Xin; Li, Yibin

2017-01-01

In visual tracking, learning a robust and efficient appearance model is a challenging task. Model learning determines both the strategy and the frequency of model updating, which contains many details that could affect the tracking results. Self-paced learning (SPL) has recently been attracting considerable interest in the fields of machine learning and computer vision. SPL is inspired by the learning principle underlying the cognitive process of humans, whose learning process is generally from easier samples to more complex aspects of a task. We propose a tracking method that integrates the learning paradigm of SPL into visual tracking, so reliable samples can be automatically selected for model learning. In contrast to many existing model learning strategies in visual tracking, we discover the missing link between sample selection and model learning, which are combined into a single objective function in our approach. Sample weights and model parameters can be learned by minimizing this single objective function. Additionally, to solve the real-valued learning weight of samples, an error-tolerant self-paced function that considers the characteristics of visual tracking is proposed. We demonstrate the robustness and efficiency of our tracker on a recent tracking benchmark data set with 50 video sequences.

Real-time prediction of hand trajectory by ensembles of cortical neurons in primates

NASA Astrophysics Data System (ADS)

Wessberg, Johan; Stambaugh, Christopher R.; Kralik, Jerald D.; Beck, Pamela D.; Laubach, Mark; Chapin, John K.; Kim, Jung; Biggs, S. James; Srinivasan, Mandayam A.; Nicolelis, Miguel A. L.

2000-11-01

Signals derived from the rat motor cortex can be used for controlling one-dimensional movements of a robot arm. It remains unknown, however, whether real-time processing of cortical signals can be employed to reproduce, in a robotic device, the kind of complex arm movements used by primates to reach objects in space. Here we recorded the simultaneous activity of large populations of neurons, distributed in the premotor, primary motor and posterior parietal cortical areas, as non-human primates performed two distinct motor tasks. Accurate real-time predictions of one- and three-dimensional arm movement trajectories were obtained by applying both linear and nonlinear algorithms to cortical neuronal ensemble activity recorded from each animal. In addition, cortically derived signals were successfully used for real-time control of robotic devices, both locally and through the Internet. These results suggest that long-term control of complex prosthetic robot arm movements can be achieved by simple real-time transformations of neuronal population signals derived from multiple cortical areas in primates.

Evidence for complex contagion models of social contagion from observational data

PubMed Central

Sprague, Daniel A.

2017-01-01

Social influence can lead to behavioural ‘fads’ that are briefly popular and quickly die out. Various models have been proposed for these phenomena, but empirical evidence of their accuracy as real-world predictive tools has so far been absent. Here we find that a ‘complex contagion’ model accurately describes the spread of behaviours driven by online sharing. We found that standard, ‘simple’, contagion often fails to capture both the rapid spread and the long tails of popularity seen in real fads, where our complex contagion model succeeds. Complex contagion also has predictive power: it successfully predicted the peak time and duration of the ALS Icebucket Challenge. The fast spread and longer duration of fads driven by complex contagion has important implications for activities such as publicity campaigns and charity drives. PMID:28686719

Design considerations for computationally constrained two-way real-time video communication

NASA Astrophysics Data System (ADS)

Bivolarski, Lazar M.; Saunders, Steven E.; Ralston, John D.

2009-08-01

Today's video codecs have evolved primarily to meet the requirements of the motion picture and broadcast industries, where high-complexity studio encoding can be utilized to create highly-compressed master copies that are then broadcast one-way for playback using less-expensive, lower-complexity consumer devices for decoding and playback. Related standards activities have largely ignored the computational complexity and bandwidth constraints of wireless or Internet based real-time video communications using devices such as cell phones or webcams. Telecommunications industry efforts to develop and standardize video codecs for applications such as video telephony and video conferencing have not yielded image size, quality, and frame-rate performance that match today's consumer expectations and market requirements for Internet and mobile video services. This paper reviews the constraints and the corresponding video codec requirements imposed by real-time, 2-way mobile video applications. Several promising elements of a new mobile video codec architecture are identified, and more comprehensive computational complexity metrics and video quality metrics are proposed in order to support the design, testing, and standardization of these new mobile video codecs.

Metal Cationization Extractive Electrospray Ionization Mass Spectrometry of Compounds Containing Multiple Oxygens

NASA Astrophysics Data System (ADS)

Swanson, Kenneth D.; Spencer, Sandra E.; Glish, Gary L.

2017-06-01

Extractive electrospray ionization is an ambient ionization technique that allows real-time sampling of liquid samples, including organic aerosols. Similar to electrospray ionization, the composition of the electrospray solvent used in extractive electrospray ionization can easily be altered to form metal cationized molecules during ionization simply by adding a metal salt to the electrospray solvent. An increase in sensitivity is observed for some molecules that are lithium, sodium, or silver cationized compared with the protonated molecule formed in extractive electrospray ionization with an acid additive. Tandem mass spectrometry of metal cationized molecules can also significantly improve the ability to identify a compound. Tandem mass spectrometry of lithium and silver cationized molecules can result in an increase in the number and uniqueness of dissociation pathways relative to [M + H]+. These results highlight the potential for extractive electrospray ionization with metal cationization in analyzing complex aerosol mixtures. [Figure not available: see fulltext.

Material parameter estimation with terahertz time-domain spectroscopy.

PubMed

Dorney, T D; Baraniuk, R G; Mittleman, D M

2001-07-01

Imaging systems based on terahertz (THz) time-domain spectroscopy offer a range of unique modalities owing to the broad bandwidth, subpicosecond duration, and phase-sensitive detection of the THz pulses. Furthermore, the possibility exists for combining spectroscopic characterization or identification with imaging because the radiation is broadband in nature. To achieve this, we require novel methods for real-time analysis of THz waveforms. This paper describes a robust algorithm for extracting material parameters from measured THz waveforms. Our algorithm simultaneously obtains both the thickness and the complex refractive index of an unknown sample under certain conditions. In contrast, most spectroscopic transmission measurements require knowledge of the sample's thickness for an accurate determination of its optical parameters. Our approach relies on a model-based estimation, a gradient descent search, and the total variation measure. We explore the limits of this technique and compare the results with literature data for optical parameters of several different materials.

Automated fiber tracking and tissue characterization of the anterior cruciate ligament with optical coherence tomography

NASA Astrophysics Data System (ADS)

Balasubramanian, Priya S.; Guo, Jiaqi; Yao, Xinwen; Qu, Dovina; Lu, Helen H.; Hendon, Christine P.

2017-02-01

The directionality of collagen fibers across the anterior cruciate ligament (ACL) as well as the insertion of this key ligament into bone are important for understanding the mechanical integrity and functionality of this complex tissue. Quantitative analysis of three-dimensional fiber directionality is of particular interest due to the physiological, mechanical, and biological heterogeneity inherent across the ACL-to-bone junction, the behavior of the ligament under mechanical stress, and the usefulness of this information in designing tissue engineered grafts. We have developed an algorithm to characterize Optical Coherence Tomography (OCT) image volumes of the ACL. We present an automated algorithm for measuring ligamentous fiber angles, and extracting attenuation and backscattering coefficients of ligament, interface, and bone regions within mature and immature bovine ACL insertion samples. Future directions include translating this algorithm for real time processing to allow three-dimensional volumetric analysis within dynamically moving samples.

Complexity multiscale asynchrony measure and behavior for interacting financial dynamics

NASA Astrophysics Data System (ADS)

Yang, Ge; Wang, Jun; Niu, Hongli

2016-08-01

A stochastic financial price process is proposed and investigated by the finite-range multitype contact dynamical system, in an attempt to study the nonlinear behaviors of real asset markets. The viruses spreading process in a finite-range multitype system is used to imitate the interacting behaviors of diverse investment attitudes in a financial market, and the empirical research on descriptive statistics and autocorrelation behaviors of return time series is performed for different values of propagation rates. Then the multiscale entropy analysis is adopted to study several different shuffled return series, including the original return series, the corresponding reversal series, the random shuffled series, the volatility shuffled series and the Zipf-type shuffled series. Furthermore, we propose and compare the multiscale cross-sample entropy and its modification algorithm called composite multiscale cross-sample entropy. We apply them to study the asynchrony of pairs of time series under different time scales.

Nonparametric Bayesian Segmentation of a Multivariate Inhomogeneous Space-Time Poisson Process.

PubMed

Ding, Mingtao; He, Lihan; Dunson, David; Carin, Lawrence

2012-12-01

A nonparametric Bayesian model is proposed for segmenting time-evolving multivariate spatial point process data. An inhomogeneous Poisson process is assumed, with a logistic stick-breaking process (LSBP) used to encourage piecewise-constant spatial Poisson intensities. The LSBP explicitly favors spatially contiguous segments, and infers the number of segments based on the observed data. The temporal dynamics of the segmentation and of the Poisson intensities are modeled with exponential correlation in time, implemented in the form of a first-order autoregressive model for uniformly sampled discrete data, and via a Gaussian process with an exponential kernel for general temporal sampling. We consider and compare two different inference techniques: a Markov chain Monte Carlo sampler, which has relatively high computational complexity; and an approximate and efficient variational Bayesian analysis. The model is demonstrated with a simulated example and a real example of space-time crime events in Cincinnati, Ohio, USA.

A Novel Sensitive Luminescence Probe Microspheres for Rapid and Efficient Detection of τ-Fluvalinate in Taihu Lake

PubMed Central

Wang, Jixiang; Wang, Yunyun; Qiu, Hao; Sun, Lin; Dai, Xiaohui; Pan, Jianming; Yan, Yongsheng

2017-01-01

Fluorescent molecularly imprinted polymers have shown great promise in biological or chemical separations and detection, due to their high stability, selectivity and sensitivity. In this work, fluorescent molecularly imprinted microsphere was synthesized via precipitation polymerization, which could separate efficiently and rapidly detect τ-fluvalinate (a toxic insecticide) in water samples, was reported. The fluorescent imprinted sensor showed excellent stability, outstanding selectivity and the limit of detection low to 12.14 nM, good regeneration ability which still kept good sensitivity after 8 cycling experiments and fluorescence quenching mechanism was illustrated in details. In addition, the fluorescent sensor was further used to detect τ-fluvalinate in real samples from Taihu Lake. Despite the relatively complex components of the environment water, the fluorescent imprinted microspheres sitll showed good recovery, clearly demonstrating the potental value of this smart sensor nanomaterial in environment monitoring. PMID:28485402

Reproduction and optical analysis of Morpho-inspired polymeric nanostructures

NASA Astrophysics Data System (ADS)

Tippets, Cary A.; Fu, Yulan; Jackson, Anne-Martine; Donev, Eugenii U.; Lopez, Rene

2016-06-01

The brilliant blue coloration of the Morpho rhetenor butterfly originates from complex nanostructures found on the surface of its wings. The Morpho butterfly exhibits strong short-wavelength reflection and a unique two-lobe optical signature in the incident (θ) and reflected (ϕ) angular space. Here, we report the large-area fabrication of a Morpho-like structure and its reproduction in perfluoropolyether. Reflection comparisons of periodic and quasi-random ‘polymer butterfly’ nanostructures show similar normal-incidence spectra but differ in the angular θ-ϕ dependence. The periodic sample shows strong specular reflection and simple diffraction. However, the quasi-random sample produces a two-lobe angular reflection pattern with minimal specular refection, approximating the real butterfly’s optical behavior. Finite-difference time-domain simulations confirm that this pattern results from the quasi-random periodicity and highlights the significance of the inherent randomness in the Morpho’s photonic structure.

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.

Detection of Strongylus vulgaris in equine faecal samples by real-time PCR and larval culture - method comparison and occurrence assessment.

PubMed

Kaspar, A; Pfister, K; Nielsen, M K; Silaghi, C; Fink, H; Scheuerle, M C

2017-01-11

Strongylus vulgaris has become a rare parasite in Germany during the past 50 years due to the practice of frequent prophylactic anthelmintic therapy. To date, the emerging development of resistance in Cyathostominae and Parascaris spp. to numerous equine anthelmintics has changed deworming management and the frequency of anthelmintic usage. In this regard, reliable detection of parasitic infections, especially of the highly pathogenic S. vulgaris is essential. In the current study, two diagnostic methods for the detection of infections with S. vulgaris were compared and information on the occurrence of this parasite in German horses was gained. For this purpose, faecal samples of 501 horses were screened for S. vulgaris with real-time PCR and an additional larval culture was performed in samples of 278 horses. A subset of 26 horses underwent multiple follow-up examinations with both methods in order to evaluate both the persistence of S. vulgaris infections and the reproducibility of each diagnostic method. The real-time PCR revealed S. vulgaris-DNA in ten of 501 investigated equine samples (1.9%). The larval culture demonstrated larvae of S. vulgaris in three of the 278 samples (1.1%). A direct comparison of the two methods was possible in 321 samples including 43 follow-up examinations with the result of 11 S. vulgaris-positive samples by real-time PCR and 4 S. vulgaris-positive samples by larval culture. The McNemar's test (p-value = 0.016) revealed a significant difference and the kappa values (0.525) showed a moderate agreement between real-time PCR and larval culture. The real-time PCR detected a significantly higher proportion of positives of S. vulgaris compared to larval culture and should thus be considered as a routine diagnostic method for the detection of S. vulgaris in equine samples.

EVALUATION OF DIOXIN EMISSIONS MONITORING SYSTEMS

EPA Science Inventory

Continuous samplers and real or semi-real-time continuous monitors for polychlorinated dibenzodioxins and furans provide significant advantages relative to conventional methods of extractive sampling. Continuous samplers collect long term samples over a time period of days to wee...

Dual-dimensional microscopy: real-time in vivo three-dimensional observation method using high-resolution light-field microscopy and light-field display.

PubMed

Kim, Jonghyun; Moon, Seokil; Jeong, Youngmo; Jang, Changwon; Kim, Youngmin; Lee, Byoungho

2018-06-01

Here, we present dual-dimensional microscopy that captures both two-dimensional (2-D) and light-field images of an in-vivo sample simultaneously, synthesizes an upsampled light-field image in real time, and visualizes it with a computational light-field display system in real time. Compared with conventional light-field microscopy, the additional 2-D image greatly enhances the lateral resolution at the native object plane up to the diffraction limit and compensates for the image degradation at the native object plane. The whole process from capturing to displaying is done in real time with the parallel computation algorithm, which enables the observation of the sample's three-dimensional (3-D) movement and direct interaction with the in-vivo sample. We demonstrate a real-time 3-D interactive experiment with Caenorhabditis elegans. (2018) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

Nonlinear complexity of random visibility graph and Lempel-Ziv on multitype range-intensity interacting financial dynamics

NASA Astrophysics Data System (ADS)

Zhang, Yali; Wang, Jun

2017-09-01

In an attempt to investigate the nonlinear complex evolution of financial dynamics, a new financial price model - the multitype range-intensity contact (MRIC) financial model, is developed based on the multitype range-intensity interacting contact system, in which the interaction and transmission of different types of investment attitudes in a stock market are simulated by viruses spreading. Two new random visibility graph (VG) based analyses and Lempel-Ziv complexity (LZC) are applied to study the complex behaviors of return time series and the corresponding random sorted series. The VG method is the complex network theory, and the LZC is a non-parametric measure of complexity reflecting the rate of new pattern generation of a series. In this work, the real stock market indices are considered to be comparatively studied with the simulation data of the proposed model. Further, the numerical empirical study shows the similar complexity behaviors between the model and the real markets, the research confirms that the financial model is reasonable to some extent.

Krylov Subspace Methods for Complex Non-Hermitian Linear Systems. Thesis

NASA Technical Reports Server (NTRS)

Freund, Roland W.

1991-01-01

We consider Krylov subspace methods for the solution of large sparse linear systems Ax = b with complex non-Hermitian coefficient matrices. Such linear systems arise in important applications, such as inverse scattering, numerical solution of time-dependent Schrodinger equations, underwater acoustics, eddy current computations, numerical computations in quantum chromodynamics, and numerical conformal mapping. Typically, the resulting coefficient matrices A exhibit special structures, such as complex symmetry, or they are shifted Hermitian matrices. In this paper, we first describe a Krylov subspace approach with iterates defined by a quasi-minimal residual property, the QMR method, for solving general complex non-Hermitian linear systems. Then, we study special Krylov subspace methods designed for the two families of complex symmetric respectively shifted Hermitian linear systems. We also include some results concerning the obvious approach to general complex linear systems by solving equivalent real linear systems for the real and imaginary parts of x. Finally, numerical experiments for linear systems arising from the complex Helmholtz equation are reported.

Design and Validation of a Compressive Tissue Stimulator with High-Throughput Capacity and Real-Time Modulus Measurement Capability

PubMed Central

Salvetti, David J.; Pino, Christopher J.; Manuel, Steven G.; Dallmeyer, Ian; Rangarajan, Sanjeet V.; Meyer, Tobias; Kotov, Misha

2012-01-01

Mechanical stimulation has been shown to impact the properties of engineered hyaline cartilage constructs and is relevant for engineering of cartilage and osteochondral tissues. Most mechanical stimulators developed to date emphasize precision over adaptability to standard tissue culture equipment and protocols. The realization of mechanical characteristics in engineered constructs approaching native cartilage requires the optimization of complex variables (type of stimulus, regimen, and bimolecular signals). We have proposed and validated a stimulator design that focuses on high construct capacity, compatibility with tissue culture plastic ware, and regimen adaptability to maximize throughput. This design utilizes thin force sensors in lieu of a load cell and a linear encoder to verify position. The implementation of an individual force sensor for each sample enables the measurement of Young's modulus while stimulating the sample. Removable and interchangeable Teflon plungers mounted using neodymium magnets contact each sample. Variations in plunger height and design can vary the strain and force type on individual samples. This allows for the evaluation of a myriad of culture conditions and regimens simultaneously. The system was validated using contact accuracy, and Young's modulus measurements range as key parameters. Contact accuracy for the system was excellent within 1.16% error of the construct height in comparison to measurements made with a micrometer. Biomaterials ranging from bioceramics (cancellous bone, 123 MPa) to soft gels (1% agarose, 20 KPa) can be measured without any modification to the device. The accuracy of measurements in conjunction with the wide range of moduli tested demonstrate the unique characteristics of the device and the feasibility of using this device in mapping real-time changes to Young's modulus of tissue constructs (cartilage, bone) through the developmental phases in ex vivo culture conditions. PMID:21988089

The tracing of mycobacteria in drinking water supply systems by culture, conventional, and real time PCRs.

PubMed

Klanicova, Barbora; Seda, Jaromir; Slana, Iva; Slany, Michal; Pavlik, Ivo

2013-12-01

Mycobacteria are widely present in diverse aquatic habitats, where they can survive for months or years while some species can even proliferate. The resistance of different mycobacterial species to disinfection methods like chlorination or ozonation could result in their presence in the final tap water of consumers. In this study, the culture method, Mycobacterium tuberculosis complex conventional duplex PCR for detection of non-tuberculous mycobacteria (NTM) and quantitative real-time PCR (qPCR) to detect three subspecies of M. avium species (M. a. avium, M. a. hominissuis, and M. a. paratuberculosis) were used to trace their possible path of transmission from the watershed through the reservoir and drinking water plant to raw drinking water and finally to households. A total of 124 samples from four drinking water supply systems in the Czech Republic, 52 dam sediments, 34 water treatment plant sludge samples, and 38 tap water household sediments, were analyzed. NTM of 11 different species were isolated by culture from 42 (33.9 %) samples; the most prevalent were M. gordonae (16.7 %), M. triplex (14.3 %), M. lentiflavum (9.5 %), M. a. avium (7.1 %), M. montefiorenase (7.1 %), and M. nonchromogenicum (7.1 %). NTM DNA was detected in 92 (76.7 %) samples. By qPCR analysis a statistically significant decrease (P < 0.01) was observed along the route from the reservoir (dam sediments), through water treatment sludge and finally to household sediments. The concentrations ranged from 10(0) to 10(4) DNA cells/g. It was confirmed that drinking water supply systems (watershed-reservoir-drinking water treatment plant-household) might be a potential transmission route for mycobacteria.

A Framework for Realistic Modeling and Display of Object Surface Appearance

NASA Astrophysics Data System (ADS)

Darling, Benjamin A.

With advances in screen and video hardware technology, the type of content presented on computers has progressed from text and simple shapes to high-resolution photographs, photorealistic renderings, and high-definition video. At the same time, there have been significant advances in the area of content capture, with the development of devices and methods for creating rich digital representations of real-world objects. Unlike photo or video capture, which provide a fixed record of the light in a scene, these new technologies provide information on the underlying properties of the objects, allowing their appearance to be simulated for novel lighting and viewing conditions. These capabilities provide an opportunity to continue the computer display progression, from high-fidelity image presentations to digital surrogates that recreate the experience of directly viewing objects in the real world. In this dissertation, a framework was developed for representing objects with complex color, gloss, and texture properties and displaying them onscreen to appear as if they are part of the real-world environment. At its core, there is a conceptual shift from a traditional image-based display workflow to an object-based one. Instead of presenting the stored patterns of light from a scene, the objective is to reproduce the appearance attributes of a stored object by simulating its dynamic patterns of light for the real viewing and lighting geometry. This is accomplished using a computational approach where the physical light sources are modeled and the observer and display screen are actively tracked. Surface colors are calculated for the real spectral composition of the illumination with a custom multispectral rendering pipeline. In a set of experiments, the accuracy of color and gloss reproduction was evaluated by measuring the screen directly with a spectroradiometer. Gloss reproduction was assessed by comparing gonio measurements of the screen output to measurements of the real samples in the same measurement configuration. A chromatic adaptation experiment was performed to evaluate color appearance in the framework and explore the factors that contribute to differences when viewing self-luminous displays as opposed to reflective objects. A set of sample applications was developed to demonstrate the potential utility of the object display technology for digital proofing, psychophysical testing, and artwork display.

A system for measuring complex dielectric properties of thin films at submillimeter wavelengths using an open hemispherical cavity and a vector network analyzer

NASA Astrophysics Data System (ADS)

Rahman, Rezwanur; Taylor, P. C.; Scales, John A.

2013-08-01

Quasi-optical (QO) methods of dielectric spectroscopy are well established in the millimeter and submillimeter frequency bands. These methods exploit standing wave structure in the sample produced by a transmitted Gaussian beam to achieve accurate, low-noise measurement of the complex permittivity of the sample [e.g., J. A. Scales and M. Batzle, Appl. Phys. Lett. 88, 062906 (2006);, 10.1063/1.2172403 R. N. Clarke and C. B. Rosenberg, J. Phys. E 15, 9 (1982);, 10.1088/0022-3735/15/1/002 T. M. Hirovnen, P. Vainikainen, A. Lozowski, and A. V. Raisanen, IEEE Trans. Instrum. Meas. 45, 780 (1996)], 10.1109/19.516996. In effect the sample itself becomes a low-Q cavity. On the other hand, for optically thin samples (films of thickness much less than a wavelength) or extremely low loss samples (loss tangents below 10-5) the QO approach tends to break down due to loss of signal. In such a case it is useful to put the sample in a high-Q cavity and measure the perturbation of the cavity modes. Provided that the average mode frequency divided by the shift in mode frequency is less than the Q (quality factor) of the mode, then the perturbation should be resolvable. Cavity perturbation techniques are not new, but there are technological difficulties in working in the millimeter/submillimeter wave region. In this paper we will show applications of cavity perturbation to the dielectric characterization of semi-conductor thin films of the type used in the manufacture of photovoltaics in the 100 and 350 GHz range. We measured the complex optical constants of hot-wire chemical deposition grown 1-μm thick amorphous silicon (a-Si:H) film on borosilicate glass substrate. The real part of the refractive index and dielectric constant of the glass-substrate varies from frequency-independent to linearly frequency-dependent. We also see power-law behavior of the frequency-dependent optical conductivity from 316 GHz (9.48 cm-1) down to 104 GHz (3.12 cm-1).

Class-conditional feature modeling for ignitable liquid classification with substantial substrate contribution in fire debris analysis.

PubMed

Lopatka, Martin; Sigman, Michael E; Sjerps, Marjan J; Williams, Mary R; Vivó-Truyols, Gabriel

2015-07-01

Forensic chemical analysis of fire debris addresses the question of whether ignitable liquid residue is present in a sample and, if so, what type. Evidence evaluation regarding this question is complicated by interference from pyrolysis products of the substrate materials present in a fire. A method is developed to derive a set of class-conditional features for the evaluation of such complex samples. The use of a forensic reference collection allows characterization of the variation in complex mixtures of substrate materials and ignitable liquids even when the dominant feature is not specific to an ignitable liquid. Making use of a novel method for data imputation under complex mixing conditions, a distribution is modeled for the variation between pairs of samples containing similar ignitable liquid residues. Examining the covariance of variables within the different classes allows different weights to be placed on features more important in discerning the presence of a particular ignitable liquid residue. Performance of the method is evaluated using a database of total ion spectrum (TIS) measurements of ignitable liquid and fire debris samples. These measurements include 119 nominal masses measured by GC-MS and averaged across a chromatographic profile. Ignitable liquids are labeled using the American Society for Testing and Materials (ASTM) E1618 standard class definitions. Statistical analysis is performed in the class-conditional feature space wherein new forensic traces are represented based on their likeness to known samples contained in a forensic reference collection. The demonstrated method uses forensic reference data as the basis of probabilistic statements concerning the likelihood of the obtained analytical results given the presence of ignitable liquid residue of each of the ASTM classes (including a substrate only class). When prior probabilities of these classes can be assumed, these likelihoods can be connected to class probabilities. In order to compare the performance of this method to previous work, a uniform prior was assumed, resulting in an 81% accuracy for an independent test of 129 real burn samples. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Reference data set of volcanic ash physicochemical and optical properties

NASA Astrophysics Data System (ADS)

Vogel, A.; Diplas, S.; Durant, A. J.; Azar, A. S.; Sunding, M. F.; Rose, W. I.; Sytchkova, A.; Bonadonna, C.; Krüger, K.; Stohl, A.

2017-09-01

Uncertainty in the physicochemical and optical properties of volcanic ash particles creates errors in the detection and modeling of volcanic ash clouds and in quantification of their potential impacts. In this study, we provide a data set that describes the physicochemical and optical properties of a representative selection of volcanic ash samples from nine different volcanic eruptions covering a wide range of silica contents (50-80 wt % SiO2). We measured and calculated parameters describing the physical (size distribution, complex shape, and dense-rock equivalent mass density), chemical (bulk and surface composition), and optical (complex refractive index from ultraviolet to near-infrared wavelengths) properties of the volcanic ash and classified the samples according to their SiO2 and total alkali contents into the common igneous rock types basalt to rhyolite. We found that the mass density ranges between ρ = 2.49 and 2.98 g/cm3 for rhyolitic to basaltic ash types and that the particle shape varies with changing particle size (d < 100 μm). The complex refractive indices in the wavelength range between λ = 300 nm and 1500 nm depend systematically on the composition of the samples. The real part values vary from n = 1.38 to 1.66 depending on ash type and wavelength and the imaginary part values from k = 0.00027 to 0.00268. We place our results into the context of existing data and thus provide a comprehensive data set that can be used for future and historic eruptions, when only basic information about the magma type producing the ash is known.

The R-Shell approach - Using scheduling agents in complex distributed real-time systems

NASA Technical Reports Server (NTRS)

Natarajan, Swaminathan; Zhao, Wei; Goforth, Andre

1993-01-01

Large, complex real-time systems such as space and avionics systems are extremely demanding in their scheduling requirements. The current OS design approaches are quite limited in the capabilities they provide for task scheduling. Typically, they simply implement a particular uniprocessor scheduling strategy and do not provide any special support for network scheduling, overload handling, fault tolerance, distributed processing, etc. Our design of the R-Shell real-time environment fcilitates the implementation of a variety of sophisticated but efficient scheduling strategies, including incorporation of all these capabilities. This is accomplished by the use of scheduling agents which reside in the application run-time environment and are responsible for coordinating the scheduling of the application.

A Metrics-Based Approach to Intrusion Detection System Evaluation for Distributed Real-Time Systems

DTIC Science & Technology

2002-04-01

Based Approach to Intrusion Detection System Evaluation for Distributed Real - Time Systems Authors: G. A. Fink, B. L. Chappell, T. G. Turner, and...Distributed, Security. 1 Introduction Processing and cost requirements are driving future naval combat platforms to use distributed, real - time systems of...distributed, real - time systems . As these systems grow more complex, the timing requirements do not diminish; indeed, they may become more constrained