Multi-scale occupancy estimation and modelling using multiple detection methods

USGS Publications Warehouse

Nichols, James D.; Bailey, Larissa L.; O'Connell, Allan F.; Talancy, Neil W.; Grant, Evan H. Campbell; Gilbert, Andrew T.; Annand, Elizabeth M.; Husband, Thomas P.; Hines, James E.

2008-01-01

Occupancy estimation and modelling based on detection–nondetection data provide an effective way of exploring change in a species’ distribution across time and space in cases where the species is not always detected with certainty. Today, many monitoring programmes target multiple species, or life stages within a species, requiring the use of multiple detection methods. When multiple methods or devices are used at the same sample sites, animals can be detected by more than one method.We develop occupancy models for multiple detection methods that permit simultaneous use of data from all methods for inference about method-specific detection probabilities. Moreover, the approach permits estimation of occupancy at two spatial scales: the larger scale corresponds to species’ use of a sample unit, whereas the smaller scale corresponds to presence of the species at the local sample station or site.We apply the models to data collected on two different vertebrate species: striped skunks Mephitis mephitis and red salamanders Pseudotriton ruber. For striped skunks, large-scale occupancy estimates were consistent between two sampling seasons. Small-scale occupancy probabilities were slightly lower in the late winter/spring when skunks tend to conserve energy, and movements are limited to males in search of females for breeding. There was strong evidence of method-specific detection probabilities for skunks. As anticipated, large- and small-scale occupancy areas completely overlapped for red salamanders. The analyses provided weak evidence of method-specific detection probabilities for this species.Synthesis and applications. Increasingly, many studies are utilizing multiple detection methods at sampling locations. The modelling approach presented here makes efficient use of detections from multiple methods to estimate occupancy probabilities at two spatial scales and to compare detection probabilities associated with different detection methods. The models can be viewed as another variation of Pollock's robust design and may be applicable to a wide variety of scenarios where species occur in an area but are not always near the sampled locations. The estimation approach is likely to be especially useful in multispecies conservation programmes by providing efficient estimates using multiple detection devices and by providing device-specific detection probability estimates for use in survey design.

Multiple-Targeted Graphene-based Nanocarrier for Intracellular Imaging of mRNAs

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

Wang, Ying; Li, Zhaohui; Liu, Misha

Simultaneous detection and imaging of multiple intracellular messenger RNA (mRNAs) hold great significant for early cancer diagnostics and preventive medicine development. Herein, we propose a multiple-targeted graphene oxide (GO) nanocarrier that can simultaneously detect and image different type mRNAs in living cells. First of all, in vitro detection of multiple targets have been realized successfully based on the multiple-targeted GO nanocarrier with linear relationship ranging from 3 nM to 200 nM, as well as sensitive detection limit of 1.84 nM for manganese superoxide dismutase (Mn-SOD) mRNA and 2.45 nM for β-actin mRNA. Additionally, this nanosensing platform composed of fluorescent labeledmore » single strand DNA probes and GO nanocarrier can identify Mn-SOD mRNA and endogenous mRNA of β-actin in living cancer cells, showing rapid response, high specificity, nuclease stability, and good biocompatibility during the cell imaging. Thirdly, changes of the expression levels of mRNA in living cells before or after the drug treatment can be monitored successfully. By using multiple ssDNA as probes and GO nanocarrier as the cellular delivery cargo, the proposed simultaneous multiple-targeted sensing platform will be of great potential as a powerful tool for intracellular trafficking process from basic research to clinical diagnosis.« less

Detection of BCG bacteria using a magnetoresistive biosensor: A step towards a fully electronic platform for tuberculosis point-of-care detection.

PubMed

Barroso, Teresa G; Martins, Rui C; Fernandes, Elisabete; Cardoso, Susana; Rivas, José; Freitas, Paulo P

2018-02-15

Tuberculosis is one of the major public health concerns. This highly contagious disease affects more than 10.4 million people, being a leading cause of morbidity by infection. Tuberculosis is diagnosed at the point-of-care by the Ziehl-Neelsen sputum smear microscopy test. Ziehl-Neelsen is laborious, prone to human error and infection risk, with a limit of detection of 10 4 cells/mL. In resource-poor nations, a more practical test, with lower detection limit, is paramount. This work uses a magnetoresistive biosensor to detect BCG bacteria for tuberculosis diagnosis. Herein we report: i) nanoparticle assembly method and specificity for tuberculosis detection; ii) demonstration of proportionality between BCG cell concentration and magnetoresistive voltage signal; iii) application of multiplicative signal correction for systematic effects removal; iv) investigation of calibration effectiveness using chemometrics methods; and v) comparison with state-of-the-art point-of-care tuberculosis biosensors. Results present a clear correspondence between voltage signal and cell concentration. Multiplicative signal correction removes baseline shifts within and between biochip sensors, allowing accurate and precise voltage signal between different biochips. The corrected signal was used for multivariate regression models, which significantly decreased the calibration standard error from 0.50 to 0.03log 10 (cells/mL). Results show that Ziehl-Neelsen detection limits and below are achievable with the magnetoresistive biochip, when pre-processing and chemometrics are used. Copyright © 2017 Elsevier B.V. All rights reserved.

Estimation of descriptive statistics for multiply censored water quality data

USGS Publications Warehouse

Helsel, Dennis R.; Cohn, Timothy A.

1988-01-01

This paper extends the work of Gilliom and Helsel (1986) on procedures for estimating descriptive statistics of water quality data that contain “less than” observations. Previously, procedures were evaluated when only one detection limit was present. Here we investigate the performance of estimators for data that have multiple detection limits. Probability plotting and maximum likelihood methods perform substantially better than simple substitution procedures now commonly in use. Therefore simple substitution procedures (e.g., substitution of the detection limit) should be avoided. Probability plotting methods are more robust than maximum likelihood methods to misspecification of the parent distribution and their use should be encouraged in the typical situation where the parent distribution is unknown. When utilized correctly, less than values frequently contain nearly as much information for estimating population moments and quantiles as would the same observations had the detection limit been below them.

Detection of admittivity anomaly on high-contrast heterogeneous backgrounds using frequency difference EIT.

PubMed

Jang, J; Seo, J K

2015-06-01

This paper describes a multiple background subtraction method in frequency difference electrical impedance tomography (fdEIT) to detect an admittivity anomaly from a high-contrast background conductivity distribution. The proposed method expands the use of the conventional weighted frequency difference EIT method, which has been used limitedly to detect admittivity anomalies in a roughly homogeneous background. The proposed method can be viewed as multiple weighted difference imaging in fdEIT. Although the spatial resolutions of the output images by fdEIT are very low due to the inherent ill-posedness, numerical simulations and phantom experiments of the proposed method demonstrate its feasibility to detect anomalies. It has potential application in stroke detection in a head model, which is highly heterogeneous due to the skull.

Enhanced Detectability of Community Structure in Multilayer Networks through Layer Aggregation.

PubMed

Taylor, Dane; Shai, Saray; Stanley, Natalie; Mucha, Peter J

2016-06-03

Many systems are naturally represented by a multilayer network in which edges exist in multiple layers that encode different, but potentially related, types of interactions, and it is important to understand limitations on the detectability of community structure in these networks. Using random matrix theory, we analyze detectability limitations for multilayer (specifically, multiplex) stochastic block models (SBMs) in which L layers are derived from a common SBM. We study the effect of layer aggregation on detectability for several aggregation methods, including summation of the layers' adjacency matrices for which we show the detectability limit vanishes as O(L^{-1/2}) with increasing number of layers, L. Importantly, we find a similar scaling behavior when the summation is thresholded at an optimal value, providing insight into the common-but not well understood-practice of thresholding pairwise-interaction data to obtain sparse network representations.

Quantitative Detection of Nucleoside Analogues by Multi-enzyme Biosensors using Time-Resolved Kinetic Measurements.

PubMed

Muthu, Pravin; Lutz, Stefan

2016-04-05

Fast, simple and cost-effective methods for detecting and quantifying pharmaceutical agents in patients are highly sought after to replace equipment and labor-intensive analytical procedures. The development of new diagnostic technology including portable detection devices also enables point-of-care by non-specialists in resource-limited environments. We have focused on the detection and dose monitoring of nucleoside analogues used in viral and cancer therapies. Using deoxyribonucleoside kinases (dNKs) as biosensors, our chemometric model compares observed time-resolved kinetics of unknown analytes to known substrate interactions across multiple enzymes. The resulting dataset can simultaneously identify and quantify multiple nucleosides and nucleoside analogues in complex sample mixtures. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multiple biomarkers biosensor with just-in-time functionalization: Application to prostate cancer detection.

PubMed

Parra-Cabrera, C; Samitier, J; Homs-Corbera, A

2016-03-15

We present a novel lab-on-a-chip (LOC) device for the simultaneous detection of multiple biomarkers using simple voltage measurements. The biosensor functionalization is performed in-situ, immediately before its use, facilitating reagents storage and massive devices fabrication. Sensitivity, limit of detection (LOD) and limit of quantification (LOQ) are tunable depending on the in-chip flown sample volumes. As a proof-of-concept, the system has been tested and adjusted to quantify two proteins found in blood that are susceptible to be used combined, as a screening tool, to diagnose prostate cancer (PCa): prostate-specific antigen (PSA) and spondin-2 (SPON2). This combination of biomarkers has been reported to be more specific for PCa diagnostics than the currently accepted but rather controversial PSA indicator. The range of detection for PSA and SPON2 could be adjusted to the clinically relevant range of 1 to 10 ng/ml. The system was tested for specificity to the evaluated biomarkers. This multiplex system can be modified and adapted to detect a larger quantity of biomarkers, or different ones, of relevance to other specific diseases. Copyright © 2015 Elsevier B.V. All rights reserved.

Fast Optical Hazard Detection for Planetary Rovers Using Multiple Spot Laser Triangulation

NASA Technical Reports Server (NTRS)

Matthies, L.; Balch, T.; Wilcox, B.

1997-01-01

A new laser-based optical sensor system that provides hazard detection for planetary rovers is presented. It is anticipated that the sensor can support safe travel at speeds up to 6cm/second for large (1m) rovers in full sunlight on Earth or Mars. The system overcomes limitations in an older design that require image differencing ot detect a laser stripe in full sun.

Protoplanetary Disks in Multiple Star Systems

NASA Astrophysics Data System (ADS)

Harris, Robert J.

Most stars are born in multiple systems, so the presence of a stellar companion may commonly influence planet formation. Theory indicates that companions may inhibit planet formation in two ways. First, dynamical interactions can tidally truncate circumstellar disks. Truncation reduces disk lifetimes and masses, leaving less time and material for planet formation. Second, these interactions might reduce grain-coagulation efficiency, slowing planet formation in its earliest stages. I present three observational studies investigating these issues. First is a spatially resolved Submillimeter Array (SMA) census of disks in young multiple systems in the Taurus-Auriga star-forming region to study their bulk properties. With this survey, I confirmed that disk lifetimes are preferentially decreased in multiples: single stars have detectable millimeter-wave continuum emission twice as often as components of multiples. I also verified that millimeter luminosity (proportional to disk mass) declines with decreasing stellar separation. Furthermore, by measuring resolved-disk radii, I quantitatively tested tidal-truncation theories: results were mixed, with a few disks much larger than expected. I then switch focus to the grain-growth properties of disks in multiple star systems. By combining SMA, Combined Array for Research in Millimeter Astronomy (CARMA), and Jansky Very Large Array (VLA) observations of the circumbinary disk in the UZ Tau quadruple system, I detected radial variations in the grain-size distribution: large particles preferentially inhabit the inner disk. Detections of these theoretically predicted variations have been rare. I related this to models of grain coagulation in gas disks and find that our results are consistent with growth limited by radial drift. I then present a study of grain growth in the disks of the AS 205 and UX Tau multiple systems. By combining SMA, Atacama Large Millimeter/submillimeter Array (ALMA), and VLA observations, I detected radial variations of the grain-size distribution in the AS 205 A disk, but not in the UX Tau A disk. I find that some combination of radial drift and fragmentation limits growth in the AS 205 A disk. In the final chapter, I summarize my findings that, while multiplicity clearly influences bulk disk properties, it does not obviously inhibit grain growth. Other investigations are suggested.

Multiple pathogen biomarker detection using an encoded bead array in droplet PCR.

PubMed

Periyannan Rajeswari, Prem Kumar; Soderberg, Lovisa M; Yacoub, Alia; Leijon, Mikael; Andersson Svahn, Helene; Joensson, Haakan N

2017-08-01

We present a droplet PCR workflow for detection of multiple pathogen DNA biomarkers using fluorescent color-coded Luminex® beads. This strategy enables encoding of multiple singleplex droplet PCRs using a commercially available bead set of several hundred distinguishable fluorescence codes. This workflow provides scalability beyond the limited number offered by fluorescent detection probes such as TaqMan probes, commonly used in current multiplex droplet PCRs. The workflow was validated for three different Luminex bead sets coupled to target specific capture oligos to detect hybridization of three microorganisms infecting poultry: avian influenza, infectious laryngotracheitis virus and Campylobacter jejuni. In this assay, the target DNA was amplified with fluorescently labeled primers by PCR in parallel in monodisperse picoliter droplets, to avoid amplification bias. The color codes of the Luminex detection beads allowed concurrent and accurate classification of the different bead sets used in this assay. The hybridization assay detected target DNA of all three microorganisms with high specificity, from samples with average target concentration of a single DNA template molecule per droplet. This workflow demonstrates the possibility of increasing the droplet PCR assay detection panel to detect large numbers of targets in parallel, utilizing the scalability offered by the color-coded Luminex detection beads. Copyright © 2017. Published by Elsevier B.V.

Comparison of traditional culture and molecular qPCR for detection of simultaneous carriage of multiple pneumococcal serotypes in African children.

PubMed

Olwagen, Courtney P; Adrian, Peter V; Madhi, Shabir A

2017-07-05

S. pneumoniae is a common colonizer of the human nasopharynx in high income and low-middle income countries. Due to limitations of standard culture methods, the prevalence of concurrent colonization with multiple serotypes is unclear. We evaluated the use of multiplex quantitative PCR (qPCR) to detect multiple pneumococcal serotypes/group colonization in archived nasopharyngeal swabs of pneumococcal conjugate vaccine naive children who had previously been investigated by traditional culture methods. Overall the detection of pneumococcal colonization was higher by qPCR (82%) compared to standard culture (71%; p < 0.001), with a high concordance (kappa = 0.73) of serotypes/groups identified by culture also being identified by qPCR. Also, qPCR was more sensitive in detecting multiple serotype/groups among colonized cases (28.7%) compared to culture (4.5%; p < 0.001). Of the additional serotypes detected only by qPCR, the majority were of lower density (<10 4 CFU/ml) than the dominant colonizing serotype, with serotype/group 6A/B, 19B/F and 23F being the highest density colonizers, followed by serotype 5 and serogroup 9A/L/N/V being the most common second and third colonizers respectively. The ability of qPCR to detect multiple pneumococcal serotypes at a low carriage density might provide better insight into underlying mechanism for changes in serotype colonization in PCV vaccinated children.

Sensitivity to microstimulation of somatosensory cortex distributed over multiple electrodes.

PubMed

Kim, Sungshin; Callier, Thierri; Tabot, Gregg A; Tenore, Francesco V; Bensmaia, Sliman J

2015-01-01

Meaningful and repeatable tactile sensations can be evoked by electrically stimulating primary somatosensory cortex. Intracortical microstimulation (ICMS) may thus be a viable approach to restore the sense of touch in individuals who have lost it, for example tetraplegic patients. One of the potential limitations of this approach, however, is that high levels of current can damage the neuronal tissue if the resulting current densities are too high. The limited range of safe ICMS amplitudes thus limits the dynamic range of ICMS-evoked sensations. One way to get around this limitation would be to distribute the ICMS over multiple electrodes in the hopes of intensifying the resulting percept without increasing the current density experienced by the neuronal tissue. Here, we test whether stimulating through multiple electrodes is a viable solution to increase the dynamic range of ICMS-elicited sensations without increasing the peak current density. To this end, we compare the ability of non-human primates to detect ICMS delivered through one vs. multiple electrodes. We also compare their ability to discriminate pulse trains differing in amplitude when these are delivered through one or more electrodes. We find that increasing the number of electrodes through which ICMS is delivered only has a marginal effect on detectability or discriminability despite the fact that 2-4 times more current is delivered overall. Furthermore, the impact of multielectrode stimulation (or lack thereof) is found whether pulses are delivered synchronously or asynchronously, whether the leading phase of the pulses is cathodic or anodic, and regardless of the spatial configuration of the electrode groups.

Ferrocenemonocarboxylic-HRP@Pt nanoparticles labeled RCA for multiple amplification of electro-immunosensing.

PubMed

Su, Huilan; Yuan, Ruo; Chai, Yaqin; Mao, Li; Zhuo, Ying

2011-07-15

A multiple amplification immunoassay was proposed to detect alpha-fetoprotein (AFP), which was based on ferrocenemonocarboxylic-HRP conjugated on Pt nanoparticles as labels for rolling circle amplification (RCA). Firstly, the capture antibody (anti-AFP) was immobilized on glass carbon electrode (GCE) deposited nano-sized gold particles. After a typical immuno-sandwich protocol, primary DNA was immobilized by labeling secondary antibody, which acted as a precursor to initiate RCA. The products of RCA provide large amount of sites to link detection DNAs, which were labeled by signal probes (ferrocenemonocarboxylic) and horseradish peroxidase (HRP). Moreover, the enzymatic amplification signals could be produced by the catalysis of HRP and Pt nanoparticles with the addition of H₂O₂. These lead to multiple amplification signals monitoring by electrochemical instrument and further resulted in high sensitivity of the immunoassay with the detection limit of 1.7 pg/mL. Copyright © 2011 Elsevier B.V. All rights reserved.

Detection of Salmonella enterica Serovar Typhimurium by Using a Rapid, Array-Based Immunosensor

PubMed Central

Taitt, Chris Rowe; Shubin, Yura S.; Angel, Roselina; Ligler, Frances S.

2004-01-01

The multianalyte array biosensor (MAAB) is a rapid analysis instrument capable of detecting multiple analytes simultaneously. Rapid (15-min), single-analyte sandwich immunoassays were developed for the detection of Salmonella enterica serovar Typhimurium, with a detection limit of 8 × 104 CFU/ml; the limit of detection was improved 10-fold by lengthening the assay protocol to 1 h. S. enterica serovar Typhimurium was also detected in the following spiked foodstuffs, with minimal sample preparation: sausage, cantaloupe, whole liquid egg, alfalfa sprouts, and chicken carcass rinse. Cross-reactivity tests were performed with Escherichia coli and Campylobacter jejuni. To determine whether the MAAB has potential as a screening tool for the diagnosis of asymptomatic Salmonella infection of poultry, chicken excretal samples from a private, noncommercial farm and from university poultry facilities were tested. While the private farm excreta gave rise to signals significantly above the buffer blanks, none of the university samples tested positive for S. enterica serovar Typhimurium without spiking; dose-response curves of spiked excretal samples from university-raised poultry gave limits of detection of 8 × 103 CFU/g. PMID:14711637

A multiple technique approach to the analysis of urinary calculi.

PubMed

Rodgers, A L; Nassimbeni, L R; Mulder, K J

1982-01-01

10 urinary calculi have been qualitatively and quantitatively analysed using X-ray diffraction, infra-red, scanning electron microscopy, X-ray fluorescence, atomic absorption and density gradient procedures. Constituents and compositional features which often go undetected due to limitations in the particular analytical procedure being used, have been identified and a detailed picture of each stone's composition and structure has been obtained. In all cases at least two components were detected suggesting that the multiple technique approach might cast some doubt as to the existence of "pure" stones. Evidence for a continuous, non-sequential deposition mechanism has been detected. In addition, the usefulness of each technique in the analysis of urinary stones has been assessed and the multiple technique approach has been evaluated as a whole.

Multivariate objective response detectors (MORD): statistical tools for multichannel EEG analysis during rhythmic stimulation.

PubMed

Felix, Leonardo Bonato; Miranda de Sá, Antonio Mauricio Ferreira Leite; Infantosi, Antonio Fernando Catelli; Yehia, Hani Camille

2007-03-01

The presence of cerebral evoked responses can be tested by using objective response detectors. They are statistical tests that provide a threshold above which responses can be assumed to have occurred. The detection power depends on the signal-to-noise ratio (SNR) of the response and the amount of data available. However, the correlation within the background noise could also affect the power of such detectors. For a fixed SNR, the detection can only be improved at the expense of using a longer stretch of signal. This can constitute a limitation, for instance, in monitored surgeries. Alternatively, multivariate objective response detection (MORD) could be used. This work applies two MORD techniques (multiple coherence and multiple component synchrony measure) to EEG data collected during intermittent photic stimulation. They were evaluated throughout Monte Carlo simulations, which also allowed verifying that correlation in the background reduces the detection rate. Considering the N EEG derivations as close as possible to the primary visual cortex, if N = 4, 6 or 8, multiple coherence leads to a statistically significant higher detection rate in comparison with multiple component synchrony measure. With the former, the best performance was obtained with six signals (O1, O2, T5, T6, P3 and P4).

[High-sensitive detection of multiple allergenic proteins in infant food with high-resolution mass spectrometry].

PubMed

Wu, Ci; Chen, Xi; Liu, Jianhui; Zhang, Xiaolin; Xue, Weifeng; Liang, Zhen; Liu, Mengyao; Cui, Yan; Huang, Daliang; Zhang, Lihua

2017-10-08

A novel method of the simultaneous detection of multiple kinds of allergenic proteins in infant food with parallel reaction monitoring (PRM) mode using liquid chromatography-tandem mass spectrometry (LC-MS/MS) was established. In this method, unique peptides with good stability and high sensibility were used to quantify the corresponding allergenic proteins. Furthermore, multiple kinds of allergenic proteins are inspected simultaneously with high sensitivity. In addition, such method was successfully used for the detection of multiple allergenic proteins in infant food. As for the sample preparation for infant food, compared with the traditional acetone precipitation strategy, the protein extraction efficiency and capacity of resisting disturbance are both higher with in-situ filter-aided sample pretreatment (i-FASP) method. All allergenic proteins gave a good linear response with the correlation coefficients ( R 2 ) ≥ 0.99, and the largest concentration range of the allergenic proteins could be four orders of magnitude, and the lowest detection limit was 0.028 mg/L, which was better than that reported in references. Finally, the method was conveniently used to detect the allergens from four imported infant food real samples. All the results demonstrate that this novel strategy is of great significance for providing a rapid and reliable analytical technique for allergen proteomics.

Indoor determinants of dustborne allergens in Mexican homes

PubMed Central

Hernández-Cadena, Leticia; Zeldin, Darryl C.; Sever, Michelle L.; Sly, Peter D.; London, Stephanie J.; Escamilla-Nuñez, María Consuelo; Romieu, Isabelle

2015-01-01

Exposure to indoor allergens represents a significant risk factor for allergies and asthma in several parts of the world. In Mexico, few studies have evaluated indoor allergens, including cat, dog, and mouse allergens and the factors that predict their presence. This study evaluates the main environmental and household predictors of high prenatal allergen levels and multiple allergen exposures in a birth cohort from Mexico City. A cross-sectional study was conducted as part of a birth cohort study of 1094 infants recruited during pregnancy and followed until delivery. We collected dust samples in a subset of 264 homes and assessed environmental factors. Der p 1, Der f 1, dust mite group 2, Fel d 1, Can f 1, Rat n 1, Mus m 1, and Bla g 2 concentrations in dust samples were measured using immunoassays. To define detectable allergen levels, the lowest limits of detection for each allergen were taken as cutoff points. Overall allergen exposure was considered high when four or more allergens exceeded detectable levels in the same household. Logistic regression was used for predictive models. Eighty-five percent of homes had at least one allergen in dust over the detection limit, 52.1% had high exposure (four or more allergens above detectable limits), and 11.7% of homes had detectable levels for more than eight allergens. Der p 1, Der p 2, Mus m 1, and Fel d 1 were the most frequent allergens detected. Each allergen had both common and distinct predictors. The main predictors of a high multiple allergen index were the size of the home, pesticide use, mother's age, mother as homemaker, and season. Increased indoor environmental allergen exposure is mainly related to sociodemographic factors and household cleaning. PMID:25715241

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.

Variation in the limit-of-detection of the ProSpecT Campylobacter microplate enzyme immunoassay in stools spiked with emerging Campylobacter species.

PubMed

Bojanić, Krunoslav; Midwinter, Anne Camilla; Marshall, Jonathan Craig; Rogers, Lynn Elizabeth; Biggs, Patrick Jon; Acke, Els

2016-08-01

Campylobacter enteritis in humans is primarily associated with C. jejuni/coli infection. The impact of other Campylobacter spp. is likely to be underestimated due to the bias of culture methods towards Campylobacter jejuni/coli diagnosis. Stool antigen tests are becoming increasingly popular and appear generally less species-specific. A review of independent studies of the ProSpecT® Campylobacter Microplate enzyme immunoassay (EIA) developed for C. jejuni/coli showed comparable diagnostic results to culture methods but the examination of non-jejuni/coli Campylobacter spp. was limited and the limit-of-detection (LOD), where reported, varied between studies. This study investigated LOD of EIA for Campylobacter upsaliensis, Campylobacter hyointestinalis and Campylobacter helveticus spiked in human stools. Multiple stools and Campylobacter isolates were used in three different concentrations (10(4)-10(9)CFU/ml) to reflect sample heterogeneity. All Campylobacter species evaluated were detectable by EIA. Multivariate analysis showed LOD varied between Campylobacter spp. and faecal consistency as fixed effects and individual faecal samples as random effects. EIA showed excellent performance in replicate testing for both within and between batches of reagents, in agreement between visual and spectrophotometric reading of results, and returned no discordance between the bacterial concentrations within independent dilution test runs (positive results with lower but not higher concentrations). This study shows how limitations in experimental procedures lead to an overestimation of consistency and uniformity of LOD for EIA that may not hold under routine use in diagnostic laboratories. Benefits and limitations for clinical practice and the influence on estimates of performance characteristics from detection of multiple Campylobacter spp. by EIA are discussed. Copyright © 2016 Elsevier B.V. All rights reserved.

Part-per-trillion level detection of estradiol by competitive fluorescence immunoassay using DNA/dye conjugate as antibody multiple labels.

PubMed

Zhu, Shengchao; Zhang, Qin; Guo, Liang-Hong

2008-08-22

Fluorescent organic dyes are currently the standard signal-generating labels used in microarray quantification. However, new labeling strategies are needed to meet the demand for high sensitivity in the detection of low-abundance proteins and small molecules. In this report, a long-chain DNA/dye conjugate was used to attach multiple fluorescence labels on antibodies to improve signal intensity and immunoassay sensitivity. Compared with the 30 base-pair (bp) oligonucleotide used in our previous work [Q. Zhang, L.-H. Guo, Bioconjugate Chem. 18 (2007) 1668-1672], conjugation of a 219 bp DNA in solution with a fluorescent DNA binder SYBR Green I resulted in more than sixfold increase in signal intensity, consistent with the increase in bp number. In a direct immunoassay for the detection of goat anti-mouse IgG in a mouse IgG-coated 96-well plate, the long DNA conjugate label also produced higher fluorescence than the short one, accompanied by about 15-fold improvement in the detection limit. To demonstrate its advantage in real applications, the DNA/dye conjugate was employed in the competitive immunoassay of 17beta-estradiol, a clinically and environmentally important analyte. The biotin-terminated DNA was attached to biotinylated anti-estradiol antibody through the biotin/streptavidin/biotin bridge after the immuno-reaction was completed, followed by conjugation with SYBR Green I. The limit of detection for 17beta-estradiol is 1.9 pg mL(-1), which is 200-fold lower than the assay using fluorescein-labeled antibodies. The new multiple labeling strategy uses readily available reagents, and is also compatible with current biochip platform. It has great potential in the sensitive detection of protein and antibody microarrays.

Eccentricity in planetary systems and the role of binarity. Sample definition, initial results, and the system of HD 211847

NASA Astrophysics Data System (ADS)

Moutou, C.; Vigan, A.; Mesa, D.; Desidera, S.; Thébault, P.; Zurlo, A.; Salter, G.

2017-06-01

We explore the multiplicity of exoplanet host stars with high-resolution images obtained with VLT/SPHERE. Two different samples of systems were observed: one containing low-eccentricity outer planets, and the other containing high-eccentricity outer planets. We find that 10 out of 34 stars in the high-eccentricity systems are members of a binary, while the proportion is 3 out of 27 for circular systems. Eccentric-exoplanet hosts are, therefore, significantly more likely to have a stellar companion than circular-exoplanet hosts. The median magnitude contrast over the 68 data sets is 11.26 and 9.25, in H and K, respectively, at 0.30 arcsec. The derived detection limits reveal that binaries with separations of less than 50 au are rarer for exoplanet hosts than for field stars. Our results also imply that the majority of high-eccentricity planets are not embedded in multiple stellar systems (24 out of 34), since our detection limits exclude the presence of a stellar companion. We detect the low-mass stellar companions of HD 7449 and HD 211847, both members of our high-eccentricity sample. HD 7449B was already detected and our independent observation is in agreement with this earlier work. HD 211847's substellar companion, previously detected by the radial velocity method, is actually a low-mass star seen face-on. The role of stellar multiplicity in shaping planetary systems is confirmed by this work, although it does not appear as the only source of dynamical excitation. Based on observations collected with SPHERE on the Very Large Telescope (ESO, Chile).

Repurposing environmental DNA samples: Detecting the western pearlshell (Margaritifera falcata) as a proof of concept

Treesearch

Joseph C. Dysthe; Torrey Rodgers; Thomas W. Franklin; Kellie J. Carim; Michael K. Young; Kevin S. McKelvey; Karen E. Mock; Michael K. Schwartz

2018-01-01

Information on the distribution of multiple species in a common landscape is fundamental to effective conservation and management. However, distribution data are expensive to obtain and often limited to high-profile species in a system. A recently developed technique, environmental DNA (eDNA) sampling, has been shown to be more sensitive than traditional detection...

An Integrated Quantum Dot Barcode Smartphone Optical Device for Wireless Multiplexed Diagnosis of Infected Patients

NASA Astrophysics Data System (ADS)

Ming, Kevin

Integrating mobile-cellular devices with multiplex molecular diagnostics can potentially provide the most powerful platform for tracking, managing and preventing the transmission of infectious diseases. With over 6.9 billion subscriptions globally, handheld mobile-cellular devices can be programmed to spatially map, temporally track, and transmit information on infections over wide geographical space and boundaries. Current cell phone diagnostic technologies have poor limit of detection, dynamic range, and cannot detect multiple pathogen targets simultaneously, limiting their utility to single infections with high load. Here we combined recent advances in quantum dot barcode technology for molecular detection with smartphones to engineer a simple and low-cost chip-based wireless multiplex diagnostic device. We validated our device using a variety of synthetic genomic targets for the respiratory virus and blood-borne pathogens, and demonstrated that it could detect clinical samples after simple amplification. More importantly, we confirmed that the device is capable of detecting patients infected with a single or multiple infectious pathogens (e.g., HIV and hepatitis B) in a single test. This device advances the capacity for global surveillance of infectious diseases and has the potential to accelerate knowledge exchange-transfer of emerging or exigent disease threats with healthcare and military organizations in real-time.

Liquid chromatography-electrospray ionization tandem mass spectrometry and dynamic multiple reaction monitoring method for determining multiple pesticide residues in tomato.

PubMed

Andrade, G C R M; Monteiro, S H; Francisco, J G; Figueiredo, L A; Botelho, R G; Tornisielo, V L

2015-05-15

A quick and sensitive liquid chromatography-electrospray ionization tandem mass spectrometry method, using dynamic multiple reaction monitoring and a 1.8-μm particle size analytical column, was developed to determine 57 pesticides in tomato in a 13-min run. QuEChERS (quick, easy, cheap, effective, rugged, and safe) method for samples preparations and validations was carried out in compliance with EU SANCO guidelines. The method was applied to 58 tomato samples. More than 84% of the compounds investigated showed limits of detection equal to or lower than 5 mg kg(-1). A mild (<20%), medium (20-50%), and strong (>50%) matrix effect was observed for 72%, 25%, and 3% of the pesticides studied, respectively. Eighty-one percent of the pesticides showed recoveries ranging between 70% and 120%. Twelve pesticides were detected in 35 samples, all below the maximum residue levels permitted in the Brazilian legislation; 15 samples exceeded the maximum residue levels established by the EU legislation for methamidophos; and 10 exceeded limits for acephate and four for bromuconazole. Copyright © 2014 Elsevier Ltd. All rights reserved.

Gaussian process surrogates for failure detection: A Bayesian experimental design approach

NASA Astrophysics Data System (ADS)

Wang, Hongqiao; Lin, Guang; Li, Jinglai

2016-05-01

An important task of uncertainty quantification is to identify the probability of undesired events, in particular, system failures, caused by various sources of uncertainties. In this work we consider the construction of Gaussian process surrogates for failure detection and failure probability estimation. In particular, we consider the situation that the underlying computer models are extremely expensive, and in this setting, determining the sampling points in the state space is of essential importance. We formulate the problem as an optimal experimental design for Bayesian inferences of the limit state (i.e., the failure boundary) and propose an efficient numerical scheme to solve the resulting optimization problem. In particular, the proposed limit-state inference method is capable of determining multiple sampling points at a time, and thus it is well suited for problems where multiple computer simulations can be performed in parallel. The accuracy and performance of the proposed method is demonstrated by both academic and practical examples.

A Fast EM Algorithm for Fitting Joint Models of a Binary Response and Multiple Longitudinal Covariates Subject to Detection Limits

PubMed Central

Bernhardt, Paul W.; Zhang, Daowen; Wang, Huixia Judy

2014-01-01

Joint modeling techniques have become a popular strategy for studying the association between a response and one or more longitudinal covariates. Motivated by the GenIMS study, where it is of interest to model the event of survival using censored longitudinal biomarkers, a joint model is proposed for describing the relationship between a binary outcome and multiple longitudinal covariates subject to detection limits. A fast, approximate EM algorithm is developed that reduces the dimension of integration in the E-step of the algorithm to one, regardless of the number of random effects in the joint model. Numerical studies demonstrate that the proposed approximate EM algorithm leads to satisfactory parameter and variance estimates in situations with and without censoring on the longitudinal covariates. The approximate EM algorithm is applied to analyze the GenIMS data set. PMID:25598564

Cognitive foundations for model-based sensor fusion

NASA Astrophysics Data System (ADS)

Perlovsky, Leonid I.; Weijers, Bertus; Mutz, Chris W.

2003-08-01

Target detection, tracking, and sensor fusion are complicated problems, which usually are performed sequentially. First detecting targets, then tracking, then fusing multiple sensors reduces computations. This procedure however is inapplicable to difficult targets which cannot be reliably detected using individual sensors, on individual scans or frames. In such more complicated cases one has to perform functions of fusing, tracking, and detecting concurrently. This often has led to prohibitive combinatorial complexity and, as a consequence, to sub-optimal performance as compared to the information-theoretic content of all the available data. It is well appreciated that in this task the human mind is by far superior qualitatively to existing mathematical methods of sensor fusion, however, the human mind is limited in the amount of information and speed of computation it can cope with. Therefore, research efforts have been devoted toward incorporating "biological lessons" into smart algorithms, yet success has been limited. Why is this so, and how to overcome existing limitations? The fundamental reasons for current limitations are analyzed and a potentially breakthrough research and development effort is outlined. We utilize the way our mind combines emotions and concepts in the thinking process and present the mathematical approach to accomplishing this in the current technology computers. The presentation will summarize the difficulties encountered by intelligent systems over the last 50 years related to combinatorial complexity, analyze the fundamental limitations of existing algorithms and neural networks, and relate it to the type of logic underlying the computational structure: formal, multivalued, and fuzzy logic. A new concept of dynamic logic will be introduced along with algorithms capable of pulling together all the available information from multiple sources. This new mathematical technique, like our brain, combines conceptual understanding with emotional evaluation and overcomes the combinatorial complexity of concurrent fusion, tracking, and detection. The presentation will discuss examples of performance, where computational speedups of many orders of magnitude were attained leading to performance improvements of up to 10 dB (and better).

A Shadowing Problem in the Detection of Overlapping Communities: Lifting the Resolution Limit through a Cascading Procedure

PubMed Central

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

2015-01-01

Community detection is the process of assigning nodes and links in significant communities (e.g. clusters, function modules) and its development has led to a better understanding of complex networks. When applied to sizable networks, we argue that most detection algorithms correctly identify prominent communities, but fail to do so across multiple scales. As a result, a significant fraction of the network is left uncharted. We show that this problem stems from larger or denser communities overshadowing smaller or sparser ones, and that this effect accounts for most of the undetected communities and unassigned links. We propose a generic cascading approach to community detection that circumvents the problem. Using real and artificial network datasets with three widely used community detection algorithms, we show how a simple cascading procedure allows for the detection of the missing communities. This work highlights a new detection limit of community structure, and we hope that our approach can inspire better community detection algorithms. PMID:26461919

Simultaneous fluorescent detection of multiple metal ions based on the DNAzymes and graphene oxide.

PubMed

Yun, Wen; Wu, Hong; Liu, Xingyan; Fu, Min; Jiang, Jiaolai; Du, Yunfeng; Yang, Lizhu; Huang, Yu

2017-09-15

A novel fluorescent detection strategy for simultaneous detection of Cu 2+ , Pb 2+ and Mg 2+ based on DNAzyme branched junction structure with three kinds of DNAzymes and graphene oxide (GO) was presented. Three fluorophores labeled DNA sequences consisted with enzyme-strand (E-DNA) and substrate strand (S-DNA) were annealed to form DNAzyme branched junction structure. In the presence of target metal ion, the DNAzyme was activated to cleave the fluorophore labeled S-DNA. The S-DNA fragments were released and adsorbed onto GO surface to quench the fluorescent signal. The detection limit was calculated to be 1 nM for Cu 2+ , 200 nM for Mg 2+ , and 0.3 nM for Pb 2+ , respectively. This strategy was successfully used for simultaneous detection of Cu 2+ , Mg 2+ and Pb 2+ in human serum. Moreover, it had potential application for simultaneous detection of multiple metal ions in environmental and biological samples. Copyright © 2017 Elsevier B.V. All rights reserved.

Model observer for assessing digital breast tomosynthesis for multi-lesion detection in the presence of anatomical noise

NASA Astrophysics Data System (ADS)

Wen, Gezheng; Markey, Mia K.; Miner Haygood, Tamara; Park, Subok

2018-02-01

Model observers are widely used in task-based assessments of medical image quality. The presence of multiple abnormalities in a single set of images, such as in multifocal multicentric breast cancer (MFMC), has an immense clinical impact on treatment planning and survival outcomes. Detecting multiple breast tumors is challenging as MFMC is relatively uncommon, and human observers do not know the number or locations of tumors a priori. Digital breast tomosynthesis (DBT), in which an x-ray beam sweeps over a limited angular range across the breast, has the potential to improve the detection of multiple tumors. However, prior studies of DBT image quality all focus on unifocal breast cancers. In this study, we extended our 2D multi-lesion (ML) channelized Hotelling observer (CHO) into a 3D ML-CHO that detects multiple lesions from volumetric imaging data. Then we employed the 3D ML-CHO to identify optimal DBT acquisition geometries for detection of MFMC. Digital breast phantoms with multiple embedded synthetic lesions were scanned by simulated DBT scanners of different geometries (wide/narrow angular span, different number of projections per scan) to simulate MFMC cases. With new implementations of 3D partial least squares (PLS) and modified Laguerre-Gauss (LG) channels, the 3D ML-CHO made detection decisions based upon the overall information from individual DBT slices and their correlations. Our evaluation results show that: (1) the 3D ML-CHO could achieve good detection performance with a small number of channels, and 3D PLS channels on average outperform the counterpart LG channels; (2) incorporating locally varying anatomical backgrounds and their correlations as in the 3D ML-CHO is essential for multi-lesion detection; (3) the most effective DBT geometry for detection of MFMC may vary when the task of clinical interest changes, and a given DBT geometry may not yield images that are equally informative for detecting MF, MC, and unifocal cancers.

Radiometric Short-Term Fourier Transform analysis of photonic Doppler velocimetry recordings and detectivity limit

NASA Astrophysics Data System (ADS)

Prudhomme, G.; Berthe, L.; Bénier, J.; Bozier, O.; Mercier, P.

2017-01-01

Photonic Doppler Velocimetry is a plug-and-play and versatile diagnostic used in dynamic physic experiments to measure velocities. When signals are analyzed using a Short-Time Fourier Transform, multiple velocities can be distinguished: for example, the velocities of moving particle-cloud appear on spectrograms. In order to estimate the back-scattering fluxes of target, we propose an original approach "PDV Radiometric analysis" resulting in an expression of time-velocity spectrograms coded in power units. Experiments involving micron-sized particles raise the issue of detection limit; particle-size limit is very difficult to evaluate. From the quantification of noise sources, we derive an estimation of the spectrogram noise leading to a detectivity limit, which may be compared to the fraction of the incoming power which has been back-scattered by the particle and then collected by the probe. This fraction increases with their size. At last, some results from laser-shock accelerated particles using two different PDV systems are compared: it shows the improvement of detectivity with respect to the Effective Number of Bits (ENOB) of the digitizer.

Activity Detection and Retrieval for Image and Video Data with Limited Training

DTIC Science & Technology

2015-06-10

applications. Here we propose two techniques for image segmentation. The first involves an automata based multiple threshold selection scheme, where a... automata . For our second approach to segmentation, we employ a region based segmentation technique that is capable of handling intensity inhomogeneity...techniques for image segmentation. The first involves an automata based multiple threshold selection scheme, where a mixture of Gaussian is fitted to the

Track Score Processing of Multiple Dissimilar Sensors

DTIC Science & Technology

2007-06-01

sensors ( infrared and light detection and ranging system) and one radio frenquency sensor (radar). The signal to noise ratio and design considerations...categorized as Johnson noise , shot noise , generation-recombination noise , temperature noise , microphonic noise , 1/f noise , and finally electronic...of 2.1 µm. The values of detectivity in this figure were derived from an analysis of commercial detectors , under background- limited conditions, at

Study and realization of an obstacle detection infrared system for automotive use

NASA Astrophysics Data System (ADS)

Alaouiamine, Mohammed

1991-08-01

The main technological options available in the field of obstacle detection are presented. Ultrasound, microwave, and infrared detection systems are reviewed. The reasons for choosing an infrared solution are outlined. The problems involved in developing an obstacle detection system in the near infrared are discussed. Weather condition effects, interference limitations due to multiple onboard sensors, and range detection influence are some of the problems studied. A collimated, mechanically scanned, and pulsed infrared beam is proposed to overcome some of these problems. Performances of a first and second prototype made using this system are presented.

A satellite mobile communication system based on Band-Limited Quasi-Synchronous Code Division Multiple Access (BLQS-CDMA)

NASA Technical Reports Server (NTRS)

Degaudenzi, R.; Elia, C.; Viola, R.

1990-01-01

Discussed here is a new approach to code division multiple access applied to a mobile system for voice (and data) services based on Band Limited Quasi Synchronous Code Division Multiple Access (BLQS-CDMA). The system requires users to be chip synchronized to reduce the contribution of self-interference and to make use of voice activation in order to increase the satellite power efficiency. In order to achieve spectral efficiency, Nyquist chip pulse shaping is used with no detection performance impairment. The synchronization problems are solved in the forward link by distributing a master code, whereas carrier forced activation and closed loop control techniques have been adopted in the return link. System performance sensitivity to nonlinear amplification and timing/frequency synchronization errors are analyzed.

How to limit false positives in environmental DNA and metabarcoding?

PubMed

Ficetola, Gentile Francesco; Taberlet, Pierre; Coissac, Eric

2016-05-01

Environmental DNA (eDNA) and metabarcoding are boosting our ability to acquire data on species distribution in a variety of ecosystems. Nevertheless, as most of sampling approaches, eDNA is not perfect. It can fail to detect species that are actually present, and even false positives are possible: a species may be apparently detected in areas where it is actually absent. Controlling false positives remains a main challenge for eDNA analyses: in this issue of Molecular Ecology Resources, Lahoz-Monfort et al. () test the performance of multiple statistical modelling approaches to estimate the rate of detection and false positives from eDNA data. Here, we discuss the importance of controlling for false detection from early steps of eDNA analyses (laboratory, bioinformatics), to improve the quality of results and allow an efficient use of the site occupancy-detection modelling (SODM) framework for limiting false presences in eDNA analysis. © 2016 John Wiley & Sons Ltd.

Detection and quantification of beef and pork materials in meat products by duplex droplet digital PCR.

PubMed

Cai, Yicun; He, Yuping; Lv, Rong; Chen, Hongchao; Wang, Qiang; Pan, Liangwen

2017-01-01

Meat products often consist of meat from multiple animal species, and inaccurate food product adulteration and mislabeling can negatively affect consumers. Therefore, a cost-effective and reliable method for identification and quantification of animal species in meat products is required. In this study, we developed a duplex droplet digital PCR (dddPCR) detection and quantification system to simultaneously identify and quantify the source of meat in samples containing a mixture of beef (Bos taurus) and pork (Sus scrofa) in a single digital PCR reaction tube. Mixed meat samples of known composition were used to test the accuracy and applicability of this method. The limit of detection (LOD) and the limit of quantification (LOQ) of this detection and quantification system were also identified. We conclude that our dddPCR detection and quantification system is suitable for quality control and routine analyses of meat products.

A new paper-based platform technology for point-of-care diagnostics.

PubMed

Gerbers, Roman; Foellscher, Wilke; Chen, Hong; Anagnostopoulos, Constantine; Faghri, Mohammad

2014-10-21

Currently, the Lateral flow Immunoassays (LFIAs) are not able to perform complex multi-step immunodetection tests because of their inability to introduce multiple reagents in a controlled manner to the detection area autonomously. In this research, a point-of-care (POC) paper-based lateral flow immunosensor was developed incorporating a novel microfluidic valve technology. Layers of paper and tape were used to create a three-dimensional structure to form the fluidic network. Unlike the existing LFIAs, multiple directional valves are embedded in the test strip layers to control the order and the timing of mixing for the sample and multiple reagents. In this paper, we report a four-valve device which autonomously directs three different fluids to flow sequentially over the detection area. As proof of concept, a three-step alkaline phosphatase based Enzyme-Linked ImmunoSorbent Assay (ELISA) protocol with Rabbit IgG as the model analyte was conducted to prove the suitability of the device for immunoassays. The detection limit of about 4.8 fm was obtained.

Ultrasensitive electrochemical detection of tumor cells based on multiple layer CdS quantum dots-functionalized polystyrene microspheres and graphene oxide - polyaniline composite.

PubMed

Wang, Jidong; Wang, Xiaoyu; Tang, Hengshan; Gao, Zehua; He, Shengquan; Li, Jian; Han, Shumin

2018-02-15

In this work, a novel ultrasensitive electrochemical biosensor was developed for the detection of K562 cell by a signal amplification strategy based on multiple layer CdS QDs functionalized polystyrene microspheres(PS) as bioprobe and graphene oxide(GO) -polyaniline(PANI) composite as modified materials of capture electrode. Due to electrostatic force of different charge, CdS QDs were decorated on the surface of PS by PDDA (poly(diallyldimethyl-ammonium chloride)) through a layer-by-layer(LBL) assemble technology, in which the structure of multiple layer CdS QDs increased the detection signal intensity. Moreover, GO-PANI composite not only enhanced the electron transfer rate, but also increased tumor cells load ratio. The resulting electrochemical biosensor was used to detect K562 cells with a lower detection limit of 3 cellsmL -1 (S/N = 3) and a wider linear range from 10 to 1.0 × 10 7 cellsmL -1 . This sensor was also used for mannosyl groups on HeLa cells and Hct116 cells, which showed high specificity and sensitivity. This signal amplification strategy would provide a novel approach for detection, diagnosis and treatment for tumor cells. Copyright © 2017 Elsevier B.V. All rights reserved.

SIRE: a MIMO radar for landmine/IED detection

NASA Astrophysics Data System (ADS)

Ojowu, Ode; Wu, Yue; Li, Jian; Nguyen, Lam

2013-05-01

Multiple-input multiple-output (MIMO) radar systems have been shown to have significant performance improvements over their single-input multiple-output (SIMO) counterparts. For transmit and receive elements that are collocated, the waveform diversity afforded by this radar is exploited for performance improvements. These improvements include but are not limited to improved target detection, improved parameter identifiability and better resolvability. In this paper, we present the Synchronous Impulse Reconstruction Radar (SIRE) Ultra-wideband (UWB) radar designed by the Army Research Lab (ARL) for landmine and improvised explosive device (IED) detection as a 2 by 16 MIMO radar (with collocated antennas). Its improvement over its SIMO counterpart in terms of beampattern/cross range resolution are discussed and demonstrated using simulated data herein. The limitations of this radar for Radio Frequency Interference (RFI) suppression are also discussed in this paper. A relaxation method (RELAX) combined with averaging of multiple realizations of the measured data is presented for RFI suppression; results show no noticeable target signature distortion after suppression. In this paper, the back-projection (delay and sum) data independent method is used for generating SAR images. A side-lobe minimization technique called recursive side-lobe minimization (RSM) is also discussed for reducing side-lobes in this data independent approach. We introduce a data-dependent sparsity based spectral estimation technique called Sparse Learning via Iterative Minimization (SLIM) as well as a data-dependent CLEAN approach for generating SAR images for the SIRE radar. These data-adaptive techniques show improvement in side-lobe reduction and resolution for simulated data for the SIRE radar.

Improved detection of multiple environmental antibiotics through an optimized sample extraction strategy in liquid chromatography-mass spectrometry analysis.

PubMed

Yi, Xinzhu; Bayen, Stéphane; Kelly, Barry C; Li, Xu; Zhou, Zhi

2015-12-01

A solid-phase extraction/liquid chromatography/electrospray ionization/multi-stage mass spectrometry (SPE-LC-ESI-MS/MS) method was optimized in this study for sensitive and simultaneous detection of multiple antibiotics in urban surface waters and soils. Among the seven classes of tested antibiotics, extraction efficiencies of macrolides, lincosamide, chloramphenicol, and polyether antibiotics were significantly improved under optimized sample extraction pH. Instead of only using acidic extraction in many existing studies, the results indicated that antibiotics with low pK a values (<7) were extracted more efficiently under acidic conditions and antibiotics with high pK a values (>7) were extracted more efficiently under neutral conditions. The effects of pH were more obvious on polar compounds than those on non-polar compounds. Optimization of extraction pH resulted in significantly improved sample recovery and better detection limits. Compared with reported values in the literature, the average reduction of minimal detection limits obtained in this study was 87.6% in surface waters (0.06-2.28 ng/L) and 67.1% in soils (0.01-18.16 ng/g dry wt). This method was subsequently applied to detect antibiotics in environmental samples in a heavily populated urban city, and macrolides, sulfonamides, and lincomycin were frequently detected. Antibiotics with highest detected concentrations were sulfamethazine (82.5 ng/L) in surface waters and erythromycin (6.6 ng/g dry wt) in soils. The optimized sample extraction strategy can be used to improve the detection of a variety of antibiotics in environmental surface waters and soils.

Toward multimodal signal detection of adverse drug reactions.

PubMed

Harpaz, Rave; DuMouchel, William; Schuemie, Martijn; Bodenreider, Olivier; Friedman, Carol; Horvitz, Eric; Ripple, Anna; Sorbello, Alfred; White, Ryen W; Winnenburg, Rainer; Shah, Nigam H

2017-12-01

Improving mechanisms to detect adverse drug reactions (ADRs) is key to strengthening post-marketing drug safety surveillance. Signal detection is presently unimodal, relying on a single information source. Multimodal signal detection is based on jointly analyzing multiple information sources. Building on, and expanding the work done in prior studies, the aim of the article is to further research on multimodal signal detection, explore its potential benefits, and propose methods for its construction and evaluation. Four data sources are investigated; FDA's adverse event reporting system, insurance claims, the MEDLINE citation database, and the logs of major Web search engines. Published methods are used to generate and combine signals from each data source. Two distinct reference benchmarks corresponding to well-established and recently labeled ADRs respectively are used to evaluate the performance of multimodal signal detection in terms of area under the ROC curve (AUC) and lead-time-to-detection, with the latter relative to labeling revision dates. Limited to our reference benchmarks, multimodal signal detection provides AUC improvements ranging from 0.04 to 0.09 based on a widely used evaluation benchmark, and a comparative added lead-time of 7-22 months relative to labeling revision dates from a time-indexed benchmark. The results support the notion that utilizing and jointly analyzing multiple data sources may lead to improved signal detection. Given certain data and benchmark limitations, the early stage of development, and the complexity of ADRs, it is currently not possible to make definitive statements about the ultimate utility of the concept. Continued development of multimodal signal detection requires a deeper understanding the data sources used, additional benchmarks, and further research on methods to generate and synthesize signals. Copyright © 2017 Elsevier Inc. All rights reserved.

Application of fluorescence spectroscopy and imaging in the detection of a photosensitizer in photodynamic therapy

NASA Astrophysics Data System (ADS)

Zang, Lixin; Zhao, Huimin; Zhang, Zhiguo; Cao, Wenwu

2017-02-01

Photodynamic therapy (PDT) is currently an advanced optical technology in medical applications. However, the application of PDT is limited by the detection of photosensitizers. This work focuses on the application of fluorescence spectroscopy and imaging in the detection of an effective photosenzitizer, hematoporphyrin monomethyl ether (HMME). Optical properties of HMME were measured and analyzed based on its absorption and fluorescence spectra. The production mechanism of its fluorescence emission was analyzed. The detection device for HMME based on fluorescence spectroscopy was designed. Ratiometric method was applied to eliminate the influence of intensity change of excitation sources, fluctuates of excitation sources and photo detectors, and background emissions. The detection limit of this device is 6 μg/L, and it was successfully applied to the diagnosis of the metabolism of HMME in the esophageal cancer cells. To overcome the limitation of the point measurement using fluorescence spectroscopy, a two-dimensional (2D) fluorescence imaging system was established. The algorithm of the 2D fluorescence imaging system is deduced according to the fluorescence ratiometric method using bandpass filters. The method of multiple pixel point addition (MPPA) was used to eliminate fluctuates of signals. Using the method of MPPA, SNR was improved by about 30 times. The detection limit of this imaging system is 1.9 μg/L. Our systems can be used in the detection of porphyrins to improve the PDT effect.

A rapid assay for detection of Rose rosette virus using reverse transcription-recombinase polymerase amplification using multiple gene targets.

PubMed

Babu, Binoy; Washburn, Brian K; Miller, Steven H; Poduch, Kristina; Sarigul, Tulin; Knox, Gary W; Ochoa-Corona, Francisco M; Paret, Mathews L

2017-02-01

Rose rosette disease caused by Rose rosette virus (RRV; genus Emaravirus) is the most economically relevant disease of Knock Out ® series roses in the U.S. As there are no effective chemical control options for the disease, the most critical disease management strategies include the use of virus free clean plants for propagation and early detection and destruction of infected plants. The current diagnostic techniques for RRV including end-point reverse transcription-polymerase chain reaction (RT-PCR) and real-time PCR (RT-qPCR) are highly sensitive, but limited to diagnostic labs with the equipment and expertise; and is time consuming. To address this limitation, an isothermal reverse transcription-recombinase polymerase amplification (RT-RPA) assay based on multiple gene targets for specific detection of RRV was developed. The assay is highly specific and did not cross react with other viruses belonging to the inclusive and exclusive genus. Dilution assays using the in vitro transcripts showed that the primer sets designed (RPA-267, RPA-131, and RPA-321) are highly sensitive, consistently detecting RRV with a detection limit of 1fg/μL. Testing of the infected plants using the primer sets indicated that the virus could be detected from leaves, stems and petals of roses. The primer pair RPA-267 produced 100% positive detection of the virus from infected leaf tissues, while primer set RPA-131 produced 100% detection from stems and petals. The primer set RPA-321 produced 83%, 87.5% and 75% positive detection from leaves, petals and stem tissues, respectively. In addition, the assay has been efficiently used in the detection of RRV infecting Knock Out ® roses, collected from different states in the U.S. The assay can be completed in 20min as compared to the end-point RT-PCR assay (3-4h) and RT-qPCR (1.5h). The RT-RPA assay is reliable, rapid, highly sensitive, and can be easily used in diagnostic laboratories for detection of RRV with no need for any special equipment. Copyright © 2016 Elsevier B.V. All rights reserved.

Prevalence and multiplicity of cutaneous beta papilloma viruses in plucked hairs depend on cellular DNA input.

PubMed

Weissenborn, S J; Neale, R; de Koning, M N C; Waterboer, T; Abeni, D; Bouwes Bavinck, J N; Wieland, U; Pfister, H J

2009-11-01

In view of the low loads of beta human papillomaviruses in skin samples, amounts of cellular DNA used in qualitative PCR may become limiting for virus detection and introduce variations in prevalence and multiplicity. This issue was explored within the context of a multicentre study and increasing prevalence and multiplicity was found with increasing input amounts of cellular DNA extracted from hair bulbs. To improve the quality and comparability between different epidemiologic studies ideally equal amounts of cellular DNA should be employed. When cellular DNA input varies this should be clearly taken into account in assessing viral prevalence and multiplicity.

Determining the 95% limit of detection for waterborne pathogen analyses from primary concentration to qPCR.

PubMed

Stokdyk, Joel P; Firnstahl, Aaron D; Spencer, Susan K; Burch, Tucker R; Borchardt, Mark A

2016-06-01

The limit of detection (LOD) for qPCR-based analyses is not consistently defined or determined in studies on waterborne pathogens. Moreover, the LODs reported often reflect the qPCR assay alone rather than the entire sample process. Our objective was to develop an approach to determine the 95% LOD (lowest concentration at which 95% of positive samples are detected) for the entire process of waterborne pathogen detection. We began by spiking the lowest concentration that was consistently positive at the qPCR step (based on its standard curve) into each procedural step working backwards (i.e., extraction, secondary concentration, primary concentration), which established a concentration that was detectable following losses of the pathogen from processing. Using the fraction of positive replicates (n = 10) at this concentration, we selected and analyzed a second, and then third, concentration. If the fraction of positive replicates equaled 1 or 0 for two concentrations, we selected another. We calculated the LOD using probit analysis. To demonstrate our approach we determined the 95% LOD for Salmonella enterica serovar Typhimurium, adenovirus 41, and vaccine-derived poliovirus Sabin 3, which were 11, 12, and 6 genomic copies (gc) per reaction (rxn), respectively (equivalent to 1.3, 1.5, and 4.0 gc L(-1) assuming the 1500 L tap-water sample volume prescribed in EPA Method 1615). This approach limited the number of analyses required and was amenable to testing multiple genetic targets simultaneously (i.e., spiking a single sample with multiple microorganisms). An LOD determined this way can facilitate study design, guide the number of required technical replicates, aid method evaluation, and inform data interpretation. Published by Elsevier Ltd.

Determining the 95% limit of detection for waterborne pathogen analyses from primary concentration to qPCR

USGS Publications Warehouse

Stokdyk, Joel P.; Firnstahl, Aaron; Spencer, Susan K.; Burch, Tucker R; Borchardt, Mark A.

2016-01-01

The limit of detection (LOD) for qPCR-based analyses is not consistently defined or determined in studies on waterborne pathogens. Moreover, the LODs reported often reflect the qPCR assay alone rather than the entire sample process. Our objective was to develop an approach to determine the 95% LOD (lowest concentration at which 95% of positive samples are detected) for the entire process of waterborne pathogen detection. We began by spiking the lowest concentration that was consistently positive at the qPCR step (based on its standard curve) into each procedural step working backwards (i.e., extraction, secondary concentration, primary concentration), which established a concentration that was detectable following losses of the pathogen from processing. Using the fraction of positive replicates (n = 10) at this concentration, we selected and analyzed a second, and then third, concentration. If the fraction of positive replicates equaled 1 or 0 for two concentrations, we selected another. We calculated the LOD using probit analysis. To demonstrate our approach we determined the 95% LOD for Salmonella enterica serovar Typhimurium, adenovirus 41, and vaccine-derived poliovirus Sabin 3, which were 11, 12, and 6 genomic copies (gc) per reaction (rxn), respectively (equivalent to 1.3, 1.5, and 4.0 gc L−1 assuming the 1500 L tap-water sample volume prescribed in EPA Method 1615). This approach limited the number of analyses required and was amenable to testing multiple genetic targets simultaneously (i.e., spiking a single sample with multiple microorganisms). An LOD determined this way can facilitate study design, guide the number of required technical replicates, aid method evaluation, and inform data interpretation.

A universal DNA-based protein detection system.

PubMed

Tran, Thua N N; Cui, Jinhui; Hartman, Mark R; Peng, Songming; Funabashi, Hisakage; Duan, Faping; Yang, Dayong; March, John C; Lis, John T; Cui, Haixin; Luo, Dan

2013-09-25

Protein immune detection requires secondary antibodies which must be carefully selected in order to avoid interspecies cross-reactivity, and is therefore restricted by the limited availability of primary/secondary antibody pairs. Here we present a versatile DNA-based protein detection system using a universal adapter to interface between IgG antibodies and DNA-modified reporter molecules. As a demonstration of this capability, we successfully used DNA nano-barcodes, quantum dots, and horseradish peroxidase enzyme to detect multiple proteins using our DNA-based labeling system. Our system not only eliminates secondary antibodies but also serves as a novel method platform for protein detection with modularity, high capacity, and multiplexed capability.

A Universal DNA-Based Protein Detection System

PubMed Central

Tran, Thua N. N.; Cui, Jinhui; Hartman, Mark R.; Peng, Songming; Funabashi, Hisakage; Duan, Faping; Yang, Dayong; March, John C.; Lis, John T.; Cui, Haixin; Luo, Dan

2014-01-01

Protein immune detection requires secondary antibodies which must be carefully selected in order to avoid interspecies cross-reactivity, and is therefore restricted by the limited availability of primary/secondary antibody pairs. Here we present a versatile DNA-based protein detection system using a universal adapter to interface between IgG antibodies and DNA-modified reporter molecules. As a demonstration of this capability, we successfully used DNA nano-barcodes, quantum dots, and horseradish peroxidase enzyme to detect multiple proteins using our DNA-based labeling system. Our system not only eliminates secondary antibodies but also serves as a novel method platform for protein detection with modularity, high capacity, and multiplexed capability. PMID:23978265

Usefulness of esophagogastroduodenoscopy and 18F-fluorodeoxyglucose positron-emission tomography in detecting synchronous multiple primary cancers with oral cancer.

PubMed

Ishibashi-Kanno, Naomi; Yamagata, Kenji; Uchida, Fumihiko; Hasegawa, Shogo; Yanagawa, Toru; Bukawa, Hiroki

2017-12-01

The purpose of this study is to compare the value of screening for synchronous multiple primary cancers in other organs by esophagogastroduodenoscopy (EGD) or 18 F-fluorodeoxyglucose positron-emission tomography (PET-CT) in patients newly diagnosed with oral cancer. We retrospectively examined consecutive Japanese patients who were diagnosed with oral squamous cell carcinoma (OSCC) and were screened for synchronous multiple primary cancers in other organs by EGD and/or PET-CT between January 2010 and December 2015 at our institution. The study included 190 patients (106 males and 84 females) from 36 to 93 years of age (median age 68.8 years). The patients were screened by EGD, PET-CT, or both before beginning treatment for OSCC. Of 190 Japanese patients with OSCC, 15 had multiple primary cancers: 13 patients had double cancer and two had triple cancers. The sites of the 17 multiple primary cancers were gastric (6), esophageal (4), and lung (3), and ovarian, colon, liver, and thyroid (1 each). All of the gastric and esophageal cancers were found by EGD and were not detected by PET-CT. For three patients, the detection of multiple cancers affected the treatment modality or order of treatment selected for the OSCC. In two cases, the oral cancer and multiple primary cancer(s) in another organ were resected simultaneously by joint surgical teams. PET-CT for oral cancer patients is an effective supporting diagnostic tool. However, the ability of PET-CT has some limitations. Especially for early detection of the upper gastrointestinal cancers, it is necessary to be supplemented by EGD.

Analysis of the accuracy and precision of the McMaster method in detection of the eggs of Toxocara and Trichuris species (Nematoda) in dog faeces.

PubMed

Kochanowski, Maciej; Dabrowska, Joanna; Karamon, Jacek; Cencek, Tomasz; Osiński, Zbigniew

2013-07-01

The aim of this study was to determine the accuracy and precision of McMaster method with Raynaud's modification in the detection of the eggs of the nematodes Toxocara canis (Werner, 1782) and Trichuris ovis (Abildgaard, 1795) in faeces of dogs. Four variants of McMaster method were used for counting: in one grid, two grids, the whole McMaster chamber and flotation in the tube. One hundred sixty samples were prepared from dog faeces (20 repetitions for each egg quantity) containing 15, 25, 50, 100, 150, 200, 250 and 300 eggs of T. canis and T. ovis in 1 g of faeces. To compare the influence of kind of faeces on the results, samples of dog faeces were enriched at the same levels with the eggs of another nematode, Ascaris suum Goeze, 1782. In addition, 160 samples of pig faeces were prepared and enriched only with A. suum eggs in the same way. The highest limit of detection (the lowest level of eggs that were detected in at least 50% of repetitions) in all McMaster chamber variants were obtained for T. canis eggs (25-250 eggs/g faeces). In the variant with flotation in the tube, the highest limit of detection was obtained for T. ovis eggs (100 eggs/g). The best results of the limit of detection, sensitivity and the lowest coefficients of variation were obtained with the use of the whole McMaster chamber variant. There was no significant impact of properties of faeces on the obtained results. Multiplication factors for the whole chamber were calculated on the basis of the transformed equation of the regression line, illustrating the relationship between the number of detected eggs and that of the eggs added to the'sample. Multiplication factors calculated for T. canis and T. ovis eggs were higher than those expected using McMaster method with Raynaud modification.

A multiple hollow fibre liquid-phase microextraction method for the determination of halogenated solvent residues in olive oil.

PubMed

Manso, J; García-Barrera, T; Gómez-Ariza, J L; González, A G

2014-02-01

The present paper describes a method based on the extraction of analytes by multiple hollow fibre liquid-phase microextraction and detection by ion-trap mass spectrometry and electron capture detectors after gas chromatographic separation. The limits of detection are in the range of 0.13-0.67 μg kg(-1), five orders of magnitude lower than those reached with the European Commission Official method of analysis, with three orders of magnitude of linear range (from the quantification limits to 400 μg kg(-1) for all the analytes) and recoveries in fortified olive oils in the range of 78-104 %. The main advantages of the analytical method are the absence of sample carryover (due to the disposable nature of the membranes), high enrichment factors in the range of 79-488, high throughput and low cost. The repeatability of the analytical method ranged from 8 to 15 % for all the analytes, showing a good performance.

Elaborately designed diblock nanoprobes for simultaneous multicolor detection of microRNAs

NASA Astrophysics Data System (ADS)

Wang, Chenguang; Zhang, Huan; Zeng, Dongdong; Sun, Wenliang; Zhang, Honglu; Aldalbahi, Ali; Wang, Yunsheng; San, Lili; Fan, Chunhai; Zuo, Xiaolei; Mi, Xianqiang

2015-09-01

Simultaneous detection of multiple biomarkers has important prospects in the biomedical field. In this work, we demonstrated a novel strategy for the detection of multiple microRNAs (miRNAs) based on gold nanoparticles (Au NPs) and polyadenine (polyA) mediated nanoscale molecular beacon (MB) probes (denoted p-nanoMBs). Novel fluorescent labeled p-nanoMBs bearing consecutive adenines were designed, of which polyA served as an effective anchoring block binding to the surface of Au NPs, and the appended hairpin block formed an upright conformation that favored the hybridization with targets. Using the co-assembling method and the improved hybridization conformation of the hairpin probes, we achieved high selectivity for specifically distinguishing DNA targets from single-base mismatched DNA targets. We also realized multicolor detection of three different synthetic miRNAs in a wide dynamic range from 0.01 nM to 200 nM with a detection limit of 10 pM. What's more, we even detected miRNAs in a simulated serum environment, which indicated that our method could be used in complex media. Compared with the traditional method, our strategy provides a promising alternative method for the qualitative and quantitative detection of miRNAs.Simultaneous detection of multiple biomarkers has important prospects in the biomedical field. In this work, we demonstrated a novel strategy for the detection of multiple microRNAs (miRNAs) based on gold nanoparticles (Au NPs) and polyadenine (polyA) mediated nanoscale molecular beacon (MB) probes (denoted p-nanoMBs). Novel fluorescent labeled p-nanoMBs bearing consecutive adenines were designed, of which polyA served as an effective anchoring block binding to the surface of Au NPs, and the appended hairpin block formed an upright conformation that favored the hybridization with targets. Using the co-assembling method and the improved hybridization conformation of the hairpin probes, we achieved high selectivity for specifically distinguishing DNA targets from single-base mismatched DNA targets. We also realized multicolor detection of three different synthetic miRNAs in a wide dynamic range from 0.01 nM to 200 nM with a detection limit of 10 pM. What's more, we even detected miRNAs in a simulated serum environment, which indicated that our method could be used in complex media. Compared with the traditional method, our strategy provides a promising alternative method for the qualitative and quantitative detection of miRNAs. Electronic supplementary information (ESI) available: Sequences for oligonucleotides used for this work, dynamic light scattering (DLS) measurements, fluorescent signal intensity with different ratios between p-MBs and A5 oligonucleotides, quantification of the fluorescent p-MB, and UV-Vis spectra for naked AuNPs and the p-nanoMB. See DOI: 10.1039/c5nr04618a

Sensitive SERS detection of DNA methyltransferase by target triggering primer generation-based multiple signal amplification strategy.

PubMed

Li, Ying; Yu, Chuanfeng; Han, Huixia; Zhao, Caisheng; Zhang, Xiaoru

2016-07-15

A novel and sensitive surface-enhanced Raman scattering (SERS) method is proposed for the assay of DNA methyltransferase (MTase) activity and evaluation of inhibitors by developing a target triggering primer generation-based multiple signal amplification strategy. By using of a duplex substrate for Dam MTase, two hairpin templates and a Raman probe, multiple signal amplification mode is achieved. Once recognized by Dam MTase, the duplex substrate can be cleaved by Dpn I endonuclease and two primers are released for triggering the multiple signal amplification reaction. Consequently, a wide dynamic range and remarkably high sensitivity are obtained under isothermal conditions. The detection limit is 2.57×10(-4)UmL(-1). This assay exhibits an excellent selectivity and is successfully applied in the screening of inhibitors for Dam MTase. In addition, this novel sensing system is potentially universal as the recognition element can be conveniently designed for other target analytes by changing the substrate of DNA MTase. Copyright © 2016 Elsevier B.V. All rights reserved.

Effects of capacity limits, memory loss, and sound type in change deafness.

PubMed

Gregg, Melissa K; Irsik, Vanessa C; Snyder, Joel S

2017-11-01

Change deafness, the inability to notice changes to auditory scenes, has the potential to provide insights about sound perception in busy situations typical of everyday life. We determined the extent to which change deafness to sounds is due to the capacity of processing multiple sounds and the loss of memory for sounds over time. We also determined whether these processing limitations work differently for varying types of sounds within a scene. Auditory scenes composed of naturalistic sounds, spectrally dynamic unrecognizable sounds, tones, and noise rhythms were presented in a change-detection task. On each trial, two scenes were presented that were same or different. We manipulated the number of sounds within each scene to measure memory capacity and the silent interval between scenes to measure memory loss. For all sounds, change detection was worse as scene size increased, demonstrating the importance of capacity limits. Change detection to the natural sounds did not deteriorate much as the interval between scenes increased up to 2,000 ms, but it did deteriorate substantially with longer intervals. For artificial sounds, in contrast, change-detection performance suffered even for very short intervals. The results suggest that change detection is generally limited by capacity, regardless of sound type, but that auditory memory is more enduring for sounds with naturalistic acoustic structures.

A fast stir bar sorptive extraction method for the analysis of geosmin and 2-methylisoborneol in source and drinking water.

PubMed

Bauld, T; Teasdale, P; Stratton, H; Uwins, H

2007-01-01

The presence of unpleasant taste and odour in drinking water is an ongoing aesthetic concern for water providers worldwide. The need for a sensitive and robust method capable of analysis in both natural and treated waters is essential for early detection of taste and odour events. The purpose of this study was to develop and optimise a fast stir bar sorptive extraction (SBSE) method for the analysis of geosmin and 2-methylisoborneol (MIB) in both natural water and drinking water. Limits of detection with the optimised fast method (45 min extraction time at 60 degrees C using 24 microL stir bars) were 1.1 ng/L for geosmin and 4.2 ng/L for MIB. Relative standard deviations at the detection limits were under 17% for both compounds. Use of multiple stir bars can be used to decrease the detection limits further. The use of 25% NaCl and 5% methanol sample modifiers decreased the experimental recoveries. Likewise, addition of 1 mg/L and 1.5 mg/L NaOCI decreased the recoveries and this effect was not reversed by addition of 10% thiosulphate. The optimised method was used to measure geosmin concentrations in treated and untreated drinking water. MIB concentrations were below the detection limits in these waters.

Predictive inference for best linear combination of biomarkers subject to limits of detection.

PubMed

Coolen-Maturi, Tahani

2017-08-15

Measuring the accuracy of diagnostic tests is crucial in many application areas including medicine, machine learning and credit scoring. The receiver operating characteristic (ROC) curve is a useful tool to assess the ability of a diagnostic test to discriminate between two classes or groups. In practice, multiple diagnostic tests or biomarkers are combined to improve diagnostic accuracy. Often, biomarker measurements are undetectable either below or above the so-called limits of detection (LoD). In this paper, nonparametric predictive inference (NPI) for best linear combination of two or more biomarkers subject to limits of detection is presented. NPI is a frequentist statistical method that is explicitly aimed at using few modelling assumptions, enabled through the use of lower and upper probabilities to quantify uncertainty. The NPI lower and upper bounds for the ROC curve subject to limits of detection are derived, where the objective function to maximize is the area under the ROC curve. In addition, the paper discusses the effect of restriction on the linear combination's coefficients on the analysis. Examples are provided to illustrate the proposed method. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Dark matter effective field theory scattering in direct detection experiments

DOE PAGES

Schneck, K.

2015-05-01

We examine the consequences of the effective field theory (EFT) of dark matter–nucleon scattering for current and proposed direct detection experiments. Exclusion limits on EFT coupling constants computed using the optimum interval method are presented for SuperCDMS Soudan, CDMS II, and LUX, and the necessity of combining results from multiple experiments in order to determine dark matter parameters is discussed. We demonstrate that spectral differences between the standard dark matter model and a general EFT interaction can produce a bias when calculating exclusion limits and when developing signal models for likelihood and machine learning techniques. We also discuss the implicationsmore » of the EFT for the next-generation (G2) direct detection experiments and point out regions of complementarity in the EFT parameter space.« less

Dark matter effective field theory scattering in direct detection experiments

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

Schneck, K.; Cabrera, B.; Cerdeño, D. G.

2015-05-18

We examine the consequences of the effective field theory (EFT) of dark matter-nucleon scattering for current and proposed direct detection experiments. Exclusion limits on EFT coupling constants computed using the optimum interval method are presented for SuperCDMS Soudan, CDMS II, and LUX, and the necessity of combining results from multiple experiments in order to determine dark matter parameters is discussed. Here. we demonstrate that spectral differences between the standard dark matter model and a general EFT interaction can produce a bias when calculating exclusion limits and when developing signal models for likelihood and machine learning techniques. In conclusion, we discussmore » the implications of the EFT for the next-generation (G2) direct detection experiments and point out regions of complementarity in the EFT parameter space.« less

Dark matter effective field theory scattering in direct detection experiments

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

Schneck, K.; Cabrera, B.; Cerdeño, D. G.

2015-05-18

We examine the consequences of the effective field theory (EFT) of dark matter–nucleon scattering for current and proposed direct detection experiments. Exclusion limits on EFT coupling constants computed using the optimum interval method are presented for SuperCDMS Soudan, CDMS II, and LUX, and the necessity of combining results from multiple experiments in order to determine dark matter parameters is discussed. We demonstrate that spectral differences between the standard dark matter model and a general EFT interaction can produce a bias when calculating exclusion limits and when developing signal models for likelihood and machine learning techniques. We also discuss the implicationsmore » of the EFT for the next-generation (G2) direct detection experiments and point out regions of complementarity in the EFT parameter space.« less

Microfluidic CODES: a scalable multiplexed electronic sensor for orthogonal detection of particles in microfluidic channels.

PubMed

Liu, Ruxiu; Wang, Ningquan; Kamili, Farhan; Sarioglu, A Fatih

2016-04-21

Numerous biophysical and biochemical assays rely on spatial manipulation of particles/cells as they are processed on lab-on-a-chip devices. Analysis of spatially distributed particles on these devices typically requires microscopy negating the cost and size advantages of microfluidic assays. In this paper, we introduce a scalable electronic sensor technology, called microfluidic CODES, that utilizes resistive pulse sensing to orthogonally detect particles in multiple microfluidic channels from a single electrical output. Combining the techniques from telecommunications and microfluidics, we route three coplanar electrodes on a glass substrate to create multiple Coulter counters producing distinct orthogonal digital codes when they detect particles. We specifically design a digital code set using the mathematical principles of Code Division Multiple Access (CDMA) telecommunication networks and can decode signals from different microfluidic channels with >90% accuracy through computation even if these signals overlap. As a proof of principle, we use this technology to detect human ovarian cancer cells in four different microfluidic channels fabricated using soft lithography. Microfluidic CODES offers a simple, all-electronic interface that is well suited to create integrated, low-cost lab-on-a-chip devices for cell- or particle-based assays in resource-limited settings.

Multicolor Super-Resolution Fluorescence Imaging via Multi-Parameter Fluorophore Detection

PubMed Central

Bates, Mark; Dempsey, Graham T; Chen, Kok Hao; Zhuang, Xiaowei

2012-01-01

Understanding the complexity of the cellular environment will benefit from the ability to unambiguously resolve multiple cellular components, simultaneously and with nanometer-scale spatial resolution. Multicolor super-resolution fluorescence microscopy techniques have been developed to achieve this goal, yet challenges remain in terms of the number of targets that can be simultaneously imaged and the crosstalk between color channels. Herein, we demonstrate multicolor stochastic optical reconstruction microscopy (STORM) based on a multi-parameter detection strategy, which uses both the fluorescence activation wavelength and the emission color to discriminate between photo-activatable fluorescent probes. First, we obtained two-color super-resolution images using the near-infrared cyanine dye Alexa 750 in conjunction with a red cyanine dye Alexa 647, and quantified color crosstalk levels and image registration accuracy. Combinatorial pairing of these two switchable dyes with fluorophores which enhance photo-activation enabled multi-parameter detection of six different probes. Using this approach, we obtained six-color super-resolution fluorescence images of a model sample. The combination of multiple fluorescence detection parameters for improved fluorophore discrimination promises to substantially enhance our ability to visualize multiple cellular targets with sub-diffraction-limit resolution. PMID:22213647

Sensitivity and accuracy of high-throughput metabarcoding methods for early detection of invasive fish species

NASA Astrophysics Data System (ADS)

Hatzenbuhler, Chelsea; Kelly, John R.; Martinson, John; Okum, Sara; Pilgrim, Erik

2017-04-01

High-throughput DNA metabarcoding has gained recognition as a potentially powerful tool for biomonitoring, including early detection of aquatic invasive species (AIS). DNA based techniques are advancing, but our understanding of the limits to detection for metabarcoding complex samples is inadequate. For detecting AIS at an early stage of invasion when the species is rare, accuracy at low detection limits is key. To evaluate the utility of metabarcoding in future fish community monitoring programs, we conducted several experiments to determine the sensitivity and accuracy of routine metabarcoding methods. Experimental mixes used larval fish tissue from multiple “common” species spiked with varying proportions of tissue from an additional “rare” species. Pyrosequencing of genetic marker, COI (cytochrome c oxidase subunit I) and subsequent sequence data analysis provided experimental evidence of low-level detection of the target “rare” species at biomass percentages as low as 0.02% of total sample biomass. Limits to detection varied interspecifically and were susceptible to amplification bias. Moreover, results showed some data processing methods can skew sequence-based biodiversity measurements from corresponding relative biomass abundances and increase false absences. We suggest caution in interpreting presence/absence and relative abundance in larval fish assemblages until metabarcoding methods are optimized for accuracy and precision.

Performance Evaluation of Solar Blind NLOS Ultraviolet Communication Systems

DTIC Science & Technology

2008-12-01

noise and signal count statistical distributions . Then we further link key system parameters such as path loss and communication bit error rate (BER... quantum noise limited photon-counting detection. These benefits can now begin to be realized based on technological advances in both miniaturized...multiplication gain of 105~107, high responsivity of 62 A/W, large detection area of a few cm2, reasonable quantum efficiency of 15%, and low dark current

Silver nanoclusters-assisted ion-exchange reaction with CdTe quantum dots for photoelectrochemical detection of adenosine by target-triggering multiple-cycle amplification strategy.

PubMed

Zhao, Yang; Tan, Lu; Gao, Xiaoshan; Jie, Guifen; Huang, Tingyu

2018-07-01

Herein, we successfully devised a novel photoelectrochemical (PEC) platform for ultrasensitive detection of adenosine by target-triggering cascade multiple cycle amplification based on the silver nanoparticles-assisted ion-exchange reaction with CdTe quantum dots (QDs). In the presence of target adenosine, DNA s1 is released from the aptamer and then hybridizes with hairpin DNA (HP1), which could initiate the cycling cleavage process under the reaction of nicking endonuclease. Then the product (DNA b) of cycle I could act as the "DNA trigger" of cycle II to further generate a large number of DNA s1, which again go back to cycle I, thus a cascade multiple DNA cycle amplification was carried out to produce abundant DNA c. These DNA c fragments with the cytosine (C)-rich loop were captured by magnetic beads, and numerous silver nanoclusters (Ag NCs) were synthesized by AgNO 3 and sodium borohydride. The dissolved AgNCs released numerous silver ions which could induce ion exchange reaction with the CdTe QDs, thus resulting in greatly amplified change of photocurrent for target detection. The detection linear range for adenosine was 1.0 fM ~10 nM with the detection limit of 0.5 fM. The present PEC strategy combining cascade multiple DNA cycle amplification and AgNCs-induced ion-exchange reaction with QDs provides new insight into rapid, and ultrasensitive PEC detection of different biomolecules, which showed great potential for detecting trace amounts in bioanalysis and clinical biomedicine. Copyright © 2018 Elsevier B.V. All rights reserved.

Speckle Interferometry at the Blanco and SOAR Telescopes in 2008 and 2009

NASA Technical Reports Server (NTRS)

Tokovinin, Andrei; Mason, Brian D.; Hartkopf, William I.

2010-01-01

The results of speckle interferometric measurements of binary and multiple stars conducted in 2008 and 2009 at the Blanco and Southern Astrophysical Research (SOAR) 4 m telescopes in Chile are presented. A tot al of 1898 measurements of 1189 resolved pairs or sub-systems and 394 observations of 285 un-resolved targets are listed. We resolved for the first time 48 new pairs, 21 of which are new sub-systems in close visual multiple stars. Typical internal measurement precision is 0.3 mas in both coordinates, typical companion detection capability is delta m approximately 4.2 at 0.15 degree separation. These data were obtained with a new electron-multiplication CCD camera; data processing is described in detail, including estimation of magnitude difference, observational errors, detection limits, and analysis of artifacts. We comment on some newly discovered pairs and objects of special interest.

SPECKLE INTERFEROMETRY AT THE BLANCO AND SOAR TELESCOPES IN 2008 AND 2009

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

Tokovinin, Andrei; Mason, Brian D.; Hartkopf, William I.

2010-02-15

The results of speckle interferometric measurements of binary and multiple stars conducted in 2008 and 2009 at the Blanco and SOAR 4 m telescopes in Chile are presented. A total of 1898 measurements of 1189 resolved pairs or sub-systems and 394 observations of 285 un-resolved targets are listed. We resolved for the first time 48 new pairs, 21 of which are new sub-systems in close visual multiple stars. Typical internal measurement precision is 0.3 mas in both coordinates, typical companion detection capability is {delta}m {approx} 4.2 at 0.''15 separation. These data were obtained with a new electron-multiplication CCD camera; datamore » processing is described in detail, including estimation of magnitude difference, observational errors, detection limits, and analysis of artifacts. We comment on some newly discovered pairs and objects of special interest.« less

Remembering Complex Objects in Visual Working Memory: Do Capacity Limits Restrict Objects or Features?

PubMed Central

Hardman, Kyle; Cowan, Nelson

2014-01-01

Visual working memory stores stimuli from our environment as representations that can be accessed by high-level control processes. This study addresses a longstanding debate in the literature about whether storage limits in visual working memory include a limit to the complexity of discrete items. We examined the issue with a number of change-detection experiments that used complex stimuli which possessed multiple features per stimulus item. We manipulated the number of relevant features of the stimulus objects in order to vary feature load. In all of our experiments, we found that increased feature load led to a reduction in change-detection accuracy. However, we found that feature load alone could not account for the results, but that a consideration of the number of relevant objects was also required. This study supports capacity limits for both feature and object storage in visual working memory. PMID:25089739

Overcoming Pose Limitations of a Skin-Cued Histograms of Oriented Gradients Dismount Detector Through Contextual Use of Skin Islands and Multiple Support Vector Machines

DTIC Science & Technology

2011-03-24

HOG) dismount detector that cues based off of the presence of human skin (to limit false detections and to reduce the search space complexity). While...wave infrared wavelengths in addition to the visible spectra in order to identify human skin [29] and selectively scan the image for the presence of...and the angle of the acqui- sition camera. Consequently, it is expected that limitations exist on the humans ’ range of motion or stance that still

Application of flat panel OLED display technology for the point-of-care detection of circulating cancer biomarkers

PubMed Central

Katchman, Benjamin A.; Smith, Joseph T.; Obahiagbon, Uwadiae; Kesiraju, Sailaja; Lee, Yong-Kyun; O’Brien, Barry; Kaftanoglu, Korhan; Blain Christen, Jennifer; Anderson, Karen S.

2016-01-01

Point-of-care molecular diagnostics can provide efficient and cost-effective medical care, and they have the potential to fundamentally change our approach to global health. However, most existing approaches are not scalable to include multiple biomarkers. As a solution, we have combined commercial flat panel OLED display technology with protein microarray technology to enable high-density fluorescent, programmable, multiplexed biorecognition in a compact and disposable configuration with clinical-level sensitivity. Our approach leverages advances in commercial display technology to reduce pre-functionalized biosensor substrate costs to pennies per cm2. Here, we demonstrate quantitative detection of IgG antibodies to multiple viral antigens in patient serum samples with detection limits for human IgG in the 10 pg/mL range. We also demonstrate multiplexed detection of antibodies to the HPV16 proteins E2, E6, and E7, which are circulating biomarkers for cervical as well as head and neck cancers. PMID:27374875

Application of flat panel OLED display technology for the point-of-care detection of circulating cancer biomarkers.

PubMed

Katchman, Benjamin A; Smith, Joseph T; Obahiagbon, Uwadiae; Kesiraju, Sailaja; Lee, Yong-Kyun; O'Brien, Barry; Kaftanoglu, Korhan; Blain Christen, Jennifer; Anderson, Karen S

2016-07-04

Point-of-care molecular diagnostics can provide efficient and cost-effective medical care, and they have the potential to fundamentally change our approach to global health. However, most existing approaches are not scalable to include multiple biomarkers. As a solution, we have combined commercial flat panel OLED display technology with protein microarray technology to enable high-density fluorescent, programmable, multiplexed biorecognition in a compact and disposable configuration with clinical-level sensitivity. Our approach leverages advances in commercial display technology to reduce pre-functionalized biosensor substrate costs to pennies per cm(2). Here, we demonstrate quantitative detection of IgG antibodies to multiple viral antigens in patient serum samples with detection limits for human IgG in the 10 pg/mL range. We also demonstrate multiplexed detection of antibodies to the HPV16 proteins E2, E6, and E7, which are circulating biomarkers for cervical as well as head and neck cancers.

Statistical significance of combinatorial regulations

PubMed Central

Terada, Aika; Okada-Hatakeyama, Mariko; Tsuda, Koji; Sese, Jun

2013-01-01

More than three transcription factors often work together to enable cells to respond to various signals. The detection of combinatorial regulation by multiple transcription factors, however, is not only computationally nontrivial but also extremely unlikely because of multiple testing correction. The exponential growth in the number of tests forces us to set a strict limit on the maximum arity. Here, we propose an efficient branch-and-bound algorithm called the “limitless arity multiple-testing procedure” (LAMP) to count the exact number of testable combinations and calibrate the Bonferroni factor to the smallest possible value. LAMP lists significant combinations without any limit, whereas the family-wise error rate is rigorously controlled under the threshold. In the human breast cancer transcriptome, LAMP discovered statistically significant combinations of as many as eight binding motifs. This method may contribute to uncover pathways regulated in a coordinated fashion and find hidden associations in heterogeneous data. PMID:23882073

Multiple Hotspot Mutations Scanning by Single Droplet Digital PCR.

PubMed

Decraene, Charles; Silveira, Amanda B; Bidard, François-Clément; Vallée, Audrey; Michel, Marc; Melaabi, Samia; Vincent-Salomon, Anne; Saliou, Adrien; Houy, Alexandre; Milder, Maud; Lantz, Olivier; Ychou, Marc; Denis, Marc G; Pierga, Jean-Yves; Stern, Marc-Henri; Proudhon, Charlotte

2018-02-01

Progress in the liquid biopsy field, combined with the development of droplet digital PCR (ddPCR), has enabled noninvasive monitoring of mutations with high detection accuracy. However, current assays detect a restricted number of mutations per reaction. ddPCR is a recognized method for detecting alterations previously characterized in tumor tissues, but its use as a discovery tool when the mutation is unknown a priori remains limited. We established 2 ddPCR assays detecting all genomic alterations within KRAS exon 2 and EGFR exon 19 mutation hotspots, which are of clinical importance in colorectal and lung cancer, with use of a unique pair of TaqMan ® oligoprobes. The KRAS assay scanned for the 7 most common mutations in codons 12/13 but also all other mutations found in that region. The EGFR assay screened for all in-frame deletions of exon 19, which are frequent EGFR-activating events. The KRAS and EGFR assays were highly specific and both reached a limit of detection of <0.1% in mutant allele frequency. We further validated their performance on multiple plasma and formalin-fixed and paraffin-embedded tumor samples harboring a panel of different KRAS or EGFR mutations. This method presents the advantage of detecting a higher number of mutations with single-reaction ddPCRs while consuming a minimum of patient sample. This is particularly useful in the context of liquid biopsy because the amount of circulating tumor DNA is often low. This method should be useful as a discovery tool when the tumor tissue is unavailable or to monitor disease during therapy. © 2017 American Association for Clinical Chemistry.

Tight Analysis of a Collisionless Robot Gathering Algorithm

DTIC Science & Technology

2015-09-28

local-multiplicity detection. In SSS , pages 384– 398, Berlin, Heidelberg, 2009. Springer-Verlag. [20] T. Izumi, Y. Katayama, N. Inuzuka, and K. Wada...T. Izumi, M. G. Potop-Butucaru, and S. Tixeuil. Connectivity- preserving scattering of mobile robots with limited visibility. In SSS , pages 319–331

Quantitative multiplex detection of biomarkers on a waveguide-based biosensor using quantum dots

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

Xie, Hongzhi; Mukundan, Harshini; Martinez, Jennifer S

2009-01-01

The quantitative, simultaneous detection of multiple biomarkers with high sensitivity and specificity is critical for biomedical diagnostics, drug discovery and biomarker characterization [Wilson 2006, Tok 2006, Straub 2005, Joos 2002, Jani 2000]. Detection systems relying on optical signal transduction are, in general, advantageous because they are fast, portable, inexpensive, sensitive, and have the potential for multiplex detection of analytes of interest. However, conventional immunoassays for the detection of biomarkers, such as the Enzyme Linked Immunosorbant Assays (ELISAs) are semi-quantitative, time consuming and insensitive. ELISA assays are also limited by high non-specific binding, especially when used with complex biological samples suchmore » as serum and urine (REF). Organic fluorophores that are commonly used in such applications lack photostability and possess a narrow Stoke's shift that makes simultaneous detection of multiple fluorophores with a single excitation source difficult, thereby restricting their use in multiplex assays. The above limitations with traditional assay platforms have resulted in the increased use of nanotechnology-based tools and techniques in the fields of medical imaging [ref], targeted drug delivery [Caruthers 2007, Liu 2007], and sensing [ref]. One such area of increasing interest is the use of semiconductor quantum dots (QDs) for biomedical research and diagnostics [Gao and Cui 2004, Voura 2004, Michalet 2005, Chan 2002, Jaiswal 2004, Gao 2005, Medintz 2005, So 2006 2006, Wu 2003]. Compared to organic dyes, QDs provide several advantages for use in immunoassay platforms, including broad absorption bands with high extinction coefficients, narrow and symmetric emission bands with high quantum yields, high photostablility, and a large Stokes shift [Michalet 2005, Gu 2002]. These features prompted the use of QDs as probes in biodetection [Michalet 2005, Medintz 2005]. For example, Jaiswal et al. reported long term multiple color imaging of live cells using QD-bioconjugates [Jaiswal 2003]. Gao [Gao 2004] and So [So 2006] have used QDs as probes for in-vivo cancer targeting and imaging. Medintz et al. reported self-assembled QD-based biosensors for detection of analytes based on energy transfer [Medintz 2003]. Others have developed an approach for multiplex optical encoding of biomolecules using QDs [Han 2001]. Immunoassays have also benefited from the advantages of QDs. Recently, dihydrolipoic acid (DHLA) capped-QDs have been attached to antibodies and used as fluorescence reporters in plate-based multiplex immunoassays [Goodman 2004]. However, DHLA-QDs are associated with low quantum efficiency and are unstable at neutral pH. These problems limit the application of this technology to the sensitive detection of biomolecules, especially in complex biological samples. Thus, the development of a rapid, sensitive, quantitative, and specific multiplex platform for the detection of biomarkers in difficult samples remains an elusive target. The goal stated above has applications in many fields including medical diagnostics, biological research, and threat reduction. The current decade alone has seen the development of a need to rapidly and accurately detect potential biological warfare agents. For example, current methods for the detection of anthrax are grossly inadequate for a variety of reasons including long incubation time (5 days from time of exposure to onset of symptoms) and non-specific ('flu-like') symptoms. When five employees of the United State Senate were exposed to B. anthracis in the mail (2001), only one patient had a confirmed diagnosis before death. Since then, sandwich immunoassays using both colorimetric and fluorescence detectors have been developed for key components of the anthrax lethal toxin, namely protective antigen (PA), lethal factor (LF), and the edema factor [Mourez 2001]. While these platforms were successful in assays against anthrax toxins, the sensitivity was poor. Furthermore, no single platform exists for the simultaneous and quantitative detection of multiple components of the B. anthracis toxin. Addressing multiple biomarkers at the same time will increase confidence in a positive result, and may lead to application in the simultaneous detection of anthrax and other biowarfare agents.« less

Development and immunochemical evaluation of a novel chicken IgY antibody specific for KLK6.

PubMed

Sotiropoulou, Georgia; Pampalakis, Georgios; Prosnikli, Evangelia; Evangelatos, Gregory P; Livaniou, Evangelia

2012-12-05

Human kallikrein-related peptidase 6 (KLK6) has been implicated in various types of cancer and in neurodegenerative and demyelinating diseases including multiple sclerosis. Further, anti-KLK6 antibodies attenuated disease manifestations in the mouse model of multiple sclerosis. Availability of specific antibodies against KLK6 is fundamental to the development of improved diagnostic and/or immunotherapeutic applications. Here, we exploited the enhanced immunogenicity of mammalian proteins in avian species to generate a polyclonal antibody against KLK6. Chicken were immunized with recombinant KLK6 and antibodies Y (IgYs) were purified from egg yolk with a simple procedure and evaluated for KLK6 detection by ELISA and Western blot using recombinant proteins and human cell lysates and supernatants. The anti-KLK6 Y polyclonal exhibited high affinity for KLK6 with a detection limit of 30 fmol. On the other hand, the widely used rabbit polyclonal antibody that was raised against the same recombinant KLK6 had a detection limit of 300 fmol. Moreover, the IgYs did not display any crossreactivity with recombinant KLKs or endogenous KLKs and other cellular proteins. Based on its high specificity and sensitivity the developed anti-KLK6 IgY is expected to aid the development of improved diagnostic tools for the detection of KLK6 in biological and clinical samples.

Development and immunochemical evaluation of a novel chicken IgY antibody specific for KLK6

PubMed Central

2012-01-01

Background Human kallikrein-related peptidase 6 (KLK6) has been implicated in various types of cancer and in neurodegenerative and demyelinating diseases including multiple sclerosis. Further, anti-KLK6 antibodies attenuated disease manifestations in the mouse model of multiple sclerosis. Availability of specific antibodies against KLK6 is fundamental to the development of improved diagnostic and/or immunotherapeutic applications. Here, we exploited the enhanced immunogenicity of mammalian proteins in avian species to generate a polyclonal antibody against KLK6. Results Chicken were immunized with recombinant KLK6 and antibodies Y (IgYs) were purified from egg yolk with a simple procedure and evaluated for KLK6 detection by ELISA and Western blot using recombinant proteins and human cell lysates and supernatants. The anti-KLK6 Y polyclonal exhibited high affinity for KLK6 with a detection limit of 30 fmol. On the other hand, the widely used rabbit polyclonal antibody that was raised against the same recombinant KLK6 had a detection limit of 300 fmol. Moreover, the IgYs did not display any crossreactivity with recombinant KLKs or endogenous KLKs and other cellular proteins. Conclusions Based on its high specificity and sensitivity the developed anti-KLK6 IgY is expected to aid the development of improved diagnostic tools for the detection of KLK6 in biological and clinical samples. PMID:23216878

FERMI/LAT OBSERVATIONS OF SWIFT/BAT SEYFERT GALAXIES: ON THE CONTRIBUTION OF RADIO-QUIET ACTIVE GALACTIC NUCLEI TO THE EXTRAGALACTIC {gamma}-RAY BACKGROUND

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

Teng, Stacy H.; Mushotzky, Richard F.; Reynolds, Christopher S.

2011-12-01

We present the analysis of 2.1 years of Fermi Large Area Telescope (LAT) data on 491 Seyfert galaxies detected by the Swift Burst Alert Telescope (BAT) survey. Only the two nearest objects, NGC 1068 and NGC 4945, which were identified in the Fermi first year catalog, are detected. Using Swift/BAT and radio 20 cm fluxes, we define a new radio-loudness parameter R{sub X,BAT} where radio-loud objects have log R{sub X,BAT} > -4.7. Based on this parameter, only radio-loud sources are detected by Fermi/LAT. An upper limit to the flux of the undetected sources is derived to be {approx}2 Multiplication-Sign 10{supmore » -11} photons cm{sup -2} s{sup -1}, approximately seven times lower than the observed flux of NGC 1068. Assuming a median redshift of 0.031, this implies an upper limit to the {gamma}-ray (1-100 GeV) luminosity of {approx}< 3 Multiplication-Sign 10{sup 41} erg s{sup -1}. In addition, we identified 120 new Fermi/LAT sources near the Swift/BAT Seyfert galaxies with significant Fermi/LAT detections. A majority of these objects do not have Swift/BAT counterparts, but their possible optical counterparts include blazars, flat-spectrum radio quasars, and quasars.« less

Functionalized xenon as a biosensor

PubMed Central

Spence, Megan M.; Rubin, Seth M.; Dimitrov, Ivan E.; Ruiz, E. Janette; Wemmer, David E.; Pines, Alexander; Yao, Shao Qin; Tian, Feng; Schultz, Peter G.

2001-01-01

The detection of biological molecules and their interactions is a significant component of modern biomedical research. In current biosensor technologies, simultaneous detection is limited to a small number of analytes by the spectral overlap of their signals. We have developed an NMR-based xenon biosensor that capitalizes on the enhanced signal-to-noise, spectral simplicity, and chemical-shift sensitivity of laser-polarized xenon to detect specific biomolecules at the level of tens of nanomoles. We present results using xenon “functionalized” by a biotin-modified supramolecular cage to detect biotin–avidin binding. This biosensor methodology can be extended to a multiplexing assay for multiple analytes. PMID:11535830

Integrated Multi-process Microfluidic Systems for Automating Analysis

PubMed Central

Yang, Weichun; Woolley, Adam T.

2010-01-01

Microfluidic technologies have been applied extensively in rapid sample analysis. Some current challenges for standard microfluidic systems are relatively high detection limits, and reduced resolving power and peak capacity compared to conventional approaches. The integration of multiple functions and components onto a single platform can overcome these separation and detection limitations of microfluidics. Multiplexed systems can greatly increase peak capacity in multidimensional separations and can increase sample throughput by analyzing many samples simultaneously. On-chip sample preparation, including labeling, preconcentration, cleanup and amplification, can all serve to speed up and automate processes in integrated microfluidic systems. This paper summarizes advances in integrated multi-process microfluidic systems for automated analysis, their benefits and areas for needed improvement. PMID:20514343

HSV1 and 2 detection in the CSF of multiple sclerosis patients by real-time PCR.

PubMed

Koros, Christos; Ioannidis, Anastasios; Acquaviva, Tereza; Zoga, Margarita; Nikolaou, Chryssoula; Chatzipanagiotou, Stylianos; Kossyvakis, Athanassios; Anagnostouli, Maria

2014-01-01

The pathogenic role of Herpes Simplex Virus (HSV) 1 and 2 in Multiple Sclerosis (MS) still remains obscure. The aim of our study was the assessment of HSV1 and 2 DNA prevalence in the cerebrospinal fluid (CSF) of MS patients compared to patients with other neurological disorders (OND). HSV1 and HSV2 DNA detection in the CSF of patients was performed by real time polymerase chain reaction (PCR). The genome of HSV1 was present in the CSF of 4.7% of MS patients (4 out of 85), while HSV2 was not detected in any patient. In the sub-group of OND patients, HSV1 was detected in 7.9% of patients (3 out of 38) and HSV2 was detected in 5.3% of patients (2 out of 38). Our data are in accordance with a limited number of previous reports, supporting a prevalence of HSV1 genome in less than 5% of MS patients. Copyright © 2014 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

Limited copy number - high resolution melting (LCN-HRM) enables the detection and identification by sequencing of low level mutations in cancer biopsies

PubMed Central

Do, Hongdo; Dobrovic, Alexander

2009-01-01

Background Mutation detection in clinical tumour samples is challenging when the proportion of tumour cells, and thus mutant alleles, is low. The limited sensitivity of conventional sequencing necessitates the adoption of more sensitive approaches. High resolution melting (HRM) is more sensitive than sequencing but identification of the mutation is desirable, particularly when it is important to discriminate false positives due to PCR errors or template degradation from true mutations. We thus developed limited copy number - high resolution melting (LCN-HRM) which applies limiting dilution to HRM. Multiple replicate reactions with a limited number of target sequences per reaction allow low level mutations to be detected. The dilutions used (based on Ct values) are chosen such that mutations, if present, can be detected by the direct sequencing of amplicons with aberrant melting patterns. Results Using cell lines heterozygous for mutations, we found that the mutations were not readily detected when they comprised 10% of total alleles (20% tumour cells) by sequencing, whereas they were readily detectable at 5% total alleles by standard HRM. LCN-HRM allowed these mutations to be identified by direct sequencing of those positive reactions. LCN-HRM was then used to review formalin-fixed paraffin-embedded (FFPE) clinical samples showing discordant findings between sequencing and HRM for KRAS exon 2 and EGFR exons 19 and 21. Both true mutations present at low levels and sequence changes due to artefacts were detected by LCN-HRM. The use of high fidelity polymerases showed that the majority of the artefacts were derived from the damaged template rather than replication errors during amplification. Conclusion LCN-HRM bridges the sensitivity gap between HRM and sequencing and is effective in distinguishing between artefacts and true mutations. PMID:19811662

Limited copy number-high resolution melting (LCN-HRM) enables the detection and identification by sequencing of low level mutations in cancer biopsies.

PubMed

Do, Hongdo; Dobrovic, Alexander

2009-10-08

Mutation detection in clinical tumour samples is challenging when the proportion of tumour cells, and thus mutant alleles, is low. The limited sensitivity of conventional sequencing necessitates the adoption of more sensitive approaches. High resolution melting (HRM) is more sensitive than sequencing but identification of the mutation is desirable, particularly when it is important to discriminate false positives due to PCR errors or template degradation from true mutations.We thus developed limited copy number - high resolution melting (LCN-HRM) which applies limiting dilution to HRM. Multiple replicate reactions with a limited number of target sequences per reaction allow low level mutations to be detected. The dilutions used (based on Ct values) are chosen such that mutations, if present, can be detected by the direct sequencing of amplicons with aberrant melting patterns. Using cell lines heterozygous for mutations, we found that the mutations were not readily detected when they comprised 10% of total alleles (20% tumour cells) by sequencing, whereas they were readily detectable at 5% total alleles by standard HRM. LCN-HRM allowed these mutations to be identified by direct sequencing of those positive reactions.LCN-HRM was then used to review formalin-fixed paraffin-embedded (FFPE) clinical samples showing discordant findings between sequencing and HRM for KRAS exon 2 and EGFR exons 19 and 21. Both true mutations present at low levels and sequence changes due to artefacts were detected by LCN-HRM. The use of high fidelity polymerases showed that the majority of the artefacts were derived from the damaged template rather than replication errors during amplification. LCN-HRM bridges the sensitivity gap between HRM and sequencing and is effective in distinguishing between artefacts and true mutations.

Diagnostic Accuracy of Full-Body Linear X-Ray Scanning in Multiple Trauma Patients in Comparison to Computed Tomography.

PubMed

Jöres, A P W; Heverhagen, J T; Bonél, H; Exadaktylos, A; Klink, T

2016-02-01

The purpose of this study was to evaluate the diagnostic accuracy of full-body linear X-ray scanning (LS) in multiple trauma patients in comparison to 128-multislice computed tomography (MSCT). 106 multiple trauma patients (female: 33; male: 73) were retrospectively included in this study. All patients underwent LS of the whole body, including extremities, and MSCT covering the neck, thorax, abdomen, and pelvis. The diagnostic accuracy of LS for the detection of fractures of the truncal skeleton and pneumothoraces was evaluated in comparison to MSCT by two observers in consensus. Extremity fractures detected by LS were documented. The overall sensitivity of LS was 49.2 %, the specificity was 93.3 %, the positive predictive value was 91 %, and the negative predictive value was 57.5 %. The overall sensitivity for vertebral fractures was 16.7 %, and the specificity was 100 %. The sensitivity was 48.7 % and the specificity 98.2 % for all other fractures. Pneumothoraces were detected in 12 patients by CT, but not by LS. 40 extremity fractures were detected by LS, of which 4 fractures were dislocated, and 2 were fully covered by MSCT. The diagnostic accuracy of LS is limited in the evaluation of acute trauma of the truncal skeleton. LS allows fast whole-body X-ray imaging, and may be valuable for detecting extremity fractures in trauma patients in addition to MSCT.  The overall sensitivity of LS for truncal skeleton injuries in multiple-trauma patients was < 50 %. The diagnostic reference standard MSCT is the preferred and reliable imaging modality. LS may be valuable for quick detection of extremity fractures. © Georg Thieme Verlag KG Stuttgart · New York.

Multi-pinhole SPECT Imaging with Silicon Strip Detectors

PubMed Central

Peterson, Todd E.; Shokouhi, Sepideh; Furenlid, Lars R.; Wilson, Donald W.

2010-01-01

Silicon double-sided strip detectors offer outstanding instrinsic spatial resolution with reasonable detection efficiency for iodine-125 emissions. This spatial resolution allows for multiple-pinhole imaging at low magnification, minimizing the problem of multiplexing. We have conducted imaging studies using a prototype system that utilizes a detector of 300-micrometer thickness and 50-micrometer strip pitch together with a 23-pinhole collimator. These studies include an investigation of the synthetic-collimator imaging approach, which combines multiple-pinhole projections acquired at multiple magnifications to obtain tomographic reconstructions from limited-angle data using the ML-EM algorithm. Sub-millimeter spatial resolution was obtained, demonstrating the basic validity of this approach. PMID:20953300

The Dynamic Mutation Characteristics of Thermonuclear Reaction in Tokamak

PubMed Central

Li, Jing; Quan, Tingting; Zhang, Wei; Deng, Wei

2014-01-01

The stability and bifurcations of multiple limit cycles for the physical model of thermonuclear reaction in Tokamak are investigated in this paper. The one-dimensional Ginzburg-Landau type perturbed diffusion equations for the density of the plasma and the radial electric field near the plasma edge in Tokamak are established. First, the equations are transformed to the average equations with the method of multiple scales and the average equations turn to be a Z 2-symmetric perturbed polynomial Hamiltonian system of degree 5. Then, with the bifurcations theory and method of detection function, the qualitative behavior of the unperturbed system and the number of the limit cycles of the perturbed system for certain groups of parameter are analyzed. At last, the stability of the limit cycles is studied and the physical meaning of Tokamak equations under these parameter groups is given. PMID:24892099

Rapid detection of multiple class pharmaceuticals in both municipal wastewater and sludge with ultra high performance liquid chromatography tandem mass spectrometry.

PubMed

Yuan, Xiangjuan; Qiang, Zhimin; Ben, Weiwei; Zhu, Bing; Liu, Junxin

2014-09-01

This work described the development, optimization and validation of an analytical method for rapid detection of multiple-class pharmaceuticals in both municipal wastewater and sludge samples based on ultrasonic solvent extraction, solid-phase extraction, and ultra high performance liquid chromatography-tandem mass spectrometry quantification. The results indicated that the developed method could effectively extract all the target pharmaceuticals (25) in a single process and analyze them within 24min. The recoveries of the target pharmaceuticals were in the range of 69%-131% for wastewater and 54%-130% for sludge at different spiked concentration levels. The method quantification limits in wastewater and sludge ranged from 0.02 to 0.73ng/L and from 0.02 to 1.00μg/kg, respectively. Subsequently, this method was validated and applied for residual pharmaceutical analysis in a wastewater treatment plant located in Beijing, China. All the target pharmaceuticals were detected in the influent samples with concentrations varying from 0.09ng/L (tiamulin) to 15.24μg/L (caffeine); meanwhile, up to 23 pharmaceuticals were detected in sludge samples with concentrations varying from 60ng/kg (sulfamethizole) to 8.55mg/kg (ofloxacin). The developed method demonstrated its selectivity, sensitivity, and reliability for detecting multiple-class pharmaceuticals in complex matrices such as municipal wastewater and sludge. Copyright © 2014. Published by Elsevier B.V.

Detection of diethylene glycol adulteration in propylene glycol--method validation through a multi-instrument collaborative study.

PubMed

Li, Xiang; Arzhantsev, Sergey; Kauffman, John F; Spencer, John A

2011-04-05

Four portable NIR instruments from the same manufacturer that were nominally identical were programmed with a PLS model for the detection of diethylene glycol (DEG) contamination in propylene glycol (PG)-water mixtures. The model was developed on one spectrometer and used on other units after a calibration transfer procedure that used piecewise direct standardization. Although quantitative results were produced, in practice the instrument interface was programmed to report in Pass/Fail mode. The Pass/Fail determinations were made within 10s and were based on a threshold that passed a blank sample with 95% confidence. The detection limit was then established as the concentration at which a sample would fail with 95% confidence. For a 1% DEG threshold one false negative (Type II) and eight false positive (Type I) errors were found in over 500 samples measured. A representative test set produced standard errors of less than 2%. Since the range of diethylene glycol for economically motivated adulteration (EMA) is expected to be above 1%, the sensitivity of field calibrated portable NIR instruments is sufficient to rapidly screen out potentially problematic materials. Following method development, the instruments were shipped to different sites around the country for a collaborative study with a fixed protocol to be carried out by different analysts. NIR spectra of replicate sets of calibration transfer, system suitability and test samples were all processed with the same chemometric model on multiple instruments to determine the overall analytical precision of the method. The combined results collected for all participants were statistically analyzed to determine a limit of detection (2.0% DEG) and limit of quantitation (6.5%) that can be expected for a method distributed to multiple field laboratories. Published by Elsevier B.V.

The MAX Statistic is Less Powerful for Genome Wide Association Studies Under Most Alternative Hypotheses.

PubMed

Shifflett, Benjamin; Huang, Rong; Edland, Steven D

2017-01-01

Genotypic association studies are prone to inflated type I error rates if multiple hypothesis testing is performed, e.g., sequentially testing for recessive, multiplicative, and dominant risk. Alternatives to multiple hypothesis testing include the model independent genotypic χ 2 test, the efficiency robust MAX statistic, which corrects for multiple comparisons but with some loss of power, or a single Armitage test for multiplicative trend, which has optimal power when the multiplicative model holds but with some loss of power when dominant or recessive models underlie the genetic association. We used Monte Carlo simulations to describe the relative performance of these three approaches under a range of scenarios. All three approaches maintained their nominal type I error rates. The genotypic χ 2 and MAX statistics were more powerful when testing a strictly recessive genetic effect or when testing a dominant effect when the allele frequency was high. The Armitage test for multiplicative trend was most powerful for the broad range of scenarios where heterozygote risk is intermediate between recessive and dominant risk. Moreover, all tests had limited power to detect recessive genetic risk unless the sample size was large, and conversely all tests were relatively well powered to detect dominant risk. Taken together, these results suggest the general utility of the multiplicative trend test when the underlying genetic model is unknown.

Detection of Stimulus Displacements Across Saccades is Capacity-Limited and Biased in Favor of the Saccade Target

PubMed Central

Irwin, David E.; Robinson, Maria M.

2015-01-01

Retinal image displacements caused by saccadic eye movements are generally unnoticed. Recent theories have proposed that perceptual stability across saccades depends on a local evaluation process centered on the saccade target object rather than on remapping and evaluating the positions of all objects in a display. In three experiments, we examined whether objects other than the saccade target also influence perceptual stability by measuring displacement detection thresholds across saccades for saccade targets and a variable number of non-saccade objects. We found that the positions of multiple objects are maintained across saccades, but with variable precision, with the saccade target object having priority in the perception of displacement, most likely because it is the focus of attention before the saccade and resides near the fovea after the saccade. The perception of displacement of objects that are not the saccade target is affected by acuity limitations, attentional limitations, and limitations on memory capacity. Unlike previous studies that have found that a postsaccadic blank improves the detection of displacement direction across saccades, we found that postsaccadic blanking hurt the detection of displacement per se by increasing false alarms. Overall, our results are consistent with the hypothesis that visual working memory underlies the perception of stability across saccades. PMID:26640430

Development and Comparison of Two Assay Formats for Parallel Detection of Four Biothreat Pathogens by Using Suspension Microarrays

PubMed Central

Janse, Ingmar; Bok, Jasper M.; Hamidjaja, Raditijo A.; Hodemaekers, Hennie M.; van Rotterdam, Bart J.

2012-01-01

Microarrays provide a powerful analytical tool for the simultaneous detection of multiple pathogens. We developed diagnostic suspension microarrays for sensitive and specific detection of the biothreat pathogens Bacillus anthracis, Yersinia pestis, Francisella tularensis and Coxiella burnetii. Two assay chemistries for amplification and labeling were developed, one method using direct hybridization and the other using target-specific primer extension, combined with hybridization to universal arrays. Asymmetric PCR products for both assay chemistries were produced by using a multiplex asymmetric PCR amplifying 16 DNA signatures (16-plex). The performances of both assay chemistries were compared and their advantages and disadvantages are discussed. The developed microarrays detected multiple signature sequences and an internal control which made it possible to confidently identify the targeted pathogens and assess their virulence potential. The microarrays were highly specific and detected various strains of the targeted pathogens. Detection limits for the different pathogen signatures were similar or slightly higher compared to real-time PCR. Probit analysis showed that even a few genomic copies could be detected with 95% confidence. The microarrays detected DNA from different pathogens mixed in different ratios and from spiked or naturally contaminated samples. The assays that were developed have a potential for application in surveillance and diagnostics. PMID:22355407

Development and comparison of two assay formats for parallel detection of four biothreat pathogens by using suspension microarrays.

PubMed

Janse, Ingmar; Bok, Jasper M; Hamidjaja, Raditijo A; Hodemaekers, Hennie M; van Rotterdam, Bart J

2012-01-01

Microarrays provide a powerful analytical tool for the simultaneous detection of multiple pathogens. We developed diagnostic suspension microarrays for sensitive and specific detection of the biothreat pathogens Bacillus anthracis, Yersinia pestis, Francisella tularensis and Coxiella burnetii. Two assay chemistries for amplification and labeling were developed, one method using direct hybridization and the other using target-specific primer extension, combined with hybridization to universal arrays. Asymmetric PCR products for both assay chemistries were produced by using a multiplex asymmetric PCR amplifying 16 DNA signatures (16-plex). The performances of both assay chemistries were compared and their advantages and disadvantages are discussed. The developed microarrays detected multiple signature sequences and an internal control which made it possible to confidently identify the targeted pathogens and assess their virulence potential. The microarrays were highly specific and detected various strains of the targeted pathogens. Detection limits for the different pathogen signatures were similar or slightly higher compared to real-time PCR. Probit analysis showed that even a few genomic copies could be detected with 95% confidence. The microarrays detected DNA from different pathogens mixed in different ratios and from spiked or naturally contaminated samples. The assays that were developed have a potential for application in surveillance and diagnostics.

Enhanced speed in fluorescence imaging using beat frequency multiplexing

NASA Astrophysics Data System (ADS)

Mikami, Hideharu; Kobayashi, Hirofumi; Wang, Yisen; Hamad, Syed; Ozeki, Yasuyuki; Goda, Keisuke

2016-03-01

Fluorescence imaging using radiofrequency-tagged emission (FIRE) is an emerging technique that enables higher imaging speed (namely, temporal resolution) in fluorescence microscopy compared to conventional fluorescence imaging techniques such as confocal microscopy and wide-field microscopy. It works based on the principle that it uses multiple intensity-modulated fields in an interferometric setup as excitation fields and applies frequency-division multiplexing to fluorescence signals. Unfortunately, despite its high potential, FIRE has limited imaging speed due to two practical limitations: signal bandwidth and signal detection efficiency. The signal bandwidth is limited by that of an acousto-optic deflector (AOD) employed in the setup, which is typically 100-200 MHz for the spectral range of fluorescence excitation (400-600 nm). The signal detection efficiency is limited by poor spatial mode-matching between two interfering fields to produce a modulated excitation field. Here we present a method to overcome these limitations and thus to achieve higher imaging speed than the prior version of FIRE. Our method achieves an increase in signal bandwidth by a factor of two and nearly optimal mode matching, which enables the imaging speed limited by the lifetime of the target fluorophore rather than the imaging system itself. The higher bandwidth and better signal detection efficiency work synergistically because higher bandwidth requires higher signal levels to avoid the contribution of shot noise and amplifier noise to the fluorescence signal. Due to its unprecedentedly high-speed performance, our method has a wide variety of applications in cancer detection, drug discovery, and regenerative medicine.

A widely-tunable and sensitive optical sensor for multi-species detection in the mid-IR

NASA Astrophysics Data System (ADS)

Alquaity, Awad B. S.; Al-Saif, Bidoor; Farooq, Aamir

2018-01-01

Pulsed cavity ringdown spectroscopy (CRDS) technique was used to develop a novel widely-tunable laser-based sensor for sensitive measurements of ethylene, propene, 1-butene and allene in the mid-IR. The use of an external-cavity quantum cascade laser (EC-QCL) enabled the sensor to cover a wide wavelength range from 10 to 11.1 µm (900-1000 cm-1) to detect multiple gases relevant to combustion and environment. The sensor operation was validated in a room-temperature static cell using well-characterized absorption lines of carbon dioxide near 938.69 cm-1 and 974.62 cm-1. Detection limits for ethylene, propene, 1-butene, and allene were measured to be 17, 134, 754 and 378 ppb, respectively, at 296 K and 760 Torr for a single-pass path-length of 70 cm with averaging time of 4 ms. The excellent sensitivity of the optical sensor enabled it to measure the aforementioned gases at levels smaller than 1% of their recommended exposure limits. To the best of our knowledge, this is one of the first successful applications of the pulsed CRDS technique to measure trace levels of multiple gases in the 10-11 µm wavelength region.

Estimating weak ratiometric signals in imaging data. II. Meta-analysis with multiple, dual-channel datasets.

PubMed

Sornborger, Andrew; Broder, Josef; Majumder, Anirban; Srinivasamoorthy, Ganesh; Porter, Erika; Reagin, Sean S; Keith, Charles; Lauderdale, James D

2008-09-01

Ratiometric fluorescent indicators are used for making quantitative measurements of a variety of physiological variables. Their utility is often limited by noise. This is the second in a series of papers describing statistical methods for denoising ratiometric data with the aim of obtaining improved quantitative estimates of variables of interest. Here, we outline a statistical optimization method that is designed for the analysis of ratiometric imaging data in which multiple measurements have been taken of systems responding to the same stimulation protocol. This method takes advantage of correlated information across multiple datasets for objectively detecting and estimating ratiometric signals. We demonstrate our method by showing results of its application on multiple, ratiometric calcium imaging experiments.

A New Internet Tool for Automatic Evaluation in Control Systems and Programming

ERIC Educational Resources Information Center

Munoz de la Pena, D.; Gomez-Estern, F.; Dormido, S.

2012-01-01

In this paper we present a web-based innovative education tool designed for automating the collection, evaluation and error detection in practical exercises assigned to computer programming and control engineering students. By using a student/instructor code-fusion architecture, the conceptual limits of multiple-choice tests are overcome by far.…

A New Methodology for 3D Target Detection in Automotive Radar Applications

PubMed Central

Baselice, Fabio; Ferraioli, Giampaolo; Lukin, Sergyi; Matuozzo, Gianfranco; Pascazio, Vito; Schirinzi, Gilda

2016-01-01

Today there is a growing interest in automotive sensor monitoring systems. One of the main challenges is to make them an effective and valuable aid in dangerous situations, improving transportation safety. The main limitation of visual aid systems is that they do not produce accurate results in critical visibility conditions, such as in presence of rain, fog or smoke. Radar systems can greatly help in overcoming such limitations. In particular, imaging radar is gaining interest in the framework of Driver Assistance Systems (DAS). In this manuscript, a new methodology able to reconstruct the 3D imaged scene and to detect the presence of multiple targets within each line of sight is proposed. The technique is based on the use of Compressive Sensing (CS) theory and produces the estimation of multiple targets for each line of sight, their range distance and their reflectivities. Moreover, a fast approach for 2D focus based on the FFT algorithm is proposed. After the description of the proposed methodology, different simulated case studies are reported in order to evaluate the performances of the proposed approach. PMID:27136558

Multiple headspace-solid-phase microextraction: an application to quantification of mushroom volatiles.

PubMed

Costa, Rosaria; Tedone, Laura; De Grazia, Selenia; Dugo, Paola; Mondello, Luigi

2013-04-03

Multiple headspace-solid phase microextraction (MHS-SPME) followed by gas chromatography/mass spectrometry (GC-MS) and flame ionization detection (GC-FID) was applied to the identification and quantification of volatiles released by the mushroom Agaricus bisporus, also known as champignon. MHS-SPME allows to perform quantitative analysis of volatiles from solid matrices, free of matrix interferences. Samples analyzed were fresh mushrooms (chopped and homogenized) and mushroom-containing food dressings. 1-Octen-3-ol, 3-octanol, 3-octanone, 1-octen-3-one and benzaldehyde were common constituents of the samples analyzed. Method performance has been tested through the evaluation of limit of detection (LoD, range 0.033-0.078 ng), limit of quantification (LoQ, range 0.111-0.259 ng) and analyte recovery (92.3-108.5%). The results obtained showed quantitative differences among the samples, which can be attributed to critical factors, such as the degree of cell damage upon sample preparation, that are here discussed. Considerations on the mushrooms biochemistry and on the basic principles of MHS analysis are also presented. Copyright © 2013 Elsevier B.V. All rights reserved.

High Speed Intact Protein Characterization Using 4X Frequency Multiplication, Ion Trap Harmonization, and 21 Tesla FTICR-MS.

PubMed

Shaw, Jared B; Gorshkov, Mikhail V; Wu, Qinghao; Paša-Tolić, Ljiljana

2018-05-01

Mass spectrometric characterization of large biomolecules, such as intact proteins, requires the specificity afforded by ultrahigh resolution mass measurements performed at both the intact mass and product ion levels. Although the performance of time-of-flight mass analyzers is steadily increasing, the choice of mass analyzer for large biomolecules (e.g., proteins >50 kDa) is generally limited to the Fourier transform family of mass analyzers such as Orbitrap and ion cyclotron resonance (FTICR-MS), with the latter providing unmatched mass resolving power and measurement accuracy. Yet, protein analyses using FTMS are largely hindered by the low acquisition rates of spectra with ultrahigh resolving power. Frequency multiple detection schemes enable FTICR-MS to overcome this fundamental barrier and achieve resolving powers and acquisition speeds 4× greater than the limits imposed by magnetic field strength. Here we expand upon earlier work on the implementation of this technique for biomolecular characterization. We report the coupling of 21T FTICR-MS, 4X frequency multiplication, ion trapping field harmonization technology, and spectral data processing methods to achieve unprecedented acquisition rates and resolving power in mass spectrometry of large intact proteins. Isotopically resolved spectra of multiply charged ubiquitin ions were acquired using detection periods as short as 12 ms. Large proteins such as apo-transferrin (MW = 78 kDa) and monoclonal antibody (MW = 150 kDa) were isotopically resolved with detection periods of 384 and 768 ms, respectively. These results illustrate the future capability of accurate characterization of large proteins on time scales compatible with online separations.

History, rare, and multiple events of mechanical unfolding of repeat proteins

NASA Astrophysics Data System (ADS)

Sumbul, Fidan; Marchesi, Arin; Rico, Felix

2018-03-01

Mechanical unfolding of proteins consisting of repeat domains is an excellent tool to obtain large statistics. Force spectroscopy experiments using atomic force microscopy on proteins presenting multiple domains have revealed that unfolding forces depend on the number of folded domains (history) and have reported intermediate states and rare events. However, the common use of unspecific attachment approaches to pull the protein of interest holds important limitations to study unfolding history and may lead to discarding rare and multiple probing events due to the presence of unspecific adhesion and uncertainty on the pulling site. Site-specific methods that have recently emerged minimize this uncertainty and would be excellent tools to probe unfolding history and rare events. However, detailed characterization of these approaches is required to identify their advantages and limitations. Here, we characterize a site-specific binding approach based on the ultrastable complex dockerin/cohesin III revealing its advantages and limitations to assess the unfolding history and to investigate rare and multiple events during the unfolding of repeated domains. We show that this approach is more robust, reproducible, and provides larger statistics than conventional unspecific methods. We show that the method is optimal to reveal the history of unfolding from the very first domain and to detect rare events, while being more limited to assess intermediate states. Finally, we quantify the forces required to unfold two molecules pulled in parallel, difficult when using unspecific approaches. The proposed method represents a step forward toward more reproducible measurements to probe protein unfolding history and opens the door to systematic probing of rare and multiple molecule unfolding mechanisms.

Detecting Visually Observable Disease Symptoms from Faces.

PubMed

Wang, Kuan; Luo, Jiebo

2016-12-01

Recent years have witnessed an increasing interest in the application of machine learning to clinical informatics and healthcare systems. A significant amount of research has been done on healthcare systems based on supervised learning. In this study, we present a generalized solution to detect visually observable symptoms on faces using semi-supervised anomaly detection combined with machine vision algorithms. We rely on the disease-related statistical facts to detect abnormalities and classify them into multiple categories to narrow down the possible medical reasons of detecting. Our method is in contrast with most existing approaches, which are limited by the availability of labeled training data required for supervised learning, and therefore offers the major advantage of flagging any unusual and visually observable symptoms.

Introduction of the ASGARD Code

NASA Technical Reports Server (NTRS)

Bethge, Christian; Winebarger, Amy; Tiwari, Sanjiv; Fayock, Brian

2017-01-01

ASGARD stands for 'Automated Selection and Grouping of events in AIA Regional Data'. The code is a refinement of the event detection method in Ugarte-Urra & Warren (2014). It is intended to automatically detect and group brightenings ('events') in the AIA EUV channels, to record event parameters, and to find related events over multiple channels. Ultimately, the goal is to automatically determine heating and cooling timescales in the corona and to significantly increase statistics in this respect. The code is written in IDL and requires the SolarSoft library. It is parallelized and can run with multiple CPUs. Input files are regions of interest (ROIs) in time series of AIA images from the JSOC cutout service (http://jsoc.stanford.edu/ajax/exportdata.html). The ROIs need to be tracked, co-registered, and limited in time (typically 12 hours).

Trace detection of oxygen--ionic liquids in gas sensor design.

PubMed

Baltes, N; Beyle, F; Freiner, S; Geier, F; Joos, M; Pinkwart, K; Rabenecker, P

2013-11-15

This paper presents a novel electrochemical membrane sensor on basis of ionic liquids for trace analysis of oxygen in gaseous atmospheres. The faradaic response currents for the reduction of oxygen which were obtained by multiple-potential-step-chronoamperometry could be used for real time detection of oxygen down to concentrations of 30 ppm. The theoretical limit of detection was 5 ppm. The simple, non-expensive sensors varied in electrolyte composition and demonstrated a high sensitivity, a rapid response time and an excellent reproducibility at room temperature. Some of them were continuously used for at least one week and first results promise good long term stability. Voltammetric, impedance and oxygen detection studies at temperatures up to 200 °C (in the presence and absence of humidity and CO2) revealed also the limitations of certain ionic liquids for some electrochemical high temperature applications. Application areas of the developed sensors are control and analysis processes of non oxidative and oxygen free atmospheres. Copyright © 2013 Elsevier B.V. All rights reserved.

Detection of increased vasa vasorum in artery walls: improving CT number accuracy using image deconvolution

NASA Astrophysics Data System (ADS)

Rajendran, Kishore; Leng, Shuai; Jorgensen, Steven M.; Abdurakhimova, Dilbar; Ritman, Erik L.; McCollough, Cynthia H.

2017-03-01

Changes in arterial wall perfusion are an indicator of early atherosclerosis. This is characterized by an increased spatial density of vasa vasorum (VV), the micro-vessels that supply oxygen and nutrients to the arterial wall. Detection of increased VV during contrast-enhanced computed tomography (CT) imaging is limited due to contamination from blooming effect from the contrast-enhanced lumen. We report the application of an image deconvolution technique using a measured system point-spread function, on CT data obtained from a photon-counting CT system to reduce blooming and to improve the CT number accuracy of arterial wall, which enhances detection of increased VV. A phantom study was performed to assess the accuracy of the deconvolution technique. A porcine model was created with enhanced VV in one carotid artery; the other carotid artery served as a control. CT images at an energy range of 25-120 keV were reconstructed. CT numbers were measured for multiple locations in the carotid walls and for multiple time points, pre and post contrast injection. The mean CT number in the carotid wall was compared between the left (increased VV) and right (control) carotid arteries. Prior to deconvolution, results showed similar mean CT numbers in the left and right carotid wall due to the contamination from blooming effect, limiting the detection of increased VV in the left carotid artery. After deconvolution, the mean CT number difference between the left and right carotid arteries was substantially increased at all the time points, enabling detection of the increased VV in the artery wall.

Detection and measurement of surface contamination by multiple antineoplastic drugs using multiplex bead assay

PubMed Central

Smith, Jerome P; Sammons, Deborah L; Robertson, Shirley A; Pretty, Jack; Debord, D Gayle; Connor, Thomas H; Snawder, John

2015-01-01

Objectives Contamination of workplace surfaces by antineoplastic drugs presents an exposure risk for healthcare workers. Traditional instrumental methods to detect contamination such as liquid chromatography-tandem mass spectrometry (LC-MS/MS) are sensitive and accurate but expensive. Since immunochemical methods may be cheaper and faster than instrumental methods, we wanted to explore their use for routine drug residue detection for preventing worker exposure. Methods In this study we examined the feasibility of using fluorescence covalent microbead immunosorbent assay (FCMIA) for simultaneous detection and semi-quantitative measurement of three antineoplastic drugs (5-fluorouracil, paclitaxel, and doxorubicin). The concentration ranges for the assay were 0–1000 ng/ml for 5-fluorouracil, 0–100 ng/ml for paclitaxel, and 0–2 ng/ml for doxorubicin. The surface sampling technique involved wiping a loaded surface with a swab wetted with wash buffer, extracting the swab in storage/blocking buffer, and measuring drugs in the extract using FCMIA. Results There was no significant cross reactivity between these drugs at the ranges studied indicated by a lack of response in the assay to cross analytes. The limit of detection (LOD) for 5-fluorouracil on the surface studied was 0.93 ng/cm2 with a limit of quantitation (LOQ) of 2.8 ng/cm2, the LOD for paclitaxel was 0.57 ng/cm2 with an LOQ of 2.06 ng/cm2, and the LOD for doxorubicin was 0.0036 ng/cm2 with an LOQ of 0.013 ng/cm2. Conclusion The use of FCMIA with a simple sampling technique has potential for low cost simultaneous detection and semi-quantitative measurement of surface contamination from multiple antineoplastic drugs. PMID:25293722

First Limit on the Direct Detection of Lightly Ionizing Particles for Electric Charge as Low as e / 1000 with the Majorana Demonstrator

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

Alvis, S. I.; Arnquist, I. J.; Avignone, F. T.

The Majorana Demonstrator is an ultralow-background experiment searching for neutrinoless double-beta decay in 76Ge. The heavily shielded array of germanium detectors, placed nearly a mile underground at the Sanford Underground Research Facility in Lead, South Dakota, also allows searches for new exotic physics. Free, relativistic, lightly ionizing particles with an electrical charge less than e are forbidden by the standard model but predicted by some of its extensions. If such particles exist, they might be detected in the Majorana Demonstrator by searching for multiple-detector events with individual-detector energy depositions down to 1 keV. This search is background-free, and no candidatemore » events have been found in 285 days of data taking. As a result, new direct-detection limits are set for the flux of lightly ionizing particles for charges as low as e/1000.« less

First Limit on the Direct Detection of Lightly Ionizing Particles for Electric Charge as Low as e /1000 with the Majorana Demonstrator

NASA Astrophysics Data System (ADS)

Alvis, S. I.; Arnquist, I. J.; Avignone, F. T.; Barabash, A. S.; Barton, C. J.; Bertrand, F. E.; Brudanin, V.; Busch, M.; Buuck, M.; Caldwell, T. S.; Chan, Y.-D.; Christofferson, C. D.; Chu, P.-H.; Cuesta, C.; Detwiler, J. A.; Dunagan, C.; Efremenko, Yu.; Ejiri, H.; Elliott, S. R.; Gilliss, T.; Giovanetti, G. K.; Green, M. P.; Gruszko, J.; Guinn, I. S.; Guiseppe, V. E.; Haufe, C. R.; Hehn, L.; Henning, R.; Hoppe, E. W.; Howe, M. A.; Konovalov, S. I.; Kouzes, R. T.; Lopez, A. M.; Martin, R. D.; Massarczyk, R.; Meijer, S. J.; Mertens, S.; Myslik, J.; O'Shaughnessy, C.; Othman, G.; Pettus, W.; Poon, A. W. P.; Radford, D. C.; Rager, J.; Reine, A. L.; Rielage, K.; Robertson, R. G. H.; Ruof, N. W.; Shanks, B.; Shirchenko, M.; Suriano, A. M.; Tedeschi, D.; Varner, R. L.; Vasilyev, S.; Vorren, K.; White, B. R.; Wilkerson, J. F.; Wiseman, C.; Xu, W.; Yakushev, E.; Yu, C.-H.; Yumatov, V.; Zhitnikov, I.; Zhu, B. X.; Majorana Collaboration

2018-05-01

The Majorana Demonstrator is an ultralow-background experiment searching for neutrinoless double-beta decay in 76Ge. The heavily shielded array of germanium detectors, placed nearly a mile underground at the Sanford Underground Research Facility in Lead, South Dakota, also allows searches for new exotic physics. Free, relativistic, lightly ionizing particles with an electrical charge less than e are forbidden by the standard model but predicted by some of its extensions. If such particles exist, they might be detected in the Majorana Demonstrator by searching for multiple-detector events with individual-detector energy depositions down to 1 keV. This search is background-free, and no candidate events have been found in 285 days of data taking. New direct-detection limits are set for the flux of lightly ionizing particles for charges as low as e /1000 .

First Limit on the Direct Detection of Lightly Ionizing Particles for Electric Charge as Low as e / 1000 with the Majorana Demonstrator

DOE PAGES

Alvis, S. I.; Arnquist, I. J.; Avignone, F. T.; ...

2018-05-25

The Majorana Demonstrator is an ultralow-background experiment searching for neutrinoless double-beta decay in 76Ge. The heavily shielded array of germanium detectors, placed nearly a mile underground at the Sanford Underground Research Facility in Lead, South Dakota, also allows searches for new exotic physics. Free, relativistic, lightly ionizing particles with an electrical charge less than e are forbidden by the standard model but predicted by some of its extensions. If such particles exist, they might be detected in the Majorana Demonstrator by searching for multiple-detector events with individual-detector energy depositions down to 1 keV. This search is background-free, and no candidatemore » events have been found in 285 days of data taking. As a result, new direct-detection limits are set for the flux of lightly ionizing particles for charges as low as e/1000.« less

Combined acquisition technique (CAT) for neuroimaging of multiple sclerosis at low specific absorption rates (SAR).

PubMed

Biller, Armin; Choli, Morwan; Blaimer, Martin; Breuer, Felix A; Jakob, Peter M; Bartsch, Andreas J

2014-01-01

To compare a novel combined acquisition technique (CAT) of turbo-spin-echo (TSE) and echo-planar-imaging (EPI) with conventional TSE. CAT reduces the electromagnetic energy load transmitted for spin excitation. This radiofrequency (RF) burden is limited by the specific absorption rate (SAR) for patient safety. SAR limits restrict high-field MRI applications, in particular. The study was approved by the local Medical Ethics Committee. Written informed consent was obtained from all participants. T2- and PD-weighted brain images of n = 40 Multiple Sclerosis (MS) patients were acquired by CAT and TSE at 3 Tesla. Lesions were recorded by two blinded, board-certificated neuroradiologists. Diagnostic equivalence of CAT and TSE to detect MS lesions was evaluated along with their SAR, sound pressure level (SPL) and sensations of acoustic noise, heating, vibration and peripheral nerve stimulation. Every MS lesion revealed on TSE was detected by CAT according to both raters (Cohen's kappa of within-rater/across-CAT/TSE lesion detection κCAT = 1.00, at an inter-rater lesion detection agreement of κLES = 0.82). CAT reduced the SAR burden significantly compared to TSE (p<0.001). Mean SAR differences between TSE and CAT were 29.0 (± 5.7) % for the T2-contrast and 32.7 (± 21.9) % for the PD-contrast (expressed as percentages of the effective SAR limit of 3.2 W/kg for head examinations). Average SPL of CAT was no louder than during TSE. Sensations of CAT- vs. TSE-induced heating, noise and scanning vibrations did not differ. T2-/PD-CAT is diagnostically equivalent to TSE for MS lesion detection yet substantially reduces the RF exposure. Such SAR reduction facilitates high-field MRI applications at 3 Tesla or above and corresponding protocol standardizations but CAT can also be used to scan faster, at higher resolution or with more slices. According to our data, CAT is no more uncomfortable than TSE scanning.

Conjugated Polymer Nanoparticles for the Amplified Detection of Nitro-explosive Picric Acid on Multiple Platforms.

PubMed

Malik, Akhtar Hussain; Hussain, Sameer; Kalita, Anamika; Iyer, Parameswar Krishnan

2015-12-09

Spontaneously formed conjugated polymer nanoparticles (CPNs) or polymer dots displayed remarkable fluorescence response toward nitroexplosive-picric acid (PA) in multiple environments including 100% aqueous media, solid support using portable paper strips and vapor phase detection via two terminal device. This new cationic conjugated polyelectrolyte (CPE) poly(3,3'-((2-phenyl-9H-fluorene-9,9-diyl)bis(hexane-6,1-diyl))bis(1-methyl-1H-imidazol-3-ium)bromide) (PFMI) was synthesized by Suzuki coupling polymerization followed by post functionalization method without employing any hectic purification technique. Highest quenching constant value (K(sv)) of 1.12 × 10(8) M(-1) and a very low detection limit of 30.9 pM/7.07 ppt were obtained exclusively for PA in 100% aqueous environment which is rare and unique for any CPE/CPNs. Contact mode detection of PA was also performed using simple, cost-effective and portable fluorescent paper strips for achieving on-site detection. Furthermore, the two terminal sensor device fabricated with nanoparticles of PFMI (PFMI-NPs) provides an exceptional and unprecedented platform for the vapor mode detection of PA under ambient conditions. The mechanism for the ultrasensitivity of PFMI-NPs probe to detect PA is attributed to the "molecular-wire effect", electrostatic interaction, photoinduced electron transfer (PET), and possible resonance energy transfer (RET).

A MULTIPLICITY CENSUS OF INTERMEDIATE-MASS STARS IN SCORPIUS-CENTAURUS

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

Janson, Markus; Lafreniere, David; Jayawardhana, Ray

2013-08-20

Stellar multiplicity properties have been studied for the lowest and the highest stellar masses, but intermediate-mass stars from F-type to late A-type have received relatively little attention. Here, we report on a Gemini/NICI snapshot imaging survey of 138 such stars in the young Scorpius-Centaurus (Sco-Cen) region, for the purpose of studying multiplicity with sensitivity down to planetary masses at wide separations. In addition to two brown dwarfs and a companion straddling the hydrogen-burning limit which we reported previously, here we present 26 new stellar companions and determine a multiplicity fraction within 0.''1-5.''0 of 21% {+-} 4%. Depending on the adoptedmore » semimajor axis distribution, our results imply a total multiplicity in the range of {approx}60%-80%, which further supports the known trend of a smooth continuous increase in the multiplicity fraction as a function of primary stellar mass. A surprising feature in the sample is a distinct lack of nearly equal-mass binaries, for which we discuss possible reasons. The survey yielded no additional companions below or near the deuterium-burning limit, implying that their frequency at >200 AU separations is not quite as high as might be inferred from previous detections of such objects within the Sco-Cen region.« less

Development of a multiple immunoaffinity column for simultaneous determination of multiple mycotoxins in feeds using UPLC-MS/MS.

PubMed

Hu, Xiaofeng; Hu, Rui; Zhang, Zhaowei; Li, Peiwu; Zhang, Qi; Wang, Min

2016-09-01

A sensitive and specific immunoaffinity column to clean up and isolate multiple mycotoxins was developed along with a rapid one-step sample preparation procedure for ultra-performance liquid chromatography-tandem mass spectrometry analysis. Monoclonal antibodies against aflatoxin B1, aflatoxin B2, aflatoxin G1, aflatoxin G2, zearalenone, ochratoxin A, sterigmatocystin, and T-2 toxin were coupled to microbeads for mycotoxin purification. We optimized a homogenization and extraction procedure as well as column loading and elution conditions to maximize recoveries from complex feed matrices. This method allowed rapid, simple, and simultaneous determination of mycotoxins in feeds with a single chromatographic run. Detection limits for these toxins ranged from 0.006 to 0.12 ng mL(-1), and quantitation limits ranged from 0.06 to 0.75 ng mL(-1). Concentration curves were linear from 0.12 to 40 μg kg(-1) with correlation coefficients of R (2) > 0.99. Intra-assay and inter-assay comparisons indicated excellent repeatability and reproducibility of the multiple immunoaffinity columns. As a proof of principle, 80 feed samples were tested and several contained multiple mycotoxins. This method is sensitive, rapid, and durable enough for multiple mycotoxin determinations that fulfill European Union and Chinese testing criteria.

Multiple imputation for multivariate data with missing and below-threshold measurements: time-series concentrations of pollutants in the Arctic.

PubMed

Hopke, P K; Liu, C; Rubin, D B

2001-03-01

Many chemical and environmental data sets are complicated by the existence of fully missing values or censored values known to lie below detection thresholds. For example, week-long samples of airborne particulate matter were obtained at Alert, NWT, Canada, between 1980 and 1991, where some of the concentrations of 24 particulate constituents were coarsened in the sense of being either fully missing or below detection limits. To facilitate scientific analysis, it is appealing to create complete data by filling in missing values so that standard complete-data methods can be applied. We briefly review commonly used strategies for handling missing values and focus on the multiple-imputation approach, which generally leads to valid inferences when faced with missing data. Three statistical models are developed for multiply imputing the missing values of airborne particulate matter. We expect that these models are useful for creating multiple imputations in a variety of incomplete multivariate time series data sets.

Using a two-phase evolutionary framework to select multiple network spreaders based on community structure

NASA Astrophysics Data System (ADS)

Fu, Yu-Hsiang; Huang, Chung-Yuan; Sun, Chuen-Tsai

2016-11-01

Using network community structures to identify multiple influential spreaders is an appropriate method for analyzing the dissemination of information, ideas and infectious diseases. For example, data on spreaders selected from groups of customers who make similar purchases may be used to advertise products and to optimize limited resource allocation. Other examples include community detection approaches aimed at identifying structures and groups in social or complex networks. However, determining the number of communities in a network remains a challenge. In this paper we describe our proposal for a two-phase evolutionary framework (TPEF) for determining community numbers and maximizing community modularity. Lancichinetti-Fortunato-Radicchi benchmark networks were used to test our proposed method and to analyze execution time, community structure quality, convergence, and the network spreading effect. Results indicate that our proposed TPEF generates satisfactory levels of community quality and convergence. They also suggest a need for an index, mechanism or sampling technique to determine whether a community detection approach should be used for selecting multiple network spreaders.

Impedimetric Zika and Dengue Biosensor based on Functionalized Graphene Oxide Wrapped Silica Particles

NASA Astrophysics Data System (ADS)

Jin, Seon-Ah; Marinero, Ernesto E.; Stanciu, Lia A. Stanciu; Poudyal, Shishir; Kuhn, Richard J.

A composite of 3-Aminopropyltriethoxysilane (APTES) functionalized graphene oxide (APTES-GO) wrapped on SiO2 particles (SiO2@APTES-GO) was prepared via self-assembly. Transmission electron microscopy (TEM) and ATR-Fourier Transform Infrared spectroscopy (ATR-FTIR) confirmed wrapping of the SiO2 particles by the APTES-GO sheets. An impedimetric biosensor was constructed and used to sensitively detect Zika and dengue DNA and RNA via primer hybridization using different oligonucleotide sequences. The results demonstrate that the SiO2@APTES-GO electrode materials provide enhanced RNA detection sensitivity with selectivity and detection limit (1 femto-Molar), compared to both APTES-GO and APTES-SiO2. The three-dimensional structure, higher contact area, electrical properties and the ability for rapid hybridization offered by the SiO2@APTES-GO resulted in a successful design of a Zika and dengue biosensor with the lowest detection limit reported to date. We are in the process of developing a platform for multiple viral detection for point-of-care diagnostics for arthropode borne viral infectious diseases.

Comprehensive sample analysis using high performance liquid chromatography with multi-detection.

PubMed

Pravadali, Sercan; Bassanese, Danielle N; Conlan, Xavier A; Francis, Paul S; Smith, Zoe M; Terry, Jessica M; Shalliker, R Andrew

2013-11-25

Herein we assess the separation space offered by a liquid chromatography system with an optimised uni-dimensional separation for the determination of the key chemical entities in the highly complex matrix of a tobacco leaf extract. Multiple modes of detection, including UV-visible absorbance, chemiluminescence (acidic potassium permanganate, manganese(IV), and tris(2,2'-bipyridine)ruthenium(III)), mass spectrometry and DPPH radical scavenging were used in an attempt to systematically reduce the data complexity of the sample whilst obtaining a greater degree of molecule-specific information. A large amount of chemical data was obtained, but several limitations in the ability to assign detector responses to particular compounds, even with the aid of complementary detection systems, were observed. Thirty-three compounds were detected via MS on the tobacco extract and 12 out of 32 compounds gave a peak height ratio (PHR) greater than 0.33 on one or more detectors. This paper serves as a case study of these limitations, illustrating why multidimensional chromatography is an important consideration when developing a comprehensive chemical detection system. Copyright © 2013 Elsevier B.V. All rights reserved.

Analysis of eight glycols in serum using LC-ESI-MS-MS.

PubMed

Imbert, Laurent; Saussereau, Elodie; Lacroix, Christian

2014-01-01

A liquid chromatography coupled with electrospray tandem mass spectrometry method was developed for the analysis of ethylene glycol, diethylene glycol, triethylene glycol, 1,4-butanediol, 1,2-butanediol, 2,3-butanediol, 1,2-propanediol and 1,3-propanediol, in serum after a Schotten-Baumann derivatization by benzoyl chloride. Usual validation parameters were tested: linearity, repeatability and intermediate precision, limits of detection and quantification, carry over and ion suppression. Limits of detection were between 0.18 and 1.1 mg/L, and limits of quantification were between 0.4 and 2.3 mg/L. Separation of isomers was possible either chromatographically or by selecting specific multiple reaction monitoring transitions. This method could be a useful tool in case of suspected intoxication with antifreeze agents, solvents, dietary supplements or some medical drug compounds. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Remembering complex objects in visual working memory: do capacity limits restrict objects or features?

PubMed

Hardman, Kyle O; Cowan, Nelson

2015-03-01

Visual working memory stores stimuli from our environment as representations that can be accessed by high-level control processes. This study addresses a longstanding debate in the literature about whether storage limits in visual working memory include a limit to the complexity of discrete items. We examined the issue with a number of change-detection experiments that used complex stimuli that possessed multiple features per stimulus item. We manipulated the number of relevant features of the stimulus objects in order to vary feature load. In all of our experiments, we found that increased feature load led to a reduction in change-detection accuracy. However, we found that feature load alone could not account for the results but that a consideration of the number of relevant objects was also required. This study supports capacity limits for both feature and object storage in visual working memory. PsycINFO Database Record (c) 2015 APA, all rights reserved.

Mass detection in digital breast tomosynthesis data using convolutional neural networks and multiple instance learning.

PubMed

Yousefi, Mina; Krzyżak, Adam; Suen, Ching Y

2018-05-01

Digital breast tomosynthesis (DBT) was developed in the field of breast cancer screening as a new tomographic technique to minimize the limitations of conventional digital mammography breast screening methods. A computer-aided detection (CAD) framework for mass detection in DBT has been developed and is described in this paper. The proposed framework operates on a set of two-dimensional (2D) slices. With plane-to-plane analysis on corresponding 2D slices from each DBT, it automatically learns complex patterns of 2D slices through a deep convolutional neural network (DCNN). It then applies multiple instance learning (MIL) with a randomized trees approach to classify DBT images based on extracted information from 2D slices. This CAD framework was developed and evaluated using 5040 2D image slices derived from 87 DBT volumes. The empirical results demonstrate that this proposed CAD framework achieves much better performance than CAD systems that use hand-crafted features and deep cardinality-restricted Bolzmann machines to detect masses in DBTs. Copyright © 2018 Elsevier Ltd. All rights reserved.

A method based on multi-sensor data fusion for fault detection of planetary gearboxes.

PubMed

Lei, Yaguo; Lin, Jing; He, Zhengjia; Kong, Detong

2012-01-01

Studies on fault detection and diagnosis of planetary gearboxes are quite limited compared with those of fixed-axis gearboxes. Different from fixed-axis gearboxes, planetary gearboxes exhibit unique behaviors, which invalidate fault diagnosis methods that work well for fixed-axis gearboxes. It is a fact that for systems as complex as planetary gearboxes, multiple sensors mounted on different locations provide complementary information on the health condition of the systems. On this basis, a fault detection method based on multi-sensor data fusion is introduced in this paper. In this method, two features developed for planetary gearboxes are used to characterize the gear health conditions, and an adaptive neuro-fuzzy inference system (ANFIS) is utilized to fuse all features from different sensors. In order to demonstrate the effectiveness of the proposed method, experiments are carried out on a planetary gearbox test rig, on which multiple accelerometers are mounted for data collection. The comparisons between the proposed method and the methods based on individual sensors show that the former achieves much higher accuracies in detecting planetary gearbox faults.

Ultrasensitive Immunosensor for Cancer Biomarker Proteins using Gold Nanoparticle Film Electrodes and Multienzyme-Particle Amplification

PubMed Central

Mani, Vigneshwaran; Chikkaveeraiah, Bhaskara V.; Patel, Vyomesh; Gutkind, J. Silvio; Rusling, James F.

2009-01-01

A densely packed gold nanoparticle platform combined with a multiple-enzyme labeled detection antibody-magnetic bead bioconjugate was used as the basis for an ultrasensitive electrochemical immunosensor to detect cancer biomarkers in serum. Sensitivity was greatly amplified by synthesizing magnetic bioconjugates particles containing 7500 horseradish peroxidase (HRP) labels along with detection antibodies (Ab2) attached to activated carboxyl groups on 1 µm diameter magnetic beads. These sensors had sensitivity of 31.5 µA mL ng−1 and detection limit (DL) of 0.5 pg mL−1 for prostate specific antigen (PSA) in 10 µL of undiluted serum. This represents an ultralow mass DL of 5 fg PSA, eight fold better than a previously reported carbon nanotube (CNT) forest immunosensor featuring multiple labels on carbon nanotubes, and near or below the normal serum levels of most cancer biomarkers. Measurements of PSA in cell lysates and human serum of cancer patients gave excellent correlations with standard ELISA assays. These easily fabricated AuNP immunosensors show excellent promise for future fabrication of bioelectronic arrays. PMID:19216571

40 CFR 141.23 - Inorganic chemical sampling and analytical requirements.

Code of Federal Regulations, 2011 CFR

2011-07-01

... Inorganic Contaminants Contaminant MCL (mg/l) Methodology Detection limit (mg/l) Antimony 0.006 Atomic... January 23, 2006. Unit then, the MCL is 0.05 mg/L. 7 The MDL reported for EPA method 200.9 (Atomic... higher. Using multiple depositions, EPA 200.9 is capable of obtaining MDL of 0.0001 mg/L. 8 Using...

Analytic Support of Emergency Response and Recovery for the Wide-Area Recovery & Resiliency Program (WARRP) Task 1: Medical Countermeasures Response

DTIC Science & Technology

2012-02-23

time Detect and Characterize Event Multiple Materiel No integration between national biosurveillance systems Could receive disparate signals and the...is very limited in its applicability at this time only being deployable in one city and in the process of being implemented in four more Push models

An improved multiple flame photometric detector for gas chromatography.

PubMed

Clark, Adrian G; Thurbide, Kevin B

2015-11-20

An improved multiple flame photometric detector (mFPD) is introduced, based upon interconnecting fluidic channels within a planar stainless steel (SS) plate. Relative to the previous quartz tube mFPD prototype, the SS mFPD provides a 50% reduction in background emission levels, an orthogonal analytical flame, and easier more sensitive operation. As a result, sulfur response in the SS mFPD spans 4 orders of magnitude, yields a minimum detectable limit near 9×10(-12)gS/s, and has a selectivity approaching 10(4) over carbon. The device also exhibits exceptionally large resistance to hydrocarbon response quenching. Additionally, the SS mFPD uniquely allows analyte emission monitoring in the multiple worker flames for the first time. The findings suggest that this mode can potentially further improve upon the analytical flame response of sulfur (both linear HSO, and quadratic S2) and also phosphorus. Of note, the latter is nearly 20-fold stronger in S/N in the collective worker flames response and provides 6 orders of linearity with a detection limit of about 2.0×10(-13)gP/s. Overall, the results indicate that this new SS design notably improves the analytical performance of the mFPD and can provide a versatile and beneficial monitoring tool for gas chromatography. Copyright © 2015 Elsevier B.V. All rights reserved.

Multiple fingerprinting analyses in quality control of Cassiae Semen polysaccharides.

PubMed

Cheng, Jing; He, Siyu; Wan, Qiang; Jing, Pu

2018-03-01

Quality control issue overshadows potential health benefits of Cassiae Semen due to the analytic limitations. In this study, multiple-fingerprint analysis integrated with several chemometrics was performed to assess the polysaccharide quality of Cassiae Semen harvested from different locations. FT-IR, HPLC, and GC fingerprints of polysaccharide extracts from the authentic source were established as standard profiles, applying to assess the quality of foreign sources. Analyses of FT-IR fingerprints of polysaccharide extracts using either Pearson correlation analysis or principal component analysis (PCA), or HPLC fingerprints of partially hydrolyzed polysaccharides with PCA, distinguished the foreign sources from the authentic source. However, HPLC or GC fingerprints of completely hydrolyzed polysaccharides couldn't identify all foreign sources and the methodology using GC is quite limited in determining the monosaccharide composition. This indicates that FT-IR/HPLC fingerprints of non/partially-hydrolyzed polysaccharides, respectively, accompanied by multiple chemometrics methods, might be potentially applied in detecting and differentiating sources of Cassiae Semen. Copyright © 2018 Elsevier B.V. All rights reserved.

[Investigation of RNA viral genome amplification by multiple displacement amplification technique].

PubMed

Pang, Zheng; Li, Jian-Dong; Li, Chuan; Liang, Mi-Fang; Li, De-Xin

2013-06-01

In order to facilitate the detection of newly emerging or rare viral infectious diseases, a negative-strand RNA virus-severe fever with thrombocytopenia syndrome bunyavirus, and a positive-strand RNA virus-dengue virus, were used to investigate RNA viral genome unspecific amplification by multiple displacement amplification technique from clinical samples. Series of 10-fold diluted purified viral RNA were utilized as analog samples with different pathogen loads, after a series of reactions were sequentially processed, single-strand cDNA, double-strand cDNA, double-strand cDNA treated with ligation without or with supplemental RNA were generated, then a Phi29 DNA polymerase depended isothermal amplification was employed, and finally the target gene copies were detected by real time PCR assays to evaluate the amplification efficiencies of various methods. The results showed that multiple displacement amplification effects of single-strand or double-strand cDNA templates were limited, while the fold increases of double-strand cDNA templates treated with ligation could be up to 6 X 10(3), even 2 X 10(5) when supplemental RNA existed, and better results were obtained when viral RNA loads were lower. A RNA viral genome amplification system using multiple displacement amplification technique was established in this study and effective amplification of RNA viral genome with low load was achieved, which could provide a tool to synthesize adequate viral genome for multiplex pathogens detection.

A method for release and multiple strand amplification of small quantities of DNA from endospores of the fastidious bacterium Pasteuria penetrans.

PubMed

Mauchline, T H; Mohan, S; Davies, K G; Schaff, J E; Opperman, C H; Kerry, B R; Hirsch, P R

2010-05-01

To establish a reliable protocol to extract DNA from Pasteuria penetrans endospores for use as template in multiple strand amplification, thus providing sufficient material for genetic analyses. To develop a highly sensitive PCR-based diagnostic tool for P. penetrans. An optimized method to decontaminate endospores, release and purify DNA enabled multiple strand amplification. DNA purity was assessed by cloning and sequencing gyrB and 16S rRNA gene fragments obtained from PCR using generic primers. Samples indicated to be 100%P. penetrans by the gyrB assay were estimated at 46% using the 16S rRNA gene. No bias was detected on cloning and sequencing 12 housekeeping and sporulation gene fragments from amplified DNA. The detection limit by PCR with Pasteuria-specific 16S rRNA gene primers following multiple strand amplification of DNA extracted using the method was a single endospore. Generation of large quantities DNA will facilitate genomic sequencing of P. penetrans. Apparent differences in sample purity are explained by variations in 16S rRNA gene copy number in Eubacteria leading to exaggerated estimations of sample contamination. Detection of single endospores will facilitate investigations of P. penetrans molecular ecology. These methods will advance studies on P. penetrans and facilitate research on other obligate and fastidious micro-organisms where it is currently impractical to obtain DNA in sufficient quantity and quality.

Kinetics of T-cell receptor-dependent antigen recognition determined in vivo by multi-spectral normalized epifluorescence laser scanning

NASA Astrophysics Data System (ADS)

Favicchio, Rosy; Zacharakis, Giannis; Oikonomaki, Katerina; Zacharopoulos, Athanasios; Mamalaki, Clio; Ripoll, Jorge

2012-07-01

Detection of multiple fluorophores in conditions of low signal represents a limiting factor for the application of in vivo optical imaging techniques in immunology where fluorescent labels report for different functional characteristics. A noninvasive in vivo Multi-Spectral Normalized Epifluorescence Laser scanning (M-SNELS) method was developed for the simultaneous and quantitative detection of multiple fluorophores in low signal to noise ratios and used to follow T-cell activation and clonal expansion. Colocalized DsRed- and GFP-labeled T cells were followed in tandem during the mounting of an immune response. Spectral unmixing was used to distinguish the overlapping fluorescent emissions representative of the two distinct cell populations and longitudinal data reported the discrete pattern of antigen-driven proliferation. Retrieved values were validated both in vitro and in vivo with flow cytometry and significant correlation between all methodologies was achieved. Noninvasive M-SNELS successfully quantified two colocalized fluorescent populations and provides a valid alternative imaging approach to traditional invasive methods for detecting T cell dynamics.

Damage detection of structures identified with deterministic-stochastic models using seismic data.

PubMed

Huang, Ming-Chih; Wang, Yen-Po; Chang, Ming-Lian

2014-01-01

A deterministic-stochastic subspace identification method is adopted and experimentally verified in this study to identify the equivalent single-input-multiple-output system parameters of the discrete-time state equation. The method of damage locating vector (DLV) is then considered for damage detection. A series of shaking table tests using a five-storey steel frame has been conducted. Both single and multiple damage conditions at various locations have been considered. In the system identification analysis, either full or partial observation conditions have been taken into account. It has been shown that the damaged stories can be identified from global responses of the structure to earthquakes if sufficiently observed. In addition to detecting damage(s) with respect to the intact structure, identification of new or extended damages of the as-damaged counterpart has also been studied. This study gives further insights into the scheme in terms of effectiveness, robustness, and limitation for damage localization of frame systems.

Development and Measurements of a Mid-Infrared Multi-Gas Sensor System for CO, CO₂ and CH₄ Detection.

PubMed

Dong, Ming; Zheng, Chuantao; Miao, Shuzhuo; Zhang, Yu; Du, Qiaoling; Wang, Yiding; Tittel, Frank K

2017-09-27

A multi-gas sensor system was developed that uses a single broadband light source and multiple carbon monoxide (CO), carbon dioxide (CO₂) and methane (CH₄) pyroelectric detectors by use of the time division multiplexing (TDM) technique. A stepper motor-based rotating system and a single-reflection spherical optical mirror were designed and adopted to realize and enhance multi-gas detection. Detailed measurements under static detection mode (without rotation) and dynamic mode (with rotation) were performed to study the performance of the sensor system for the three gas species. Effects of the motor rotating period on sensor performances were also investigated and a rotation speed of 0.4π rad/s was required to obtain a stable sensing performance, corresponding to a detection period of ~10 s to realize one round of detection. Based on an Allan deviation analysis, the 1 σ detection limits under static operation are 2.96, 4.54 and 2.84 parts per million in volume (ppmv) for CO, CO₂ and CH₄, respectively and the 1 σ detection limits under dynamic operations are 8.83, 8.69 and 10.29 ppmv for the three gas species, respectively. The reported sensor has potential applications in various fields requiring CO, CO₂ and CH₄ detection such as in coal mines.

A fully automated microfluidic-based electrochemical sensor for real-time bacteria detection.

PubMed

Altintas, Zeynep; Akgun, Mete; Kokturk, Guzin; Uludag, Yildiz

2018-02-15

A fully automated microfluidic-based electrochemical biosensor was designed and manufactured for pathogen detection. The quantification of Escherichia coli was investigated with standard and nanomaterial amplified immunoassays in the concentration ranges of 0.99 × 10 4 3.98 × 10 9 cfu mL -1 and 103.97 × 10 7 cfu mL -1 which resulted in detection limits of 1.99 × 10 4 cfu mL -1 and 50 cfu mL -1 , respectively. The developed methodology was then applied for E. coli quantification in water samples using nanomaterial modified assay. Same detection limit for E. coli was achieved for real sample analysis with a little decrease on the sensor signal. Cross-reactivity studies were conducted by testing Shigella, Salmonella spp., Salmonella typhimurium and Staphylococcus aureus on E. coli specific antibody surface that confirmed the high specificity of the developed immunoassays. The sensor surface could be regenerated multiple times which significantly reduces the cost of the system. Our custom-designed biosensor is capable of detecting bacteria with high sensitivity and specificity, and can serve as a promising tool for pathogen detection. Copyright © 2017 Elsevier B.V. All rights reserved.

Dual-wavelength quantum cascade laser for trace gas spectroscopy

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

Jágerská, J.; Tuzson, B.; Mangold, M.

2014-10-20

We demonstrate a sequentially operating dual-wavelength quantum cascade laser with electrically separated laser sections, emitting single-mode at 5.25 and 6.25 μm. Based on a single waveguide ridge, this laser represents a considerable asset to optical sensing and trace gas spectroscopy, as it allows probing multiple gas species with spectrally distant absorption features using conventional optical setups without any beam combining optics. The laser capability was demonstrated in simultaneous NO and NO{sub 2} detection, reaching sub-ppb detection limits and selectivity comparable to conventional high-end spectroscopic systems.

Addressing the Analytic Challenges of Cross-Sectional Pediatric Pneumonia Etiology Data.

PubMed

Hammitt, Laura L; Feikin, Daniel R; Scott, J Anthony G; Zeger, Scott L; Murdoch, David R; O'Brien, Katherine L; Deloria Knoll, Maria

2017-06-15

Despite tremendous advances in diagnostic laboratory technology, identifying the pathogen(s) causing pneumonia remains challenging because the infected lung tissue cannot usually be sampled for testing. Consequently, to obtain information about pneumonia etiology, clinicians and researchers test specimens distant to the site of infection. These tests may lack sensitivity (eg, blood culture, which is only positive in a small proportion of children with pneumonia) and/or specificity (eg, detection of pathogens in upper respiratory tract specimens, which may indicate asymptomatic carriage or a less severe syndrome, such as upper respiratory infection). While highly sensitive nucleic acid detection methods and testing of multiple specimens improve sensitivity, multiple pathogens are often detected and this adds complexity to the interpretation as the etiologic significance of results may be unclear (ie, the pneumonia may be caused by none, one, some, or all of the pathogens detected). Some of these challenges can be addressed by adjusting positivity rates to account for poor sensitivity or incorporating test results from controls without pneumonia to account for poor specificity. However, no classical analytic methods can account for measurement error (ie, sensitivity and specificity) for multiple specimen types and integrate the results of measurements for multiple pathogens to produce an accurate understanding of etiology. We describe the major analytic challenges in determining pneumonia etiology and review how the common analytical approaches (eg, descriptive, case-control, attributable fraction, latent class analysis) address some but not all challenges. We demonstrate how these limitations necessitate a new, integrated analytical approach to pneumonia etiology data. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America.

Addressing the Analytic Challenges of Cross-Sectional Pediatric Pneumonia Etiology Data

PubMed Central

Feikin, Daniel R.; Scott, J. Anthony G.; Zeger, Scott L.; Murdoch, David R.; O’Brien, Katherine L.; Deloria Knoll, Maria

2017-01-01

Abstract Despite tremendous advances in diagnostic laboratory technology, identifying the pathogen(s) causing pneumonia remains challenging because the infected lung tissue cannot usually be sampled for testing. Consequently, to obtain information about pneumonia etiology, clinicians and researchers test specimens distant to the site of infection. These tests may lack sensitivity (eg, blood culture, which is only positive in a small proportion of children with pneumonia) and/or specificity (eg, detection of pathogens in upper respiratory tract specimens, which may indicate asymptomatic carriage or a less severe syndrome, such as upper respiratory infection). While highly sensitive nucleic acid detection methods and testing of multiple specimens improve sensitivity, multiple pathogens are often detected and this adds complexity to the interpretation as the etiologic significance of results may be unclear (ie, the pneumonia may be caused by none, one, some, or all of the pathogens detected). Some of these challenges can be addressed by adjusting positivity rates to account for poor sensitivity or incorporating test results from controls without pneumonia to account for poor specificity. However, no classical analytic methods can account for measurement error (ie, sensitivity and specificity) for multiple specimen types and integrate the results of measurements for multiple pathogens to produce an accurate understanding of etiology. We describe the major analytic challenges in determining pneumonia etiology and review how the common analytical approaches (eg, descriptive, case-control, attributable fraction, latent class analysis) address some but not all challenges. We demonstrate how these limitations necessitate a new, integrated analytical approach to pneumonia etiology data. PMID:28575372

Duplex microfluidic SERS detection of pathogen antigens with nanoyeast single-chain variable fragments.

PubMed

Wang, Yuling; Rauf, Sakandar; Grewal, Yadveer S; Spadafora, Lauren J; Shiddiky, Muhammad J A; Cangelosi, Gerard A; Schlücker, Sebastian; Trau, Matt

2014-10-07

Quantitative and accurate detection of multiple biomarkers would allow for the rapid diagnosis and treatment of diseases induced by pathogens. Monoclonal antibodies are standard affinity reagents applied for biomarkers detection; however, their production is expensive and labor-intensive. Herein, we report on newly developed nanoyeast single-chain variable fragments (NYscFv) as an attractive alternative to monoclonal antibodies, which offers the unique advantage of a cost-effective production, stability in solution, and target-specificity. By combination of surface-enhanced Raman scattering (SERS) microspectroscopy using glass-coated, highly purified SERS nanoparticle clusters as labels, with a microfluidic device comprising multiple channels, a robust platform for the sensitive duplex detection of pathogen antigens has been developed. Highly sensitive detection for individual Entamoeba histolytica antigen EHI_115350 (limit of detection = 1 pg/mL, corresponding to 58.8 fM) and EHI_182030 (10 pg/mL, corresponding 453 fM) with high specificity has been achieved, employing the newly developed corresponding NYscFv as probe in combination with SERS microspectroscopy at a single laser excitation wavelength. Our first report on SERS-based immunoassays using the novel NYscFv affinity reagent demonstrates the flexibility of NYscFv fragments as viable alternatives to monoclonal antibodies in a range of bioassay platforms and paves the way for further applications.

Highly Efficient Multiple-Anchored Fluorescent Probe for the Detection of Aniline Vapor Based on Synergistic Effect: Chemical Reaction and PET.

PubMed

Jiao, Zinuo; Zhang, Yu; Xu, Wei; Zhang, Xiangtao; Jiang, Haibo; Wu, Pengcheng; Fu, Yanyan; He, Qingguo; Cao, Huimin; Cheng, Jiangong

2017-05-26

A multiple-anchored fluorescent probe ((((hexane-1,6-diylbis(2,7-bis(4-formyl)-phenyl)-9H-fluorine-9,9-diyl))-bis(hexane-6,1-diyl))-bis(9H-carbazole-9,3,6-triyl))-tetrakis(benzene-4,1-diyl))-tetraformyl-(8FP-2F) with eight aldehyde groups was designed and synthesized. The molecule has four branches and highly twisted structure. Furthermore, it tends to self-assemble into nanospheres, which is beneficial for gaseous analyte penetration and high fluorescence quantum efficiency. Among gaseous analytes, detection of aniline vapor is extraordinarily important in the control of environmental issues and human diseases. Herein, 8FP-2F was introduced to detect aniline vapor with distinguished sensitivity and selectivity via simple Schiff base reaction at room temperature. After exposure to saturate aniline vapor, the 89% fluorescence of 8FP-2F was quenched in 50 s and the detection limit was as low as 3 ppb. Further study showed the suitable HOMO/LUMO energy levels and matched orbital symmetry between probe and aniline molecules ensured chemical reaction and PET process work together. The synergistic effect resulted in a significant sensing performance and fluorescence quenching toward aniline vapor. Moreover, the multiple active sites structure of 8FP-2F means it could be applied for constructing many interesting structures and highly efficient organic optoelectronic functional materials.

Paper-based immune-affinity arrays for detection of multiple mycotoxins in cereals.

PubMed

Li, Li; Chen, Hongpu; Lv, Xiaolan; Wang, Min; Jiang, Xizhi; Jiang, Yifei; Wang, Heye; Zhao, Yongfu; Xia, Liru

2018-03-01

Mycotoxins produced by different species of fungi may coexist in cereals and feedstuffs, and could be highly toxic for humans and animals. For quantification of multiple mycotoxins in cereals, we developed a paper-based mycotoxin immune-affinity array. First, paper-based microzone arrays were fabricated by photolithography. Then, monoclonal mycotoxin antibodies were added in a copolymerization reaction with a cross-linker to form an immune-affinity monolith on the paper-based microzone array. With use of a competitive immune-response format, paper-based mycotoxin immune-affinity arrays were successfully applied to detect mycotoxins in samples. The detection limits for deoxynivalenol, zearalenone, T-2 toxin, and HT-2 toxin were 62.7, 10.8, 0.36, and 0.23 μg·kg -1 , respectively, which meet relevant requirements for these compounds in food. The recovery rates were 81-86% for deoxynivalenol, 89-117% for zearalenone, 79-86% for T-2 toxin, and 78-83% for HT-2 toxin, and showed the paper-based immune-affinity arrays had good reproducibility. In summary, the paper-based mycotoxin immune-affinity array provides a sensitive, rapid, accurate, stable, and convenient platform for detection of multiple mycotoxins in agro-foods. Graphical abstract Paper-based immune-affinity monolithic array. DON deoxynivalenol, HT-2 HT-2 toxin, T-2 T-2 toxin, PEGDA polyethylene glycol diacrylate, ZEN zearalenone.

Target-responsive DNA/RNA nanomaterials for microRNA sensing and inhibition: the jack-of-all-trades in cancer nanotheranostics?

PubMed

Conde, João; Edelman, Elazer R; Artzi, Natalie

2015-01-01

microRNAs (miRNAs) show high potential for cancer treatment, however one of the most significant bottlenecks in enabling miRNA effect is the need for an efficient vehicle capable of selective targeting to tumor cells without disrupting normal cells. Even more challenging is the ability to detect and silence multiple targets simultaneously with high sensitivity while precluding resistance to the therapeutic agents. Focusing on the pervasive role of miRNAs, herein we review the multiple nanomaterial-based systems that encapsulate DNA/RNA for miRNA sensing and inhibition in cancer therapy. Understanding the potential of miRNA detection and silencing while overcoming existing limitations will be critical to the optimization and clinical utilization of this technology. Copyright © 2014 Elsevier B.V. All rights reserved.

Environment applications for ion mobility spectrometry

NASA Technical Reports Server (NTRS)

Ritchie, Robert K.; Rudolph, Andreas

1995-01-01

The detection of environmentally important polychlorinated aromatics by ion mobility spectrometry (IMS) was investigated. Single polychlorinated biphenyl (PCB) isomers (congeners) having five or more chlorine atoms were reliably detected in isooctane solution at levels of 35 ng with a Barringer IONSCAN ion mobility spectrometer operating in negative mode; limits of detection (LOD) were extrapolated to be in the low ng region. Mixtures of up to four PCB congeners, showing characteristic multiple peaks, and complex commercial mixtures of PCBs (Aroclors) were also detected. Detection of Aroclors in transformer oil was suppressed by the presence of the antioxidant BHT (2,6-di-t-butyl4-methylphenol) in the oil. The wood preservative pentachlorophenol (PCP) was easily detected in recycled wood shavings at levels of 52 ppm with the IONSCAN; the LOD was extrapolated to be in the low ppm region.

Ultrasensitive and Multiple Disease-Related MicroRNA Detection Based on Tetrahedral DNA Nanostructures and Duplex-Specific Nuclease-Assisted Signal Amplification.

PubMed

Xu, Fang; Dong, Haifeng; Cao, Yu; Lu, Huiting; Meng, Xiangdan; Dai, Wenhao; Zhang, Xueji; Al-Ghanim, Khalid Abdullah; Mahboob, Shahid

2016-12-14

A highly sensitive and multiple microRNA (miRNA) detection method by combining three-dimensional (3D) DNA tetrahedron-structured probes (TSPs) to increase the probe reactivity and accessibility with duplex-specific nuclease (DSN) for signal amplification for sensitive miRNA detection was proposed. Briefly, 3D DNA TSPs labeled with different fluorescent dyes for specific target miRNA recognition were modified on a gold nanoparticle (GNP) surface to increase the reactivity and accessibility. Upon hybridization with a specific target, the TSPs immobilized on the GNP surface hybridized with the corresponding target miRNA to form DNA-RNA heteroduplexes, and the DSN can recognize the formed DNA-RNA heteroduplexes to hydrolyze the DNA in the heteroduplexes to produce a specific fluorescent signal corresponding to a specific miRNA, while the released target miRNA strands can initiate another cycle, resulting in a significant signal amplification for sensitive miRNA detection. Different targets can produce different fluorescent signals, leading to the development of a sensitive detection for multiple miRNAs in a homogeneous solution. Under optimized conditions, the proposed assay can simultaneously detect three different miRNAs in a homogeneous solution with a logarithmic linear range spanning 5 magnitudes (10 -12 -10 -16 ) and achieving a limit of detection down to attomolar concentrations. Meanwhile, the proposed miRNA assay exhibited the capability of discriminating single bases (three bases mismatched miRNAs) and showed good eligibility in the analysis of miRNAs extracted from cell lysates and miRNAs in cell incubation media, which indicates its potential use in biomedical research and clinical analysis.

Ultrasensitive aptamer-based protein detection via a dual amplified biocatalytic strategy

PubMed Central

Xiang, Yun; Zhang, Yuyong; Qian, Xiaoqing; Chai, Yaqin; Wang, Joseph; Yuan, Ruo

2010-01-01

We present an ultrasensitive aptasensor for electronic monitoring of proteins through a dual amplified strategy in this paper. The target protein thrombin is sandwiched between an electrode surface confined aptamer and an aptamer-enzyme-carbon nanotube bioconjugate. The analytical signal amplification is achieved by coupling the signal amplification nature of multiple enzymes with the biocatalytic signal enhancement of redox-recycling. Our novel dramatic signal amplification strategy, with a detection limit of 8.3 fM, shows about 4 orders of magnitude improvement in sensitivity for thrombin detection compared to other universal single enzyme-based assay. This makes our approach an attractive alternative to other common PCR-based signal amplification in ultralow level of protein detection. PMID:20452761

The increasing application of multiplex nucleic acid detection tests to the diagnosis of syndromic infections.

PubMed

Gray, J; Coupland, L J

2014-01-01

On 14 January 2013, the US Food and Drug Administration (FDA) announced permission for a multiplex nucleic acid test, the xTAG® Gastrointestinal Pathogen Panel (GPP) (Luminex Corporation, USA), which simultaneously detects 11 common viral, bacterial and parasitic causes of infectious gastroenteritis, to be marketed in the USA. This announcement reflects the current move towards the development and commercialization of detection technologies based on nucleic acid amplification techniques for diagnosis of syndromic infections. We discuss the limitations and advantages of nucleic acid amplification techniques and the recent advances in Conformité Européene - in-vitro diagnostic (CE-IVD)-approved multiplex real-time PCR kits for the simultaneous detection of multiple targets within the clinical diagnostics market.

Threat detection of liquid explosives and precursors from their x-ray scattering pattern using energy dispersive detector technology

NASA Astrophysics Data System (ADS)

Kehres, Jan; Lyksborg, Mark; Olsen, Ulrik L.

2017-09-01

Energy dispersive X-ray diffraction (EDXRD) can be applied for identification of liquid threats in luggage scanning in security applications. To define the instrumental design, the framework for data reduction and analysis and test the performance of the threat detection in various scenarios, a flexible laboratory EDXRD test setup was build. A data set of overall 570 EDXRD spectra has been acquired for training and testing of threat identification algorithms. The EDXRD data was acquired with limited count statistics and at multiple detector angles and merged after correction and normalization. Initial testing of the threat detection algorithms with this data set indicate the feasibility of detection levels of > 95 % true positive with < 6 % false positive alarms.

A molecular beacon based on DNA-templated silver nanoclusters for the highly sensitive and selective multiplexed detection of virulence genes.

PubMed

Han, Dan; Wei, Chunying

2018-05-01

In this work, we develop a fluorescent molecular beacon based on the DNA-templated silver nanoclusters (DNA-Ag NCs). The skillfully designed molecular beacon can be conveniently used for detection of diverse virulence genes as long as the corresponding recognition sequences are embedded. Importantly, the constructed detection system allows simultaneous detection of multiple nucleic acids, which is attributed to non-overlapping emission spectra of the as-synthesized silver nanoclusters. Based on the target-induced fluorescence enhancement, three infectious disease-related genes HIV, H1N1, and H5N1 are detected, and the corresponding detection limits are 3.53, 0.12 and 3.95nM, respectively. This design allows specific, versatile and simultaneous detection of diverse targets with easy operation and low cost. Copyright © 2017 Elsevier B.V. All rights reserved.

A new understanding of multiple-pulsed laser-induced retinal injury thresholds.

PubMed

Lund, David J; Sliney, David H

2014-04-01

Laser safety standards committees have struggled for years to formulate adequately a sound method for treating repetitive-pulse laser exposures. Safety standards for lamps and LEDs have ignored this issue because averaged irradiance appeared to treat the issue adequately for large retinal image sizes and skin exposures. Several authors have recently questioned the current approach of three test conditions (i.e., limiting single-pulse exposure, average irradiance, and a single-pulse-reduction factor) as still insufficient to treat pulses of unequal energies or certain pulse groupings. Schulmeister et al. employed thermal modeling to show that a total-on-time pulse (TOTP) rule was conservative. Lund further developed the approach of probability summation proposed by Menendez et al. to explain pulse-additivity, whereby additivity is the result of an increasing probability of detecting injury with multiple pulse exposures. This latter argument relates the increase in detection probability to the slope of the probit curve for the threshold studies. Since the uncertainty in the threshold for producing an ophthalmoscopically detectable minimal visible lesion (MVL) is large for retinal exposure to a collimated laser beam, safety committees traditionally applied large risk reduction factors ("safety factors") of one order of magnitude when deriving intrabeam, "point-source" exposure limits. This reduction factor took into account the probability of visually detecting the low-contrast lesion among other factors. The reduction factor is smaller for large spot sizes where these difficulties are quite reduced. Thus the N⁻⁰·²⁵ reduction factor may result from the difficulties in detecting the lesion. Recent studies on repetitive pulse exposures in both animal and in vitro (retinal explant) models support this interpretation of the available data.

A paper/polymer hybrid microfluidic microplate for rapid quantitative detection of multiple disease biomarkers.

PubMed

Sanjay, Sharma T; Dou, Maowei; Sun, Jianjun; Li, XiuJun

2016-07-26

Enzyme linked immunosorbent assay (ELISA) is one of the most widely used laboratory disease diagnosis methods. However, performing ELISA in low-resource settings is limited by long incubation time, large volumes of precious reagents, and well-equipped laboratories. Herein, we developed a simple, miniaturized paper/PMMA (poly(methyl methacrylate)) hybrid microfluidic microplate for low-cost, high throughput, and point-of-care (POC) infectious disease diagnosis. The novel use of porous paper in flow-through microwells facilitates rapid antibody/antigen immobilization and efficient washing, avoiding complicated surface modifications. The top reagent delivery channels can simply transfer reagents to multiple microwells thus avoiding repeated manual pipetting and costly robots. Results of colorimetric ELISA can be observed within an hour by the naked eye. Quantitative analysis was achieved by calculating the brightness of images scanned by an office scanner. Immunoglobulin G (IgG) and Hepatitis B surface Antigen (HBsAg) were quantitatively analyzed with good reliability in human serum samples. Without using any specialized equipment, the limits of detection of 1.6 ng/mL for IgG and 1.3 ng/mL for HBsAg were achieved, which were comparable to commercial ELISA kits using specialized equipment. We envisage that this simple POC hybrid microplate can have broad applications in various bioassays, especially in resource-limited settings.

A paper/polymer hybrid microfluidic microplate for rapid quantitative detection of multiple disease biomarkers

PubMed Central

Sanjay, Sharma T.; Dou, Maowei; Sun, Jianjun; Li, XiuJun

2016-01-01

Enzyme linked immunosorbent assay (ELISA) is one of the most widely used laboratory disease diagnosis methods. However, performing ELISA in low-resource settings is limited by long incubation time, large volumes of precious reagents, and well-equipped laboratories. Herein, we developed a simple, miniaturized paper/PMMA (poly(methyl methacrylate)) hybrid microfluidic microplate for low-cost, high throughput, and point-of-care (POC) infectious disease diagnosis. The novel use of porous paper in flow-through microwells facilitates rapid antibody/antigen immobilization and efficient washing, avoiding complicated surface modifications. The top reagent delivery channels can simply transfer reagents to multiple microwells thus avoiding repeated manual pipetting and costly robots. Results of colorimetric ELISA can be observed within an hour by the naked eye. Quantitative analysis was achieved by calculating the brightness of images scanned by an office scanner. Immunoglobulin G (IgG) and Hepatitis B surface Antigen (HBsAg) were quantitatively analyzed with good reliability in human serum samples. Without using any specialized equipment, the limits of detection of 1.6 ng/mL for IgG and 1.3 ng/mL for HBsAg were achieved, which were comparable to commercial ELISA kits using specialized equipment. We envisage that this simple POC hybrid microplate can have broad applications in various bioassays, especially in resource-limited settings. PMID:27456979

A paper/polymer hybrid microfluidic microplate for rapid quantitative detection of multiple disease biomarkers

NASA Astrophysics Data System (ADS)

Sanjay, Sharma T.; Dou, Maowei; Sun, Jianjun; Li, Xiujun

2016-07-01

Enzyme linked immunosorbent assay (ELISA) is one of the most widely used laboratory disease diagnosis methods. However, performing ELISA in low-resource settings is limited by long incubation time, large volumes of precious reagents, and well-equipped laboratories. Herein, we developed a simple, miniaturized paper/PMMA (poly(methyl methacrylate)) hybrid microfluidic microplate for low-cost, high throughput, and point-of-care (POC) infectious disease diagnosis. The novel use of porous paper in flow-through microwells facilitates rapid antibody/antigen immobilization and efficient washing, avoiding complicated surface modifications. The top reagent delivery channels can simply transfer reagents to multiple microwells thus avoiding repeated manual pipetting and costly robots. Results of colorimetric ELISA can be observed within an hour by the naked eye. Quantitative analysis was achieved by calculating the brightness of images scanned by an office scanner. Immunoglobulin G (IgG) and Hepatitis B surface Antigen (HBsAg) were quantitatively analyzed with good reliability in human serum samples. Without using any specialized equipment, the limits of detection of 1.6 ng/mL for IgG and 1.3 ng/mL for HBsAg were achieved, which were comparable to commercial ELISA kits using specialized equipment. We envisage that this simple POC hybrid microplate can have broad applications in various bioassays, especially in resource-limited settings.

Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays.

PubMed

Nielsen, Henrik Bjørn; Wernersson, Rasmus; Knudsen, Steen

2003-07-01

Optimal design of oligonucleotides for microarrays involves tedious and laborious work evaluating potential oligonucleotides relative to a series of parameters. The currently available tools for this purpose are limited in their flexibility and do not present the oligonucleotide designer with an overview of these parameters. We present here a flexible tool named OligoWiz for designing oligonucleotides for multiple purposes. OligoWiz presents a set of parameter scores in a graphical interface to facilitate an overview for the user. Additional custom parameter scores can easily be added to the program to extend the default parameters: homology, DeltaTm, low-complexity, position and GATC-only. Furthermore we present an analysis of the limitations in designing oligonucleotide sets that can detect transcripts from multiple organisms. OligoWiz is available at www.cbs.dtu.dk/services/OligoWiz/.

A statistical assessment of pesticide pollution in surface waters using environmental monitoring data: Chlorpyrifos in Central Valley, California.

PubMed

Wang, Dan; Singhasemanon, Nan; Goh, Kean S

2016-11-15

Pesticides are routinely monitored in surface waters and resultant data are analyzed to assess whether their uses will damage aquatic eco-systems. However, the utility of the monitoring data is limited because of the insufficiency in the temporal and spatial sampling coverage and the inability to detect and quantify trace concentrations. This study developed a novel assessment procedure that addresses those limitations by combining 1) statistical methods capable of extracting information from concentrations below changing detection limits, 2) statistical resampling techniques that account for uncertainties rooted in the non-detects and insufficient/irregular sampling coverage, and 3) multiple lines of evidence that improve confidence in the final conclusion. This procedure was demonstrated by an assessment on chlorpyrifos monitoring data in surface waters of California's Central Valley (2005-2013). We detected a significant downward trend in the concentrations, which cannot be observed by commonly-used statistical approaches. We assessed that the aquatic risk was low using a probabilistic method that works with non-detects and has the ability to differentiate indicator groups with varying sensitivity. In addition, we showed that the frequency of exceedance over ambient aquatic life water quality criteria was affected by pesticide use, precipitation and irrigation demand in certain periods anteceding the water sampling events. Copyright © 2016 Elsevier B.V. All rights reserved.

Kernel canonical-correlation Granger causality for multiple time series

NASA Astrophysics Data System (ADS)

Wu, Guorong; Duan, Xujun; Liao, Wei; Gao, Qing; Chen, Huafu

2011-04-01

Canonical-correlation analysis as a multivariate statistical technique has been applied to multivariate Granger causality analysis to infer information flow in complex systems. It shows unique appeal and great superiority over the traditional vector autoregressive method, due to the simplified procedure that detects causal interaction between multiple time series, and the avoidance of potential model estimation problems. However, it is limited to the linear case. Here, we extend the framework of canonical correlation to include the estimation of multivariate nonlinear Granger causality for drawing inference about directed interaction. Its feasibility and effectiveness are verified on simulated data.

Development of a Machine Vision Method for the Monitoring of Laying Hens and Detection of Multiple Nest Occupations.

PubMed

Zaninelli, Mauro; Redaelli, Veronica; Luzi, Fabio; Mitchell, Malcolm; Bontempo, Valentino; Cattaneo, Donata; Dell'Orto, Vittorio; Savoini, Giovanni

2018-01-05

Free range systems can improve the welfare of laying hens. However, the access to environmental resources can be partially limited by social interactions, feeding of hens, and productivity, can be not stable and damaging behaviors, or negative events, can be observed more frequently than in conventional housing systems. In order to reach a real improvement of the hens' welfare the study of their laying performances and behaviors is necessary. With this purpose, many systems have been developed. However, most of them do not detect a multiple occupation of the nest negatively affecting the accuracy of data collected. To overcome this issue, a new "nest-usage-sensor" was developed and tested. It was based on the evaluation of thermografic images, as acquired by a thermo-camera, and the performing of patter recognitions on images acquired from the nest interior. The sensor was setup with a "Multiple Nest Occupation Threshold" of 796 colored pixels and a template of triangular shape and sizes of 43 × 33 pixels (high per base). It was tested through an experimental nesting system where 10 hens were reared for a month. Results showed that the evaluation of thermografic images could increase the detection performance of a multiple occupation of the nest and to apply an image pattern recognition technique could allow for counting the number of hens in the nest in case of a multiple occupation. As a consequence, the accuracy of data collected in studies on laying performances and behaviors of hens, reared in a free-range housing system, could result to be improved.

Recovering incomplete data using Statistical Multiple Imputations (SMI): a case study in environmental chemistry.

PubMed

Mercer, Theresa G; Frostick, Lynne E; Walmsley, Anthony D

2011-10-15

This paper presents a statistical technique that can be applied to environmental chemistry data where missing values and limit of detection levels prevent the application of statistics. A working example is taken from an environmental leaching study that was set up to determine if there were significant differences in levels of leached arsenic (As), chromium (Cr) and copper (Cu) between lysimeters containing preservative treated wood waste and those containing untreated wood. Fourteen lysimeters were setup and left in natural conditions for 21 weeks. The resultant leachate was analysed by ICP-OES to determine the As, Cr and Cu concentrations. However, due to the variation inherent in each lysimeter combined with the limits of detection offered by ICP-OES, the collected quantitative data was somewhat incomplete. Initial data analysis was hampered by the number of 'missing values' in the data. To recover the dataset, the statistical tool of Statistical Multiple Imputation (SMI) was applied, and the data was re-analysed successfully. It was demonstrated that using SMI did not affect the variance in the data, but facilitated analysis of the complete dataset. Copyright © 2011 Elsevier B.V. All rights reserved.

Multiple-camera/motion stereoscopy for range estimation in helicopter flight

NASA Technical Reports Server (NTRS)

Smith, Phillip N.; Sridhar, Banavar; Suorsa, Raymond E.

1993-01-01

Aiding the pilot to improve safety and reduce pilot workload by detecting obstacles and planning obstacle-free flight paths during low-altitude helicopter flight is desirable. Computer vision techniques provide an attractive method of obstacle detection and range estimation for objects within a large field of view ahead of the helicopter. Previous research has had considerable success by using an image sequence from a single moving camera to solving this problem. The major limitations of single camera approaches are that no range information can be obtained near the instantaneous direction of motion or in the absence of motion. These limitations can be overcome through the use of multiple cameras. This paper presents a hybrid motion/stereo algorithm which allows range refinement through recursive range estimation while avoiding loss of range information in the direction of travel. A feature-based approach is used to track objects between image frames. An extended Kalman filter combines knowledge of the camera motion and measurements of a feature's image location to recursively estimate the feature's range and to predict its location in future images. Performance of the algorithm will be illustrated using an image sequence, motion information, and independent range measurements from a low-altitude helicopter flight experiment.

A simple and selective method for the measurement of azadirachtin and related azadirachtoid levels in fruits and vegetables using liquid chromatography electrospray ionization tandem mass spectrometry.

PubMed

Sarais, Giorgia; Caboni, Pierluigi; Sarritzu, Erika; Russo, Mariateresa; Cabras, Paolo

2008-05-14

Neem-based insecticides containing azadirachtin and related azadirachtoids are widely used in agriculture. Here, we report an analytical method for the rapid and accurate quantification of the insecticide azadirachtin A and B and other azadirachtoids such as salannin, nimbin, and their deacetylated analogues on tomatoes and peaches. Azadirachtoids were extracted from fruits and vegetables with acetonitrile. Using high-performance liquid chromatography/electrospray ionization tandem mass spectrometer, azadirachtoids were selectively detected monitoring the multiple reaction transitions of sodium adduct precursor ions. For azadirachtin A, calibration was linear over a working range of 1-1000 microg/L with r > 0.996. The limit of detection and limit of quantification for azadirachtin A were 0.4 and 0.8 microg/kg, respectively. The presence of interfering compounds in the peach and tomato extracts was evaluated and found to be minimal. Because of the linear behavior, it was concluded that the multiple reaction transitions of sodium adduct ions can be used for analytical purposes, that is, for the identification and quantification of azadirachtin A and B and related azadirachtoids in fruit and vegetable extracts at trace levels.

A Multiplicity Survey of Chromospherically Active and Inactive Stars

NASA Technical Reports Server (NTRS)

Mason, Brian D.; Henry, Todd J.; Hartkopf, William I.; TenBrummelaar, Theo; Soderblom, David R.

1998-01-01

Surveys of the three samples of solar-type stars, segregated by chromospheric emission level, were made to determine their multiplicity fractions and to investigate the evolution of multiplicity with age. In total, 245 stars were searched for companions with DeltaV <= 3.0 and separations of 0.035" to 1.08" using optical speckle interferometry, By incorporating the visual micrometer survey for duplicity of the LamontHussey Observatory, the angular coverage was extended to 5.0" with no change in in the DeltaV limit. This magnitude difference allows mass ratios of 0.63 and larger to be detected throughout a search region of 2-127 AU for the stars observed. The 84 primaries observed in the chromospherically active sample are presumably part of a young population and are found to have a multiplicity fraction of 17.9% +/- 4.6%. The sample of 118 inactive, presumably older, primaries were selected and observed using identical methods and are found to have a multiplicity fraction of only 8.5% +/- 2.7%. Given the known link between chromospheric activity and age, these results tentatively imply a decreasing stellar multiplicity fraction from 1 to 4 Gyr, the approximate ages of the two samples. Finally, only two of the 14 very active primaries observed were found to have a companion meeting the survey detection parameters. In this case, many of the systems are either very young, or close, RS CVn type multiples that are unresolvable using techniques employed here.

Evaluation of a TaqMan Array Card for Detection of Central Nervous System Infections.

PubMed

Onyango, Clayton O; Loparev, Vladimir; Lidechi, Shirley; Bhullar, Vinod; Schmid, D Scott; Radford, Kay; Lo, Michael K; Rota, Paul; Johnson, Barbara W; Munoz, Jorge; Oneko, Martina; Burton, Deron; Black, Carolyn M; Neatherlin, John; Montgomery, Joel M; Fields, Barry

2017-07-01

Infections of the central nervous system (CNS) are often acute, with significant morbidity and mortality. Routine diagnosis of such infections is limited in developing countries and requires modern equipment in advanced laboratories that may be unavailable to a number of patients in sub-Saharan Africa. We developed a TaqMan array card (TAC) that detects multiple pathogens simultaneously from cerebrospinal fluid. The 21-pathogen CNS multiple-pathogen TAC (CNS-TAC) assay includes two parasites ( Balamuthia mandrillaris and Acanthamoeba ), six bacterial pathogens ( Streptococcus pneumonia e, Haemophilus influenzae , Neisseria meningitidis , Mycoplasma pneumoniae , Mycobacterium tuberculosis , and Bartonella ), and 13 viruses (parechovirus, dengue virus, Nipah virus, varicella-zoster virus, mumps virus, measles virus, lyssavirus, herpes simplex viruses 1 and 2, Epstein-Barr virus, enterovirus, cytomegalovirus, and chikungunya virus). The card also includes human RNase P as a nucleic acid extraction control and an internal manufacturer control, GAPDH (glyceraldehyde-3-phosphate dehydrogenase). This CNS-TAC assay can test up to eight samples for all 21 agents within 2.5 h following nucleic acid extraction. The assay was validated for linearity, limit of detection, sensitivity, and specificity by using either live viruses (dengue, mumps, and measles viruses) or nucleic acid material (Nipah and chikungunya viruses). Of 120 samples tested by individual real-time PCR, 35 were positive for eight different targets, whereas the CNS-TAC assay detected 37 positive samples across nine different targets. The CNS-TAC assays showed 85.6% sensitivity and 96.7% specificity. Therefore, the CNS-TAC assay may be useful for outbreak investigation and surveillance of suspected neurological disease. Copyright © 2017 American Society for Microbiology.

Characterization of vitamin D3 metabolites using continuous-flow fast atom bombardment tandem mass spectrometry and high-performance liquid chromatography.

PubMed

Yeung, B; Vouros, P; Reddy, G S

1993-08-13

A mass spectrometric method for the detection of vitamin D3 metabolites is described. This method involves the derivatization of the metabolites by cycloaddition with 4-phenyl-1,2,4-triazoline-3,5-dione, followed by their characterization by continuous-flow fast atom bombardment (CF-FAB) tandem mass spectrometry (MS-MS) and high-performance liquid chromatography (HPLC). Using HPLC, this derivatization has been shown to increase the UV detectability of 25-hydroxyvitamin D3 by about 5-fold. The FAB spectra of the adducts are dominated by peaks corresponding to a protonated molecule and a fragment ion derived in part from the loss of the side chain. Multiple reaction monitoring (MRM) of this transition by MS-MS may be utilized for trace level analysis of vitamin D metabolites. Sample introduction by flow injection yields detection limits in the low nanogram to high picogram range, whereas the use of on-line capillary LC has been found to decrease the detection limits to the low picogram level.

Trace detection of meglumine and diatrizoate from Bacillus spore samples using liquid chromatography/mass spectrometry.

PubMed

Swider, Catherine; Maguire, Kelly; Rickenbach, Michael; Montgomery, Madeline; Ducote, Matthew J; Marhefka, Craig A

2012-07-01

Following the September 11, 2001 terrorist attacks, letters containing Bacillus anthracis were distributed through the United States postal system killing five people. A complex forensic investigation commenced to identify the perpetrator of these mailings. A novel liquid chromatography/mass spectrometry protocol for the qualitative detection of trace levels of meglumine and diatrizoate in dried spore preparations of B. anthracis was developed. Meglumine and diatrizoate are components of radiographic imaging products that have been used to purify bacterial spores. Two separate chromatographic assays using multiple mass spectrometric analyses were developed for the detection of meglumine and diatrizoate. The assays achieved limits of detection for meglumine and diatrizoate of 1.00 and 10.0 ng/mL, respectively. Bacillus cereus T strain spores were effectively used as a surrogate for B. anthracis spores during method development and validation. This protocol was successfully applied to limited evidentiary B. anthracis spore material, providing probative information to the investigators. 2012 American Academy of Forensic Sciences. Published 2012. This article is a U.S. Government work and is in the public domain in the U.S.A.

Sensor Data Qualification System (SDQS) Implementation Study

NASA Technical Reports Server (NTRS)

Wong, Edmond; Melcher, Kevin; Fulton, Christopher; Maul, William

2009-01-01

The Sensor Data Qualification System (SDQS) is being developed to provide a sensor fault detection capability for NASA s next-generation launch vehicles. In addition to traditional data qualification techniques (such as limit checks, rate-of-change checks and hardware redundancy checks), SDQS can provide augmented capability through additional techniques that exploit analytical redundancy relationships to enable faster and more sensitive sensor fault detection. This paper documents the results of a study that was conducted to determine the best approach for implementing a SDQS network configuration that spans multiple subsystems, similar to those that may be implemented on future vehicles. The best approach is defined as one that most minimizes computational resource requirements without impacting the detection of sensor failures.

Detection of Several Classes of Pesticides and Metabolites in Meconium by Gas Chromatography-Mass Spectrometry.

PubMed

Bielawski, D; Ostrea, E; Posecion, N; Corrion, M; Seagraves, J

2005-01-01

A solid phase extraction method was developed to isolate multiple classes of parent pesticides from meconium. A methanolic/hydrochloric acid methyl ester derivatization with liquid-liquid extraction technique was also developed for the analysis of metabolites. Identification and quantitation was by electron impact gas chromatography-mass spectrometry. For the parent compounds and metabolites, recoveries in spiked meconium ranged between 72-109%, with coefficients of variation ranging from 1.55-16.92% and limits of detection between 0.01-4.15 μg g(-1). Meconium samples obtained from infants in the Philippines were assayed using these methods, and propoxur, cypermethrin, pretilachlor, malathion, 4,4'-dichlorodiphenyltrichloroethylene, bioallethrin, and cyfluthrin were detected.

Real-Time Reverse Transcription–Polymerase Chain Reaction Assay for SARS-associated Coronavirus

PubMed Central

Emery, Shannon L.; Bowen, Michael D.; Newton, Bruce R.; Winchell, Jonas M.; Meyer, Richard F.; Tong, Suxiang; Cook, Byron T.; Holloway, Brian P.; McCaustland, Karen A.; Rota, Paul A.; Bankamp, Bettina; Lowe, Luis E.; Ksiazek, Tom G.; Bellini, William J.; Anderson, Larry J.

2004-01-01

A real-time reverse transcription–polymerase chain reaction (RT-PCR) assay was developed to rapidly detect the severe acute respiratory syndrome–associated coronavirus (SARS-CoV). The assay, based on multiple primer and probe sets located in different regions of the SARS-CoV genome, could discriminate SARS-CoV from other human and animal coronaviruses with a potential detection limit of <10 genomic copies per reaction. The real-time RT-PCR assay was more sensitive than a conventional RT-PCR assay or culture isolation and proved suitable to detect SARS-CoV in clinical specimens. Application of this assay will aid in diagnosing SARS-CoV infection. PMID:15030703

Digital PCR methods improve detection sensitivity and measurement precision of low abundance mtDNA deletions.

PubMed

Belmonte, Frances R; Martin, James L; Frescura, Kristin; Damas, Joana; Pereira, Filipe; Tarnopolsky, Mark A; Kaufman, Brett A

2016-04-28

Mitochondrial DNA (mtDNA) mutations are a common cause of primary mitochondrial disorders, and have also been implicated in a broad collection of conditions, including aging, neurodegeneration, and cancer. Prevalent among these pathogenic variants are mtDNA deletions, which show a strong bias for the loss of sequence in the major arc between, but not including, the heavy and light strand origins of replication. Because individual mtDNA deletions can accumulate focally, occur with multiple mixed breakpoints, and in the presence of normal mtDNA sequences, methods that detect broad-spectrum mutations with enhanced sensitivity and limited costs have both research and clinical applications. In this study, we evaluated semi-quantitative and digital PCR-based methods of mtDNA deletion detection using double-stranded reference templates or biological samples. Our aim was to describe key experimental assay parameters that will enable the analysis of low levels or small differences in mtDNA deletion load during disease progression, with limited false-positive detection. We determined that the digital PCR method significantly improved mtDNA deletion detection sensitivity through absolute quantitation, improved precision and reduced assay standard error.

Digital PCR methods improve detection sensitivity and measurement precision of low abundance mtDNA deletions

PubMed Central

Belmonte, Frances R.; Martin, James L.; Frescura, Kristin; Damas, Joana; Pereira, Filipe; Tarnopolsky, Mark A.; Kaufman, Brett A.

2016-01-01

Mitochondrial DNA (mtDNA) mutations are a common cause of primary mitochondrial disorders, and have also been implicated in a broad collection of conditions, including aging, neurodegeneration, and cancer. Prevalent among these pathogenic variants are mtDNA deletions, which show a strong bias for the loss of sequence in the major arc between, but not including, the heavy and light strand origins of replication. Because individual mtDNA deletions can accumulate focally, occur with multiple mixed breakpoints, and in the presence of normal mtDNA sequences, methods that detect broad-spectrum mutations with enhanced sensitivity and limited costs have both research and clinical applications. In this study, we evaluated semi-quantitative and digital PCR-based methods of mtDNA deletion detection using double-stranded reference templates or biological samples. Our aim was to describe key experimental assay parameters that will enable the analysis of low levels or small differences in mtDNA deletion load during disease progression, with limited false-positive detection. We determined that the digital PCR method significantly improved mtDNA deletion detection sensitivity through absolute quantitation, improved precision and reduced assay standard error. PMID:27122135

Parallel heuristics for scalable community detection

DOE PAGES

Lu, Hao; Halappanavar, Mahantesh; Kalyanaraman, Ananth

2015-08-14

Community detection has become a fundamental operation in numerous graph-theoretic applications. Despite its potential for application, there is only limited support for community detection on large-scale parallel computers, largely owing to the irregular and inherently sequential nature of the underlying heuristics. In this paper, we present parallelization heuristics for fast community detection using the Louvain method as the serial template. The Louvain method is an iterative heuristic for modularity optimization. Originally developed in 2008, the method has become increasingly popular owing to its ability to detect high modularity community partitions in a fast and memory-efficient manner. However, the method ismore » also inherently sequential, thereby limiting its scalability. Here, we observe certain key properties of this method that present challenges for its parallelization, and consequently propose heuristics that are designed to break the sequential barrier. For evaluation purposes, we implemented our heuristics using OpenMP multithreading, and tested them over real world graphs derived from multiple application domains. Compared to the serial Louvain implementation, our parallel implementation is able to produce community outputs with a higher modularity for most of the inputs tested, in comparable number or fewer iterations, while providing real speedups of up to 16x using 32 threads.« less

Low contrast detection in abdominal CT: comparing single-slice and multi-slice tasks

NASA Astrophysics Data System (ADS)

Ba, Alexandre; Racine, Damien; Viry, Anaïs.; Verdun, Francis R.; Schmidt, Sabine; Bochud, François O.

2017-03-01

Image quality assessment is crucial for the optimization of computed tomography (CT) protocols. Human and mathematical model observers are increasingly used for the detection of low contrast signal in abdominal CT, but are frequently limited to the use of a single image slice. Another limitation is that most of them only consider the detection of a signal embedded in a uniform background phantom. The purpose of this paper was to test if human observer performance is significantly different in CT images read in single or multiple slice modes and if these differences are the same for anatomical and uniform clinical images. We investigated detection performance and scrolling trends of human observers of a simulated liver lesion embedded in anatomical and uniform CT backgrounds. Results show that observers don't take significantly benefit of additional information provided in multi-slice reading mode. Regarding the background, performances are moderately higher for uniform than for anatomical images. Our results suggest that for low contrast detection in abdominal CT, the use of multi-slice model observers would probably only add a marginal benefit. On the other hand, the quality of a CT image is more accurately estimated with clinical anatomical backgrounds.

Automatic mine detection based on multiple features

NASA Astrophysics Data System (ADS)

Yu, Ssu-Hsin; Gandhe, Avinash; Witten, Thomas R.; Mehra, Raman K.

2000-08-01

Recent research sponsored by the Army, Navy and DARPA has significantly advanced the sensor technologies for mine detection. Several innovative sensor systems have been developed and prototypes were built to investigate their performance in practice. Most of the research has been focused on hardware design. However, in order for the systems to be in wide use instead of in limited use by a small group of well-trained experts, an automatic process for mine detection is needed to make the final decision process on mine vs. no mine easier and more straightforward. In this paper, we describe an automatic mine detection process consisting of three stage, (1) signal enhancement, (2) pixel-level mine detection, and (3) object-level mine detection. The final output of the system is a confidence measure that quantifies the presence of a mine. The resulting system was applied to real data collected using radar and acoustic technologies.

A primitive study of voxel feature generation by multiple stacked denoising autoencoders for detecting cerebral aneurysms on MRA

NASA Astrophysics Data System (ADS)

Nemoto, Mitsutaka; Hayashi, Naoto; Hanaoka, Shouhei; Nomura, Yukihiro; Miki, Soichiro; Yoshikawa, Takeharu; Ohtomo, Kuni

2016-03-01

The purpose of this study is to evaluate the feasibility of a novel feature generation, which is based on multiple deep neural networks (DNNs) with boosting, for computer-assisted detection (CADe). It is hard and time-consuming to optimize the hyperparameters for DNNs such as stacked denoising autoencoder (SdA). The proposed method allows using SdA based features without the burden of the hyperparameter setting. The proposed method was evaluated by an application for detecting cerebral aneurysms on magnetic resonance angiogram (MRA). A baseline CADe process included four components; scaling, candidate area limitation, candidate detection, and candidate classification. Proposed feature generation method was applied to extract the optimal features for candidate classification. Proposed method only required setting range of the hyperparameters for SdA. The optimal feature set was selected from a large quantity of SdA based features by multiple SdAs, each of which was trained using different hyperparameter set. The feature selection was operated through ada-boost ensemble learning method. Training of the baseline CADe process and proposed feature generation were operated with 200 MRA cases, and the evaluation was performed with 100 MRA cases. Proposed method successfully provided SdA based features just setting the range of some hyperparameters for SdA. The CADe process by using both previous voxel features and SdA based features had the best performance with 0.838 of an area under ROC curve and 0.312 of ANODE score. The results showed that proposed method was effective in the application for detecting cerebral aneurysms on MRA.

In vivo Electrochemical Biosensor for Brain Glutamate Detection: A Mini Review

PubMed Central

HAMDAN, Siti Kartika; MOHD ZAIN, ainiharyati

2014-01-01

Glutamate is one of the most prominent neurotransmitters in mammalian brains, which plays an important role in neuronal excitation. High levels of neurotransmitter cause numerous alterations, such as calcium overload and the dysfunction of mitochondrial and oxidative stress. These alterations may lead to excitotoxicity and may trigger multiple neuronal diseases, such as Alzheimer’s disease, stroke, and epilepsy. Excitotoxicity is a pathological process that damages nerve cells and kills cells via excessive stimulation by neurotransmitters. Monitoring the concentration level of brain glutamate via an implantable microbiosensor is a promising alternative approach to closely investigate in the function of glutamate as a neurotransmitter. This review outlines glutamate microbiosensor designs to enhance the sensitivity of glutamate detection with less biofouling occurrence and minimal detection of interference species. There are many challenges in the development of a reproducible and stable implantable microbiosensor because many factors and limitations may affect the detection performance. However, the incorporation of multiple scales is needed to address the basic issues and combinations across the various disciplines needed to achieve the success of the system to overcome the challenges in the development of an implantable glutamate biosensor. PMID:25941459

A novel surface-enhanced Raman scattering nanosensor for detecting multiple heavy metal ions based on 2-mercaptoisonicotinic acid functionalized gold nanoparticles.

PubMed

Tan, Enzhong; Yin, Penggang; Lang, Xiufeng; Zhang, Hongyan; Guo, Lin

2012-11-01

A novel, effective and simple surface-enhanced Raman scattering (SERS) nanosensor for selectively and sensitively detecting heavy metal ions in aqueous solution has been developed in the form of 2-mercaptoisonicotinic acid (2 MNA)-modified gold nanoparticles (AuNPs). Multiple heavy metal ions can be identified and quantified by using relative peak intensity ratios of selected vibrational bands in the SERS spectra of 2 MNA. Especially, concentration of Hg(2+) and Pb(2+) ions are determined by comparing the intensity ratios of the bands 1160/1230 cm(-1) for Hg(2+) and 861/815 cm(-1) (or 815/1392 cm(-1)) for Pb(2+), with detection limits of 3.4×10(-8) and 1.0×10(-7)M, respectively. 2 MNA-AuNPs sensors show a high selectivity for Hg(2+) without masking reagent, and they can also be highly selective for Pb(2+) when using sodium thiosulphate and l-cysteine as masking reagents. These results demonstrate that these 2 MNA-AuNPs nanosensors are promising candidates for in situ heavy metal ions detection and quantification, maybe even inside living cells. Copyright © 2012 Elsevier B.V. All rights reserved.

Microplate based optical biosensor for L-Dopa using tyrosinase from Amorphophallus campanulatus.

PubMed

Saini, Amardeep Singh; Kumar, Jitendra; Melo, Jose Savio

2014-11-07

Developing a biosensor which is capable of simultaneously monitoring l-Dopa levels in multiple samples besides requiring small reaction volume is of great value. The present study describes the detection of l-Dopa using tyrosinase enzyme extracted from Amorphophallus campanulatus and immobilized on the surface of the microplate wells. Among the different approaches used for immobilizing tyrosinase onto the microplate wells, glutaraldehyde treatment was found to be most effective. Besides enzyme activity, ESEM-EDS (environmental scanning electron microscope-energy dispersive system) and Atomic Force Microscopy (AFM) were also carried out to confirm the immobilization of tyrosinase enzyme onto the microplate well surface. This immobilized biocomponent was then integrated with an optical transducer for l-Dopa detection and it showed good reproducibility. The sensing property of the system was studied by measuring the initial rate of dopachrome formation at 475 nm. The calibration plot gave a linear range of detection from 10-1000 μM and the detection limit was calculated to be 3 μM. The immobilized biocomponent was stable for 41 days and was reused up to nine times. Spiked samples (blood plasma) were also analyzed using this biocomponent. This microplate based biosensor thus provides a convenient system for detection of multiple samples in a single run. Copyright © 2014 Elsevier B.V. All rights reserved.

Target-triggering multiple-cycle signal amplification strategy for ultrasensitive detection of DNA based on QCM and SPR.

PubMed

Song, Weiling; Yin, Wenshuo; Sun, Wenbo; Guo, Xiaoyan; He, Peng; Yang, Xiaoyan; Zhang, Xiaoru

2018-04-24

Detection of ultralow concentrations of nucleic acid sequences is a central challenge in the early diagnosis of genetic diseases. Herein, we developed a target-triggering cascade multiple cycle amplification for ultrasensitive DNA detection using quartz crystal microbalance (QCM) and surface plasmon resonance (SPR). It was based on the exonuclease Ⅲ (Exo Ⅲ)-assisted signal amplification and the hybridization chain reaction (HCR). The streptavidin-coated Au-NPs (Au-NPs-SA) were assembled on the HCR products as recognition element. Upon sensing of target DNA, the duplex DNA probe triggered the Exo Ⅲ cleavage process, accompanied by generating a new secondary target DNA and releasing target DNA. The released target DNA and the secondary target DNA were recycled. Simultaneously, numerous single strands were liberated and acted as the trigger of HCR to generate further signal amplification, resulting in the immobilization of abundant Au-NPs-SA on the gold substrate. The QCM sensor results were found to be comparable to that achieved using a SPR sensor platform. This method exhibited a high sensitivity toward target DNA with a detection limit of 0.70 fM. The high sensitivity and specificity make this method a great potential for detecting DNA with trace amounts in bioanalysis and clinical biomedicine. Copyright © 2018 Elsevier Inc. All rights reserved.

Fast experiments for structure elucidation of small molecules: Hadamard NMR with multiple receivers.

PubMed

Gierth, Peter; Codina, Anna; Schumann, Frank; Kovacs, Helena; Kupče, Ēriks

2015-11-01

We propose several significant improvements to the PANSY (Parallel NMR SpectroscopY) experiments-PANSY COSY and PANSY-TOCSY. The improved versions of these experiments provide sufficient spectral information for structure elucidation of small organic molecules from just two 2D experiments. The PANSY-TOCSY-Q experiment has been modified to allow for simultaneous acquisition of three different types of NMR spectra-1D C-13 of non-protonated carbon sites, 2D TOCSY and multiplicity edited 2D HETCOR. In addition the J-filtered 2D PANSY-gCOSY experiment records a 2D HH gCOSY spectrum in parallel with a (1) J-filtered HC long-range HETCOR spectrum as well as offers a simplified data processing. In addition to parallel acquisition, further time savings are feasible because of significantly smaller F1 spectral windows as compared to the indirect detection experiments. Use of cryoprobes and multiple receivers can significantly alleviate the sensitivity issues that are usually associated with the so called direct detection experiments. In cases where experiments are sampling limited rather than sensitivity limited further reduction of experiment time is achieved by using Hadamard encoding. In favorable cases the total recording time for the two PANSY experiments can be reduced to just 40 s. The proposed PANSY experiments provide sufficient information to allow the CMCse software package (Bruker) to solve structures of small organic molecules. Copyright © 2015 John Wiley & Sons, Ltd.

Epsilon-Q: An Automated Analyzer Interface for Mass Spectral Library Search and Label-Free Protein Quantification.

PubMed

Cho, Jin-Young; Lee, Hyoung-Joo; Jeong, Seul-Ki; Paik, Young-Ki

2017-12-01

Mass spectrometry (MS) is a widely used proteome analysis tool for biomedical science. In an MS-based bottom-up proteomic approach to protein identification, sequence database (DB) searching has been routinely used because of its simplicity and convenience. However, searching a sequence DB with multiple variable modification options can increase processing time, false-positive errors in large and complicated MS data sets. Spectral library searching is an alternative solution, avoiding the limitations of sequence DB searching and allowing the detection of more peptides with high sensitivity. Unfortunately, this technique has less proteome coverage, resulting in limitations in the detection of novel and whole peptide sequences in biological samples. To solve these problems, we previously developed the "Combo-Spec Search" method, which uses manually multiple references and simulated spectral library searching to analyze whole proteomes in a biological sample. In this study, we have developed a new analytical interface tool called "Epsilon-Q" to enhance the functions of both the Combo-Spec Search method and label-free protein quantification. Epsilon-Q performs automatically multiple spectral library searching, class-specific false-discovery rate control, and result integration. It has a user-friendly graphical interface and demonstrates good performance in identifying and quantifying proteins by supporting standard MS data formats and spectrum-to-spectrum matching powered by SpectraST. Furthermore, when the Epsilon-Q interface is combined with the Combo-Spec search method, called the Epsilon-Q system, it shows a synergistic function by outperforming other sequence DB search engines for identifying and quantifying low-abundance proteins in biological samples. The Epsilon-Q system can be a versatile tool for comparative proteome analysis based on multiple spectral libraries and label-free quantification.

Development and Measurements of a Mid-Infrared Multi-Gas Sensor System for CO, CO2 and CH4 Detection

PubMed Central

Dong, Ming; Zheng, Chuantao; Miao, Shuzhuo; Zhang, Yu; Du, Qiaoling; Wang, Yiding

2017-01-01

A multi-gas sensor system was developed that uses a single broadband light source and multiple carbon monoxide (CO), carbon dioxide (CO2) and methane (CH4) pyroelectric detectors by use of the time division multiplexing (TDM) technique. A stepper motor-based rotating system and a single-reflection spherical optical mirror were designed and adopted to realize and enhance multi-gas detection. Detailed measurements under static detection mode (without rotation) and dynamic mode (with rotation) were performed to study the performance of the sensor system for the three gas species. Effects of the motor rotating period on sensor performances were also investigated and a rotation speed of 0.4π rad/s was required to obtain a stable sensing performance, corresponding to a detection period of ~10 s to realize one round of detection. Based on an Allan deviation analysis, the 1σ detection limits under static operation are 2.96, 4.54 and 2.84 parts per million in volume (ppmv) for CO, CO2 and CH4, respectively and the 1σ detection limits under dynamic operations are 8.83, 8.69 and 10.29 ppmv for the three gas species, respectively. The reported sensor has potential applications in various fields requiring CO, CO2 and CH4 detection such as in coal mines. PMID:28953260

A nucleic acid strand displacement system for the multiplexed detection of tuberculosis-specific mRNA using quantum dots

NASA Astrophysics Data System (ADS)

Gliddon, H. D.; Howes, P. D.; Kaforou, M.; Levin, M.; Stevens, M. M.

2016-05-01

The development of rapid, robust and high performance point-of-care diagnostics relies on the advancement and combination of various areas of research. We have developed an assay for the detection of multiple mRNA molecules that combines DNA nanotechnology with fluorescent nanomaterials. The core switching mechanism is toehold-mediated strand displacement. We have used fluorescent quantum dots (QDs) as signal transducers in this assay, as they bring many benefits including bright fluorescence and multiplexing abilities. The resulting assay is capable of multiplexed detection of long RNA targets against a high concentration of background non-target RNA, with high sensitivity and specificity and limits of detection in the nanomolar range using only a standard laboratory plate reader. We demonstrate the utility of our QD-based system for the detection of two genes selected from a microarray-derived tuberculosis-specific gene expression signature. Levels of up- and downregulated gene transcripts comprising this signature can be combined to give a disease risk score, making the signature more amenable for use as a diagnostic marker. Our QD-based approach to detect these transcripts could pave the way for novel diagnostic assays for tuberculosis.The development of rapid, robust and high performance point-of-care diagnostics relies on the advancement and combination of various areas of research. We have developed an assay for the detection of multiple mRNA molecules that combines DNA nanotechnology with fluorescent nanomaterials. The core switching mechanism is toehold-mediated strand displacement. We have used fluorescent quantum dots (QDs) as signal transducers in this assay, as they bring many benefits including bright fluorescence and multiplexing abilities. The resulting assay is capable of multiplexed detection of long RNA targets against a high concentration of background non-target RNA, with high sensitivity and specificity and limits of detection in the nanomolar range using only a standard laboratory plate reader. We demonstrate the utility of our QD-based system for the detection of two genes selected from a microarray-derived tuberculosis-specific gene expression signature. Levels of up- and downregulated gene transcripts comprising this signature can be combined to give a disease risk score, making the signature more amenable for use as a diagnostic marker. Our QD-based approach to detect these transcripts could pave the way for novel diagnostic assays for tuberculosis. Electronic supplementary information (ESI) available: Base pair mismatch tuning of CProbes. Binding capacity of the QDs. Theoretical limit of detection (LOD) for the monoplex systems. Kinetics of strand displacement. Kinetics of QProbe-CProbe binding. LOD and saturation point calculations. See DOI: 10.1039/c6nr00484a

Inkjet-printed point-of-care immunoassay on a nanoscale polymer brush enables subpicomolar detection of analytes in blood

NASA Astrophysics Data System (ADS)

Joh, Daniel Y.; Hucknall, Angus M.; Wei, Qingshan; Mason, Kelly A.; Lund, Margaret L.; Fontes, Cassio M.; Hill, Ryan T.; Blair, Rebecca; Zimmers, Zackary; Achar, Rohan K.; Tseng, Derek; Gordan, Raluca; Freemark, Michael; Ozcan, Aydogan; Chilkoti, Ashutosh

2017-08-01

The ELISA is the mainstay for sensitive and quantitative detection of protein analytes. Despite its utility, ELISA is time-consuming, resource-intensive, and infrastructure-dependent, limiting its availability in resource-limited regions. Here, we describe a self-contained immunoassay platform (the “D4 assay”) that converts the sandwich immunoassay into a point-of-care test (POCT). The D4 assay is fabricated by inkjet printing assay reagents as microarrays on nanoscale polymer brushes on glass chips, so that all reagents are “on-chip,” and these chips show durable storage stability without cold storage. The D4 assay can interrogate multiple analytes from a drop of blood, is compatible with a smartphone detector, and displays analytical figures of merit that are comparable to standard laboratory-based ELISA in whole blood. These attributes of the D4 POCT have the potential to democratize access to high-performance immunoassays in resource-limited settings without sacrificing their performance.

Multiple-element semiquantitative analysis of one-milligram geochemical samples by D.C. arc emission spectrography

USGS Publications Warehouse

Rait, N.

1981-01-01

A modified method is described for a 1-mg sample multi-element semiquantitative spectrographic analysis. This method uses a direct-current arc source, carbon instead of graphite electrodes, and an 80% argon-20% oxygen atmosphere instead of air. Although this is a destructive method, an analysis can be made for 68 elements in all mineral and geochemical samples. Carbon electrodes have been an aid in improving the detection limits of many elements. The carbon has a greater resistance to heat conductance and develops a better tip, facilitating sample volatilization and counter balancing the cooling effect of a flow of the argon-oxygen mixture around the anode. Where such an argon-oxygen atmosphere is used instead of air, the cyanogen band lines are greatly diminished in intensity, and thus more spectral lines of analysis elements are available for use; the spectral background is also lower. The main advantage of using the carbon electrode and the 80% argon-20% oxygen atmosphere is the improved detection limits of 36 out of 68 elements. The detection limits remain the same for 23 elements, and are not as good for only nine elements. ?? 1981.

Comparative Study of the Detection of Chromium Content in Rice Leaves by 532 nm and 1064 nm Laser-Induced Breakdown Spectroscopy

PubMed Central

Shen, Tingting; Ye, Lanhan; Kong, Wenwen; Wang, Wei; Liu, Xiaodan

2018-01-01

Fast detection of toxic metals in crops is important for monitoring pollution and ensuring food safety. In this study, laser-induced breakdown spectroscopy (LIBS) was used to detect the chromium content in rice leaves. We investigated the influence of laser wavelength (532 nm and 1064 nm excitation), along with the variations of delay time, pulse energy, and lens-to-sample distance (LTSD), on the signal (sensitivity and stability) and plasma features (temperature and electron density). With the optimized experimental parameters, univariate analysis was used for quantifying the chromium content, and several preprocessing methods (including background normalization, area normalization, multiplicative scatter correction (MSC) transformation and standardized normal variate (SNV) transformation were used to further improve the analytical performance. The results indicated that 532 nm excitation showed better sensitivity than 1064 nm excitation, with a detection limit around two times lower. However, the prediction accuracy for both excitation wavelengths was similar. The best result, with a correlation coefficient of 0.9849, root-mean-square error of 3.89 mg/kg and detection limit of 2.72 mg/kg, was obtained using the SNV transformed signal (Cr I 425.43 nm) induced by 532 nm excitation. The results indicate the inspiring capability of LIBS for toxic metals detection in plant materials. PMID:29463032

The use of Endopep-MS to detect multiple subtypes of botulinum neurotoxins A, B, E, and F

NASA Astrophysics Data System (ADS)

Kalb, Suzanne R.; Smith, Theresa J.; Moura, Hercules; Hill, Karen; Lou, Jianlong; Geren, Isin N.; Garcia-Rodriguez, Consuelo; Marks, James D.; Smith, Leonard A.; Pirkle, James L.; Barr, John R.

2008-12-01

Botulinum neurotoxins (BoNTs) cause the disease botulism, which can be lethal if untreated. Rapid determination of exposure to BoNT is an important public health goal. Previous work in our laboratory focused on the development of Endopep-MS, a mass spectrometry-based endopeptidase method for detecting and differentiating BoNT A-G in buffer and BoNT A, B, E, and F in clinical samples. We introduce here the use of Endopep-MS to detect non-commercial subtypes of BoNT A, B, E, and F which have been associated with botulism outbreaks. We have now tested and successfully detected 15 of the 17 known subtypes of BoNT A, B, E, and F by Endopep-MS. Extraction of BoNT A and B from a complex mixture prior to analysis is accomplished by using monoclonal antibodies specific for the catalytically inactive heavy chain of the toxin. These antibodies have high-binding affinities and do not interfere with the catalytic activity of the light chain resulting in a lower limit of detection for BoNT A and B than previously reported. We also report for the first time limits of detection for BoNT A2, A3, B2, and bivalent B using Endopep-MS.

Copernicus observational searches for OH and H2O in diffuse clouds

NASA Technical Reports Server (NTRS)

Smith, W. H.; Snow, T. P., Jr.

1983-01-01

An intensive search for OH and H2O in the directions of sigma Sco, alpha Cam, and micron Per was undertaken with the Copernicus satellite. Multiple scans were carried out over the wavelength region for the expected absorption features due to the OH D-X and H2O C-X transitions. The feature due to OH was detected marginally towards sigma Sco, and only an upper limit can be given towards alpha Cam. H2O was not detected in any of the stars at the signal level accumulated. The OH abundance towards sigma Sco and the respective lower limits for the OH/H2O ratios are discussed with regard to the extant models for the steady state abundances of OH and H2O, and shown not to be inconsistent with ion-molecule schemes.

Copernicus observational searches for OH and H2O in diffuse clouds

NASA Technical Reports Server (NTRS)

Smith, W. H.; Snow, T. P., Jr.

1979-01-01

An intensive search for OH and H2O in the directions of Sigma Sco, Alpha Cam, and Omicron Per was undertaken with the Copernicus satellite. Multiple scans were carried out over the wavelength region for the expected absorption features due to the OH D-X and H2O C-X transitions. The feature due to OH was possibly detected toward Sigma Sco, and only an upper limit can be given toward Alpha Cam. H2O was not detected in any of the stars at the signal level accumulated. The OH abundance toward Sigma Sco and the respective lower limits for the OH/H2O ratios are discussed with regard to the extant models for the steady-state abundances of OH and H2O, and shown not to be inconsistent with ion-molecule schemes.

New Directions in the Digital Signal Processing of Image Data.

DTIC Science & Technology

1987-05-01

and identify by block number) FIELD GROUP SUB-GROUP Object detection and idLntification 12 01 restoration of photon noise limited imagery 15 04 image...from incomplete information, restoration of blurred images in additive and multiplicative noise , motion analysis with fast hierarchical algorithms...different resolutions. As is well known, the solution to the matched filter problem under additive white noise conditions is the correlation receiver

Combined Acquisition Technique (CAT) for Neuroimaging of Multiple Sclerosis at Low Specific Absorption Rates (SAR)

PubMed Central

Biller, Armin; Choli, Morwan; Blaimer, Martin; Breuer, Felix A.; Jakob, Peter M.; Bartsch, Andreas J.

2014-01-01

Purpose To compare a novel combined acquisition technique (CAT) of turbo-spin-echo (TSE) and echo-planar-imaging (EPI) with conventional TSE. CAT reduces the electromagnetic energy load transmitted for spin excitation. This radiofrequency (RF) burden is limited by the specific absorption rate (SAR) for patient safety. SAR limits restrict high-field MRI applications, in particular. Material and Methods The study was approved by the local Medical Ethics Committee. Written informed consent was obtained from all participants. T2- and PD-weighted brain images of n = 40 Multiple Sclerosis (MS) patients were acquired by CAT and TSE at 3 Tesla. Lesions were recorded by two blinded, board-certificated neuroradiologists. Diagnostic equivalence of CAT and TSE to detect MS lesions was evaluated along with their SAR, sound pressure level (SPL) and sensations of acoustic noise, heating, vibration and peripheral nerve stimulation. Results Every MS lesion revealed on TSE was detected by CAT according to both raters (Cohen’s kappa of within-rater/across-CAT/TSE lesion detection κCAT = 1.00, at an inter-rater lesion detection agreement of κLES = 0.82). CAT reduced the SAR burden significantly compared to TSE (p<0.001). Mean SAR differences between TSE and CAT were 29.0 (±5.7) % for the T2-contrast and 32.7 (±21.9) % for the PD-contrast (expressed as percentages of the effective SAR limit of 3.2 W/kg for head examinations). Average SPL of CAT was no louder than during TSE. Sensations of CAT- vs. TSE-induced heating, noise and scanning vibrations did not differ. Conclusion T2−/PD-CAT is diagnostically equivalent to TSE for MS lesion detection yet substantially reduces the RF exposure. Such SAR reduction facilitates high-field MRI applications at 3 Tesla or above and corresponding protocol standardizations but CAT can also be used to scan faster, at higher resolution or with more slices. According to our data, CAT is no more uncomfortable than TSE scanning. PMID:24608106

In house validation of a high resolution mass spectrometry Orbitrap-based method for multiple allergen detection in a processed model food.

PubMed

Pilolli, Rosa; De Angelis, Elisabetta; Monaci, Linda

2018-02-13

In recent years, mass spectrometry (MS) has been establishing its role in the development of analytical methods for multiple allergen detection, but most analyses are being carried out on low-resolution mass spectrometers such as triple quadrupole or ion traps. In this investigation, performance provided by a high resolution (HR) hybrid quadrupole-Orbitrap™ MS platform for the multiple allergens detection in processed food matrix is presented. In particular, three different acquisition modes were compared: full-MS, targeted-selected ion monitoring with data-dependent fragmentation (t-SIM/dd2), and parallel reaction monitoring. In order to challenge the HR-MS platform, the sample preparation was kept as simple as possible, limited to a 30-min ultrasound-aided protein extraction followed by clean-up with disposable size exclusion cartridges. Selected peptide markers tracing for five allergenic ingredients namely skim milk, whole egg, soy flour, ground hazelnut, and ground peanut were monitored in home-made cookies chosen as model processed matrix. Timed t-SIM/dd2 was found the best choice as a good compromise between sensitivity and accuracy, accomplishing the detection of 17 peptides originating from the five allergens in the same run. The optimized method was validated in-house through the evaluation of matrix and processing effects, recoveries, and precision. The selected quantitative markers for each allergenic ingredient provided quantification of 60-100 μg ingred /g allergenic ingredient/matrix in incurred cookies.

Attribution of hydrological change using the Method of Multiple Working Hypotheses

NASA Astrophysics Data System (ADS)

Harrigan, Shaun

2017-04-01

The methods we have developed for managing our long-term water supply and protection from extreme hydrological events such as droughts and floods have been founded on the assumption that the hydrological cycle operates under natural conditions. However, it increasingly recognised that humans have the potential to induce significant change in almost every component of the hydrological cycle, for example, climate change, land-use change, and river engineering. Statistical detection of change in streamflow, outside that of natural variability, is an important scientific endeavour, but it does not tell us anything about the drivers of change. Attribution is the process of establishing the most likely cause(s) of a detected change - the why. Attribution is complex due to the integrated nature of streamflow and the proliferation of multiple possible drivers. It is perhaps this complexity, combined with few proven theoretical approaches to this problem in hydrology that has led to others to call for "more efforts and scientific rigour" (Merz et al., 2012). It is easier to limit the cause of a detected change to a single driver, or use simple correlation analysis alone as evidence of causation. It is convenient when the direction of a change in streamflow is consistent with what is expected from a well-known driver such as climate change. Over a century ago, Thomas Chamberlin argued these types of issues were common in many disciplines given how the scientific method is approached in general. His 1890 article introduces the Method of Multiple Working Hypotheses (MMWH) in an attempt to limit our confirmation bias and strives for increased objectivity. This presentation will argue that the MMWH offers an attractive theoretical approach to the attribution of hydrological change in modern hydrology as demonstrated through a case study of a well-documented change point in streamflow within the Boyne Catchment in Ireland. Further Reading Chamberlin, T. C.: The Method of Multiple Working Hypotheses, Science (old series), 15(366), 92-96, doi:10.1126/science.ns-15.366.92, 1890. Harrigan, S., Murphy, C., Hall, J., Wilby, R. L. and Sweeney, J.: Attribution of detected changes in streamflow using multiple working hypotheses, Hydrol. Earth Syst. Sci., 18(5), 1935-1952, doi:10.5194/hess-18-1935-2014, 2014. Merz, B., Vorogushyn, S., Uhlemann, S., Delgado, J. and Hundecha, Y.: HESS Opinions "More efforts and scientific rigour are needed to attribute trends in flood time series," Hydrol. Earth Syst. Sci., 16(5), 1379-1387, doi:10.5194/hess-16-1379-2012, 2012.

Visual performance on detection tasks with double-targets of the same and different difficulty.

PubMed

Chan, Alan H S; Courtney, Alan J; Ma, C W

2002-10-20

This paper reports a study of measurement of horizontal visual sensitivity limits for 16 subjects in single-target and double-targets detection tasks. Two phases of tests were conducted in the double-targets task; targets of the same difficulty were tested in phase one while targets of different difficulty were tested in phase two. The range of sensitivity for the double-targets test was found to be smaller than that for single-target in both the same and different target difficulty cases. The presence of another target was found to affect performance to a marked degree. Interference effect of the difficult target on detection of the easy one was greater than that of the easy one on the detection of the difficult one. Performance decrement was noted when correct percentage detection was plotted against eccentricity of target in both the single-target and double-targets tests. Nevertheless, the non-significant correlation found between the performance for the two tasks demonstrated that it was impossible to predict quantitatively ability for detection of double targets from the data for single targets. This indicated probable problems in generalizing data for single target visual lobes to those for multiple targets. Also lobe area values obtained from measurements using a single-target task cannot be applied in a mathematical model for situations with multiple occurrences of targets.

Detection of mercury(II) ions using colorimetric gold nanoparticles on paper-based analytical devices.

PubMed

Chen, Guan-Hua; Chen, Wei-Yu; Yen, Yu-Chun; Wang, Chia-Wei; Chang, Huan-Tsung; Chen, Chien-Fu

2014-07-15

An on-field colorimetric sensing strategy employing gold nanoparticles (AuNPs) and a paper-based analytical platform was investigated for mercury ion (Hg(2+)) detection at water sources. By utilizing thymine-Hg(2+)-thymine (T-Hg(2+)-T) coordination chemistry, label-free detection oligonucleotide sequences were attached to unmodified gold nanoparticles to provide rapid mercury ion sensing without complicated and time-consuming thiolated or other costly labeled probe preparation processes. Not only is this strategy's sensing mechanism specific toward Hg(2+), rather than other metal ions, but also the conformational change in the detection oligonucleotide sequences introduces different degrees of AuNP aggregation that causes the color of AuNPs to exhibit a mixture variance. To eliminate the use of sophisticated equipment and minimize the power requirement for data analysis and transmission, the color variance of multiple detection results were transferred and concentrated on cellulose-based paper analytical devices, and the data were subsequently transmitted for the readout and storage of results using cloud computing via a smartphone. As a result, a detection limit of 50 nM for Hg(2+) spiked pond and river water could be achieved. Furthermore, multiple tests could be performed simultaneously with a 40 min turnaround time. These results suggest that the proposed platform possesses the capability for sensitive and high-throughput on-site mercury pollution monitoring in resource-constrained settings.

Electrochemical immunosensor with nanocellulose-Au composite assisted multiple signal amplification for detection of avian leukosis virus subgroup J.

PubMed

Liu, Chao; Dong, Jing; Waterhouse, Geoffrey I N; Cheng, Ziqiang; Ai, Shiyun

2018-03-15

A sensitive sandwich-type electrochemical immunosensor was developed for the detection of avian leukosis virus subgroup J (ALV-J), which benefitted from multiple signal amplification involving graphene-perylene-3,4,9,10-tetracarboxylic acid nanocomposites (GR-PTCA), nanocellulose-Au NP composites (NC-Au) and the alkaline phosphatase (ALP) catalytic reaction. GR-PTCA nanocomposites on glassy carbon electrodes served as the immunosensor platform. Due to their excellent electrical conductivity and abundant polycarboxylic sites, the GR-PTCA nanocomposites allowed fast electron transfer and good immobilization of primary antibodies, thereby affording a strong immunosensor signal in the presence of ALV-J. The detected signal could be further amplified by the introduction of NC-Au composites as a carrier of secondary antibodies (Ab 2 ) and by harnessing the catalytic properties of Au and ALP. Under optimized testing conditions, the electrochemical immunosensor displayed excellent analytical performance for the detection of ALV-J, showing a linear current response from 10 2.08 to 10 4.0 TCID 50 /mL (TCID 50 : 50% tissue culture infective dose) with a low detection limit of 10 1.98 TCID 50 /mL (S/N = 3). In addition to high sensitivity, the immunosensor showed very good selectivity, reproducibility and operational stability, demonstrating potential application for the quantitative detection of ALV-J in clinical diagnosis. Copyright © 2017 Elsevier B.V. All rights reserved.

Rapid gas chromatography with flame photometric detection of multiple organophosphorus pesticides in Salvia miltiorrhizae after ultrasonication assisted one-step extraction.

PubMed

Zhang, Shanshan; Liu, Xiaofei; Qin, Jia'an; Yang, Meihua; Zhao, Hongzheng; Wang, Yong; Guo, Weiying; Ma, Zhijie; Kong, Weijun

2017-11-15

A simple and rapid gas chromatography-flame photometric detection (GC-FPD) method was developed for the determination of 12 organophosphorus pesticides (OPPs) in Salvia miltiorrhizae by using ultrasonication assisted one-step extraction (USAE) without any clean-up steps. Some crucial parameters such as type of extraction solvent were optimized to improve the method performance for trace analysis. Any clean-up steps were negligent as no interferences were detected in the GC-FPD chromatograms for sensitive detection. Under the optimized conditions, limits of detection (LODs) and quantitation (LOQs) for all pesticides were in the range of 0.001-0.002mg/kg and 0.002-0.01mg/kg and 0.002-0.01mg/kg, respectively, which were all below the regulatory maximum residue limits suggested. RSDs for method precision (intra- and inter-day variations) were lower than 6.8% in approval with international regulations. Average recovery rates for all pesticides at three fortification levels (0.5, 1.0 and 5.0mg/kg) were in the range of 71.2-101.0% with relative standard deviations (RSDs) <13%. The developed method was evaluated for its feasibility in the simultaneous pre-concentration and determination of 12 OPPs in 32 batches of real S. miltiorrhizae samples. Only one pesticide (dimethoate) out of the 12 targets was simultaneously detected in four samples at concentrations of 0.016-0.02mg/kg. Dichlorvos and omethoate were found in the same sample from Sichuan province at 0.004 and 0.027mg/kg, respectively. Malathion and monocrotophos were determined in the other two samples at 0.014 and 0.028mg/kg, respectively. All the positive samples were confirmed by LC-MS/MS. The simple, reliable and rapid USAE-GC-FPD method with many advantages over traditional techniques would be preferred for trace analysis of multiple pesticides in more complex matrices. Copyright © 2017 Elsevier B.V. All rights reserved.

Swept-source based, single-shot, multi-detectable velocity range Doppler optical coherence tomography

PubMed Central

Meemon, Panomsak; Rolland, Jannick P.

2010-01-01

Phase-Resolved Doppler Optical Coherence Tomography (PR-DOCT) allows visualization and characterization of the location, direction, velocity, and profile of flow activity embedded in a static sample structure. The detectable Velocity Dynamic Range (VDR) of each particular PR-DOCT system is governed by a detectable Doppler phase shift, a flow angle, and an acquisition time interval used to determine the Doppler phase shift. In general, the lower boundary of the detectable Doppler phase shift is limited by the phase stability of the system, while the upper boundary is limited by the π phase ambiguity. For a given range of detectable Doppler phase shift, shortening the acquisition duration will increase not only the maximum detectable velocity but unfortunately also the minimum detectable velocity, which may lead to the invisibility of a slow flow. In this paper, we present an alternative acquisition scheme for PR-DOCT that extends the lower limit of the velocity dynamic range, while maintaining the maximum detectable velocity, hence increasing the overall VDR of PR-DOCT system. The essence of the approach is to implement a technique of multi-scale measurement to simultaneously acquire multiple VDRs in a single measurement. We demonstrate an example of implementation of the technique in a dual VDR DOCT, where two Doppler maps having different detectable VDRs were simultaneously detected, processed, and displayed in real time. One was a fixed VDR DOCT capable of measuring axial velocity of up to 10.9 mm/s without phase unwrapping. The other was a variable VDR DOCT capable of adjusting its detectable VDR to reveal slow flow information down to 11.3 μm/s. The technique is shown to effectively extend the overall detectable VDR of the PR-DOCT system. Examples of real time Doppler imaging of an African frog tadpole are demonstrated using the dual-VDR DOCT system. PMID:21258521

Edge-directed inference for microaneurysms detection in digital fundus images

NASA Astrophysics Data System (ADS)

Huang, Ke; Yan, Michelle; Aviyente, Selin

2007-03-01

Microaneurysms (MAs) detection is a critical step in diabetic retinopathy screening, since MAs are the earliest visible warning of potential future problems. A variety of algorithms have been proposed for MAs detection in mass screening. Different methods have been proposed for MAs detection. The core technology for most of existing methods is based on a directional mathematical morphological operation called "Top-Hat" filter that requires multiple filtering operations at each pixel. Background structure, uneven illumination and noise often cause confusion between MAs and some non-MA structures and limits the applicability of the filter. In this paper, a novel detection framework based on edge directed inference is proposed for MAs detection. The candidate MA regions are first delineated from the edge map of a fundus image. Features measuring shape, brightness and contrast are extracted for each candidate MA region to better exclude false detection from true MAs. Algorithmic analysis and empirical evaluation reveal that the proposed edge directed inference outperforms the "Top-Hat" based algorithm in both detection accuracy and computational speed.

THE MURCHISON WIDEFIELD ARRAY 21 cm POWER SPECTRUM ANALYSIS METHODOLOGY

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

Jacobs, Daniel C.; Beardsley, A. P.; Bowman, Judd D.

2016-07-10

We present the 21 cm power spectrum analysis approach of the Murchison Widefield Array Epoch of Reionization project. In this paper, we compare the outputs of multiple pipelines for the purpose of validating statistical limits cosmological hydrogen at redshifts between 6 and 12. Multiple independent data calibration and reduction pipelines are used to make power spectrum limits on a fiducial night of data. Comparing the outputs of imaging and power spectrum stages highlights differences in calibration, foreground subtraction, and power spectrum calculation. The power spectra found using these different methods span a space defined by the various tradeoffs between speed,more » accuracy, and systematic control. Lessons learned from comparing the pipelines range from the algorithmic to the prosaically mundane; all demonstrate the many pitfalls of neglecting reproducibility. We briefly discuss the way these different methods attempt to handle the question of evaluating a significant detection in the presence of foregrounds.« less

Simultaneous Determination of Oxysterols, Cholesterol and 25-Hydroxy-Vitamin D3 in Human Plasma by LC-UV-MS

PubMed Central

Narayanaswamy, Rohini; Iyer, Vignesh; Khare, Prachi; Bodziak, Mary Lou; Badgett, Darlene; Zivadinov, Robert; Weinstock-Guttman, Bianca; Rideout, Todd C.; Ramanathan, Murali; Browne, Richard W.

2015-01-01

Background Oxysterols are promising biomarkers of neurodegenerative diseases that are linked with cholesterol and vitamin D metabolism. There is an unmet need for methods capable of sensitive, and simultaneous quantitation of multiple oxysterols, vitamin D and cholesterol pathway biomarkers. Methods A method for simultaneous determination of 5 major oxysterols, 25-hydroxy vitamin D3 and cholesterol in human plasma was developed. Total oxysterols were prepared by room temperature saponification followed by solid phase extraction from plasma spiked with deuterated internal standards. Oxysterols were resolved by reverse phase HPLC using a methanol/water/0.1% formic acid gradient. Oxysterols and 25-hydroxy vitamin D3 were detected with atmospheric pressure chemical ionization mass spectrometry in positive ion mode; in-series photodiode array detection at 204nm was used for cholesterol. Method validation studies were performed. Oxysterol levels in 220 plasma samples from healthy control subjects, multiple sclerosis and other neurological disorders patients were quantitated. Results Our method quantitated 5 oxysterols, cholesterol and 25-hydroxy vitamin D3 from 200 μL plasma in 35 minutes. Recoveries were >85% for all analytes and internal standards. The limits of detection were 3-10 ng/mL for oxysterols and 25-hydroxy vitamin D3 and 1 μg/mL for simultaneous detection of cholesterol. Analytical imprecision was <10 %CV for 24(S)-, 25-, 27-, 7α-hydroxycholesterol (HC) and cholesterol and ≤15 % for 7-keto-cholesterol. Multiple Sclerosis and other neurological disorder patients had lower 27-hydroxycholesterol levels compared to controls whereas 7α-hydroxycholesterol was lower specifically in Multiple Sclerosis. Conclusion The method is suitable for measuring plasma oxysterols levels in human health and disease. Analysis of human plasma indicates that the oxysterol, bile acid precursors 7α-hydroxycholesterol and 27-hydroxycholesterol are lower in Multiple Sclerosis and may serve as potential biomarkers of disease. PMID:25875771

Detection of Salmonella spp. in veterinary samples by combining selective enrichment and real-time PCR.

PubMed

Goodman, Laura B; McDonough, Patrick L; Anderson, Renee R; Franklin-Guild, Rebecca J; Ryan, James R; Perkins, Gillian A; Thachil, Anil J; Glaser, Amy L; Thompson, Belinda S

2017-11-01

Rapid screening for enteric bacterial pathogens in clinical environments is essential for biosecurity. Salmonella found in veterinary hospitals, particularly Salmonella enterica serovar Dublin, can pose unique challenges for culture and testing because of its poor growth. Multiple Salmonella serovars including Dublin are emerging threats to public health given increasing prevalence and antimicrobial resistance. We adapted an automated food testing method to veterinary samples and evaluated the performance of the method in a variety of matrices including environmental samples ( n = 81), tissues ( n = 52), feces ( n = 148), and feed ( n = 29). A commercial kit was chosen as the basis for this approach in view of extensive performance characterizations published by multiple independent organizations. A workflow was established for efficiently and accurately testing veterinary matrices and environmental samples by use of real-time PCR after selective enrichment in Rappaport-Vassiliadis soya (RVS) medium. Using this method, the detection limit for S. Dublin improved by 100-fold over subculture on selective agars (eosin-methylene blue, brilliant green, and xylose-lysine-deoxycholate). Overall, the procedure was effective in detecting Salmonella spp. and provided next-day results.

Genetics of human neural tube defects

PubMed Central

Greene, Nicholas D.E.; Stanier, Philip; Copp, Andrew J.

2009-01-01

Neural tube defects (NTDs) are common, severe congenital malformations whose causation involves multiple genes and environmental factors. Although more than 200 genes are known to cause NTDs in mice, there has been rather limited progress in delineating the molecular basis underlying most human NTDs. Numerous genetic studies have been carried out to investigate candidate genes in cohorts of patients, with particular reference to those that participate in folate one-carbon metabolism. Although the homocysteine remethylation gene MTHFR has emerged as a risk factor in some human populations, few other consistent findings have resulted from this approach. Similarly, attention focused on the human homologues of mouse NTD genes has contributed only limited positive findings to date, although an emerging association between genes of the non-canonical Wnt (planar cell polarity) pathway and NTDs provides candidates for future studies. Priorities for the next phase of this research include: (i) larger studies that are sufficiently powered to detect significant associations with relatively minor risk factors; (ii) analysis of multiple candidate genes in groups of well-genotyped individuals to detect possible gene–gene interactions; (iii) use of high throughput genomic technology to evaluate the role of copy number variants and to detect ‘private’ and regulatory mutations, neither of which have been studied to date; (iv) detailed analysis of patient samples stratified by phenotype to enable, for example, hypothesis-driven testing of candidates genes in groups of NTDs with specific defects of folate metabolism, or in groups of fetuses with well-defined phenotypes such as craniorachischisis. PMID:19808787

Multiple symbol partially coherent detection of MPSK

NASA Technical Reports Server (NTRS)

Simon, M. K.; Divsalar, D.

1992-01-01

It is shown that by using the known (or estimated) value of carrier tracking loop signal to noise ratio (SNR) in the decision metric, it is possible to improve the error probability performance of a partially coherent multiple phase-shift-keying (MPSK) system relative to that corresponding to the commonly used ideal coherent decision rule. Using a maximum-likeihood approach, an optimum decision metric is derived and shown to take the form of a weighted sum of the ideal coherent decision metric (i.e., correlation) and the noncoherent decision metric which is optimum for differential detection of MPSK. The performance of a receiver based on this optimum decision rule is derived and shown to provide continued improvement with increasing length of observation interval (data symbol sequence length). Unfortunately, increasing the observation length does not eliminate the error floor associated with the finite loop SNR. Nevertheless, in the limit of infinite observation length, the average error probability performance approaches the algebraic sum of the error floor and the performance of ideal coherent detection, i.e., at any error probability above the error floor, there is no degradation due to the partial coherence. It is shown that this limiting behavior is virtually achievable with practical size observation lengths. Furthermore, the performance is quite insensitive to mismatch between the estimate of loop SNR (e.g., obtained from measurement) fed to the decision metric and its true value. These results may be of use in low-cost Earth-orbiting or deep-space missions employing coded modulations.

Pulse patterning effect in optical pulse division multiplexing for flexible single wavelength multiple access optical network

NASA Astrophysics Data System (ADS)

Jung, Sun-Young; Kim, Chang-Hun; Han, Sang-Kook

2018-05-01

A demand for high spectral efficiency requires multiple access within a single wavelength, but the uplink signals are significantly degraded because of optical beat interference (OBI) in intensity modulation/direct detection system. An optical pulse division multiplexing (OPDM) technique was proposed that could effectively reduce the OBI via a simple method as long as near-orthogonality is satisfied, but the condition was strict, and thus, the number of multiplexing units was very limited. We propose pulse pattern enhanced OPDM (e-OPDM) to reduce the OBI and improve the flexibility in multiple access within a single wavelength. The performance of the e-OPDM and patterning effect are experimentally verified after 23-km single mode fiber transmission. By employing pulse patterning in OPDM, the tight requirement was relaxed by extending the optical delay dynamic range. This could support more number of access with reduced OBI, which could eventually enhance a multiple access function.

Development of a Machine Vision Method for the Monitoring of Laying Hens and Detection of Multiple Nest Occupations

PubMed Central

Redaelli, Veronica; Luzi, Fabio; Mitchell, Malcolm; Bontempo, Valentino; Cattaneo, Donata; Dell’Orto, Vittorio; Savoini, Giovanni

2018-01-01

Free range systems can improve the welfare of laying hens. However, the access to environmental resources can be partially limited by social interactions, feeding of hens, and productivity, can be not stable and damaging behaviors, or negative events, can be observed more frequently than in conventional housing systems. In order to reach a real improvement of the hens’ welfare the study of their laying performances and behaviors is necessary. With this purpose, many systems have been developed. However, most of them do not detect a multiple occupation of the nest negatively affecting the accuracy of data collected. To overcome this issue, a new “nest-usage-sensor” was developed and tested. It was based on the evaluation of thermografic images, as acquired by a thermo-camera, and the performing of patter recognitions on images acquired from the nest interior. The sensor was setup with a “Multiple Nest Occupation Threshold” of 796 colored pixels and a template of triangular shape and sizes of 43 × 33 pixels (high per base). It was tested through an experimental nesting system where 10 hens were reared for a month. Results showed that the evaluation of thermografic images could increase the detection performance of a multiple occupation of the nest and to apply an image pattern recognition technique could allow for counting the number of hens in the nest in case of a multiple occupation. As a consequence, the accuracy of data collected in studies on laying performances and behaviors of hens, reared in a free-range housing system, could result to be improved. PMID:29303981

The cumulative burden of double-stranded DNA virus detection after allogeneic HCT is associated with increased mortality.

PubMed

Hill, Joshua A; Mayer, Bryan T; Xie, Hu; Leisenring, Wendy M; Huang, Meei-Li; Stevens-Ayers, Terry; Milano, Filippo; Delaney, Colleen; Sorror, Mohamed L; Sandmaier, Brenda M; Nichols, Garrett; Zerr, Danielle M; Jerome, Keith R; Schiffer, Joshua T; Boeckh, Michael

2017-04-20

Strategies to prevent active infection with certain double-stranded DNA (dsDNA) viruses after allogeneic hematopoietic cell transplantation (HCT) are limited by incomplete understanding of their epidemiology and clinical impact. We retrospectively tested weekly plasma samples from allogeneic HCT recipients at our center from 2007 to 2014. We used quantitative PCR to test for cytomegalovirus, BK polyomavirus, human herpesvirus 6B, HHV-6A, adenovirus, and Epstein-Barr virus between days 0 and 100 post-HCT. We evaluated risk factors for detection of multiple viruses and association of viruses with mortality through day 365 post-HCT with Cox models. Among 404 allogeneic HCT recipients, including 125 cord blood, 125 HLA-mismatched, and 154 HLA-matched HCTs, detection of multiple viruses was common through day 100: 90% had ≥1, 62% had ≥2, 28% had ≥3, and 5% had 4 or 5 viruses. Risk factors for detection of multiple viruses included cord blood or HLA-mismatched HCT, myeloablative conditioning, and acute graft-versus-host disease ( P values < .01). Absolute lymphocyte count of <200 cells/mm 3 was associated with greater virus exposure on the basis of the maximum cumulative viral load area under the curve (AUC) ( P = .054). The maximum cumulative viral load AUC was the best predictor of early (days 0-100) and late (days 101-365) overall mortality (adjusted hazard ratio [aHR] = 1.36, 95% confidence interval [CI] [1.25, 1.49], and aHR = 1.04, 95% CI [1.0, 1.08], respectively) after accounting for immune reconstitution and graft-versus-host disease. In conclusion, detection of multiple dsDNA viruses was frequent after allogeneic HCT and had a dose-dependent association with increased mortality. These data suggest opportunities to improve outcomes with better antiviral strategies. © 2017 by The American Society of Hematology.

Full-band TDM-OPDMA for OBI-reduced simultaneous multiple access in a single-wavelength optical access network.

PubMed

Jung, Sun-Young; Kim, Chang-Hun; Han, Sang-Kook

2018-05-14

Simultaneous multiple access (MA) within a single wavelength can increase the data rate and split ratio in a passive optical network while optical beat interference (OBI) becomes serious in the uplink. Previous techniques to reduce OBI were limited by their complexity and lack of extendibility; as well, bandwidth allocation among MA signals is needed for single photo diode (PD) detection. We proposed and experimentally demonstrated full-band optical pulse division multiplexing-based MA (OPDMA) in an optical access network, which can effectively reduce OBI with extendibility and fully utilize frequency resources of optical modulator without bandwidth allocation in a single-wavelength MA.

An integrated data model to estimate spatiotemporal occupancy, abundance, and colonization dynamics

USGS Publications Warehouse

Williams, Perry J.; Hooten, Mevin B.; Womble, Jamie N.; Esslinger, George G.; Bower, Michael R.; Hefley, Trevor J.

2017-01-01

Ecological invasions and colonizations occur dynamically through space and time. Estimating the distribution and abundance of colonizing species is critical for efficient management or conservation. We describe a statistical framework for simultaneously estimating spatiotemporal occupancy and abundance dynamics of a colonizing species. Our method accounts for several issues that are common when modeling spatiotemporal ecological data including multiple levels of detection probability, multiple data sources, and computational limitations that occur when making fine-scale inference over a large spatiotemporal domain. We apply the model to estimate the colonization dynamics of sea otters (Enhydra lutris) in Glacier Bay, in southeastern Alaska.

Determination of methyl mercury by aqueous phase Eehylation, followed by gas chromatographic separation with cold vapor atomic fluorescence detection

USGS Publications Warehouse

De Wild, John F.; Olsen, Mark L.; Olund, Shane D.

2002-01-01

A recent national sampling of streams in the United States revealed low methyl mercury concentrations in surface waters. The resulting median and mean concentrations, calculated from 104 samples, were 0.06 nanograms per liter (ng/L) and 0.15 ng/L, respectively. This level of methyl mercury in surface water in the United States has created a need for analytical techniques capable of detecting sub-nanogram per liter concentrations. In an attempt to create a U.S. Geological Survey approved method, the Wisconsin District Mercury Laboratory has adapted a distillation/ethylation/ gas-phase separation method with cold vapor atomic fluorescence spectroscopy detection for the determination of methyl mercury in filtered and unfiltered waters. This method is described in this report. Based on multiple analyses of surface water and ground-water samples, a method detection limit of 0.04 ng/L was established. Precision and accuracy were evaluated for the method using both spiked and unspiked ground-water and surface-water samples. The percent relative standard deviations ranged from 10.2 to 15.6 for all analyses at all concentrations. Average recoveries obtained for the spiked matrices ranged from 88.8 to 117 percent. The precision and accuracy ranges are within the acceptable method-performance limits. Considering the demonstrated detection limit, precision, and accuracy, the method is an effective means to quantify methyl mercury in waters at or below environmentally relevant concentrations

Assessing assay agreement estimation for multiple left-censored data: a multiple imputation approach.

PubMed

Lapidus, Nathanael; Chevret, Sylvie; Resche-Rigon, Matthieu

2014-12-30

Agreement between two assays is usually based on the concordance correlation coefficient (CCC), estimated from the means, standard deviations, and correlation coefficient of these assays. However, such data will often suffer from left-censoring because of lower limits of detection of these assays. To handle such data, we propose to extend a multiple imputation approach by chained equations (MICE) developed in a close setting of one left-censored assay. The performance of this two-step approach is compared with that of a previously published maximum likelihood estimation through a simulation study. Results show close estimates of the CCC by both methods, although the coverage is improved by our MICE proposal. An application to cytomegalovirus quantification data is provided. Copyright © 2014 John Wiley & Sons, Ltd.

Quantum enhanced superresolution microscopy (Conference Presentation)

NASA Astrophysics Data System (ADS)

Oron, Dan; Tenne, Ron; Israel, Yonatan; Silberberg, Yaron

2017-02-01

Far-field optical microscopy beyond the Abbe diffraction limit, making use of nonlinear excitation (e.g. STED), or temporal fluctuations in fluorescence (PALM, STORM, SOFI) is already a reality. In contrast, overcoming the diffraction limit using non-classical properties of light is very difficult to achieve due to the fragility of quantum states of light. Here, we experimentally demonstrate superresolution microscopy based on quantum properties of light naturally emitted by fluorophores used as markers in fluorescence microscopy. Our approach is based on photon antibunching, the tendency of fluorophores to emit photons one by one rather than in bursts. Although a distinctively quantum phenomenon, antibunching is readily observed in most common fluorophores even at room temperature. This nonclassical resource can be utilized directly to enhance the imaging resolution, since the non-classical far-field intensity correlations induced by antibunching carry high spatial frequency information on the spatial distribution of emitters. Detecting photon statistics simultaneously in the entire field of view, we were able to detect non-classical correlations of the second and third order, and reconstructed images with resolution significantly beyond the diffraction limit. Alternatively, we demonstrate the utilization of antibunching for augmenting the capabilities of localization-based superresolution imaging in the presence of multiple emitters, using a novel detector comprised of an array of single photon detectors connected to a densely packed fiber bundle. These features allow us to enhance the spatial and temporal resolution with which multiple emitters can be imaged compared with other techniques that rely on CCD cameras.

Habitat models to predict wetland bird occupancy influenced by scale, anthropogenic disturbance, and imperfect detection

USGS Publications Warehouse

Glisson, Wesley J.; Conway, Courtney J.; Nadeau, Christopher P.; Borgmann, Kathi L.

2017-01-01

Understanding species–habitat relationships for endangered species is critical for their conservation. However, many studies have limited value for conservation because they fail to account for habitat associations at multiple spatial scales, anthropogenic variables, and imperfect detection. We addressed these three limitations by developing models for an endangered wetland bird, Yuma Ridgway's rail (Rallus obsoletus yumanensis), that examined how the spatial scale of environmental variables, inclusion of anthropogenic disturbance variables, and accounting for imperfect detection in validation data influenced model performance. These models identified associations between environmental variables and occupancy. We used bird survey and spatial environmental data at 2473 locations throughout the species' U.S. range to create and validate occupancy models and produce predictive maps of occupancy. We compared habitat-based models at three spatial scales (100, 224, and 500 m radii buffers) with and without anthropogenic disturbance variables using validation data adjusted for imperfect detection and an unadjusted validation dataset that ignored imperfect detection. The inclusion of anthropogenic disturbance variables improved the performance of habitat models at all three spatial scales, and the 224-m-scale model performed best. All models exhibited greater predictive ability when imperfect detection was incorporated into validation data. Yuma Ridgway's rail occupancy was negatively associated with ephemeral and slow-moving riverine features and high-intensity anthropogenic development, and positively associated with emergent vegetation, agriculture, and low-intensity development. Our modeling approach accounts for common limitations in modeling species–habitat relationships and creating predictive maps of occupancy probability and, therefore, provides a useful framework for other species.

Damage detection of an in-service condensation pipeline joint

NASA Astrophysics Data System (ADS)

Briand, Julie; Rezaei, Davood; Taheri, Farid

2010-04-01

The early detection of damage in structural or mechanical systems is of vital importance. With early detection, the damage may be repaired before the integrity of the system is jeopardized, resulting in monetary losses, loss of life or limb, and environmental impacts. Among the various types of structural health monitoring techniques, vibration-based methods are of significant interest since the damage location does not need to be known beforehand, making it a more versatile approach. The non-destructive damage detection method used for the experiments herein is a novel vibration-based method which uses an index called the EMD Energy Damage Index, developed with the aim of providing improved qualitative results compared to those methods currently available. As part of an effort to establish the integrity and limitation of this novel damage detection method, field testing was completed on a mechanical pipe joint on a condensation line, located in the physical plant of Dalhousie University. Piezoceramic sensors, placed at various locations around the joint were used to monitor the free vibration of the pipe imposed through the use of an impulse hammer. Multiple damage progression scenarios were completed, each having a healthy state and multiple damage cases. Subsequently, the recorded signals from the healthy and damaged joint were processed through the EMD Energy Damage Index developed in-house in an effort to detect the inflicted damage. The proposed methodology successfully detected the inflicted damages. In this paper, the effects of impact location, sensor location, frequency bandwidth, intrinsic mode functions, and boundary conditions are discussed.

Optofluidic devices for biomolecule sensing and multiplexing

NASA Astrophysics Data System (ADS)

Ozcelik, Damla

Optofluidics which integrates photonics and microfluidics, has led to highly compact, sensitive and adaptable biomedical sensors. Optofluidic biosensors based on liquid-core anti-resonant reflecting optical waveguides (LC-ARROWs), have proven to be a highly sensitive, portable, and reconfigurable platform for fluorescence spectroscopy and detection of single biomolecules such as proteins, nucleic acids, and virus particles. However, continued improvements in sensitivity remain a major goal as we approach the ultimate limit of detecting individual bio-particles labeled by single or few fluorophores. Additionally, the ability to simultaneously detect and identify multiple biological particles or biomarkers is one of the key requirements for molecular diagnostic tests. The compactness and adaptability of these platforms can further be advanced by introducing tunability, integrating off-chip components, designing reconfigurable and customizable devices, which makes these platforms very good candidates for many different applications. The goal of this thesis was to introduce new elements in these LC-ARROW optofluidics platforms that provide major enhancements in their functionality, making them more sensitive, compact, customizable and multiplexed. First, a novel integrated tunable spectral filter that achieves effective elimination of background noise on the ARROW platform was demonstrated. A unique dual liquid-core design enabled the independent multi-wavelength tuning of the spectral filter by adjusting the refractive index and chemical properties of the liquid. In order to enhance the detection sensitivity of the platform, Y-splitter waveguides were integrated to create multiple excitation spots for each target molecule. A powerful signal processing algorithm was used to analyze the data to improve the signal-to-noise ratio (SNR) of the collected data. Next, the design, optimization and characterization of the Y-splitter waveguides are presented; and single influenza virus detection with an improved SNR was demonstrated using this platform. Finally, multiplexing capacity is introduced to the ARROW detection platform by integrating multi-mode interference (MMI) waveguides. MMI waveguides create wavelength dependent multiple excitation spots at the excitation region, allowing the spectral multiplexed detection of multiple different target molecules based on the excitation pattern, without the need for additional spectral filters. Successful spectral multiplexed detection of three different types of influenza viruses is achieved by using separate wavelengths and combination of wavelengths. This multiplexing capacity is further enhanced by taking advantage of the spatial properties of the MMI pattern, designing triple liquid-core waveguides that intersect the MMI waveguide in different locations. Furthermore, the spectral and spatial multiplexing capacities are combined in these triple liquid-core MMI platforms, allowing these devices to distinguish multiple different targets and samples simultaneously.

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

PubMed

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

2018-06-13

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

Directly detecting isospin-violating dark matter

NASA Astrophysics Data System (ADS)

Kelso, Chris; Kumar, Jason; Marfatia, Danny; Sandick, Pearl

2018-03-01

We consider the prospects for multiple dark matter direct detection experiments to determine if the interactions of a dark matter candidate are isospin-violating. We focus on theoretically well-motivated examples of isospin-violating dark matter (IVDM), including models in which dark matter interactions with nuclei are mediated by a dark photon, a Z , or a squark. We determine that the best prospects for distinguishing IVDM from the isospin-invariant scenario arise in the cases of dark photon-or Z -mediated interactions, and that the ideal experimental scenario would consist of large exposure xenon- and neon-based detectors. If such models just evade current direct detection limits, then one could distinguish such models from the standard isospin-invariant case with two detectors with of order 100 ton-year exposure.

A Portable Immunoassay Platform for Multiplexed Detection of Biotoxins in Clinical and Environmental Samples

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

Koh, Chung-Yan; Piccini, Matthew Ernest; Schaff, Ulrich Y.

Multiple cases of attempted bioterrorism events using biotoxins have highlighted the urgent need for tools capable of rapid screening of suspect samples in the field (e.g., mailroom and public events). We present a portable microfluidic device capable of analyzing environmental (e.g., white powder), food (e.g., milk) and clinical (e.g., blood) samples for multiplexed detection of biotoxins. The device is rapid (<15-30 min sample-to-answer), sensitive (< 0.08 pg/mL detection limit for botulinum toxin), multiplexed (up to 64 parallel assays) and capable of analyzing small volume samples (< 20 μL total sample input). The immunoassay approach (SpinDx) is based on binding ofmore » toxins in a sample to antibody-laden capture particles followed by sedimentation of particles through a density-media in a microfluidic disk and quantification using a laser-induced fluorescence detector. A direct, blinded comparison with a gold standard ELISA revealed a 5-fold more sensitive detection limit for botulinum toxin while requiring 250-fold less sample volume and a 30 minute assay time with a near unity correlation. A key advantage of the technique is its compatibility with a variety of sample matrices with no additional sample preparation required. Ultrasensitive quantification has been demonstrated from direct analysis of multiple clinical, environmental and food samples, including white powder, whole blood, saliva, salad dressing, whole milk, peanut butter, half and half, honey, and canned meat. We believe that this device can met an urgent need in screening both potentially exposed people as well as suspicious samples in mail-rooms, airports, public sporting venues and emergency rooms. The general-purpose immunodiagnostics device can also find applications in screening of infectious and systemic diseases or serve as a lab device for conducting rapid immunoassays.« less

Detection of Multiple Stationary Humans Using UWB MIMO Radar.

PubMed

Liang, Fulai; Qi, Fugui; An, Qiang; Lv, Hao; Chen, Fuming; Li, Zhao; Wang, Jianqi

2016-11-16

Remarkable progress has been achieved in the detection of single stationary human. However, restricted by the mutual interference of multiple humans (e.g., strong sidelobes of the torsos and the shadow effect), detection and localization of the multiple stationary humans remains a huge challenge. In this paper, ultra-wideband (UWB) multiple-input and multiple-output (MIMO) radar is exploited to improve the detection performance of multiple stationary humans for its multiple sight angles and high-resolution two-dimensional imaging capacity. A signal model of the vital sign considering both bi-static angles and attitude angle of the human body is firstly developed, and then a novel detection method is proposed to detect and localize multiple stationary humans. In this method, preprocessing is firstly implemented to improve the signal-to-noise ratio (SNR) of the vital signs, and then a vital-sign-enhanced imaging algorithm is presented to suppress the environmental clutters and mutual affection of multiple humans. Finally, an automatic detection algorithm including constant false alarm rate (CFAR), morphological filtering and clustering is implemented to improve the detection performance of weak human targets affected by heavy clutters and shadow effect. The simulation and experimental results show that the proposed method can get a high-quality image of multiple humans and we can use it to discriminate and localize multiple adjacent human targets behind brick walls.

Detection of Multiple Stationary Humans Using UWB MIMO Radar

PubMed Central

Liang, Fulai; Qi, Fugui; An, Qiang; Lv, Hao; Chen, Fuming; Li, Zhao; Wang, Jianqi

2016-01-01

Remarkable progress has been achieved in the detection of single stationary human. However, restricted by the mutual interference of multiple humans (e.g., strong sidelobes of the torsos and the shadow effect), detection and localization of the multiple stationary humans remains a huge challenge. In this paper, ultra-wideband (UWB) multiple-input and multiple-output (MIMO) radar is exploited to improve the detection performance of multiple stationary humans for its multiple sight angles and high-resolution two-dimensional imaging capacity. A signal model of the vital sign considering both bi-static angles and attitude angle of the human body is firstly developed, and then a novel detection method is proposed to detect and localize multiple stationary humans. In this method, preprocessing is firstly implemented to improve the signal-to-noise ratio (SNR) of the vital signs, and then a vital-sign-enhanced imaging algorithm is presented to suppress the environmental clutters and mutual affection of multiple humans. Finally, an automatic detection algorithm including constant false alarm rate (CFAR), morphological filtering and clustering is implemented to improve the detection performance of weak human targets affected by heavy clutters and shadow effect. The simulation and experimental results show that the proposed method can get a high-quality image of multiple humans and we can use it to discriminate and localize multiple adjacent human targets behind brick walls. PMID:27854356

Traffic light detection and intersection crossing using mobile computer vision

NASA Astrophysics Data System (ADS)

Grewei, Lynne; Lagali, Christopher

2017-05-01

The solution for Intersection Detection and Crossing to support the development of blindBike an assisted biking system for the visually impaired is discussed. Traffic light detection and intersection crossing are key needs in the task of biking. These problems are tackled through the use of mobile computer vision, in the form of a mobile application on an Android phone. This research builds on previous Traffic Light detection algorithms with a focus on efficiency and compatibility on a resource-limited platform. Light detection is achieved through blob detection algorithms utilizing training data to detect patterns of Red, Green and Yellow in complex real world scenarios where multiple lights may be present. Also, issues of obscurity and scale are addressed. Safe Intersection crossing in blindBike is also discussed. This module takes a conservative "assistive" technology approach. To achieve this blindBike use's not only the Android device but, an external bike cadence Bluetooth/Ant enabled sensor. Real world testing results are given and future work is discussed.

Single-Plex Quantitative Assays for the Detection and Quantification of Most Pneumococcal Serotypes

PubMed Central

Chochua, Sopio; Satzke, Catherine; Dunne, Eileen M.; Mulholland, Kim; Klugman, Keith P.

2015-01-01

Streptococcus pneumoniae globally kills more children than any other infectious disease every year. A prerequisite for pneumococcal disease and transmission is colonization of the nasopharynx. While the introduction of pneumococcal conjugate vaccines has reduced the burden of pneumococcal disease, understanding the impact of vaccination on nasopharyngeal colonization has been hampered by the lack of sensitive quantitative methods for the detection of >90 known S. pneumoniae serotypes. In this work, we developed 27 new quantitative (q)PCR reactions and optimized 26 for a total of 53 qPCR reactions targeting pneumococcal serotypes or serogroups, including all vaccine types. Reactions proved to be target-specific with a limit of detection of 2 genome equivalents per reaction. Given the number of probes required for these assays and their unknown shelf-life, the stability of cryopreserved reagents was evaluated. Our studies demonstrate that two-year cryopreserved probes had similar limit of detection as freshly-diluted probes. Moreover, efficiency and limit of detection of 1-month cryopreserved, ready-to-use, qPCR reaction mixtures were similar to those of freshly prepared mixtures. Using these reactions, our proof-of-concept studies utilizing nasopharyngeal samples (N=30) collected from young children detected samples containing ≥2 serotypes/serogroups. Samples colonized by multiple serotypes/serogroups always had a serotype that contributes at least 50% of the pneumococcal load. In addition, a molecular approach called S6-q(PCR)2 was developed and proven to individually detect and quantify epidemiologically-important serogroup 6 strains including 6A, 6B, 6C and 6D. This technology will be useful for epidemiological studies, diagnostic platforms and to study the pneumobiome. PMID:25798884

Simultaneous Detection of Multiple Disease States.

DTIC Science & Technology

1990-02-14

analytes to be assayed in a panel forma And due to its simplicity, OIA has been demonstrated to be generally applicable to a wide range of testing...into two distinct formats on the basis of signal generation: visual and instrumented. In both cases monocrystalline silicon wafers are employed as...Due to the limited surface area available on the monocrystalline silicon wafers, attention must be paid to efficient immobilization to ensure

Comments on the New Tesla Electromagnetics. Part I. Discrepancies in Present EM Theory,

DTIC Science & Technology

1982-01-01

reality. In this reality superluminal velocity, multiple universes, travel back and forth in time, higher dimensions, variation of all "fundamental...logic -- fitted to the photon interaction by vector light as the fundamental observation mechanism -- is incapable of describing or modeling this more...fundamental reality. Using scalar waves and scalar interactions as much subtler, far less limited * observation/detection mechanisms , we must have a

Application of data fusion technology based on D-S evidence theory in fire detection

NASA Astrophysics Data System (ADS)

Cai, Zhishan; Chen, Musheng

2015-12-01

Judgment and identification based on single fire characteristic parameter information in fire detection is subject to environmental disturbances, and accordingly its detection performance is limited with the increase of false positive rate and false negative rate. The compound fire detector employs information fusion technology to judge and identify multiple fire characteristic parameters in order to improve the reliability and accuracy of fire detection. The D-S evidence theory is applied to the multi-sensor data-fusion: first normalize the data from all sensors to obtain the normalized basic probability function of the fire occurrence; then conduct the fusion processing using the D-S evidence theory; finally give the judgment results. The results show that the method meets the goal of accurate fire signal identification and increases the accuracy of fire alarm, and therefore is simple and effective.

A review on several key problems of standoff trace explosives detection by optical-related technology

NASA Astrophysics Data System (ADS)

Chen, Zhibin; Xiao, Cheng; Xiao, Wenjian; Qin, Mengze; Liu, Xianhong

2016-01-01

To prevent tragic disasters caused by terror acts and warfare threats, security check personnel must be capable of discovering, distinguishing and eliminating the explosives at multiple circumstances. Standoff technology for the remote detection of explosives and their traces on contaminated surfaces is a research field that has become a heightened priority in recent years for homeland security and counter-terrorism applications. There has been a huge increase in research within this area, the improvement of standoff trace explosives detection by optical-related technology. This paper provides a consolidation of information relating to recent advances in several key problems of, without being limited to one specific research area or explosive type. Working laser wavelength of detection system is discussed. Generation and collection of explosives spectra signal are summarized. Techniques for analysing explosives spectra signal are summed up.

Identification of faulty sensor using relative partial decomposition via independent component analysis

NASA Astrophysics Data System (ADS)

Wang, Z.; Quek, S. T.

2015-07-01

Performance of any structural health monitoring algorithm relies heavily on good measurement data. Hence, it is necessary to employ robust faulty sensor detection approaches to isolate sensors with abnormal behaviour and exclude the highly inaccurate data in the subsequent analysis. The independent component analysis (ICA) is implemented to detect the presence of sensors showing abnormal behaviour. A normalized form of the relative partial decomposition contribution (rPDC) is proposed to identify the faulty sensor. Both additive and multiplicative types of faults are addressed and the detectability illustrated using a numerical and an experimental example. An empirical method to establish control limits for detecting and identifying the type of fault is also proposed. The results show the effectiveness of the ICA and rPDC method in identifying faulty sensor assuming that baseline cases are available.

Rapid multiple immunofluorescent staining for the simultaneous detection of cytokeratin and vimentin in the cytology of canine tumors.

PubMed

Sawa, Mariko; Yabuki, Akira; Kohyama, Moeko; Miyoshi, Noriaki; Yamato, Osamu

2018-06-01

Immunocytochemistry (ICC) is utilized as an advanced technique in veterinary cytology. In tumor diagnosis, cytokeratin and vimentin are markers used to distinguish the origin of tumor cells. Standard enzyme-based ICC has limitations in clinical use; and therefore, more convenient and reliable methods are needed. The purpose of this study was to develop a rapid multiple immunofluorescent (RMIF) detection method for dual cytokeratin and vimentin staining on cytology slides in dogs. Air-dried smear samples from solid tumors and sediments of pleural effusions were prepared from dogs (n = 14) that were admitted to the Veterinary Teaching Hospital, Kagoshima University, Japan. Mouse monoclonal anti-human cytokeratin (AE1/AE3) and rabbit monoclonal anti-human vimentin (SP20) antibodies were used as primary antibodies, followed by staining with Alexa Fluor-conjugated secondary antibodies. Staining using the RMIF method was compared with enzyme-based ICC staining. Rapid multiple immunofluorescent immunostaining was clear and specific in the evaluated smears, whereas the enzyme-based ICC showed nonspecific signals. By using the RMIF staining method, epithelial cells, mesenchymal cells, and mesothelial cells could be classified on a single smear of a pleural effusion. In smears of lymph nodes with epithelial tumor metastases, the RMIF method successfully detected metastatic epithelial tumor cells. The RMIF method might be a useful tool for diagnostic cytology in veterinary medicine. © 2018 American Society for Veterinary Clinical Pathology.

Enucleation and limited pancreatic resection provide long-term cure for insulinoma in multiple endocrine neoplasia type 1.

PubMed

Bartsch, Detlef K; Albers, Max; Knoop, Richard; Kann, Peter H; Fendrich, Volker; Waldmann, Jens

2013-01-01

To assess the characteristics and long-term outcome after surgery in patients with multiple endocrine neoplasia type 1 (MEN1)-associated insulinoma. Retrospective analysis of prospectively collected data of MEN1 patients with organic hyperinsulinism at a tertiary referral center. Thirteen (17%) of 74 patients with MEN1 had organic hyperinsulinism. The median age at diagnosis was 27 (range 9-48) years. In 7 patients insulinoma was the first manifestation of the syndrome. All patients had at least one pancreatic neuroendocrine neoplasm (pNEN) upon imaging, including CT, MRI or endoscopic ultrasonography. Seven patients had solitary lesions upon imaging, 4 patients had one dominant tumor with coexisting multiple small pNENs, and 2 patients had multiple lesions without dominance. Eight patients had limited resections (1 segmental resection, 7 enucleations), 4 subtotal distal pancreatectomies, and 1 patient a partial duodenopancreatectomy. There was no postoperative mortality. Six patients experienced complications, including pancreatic fistula in 5 patients. Pathological examination revealed median three (range 1-14) macro-pNENs sized between 6 and 40 mm, and a total of 14 potentially benign insulinomas were detected in the 13 patients. After median follow-up of 156 months, only 1 patient developed recurrent hyperinsulinism after initial enucleation. Twelve patients developed new pNENs in the pancreatic remnant and 4 patients underwent reoperations (3 for metastatic ZES, 1 for recurrent hyperinsulinism). One of 5 patients with an initial extended pancreatic resection developed insulin-dependent diabetes mellitus. Enucleation and limited resection provide long-term cure for MEN1 insulinoma in patients with solitary or dominant tumors. Subtotal distal pancreatectomy should thus be preserved for patients with multiple pNENs without dominance given the risk of exocrine and endocrine pancreas insufficiency in the mostly young patients. © 2013 S. Karger AG, Basel.

Nonlinear mechanical resonators for ultra-sensitive mass detection

NASA Astrophysics Data System (ADS)

Datskos, P. G.; Lavrik, N. V.

2014-10-01

The fundamental sensitivity limit of an appropriately scaled down mechanical resonator can approach one atomic mass unit when only thermal noise is present in the system. However, operation of such nanoscale mechanical resonators is very challenging due to minuteness of their oscillation amplitudes and presence of multiple noise sources in real experimental environments. In order to surmount these challenges, we use microscale cantilever resonators driven to large amplitudes, far beyond their nonlinear instability onset. Our experiments show that such a nonlinear cantilever resonator, described analytically as a Duffing oscillator, has mass sensing performance comparable to that of much smaller resonators operating in a linear regime. We demonstrate femtogram level mass sensing that relies on a bifurcation point tracking that does not require any complex readout means. Our approaches enable straightforward detection of mass changes that are near the fundamental limit imposed by thermo-mechanical fluctuations.

Electrochemical Detection in Stacked Paper Networks.

PubMed

Liu, Xiyuan; Lillehoj, Peter B

2015-08-01

Paper-based electrochemical biosensors are a promising technology that enables rapid, quantitative measurements on an inexpensive platform. However, the control of liquids in paper networks is generally limited to a single sample delivery step. Here, we propose a simple method to automate the loading and delivery of liquid samples to sensing electrodes on paper networks by stacking multiple layers of paper. Using these stacked paper devices (SPDs), we demonstrate a unique strategy to fully immerse planar electrodes by aqueous liquids via capillary flow. Amperometric measurements of xanthine oxidase revealed that electrochemical sensors on four-layer SPDs generated detection signals up to 75% higher compared with those on single-layer paper devices. Furthermore, measurements could be performed with minimal user involvement and completed within 30 min. Due to its simplicity, enhanced automation, and capability for quantitative measurements, stacked paper electrochemical biosensors can be useful tools for point-of-care testing in resource-limited settings. © 2015 Society for Laboratory Automation and Screening.

Mixed-effects location and scale Tobit joint models for heterogeneous longitudinal data with skewness, detection limits, and measurement errors.

PubMed

Lu, Tao

2017-01-01

The joint modeling of mean and variance for longitudinal data is an active research area. This type of model has the advantage of accounting for heteroscedasticity commonly observed in between and within subject variations. Most of researches focus on improving the estimating efficiency but ignore many data features frequently encountered in practice. In this article, we develop a mixed-effects location scale joint model that concurrently accounts for longitudinal data with multiple features. Specifically, our joint model handles heterogeneity, skewness, limit of detection, measurement errors in covariates which are typically observed in the collection of longitudinal data from many studies. We employ a Bayesian approach for making inference on the joint model. The proposed model and method are applied to an AIDS study. Simulation studies are performed to assess the performance of the proposed method. Alternative models under different conditions are compared.

Copernicus observational searches for OH and H/sub 2/O in diffuse clouds

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

Smith, W.H.; Snow, T.P. Jr.

1979-03-01

An intensive search for OH and H/sub 2/O in the directions of sigma Sco, ..cap alpha.. Cam, and omicron Per was undertaken with the Copernicus satellite. Multiple scans were carried out over the wavelength region for the expected absorption features due to the OH D--X and H/sub 2/O C--X transitions. The feature due to OH was possibly detected toward sigma Sco, and only an upper limit can be given toward ..cap alpha.. Cam. H/sub 2/O was not detected in any of the stars at the signal level accumulated. The OH abundance toward sigma Sco and the respective lower limits formore » the OH/H/sub 2/O ratios are discussed with regard to the extant models for the steady-state abundances of OH and H/sub 2/O, and shown not to be inconsistent with ion-molecule schemes.« less

Heterogeneity, histological features and DNA ploidy in oral carcinoma by image-based analysis.

PubMed

Diwakar, N; Sperandio, M; Sherriff, M; Brown, A; Odell, E W

2005-04-01

Oral squamous carcinomas appear heterogeneous on DNA ploidy analysis. However, this may be partly a result of sample dilution or the detection limit of techniques. The aim of this study was to determine whether oral squamous carcinomas are heterogeneous for ploidy status using image-based ploidy analysis and to determine whether ploidy status correlates with histological parameters. Multiple samples from 42 oral squamous carcinomas were analysed for DNA ploidy using an image-based system and scored for histological parameters. 22 were uniformly aneuploid, 1 uniformly tetraploid and 3 uniformly diploid. 16 appeared heterogeneous but only 8 appeared to be genuinely heterogeneous when minor ploidy histogram peaks were taken into account. Ploidy was closely related to nuclear pleomorphism but not differentiation. Sample variation, detection limits and diagnostic criteria account for much of the ploidy heterogeneity observed. Confident diagnosis of diploid status in an oral squamous cell carcinoma requires a minimum of 5 samples.

Statistical analysis of water-quality data containing multiple detection limits II: S-language software for nonparametric distribution modeling and hypothesis testing

USGS Publications Warehouse

Lee, L.; Helsel, D.

2007-01-01

Analysis of low concentrations of trace contaminants in environmental media often results in left-censored data that are below some limit of analytical precision. Interpretation of values becomes complicated when there are multiple detection limits in the data-perhaps as a result of changing analytical precision over time. Parametric and semi-parametric methods, such as maximum likelihood estimation and robust regression on order statistics, can be employed to model distributions of multiply censored data and provide estimates of summary statistics. However, these methods are based on assumptions about the underlying distribution of data. Nonparametric methods provide an alternative that does not require such assumptions. A standard nonparametric method for estimating summary statistics of multiply-censored data is the Kaplan-Meier (K-M) method. This method has seen widespread usage in the medical sciences within a general framework termed "survival analysis" where it is employed with right-censored time-to-failure data. However, K-M methods are equally valid for the left-censored data common in the geosciences. Our S-language software provides an analytical framework based on K-M methods that is tailored to the needs of the earth and environmental sciences community. This includes routines for the generation of empirical cumulative distribution functions, prediction or exceedance probabilities, and related confidence limits computation. Additionally, our software contains K-M-based routines for nonparametric hypothesis testing among an unlimited number of grouping variables. A primary characteristic of K-M methods is that they do not perform extrapolation and interpolation. Thus, these routines cannot be used to model statistics beyond the observed data range or when linear interpolation is desired. For such applications, the aforementioned parametric and semi-parametric methods must be used.

Optimization of a sample processing protocol for recovery of Bacillus anthracis spores from soil

USGS Publications Warehouse

Silvestri, Erin E.; Feldhake, David; Griffin, Dale; Lisle, John T.; Nichols, Tonya L.; Shah, Sanjiv; Pemberton, A; Schaefer III, Frank W

2016-01-01

Following a release of Bacillus anthracis spores into the environment, there is a potential for lasting environmental contamination in soils. There is a need for detection protocols for B. anthracis in environmental matrices. However, identification of B. anthracis within a soil is a difficult task. Processing soil samples helps to remove debris, chemical components, and biological impurities that can interfere with microbiological detection. This study aimed to optimize a previously used indirect processing protocol, which included a series of washing and centrifugation steps. Optimization of the protocol included: identifying an ideal extraction diluent, variation in the number of wash steps, variation in the initial centrifugation speed, sonication and shaking mechanisms. The optimized protocol was demonstrated at two laboratories in order to evaluate the recovery of spores from loamy and sandy soils. The new protocol demonstrated an improved limit of detection for loamy and sandy soils over the non-optimized protocol with an approximate matrix limit of detection at 14 spores/g of soil. There were no significant differences overall between the two laboratories for either soil type, suggesting that the processing protocol will be robust enough to use at multiple laboratories while achieving comparable recoveries.

Detecting target changes in multiple object tracking with peripheral vision: More pronounced eccentricity effects for changes in form than in motion.

PubMed

Vater, Christian; Kredel, Ralf; Hossner, Ernst-Joachim

2017-05-01

In the current study, dual-task performance is examined with multiple-object tracking as a primary task and target-change detection as a secondary task. The to-be-detected target changes in conditions of either change type (form vs. motion; Experiment 1) or change salience (stop vs. slowdown; Experiment 2), with changes occurring at either near (5°-10°) or far (15°-20°) eccentricities (Experiments 1 and 2). The aim of the study was to test whether changes can be detected solely with peripheral vision. By controlling for saccades and computing gaze distances, we could show that participants used peripheral vision to monitor the targets and, additionally, to perceive changes at both near and far eccentricities. Noticeably, gaze behavior was not affected by the actual target change. Detection rates as well as response times generally varied as a function of change condition and eccentricity, with faster detections for motion changes and near changes. However, in contrast to the effects found for motion changes, sharp declines in detection rates and increased response times were observed for form changes as a function of the eccentricities. This result can be ascribed to properties of the visual system, namely to the limited spatial acuity in the periphery and the comparably receptive motion sensitivity of peripheral vision. These findings show that peripheral vision is functional for simultaneous target monitoring and target-change detection as saccadic information suppression can be avoided and covert attention can be optimally distributed to all targets. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Hybridization chain reaction amplification for highly sensitive fluorescence detection of DNA with dextran coated microarrays.

PubMed

Chao, Jie; Li, Zhenhua; Li, Jing; Peng, Hongzhen; Su, Shao; Li, Qian; Zhu, Changfeng; Zuo, Xiaolei; Song, Shiping; Wang, Lianhui; Wang, Lihua

2016-07-15

Microarrays of biomolecules hold great promise in the fields of genomics, proteomics, and clinical assays on account of their remarkably parallel and high-throughput assay capability. However, the fluorescence detection used in most conventional DNA microarrays is still limited by sensitivity. In this study, we have demonstrated a novel universal and highly sensitive platform for fluorescent detection of sequence specific DNA at the femtomolar level by combining dextran-coated microarrays with hybridization chain reaction (HCR) signal amplification. Three-dimensional dextran matrix was covalently coated on glass surface as the scaffold to immobilize DNA recognition probes to increase the surface binding capacity and accessibility. DNA nanowire tentacles were formed on the matrix surface for efficient signal amplification by capturing multiple fluorescent molecules in a highly ordered way. By quantifying microscopic fluorescent signals, the synergetic effects of dextran and HCR greatly improved sensitivity of DNA microarrays, with a detection limit of 10fM (1×10(5) molecules). This detection assay could recognize one-base mismatch with fluorescence signals dropped down to ~20%. This cost-effective microarray platform also worked well with samples in serum and thus shows great potential for clinical diagnosis. Copyright © 2016 Elsevier B.V. All rights reserved.

Multiplexed detection of anthrax-related toxin genes.

PubMed

Moser, Michael J; Christensen, Deanna R; Norwood, David; Prudent, James R

2006-02-01

Simultaneous analysis of three targets in three colors on any real-time polymerase chain reaction (PCR) instrument would increase the flexibility of real-time PCR. For the detection of Bacillus strains that can cause inhalation anthrax-related illness, this ability would be valuable because two plasmids confer virulence, and internal positive controls are needed to monitor the testing in cases lacking target-specific signals. Using a real-time PCR platform called MultiCode-RTx, multiple assays were developed that specifically monitor the presence of Bacillus anthracis-specific virulence plasmid-associated genes. In particular for use on LightCycler-1, two triplex RTx systems demonstrated high sensitivity with limits of detection nearing single-copy levels for both plasmids. Specificity was established using a combination of Ct values and correct amplicon melting temperatures. All reactions were further verified by detection of an internal positive control. For these two triplex RTx assays, the analytical detection limit was one to nine plasmid copy equivalents, 100% analytical specificity with a 95% confidence interval (CI) of 9%, and 100% analytical sensitivity with a CI of 2%. Although further testing using clinical or environmental samples will be required to assess diagnostic sensitivity and specificity, the RTx platform achieves similar results to those of probe-based real-time systems.

Role of CD81 and CD58 in minimal residual disease detection in pediatric B lymphoblastic leukemia.

PubMed

Tsitsikov, E; Harris, M H; Silverman, L B; Sallan, S E; Weinberg, O K

2018-06-01

Minimal residual disease (MRD) in B lymphoblastic leukemia has been demonstrated to be a powerful predictor of clinical outcome in numerous studies in both children and adults. In this study, we evaluated 86 pediatric patients with both diagnostic and remission flow cytometry studies and compared expression of CD81, CD58, CD19, CD34, CD20, and CD38 in the detection of MRD. We evaluated 86 patients with B lymphoblastic leukemia who had both diagnostic studies and remission studies for the presence of MRD using multicolor flow cytometry. We established our detection limit for identifying abnormal lymphoblasts using serial dilutions. We also compared flow cytometry findings with molecular MRD detection in a subset of patients. We found that we can resolve differences between hematogones and lymphoblasts in 85 of 86 cases using a combination of CD45, CD19, CD34, CD10, CD20, CD38, CD58, and CD81. Our detection limit using flow cytometry is 0.002% for detecting a population of abnormal B lymphoblasts. Comparison with MRD assessment by molecular methods showed a high concordance rate with flow cytometry findings. Our study highlights importance of using multiple markers to detect MRD in B lymphoblastic leukemia. Our findings indicate that including both CD58 and CD81 markers in addition to CD19, CD34, CD20, CD38, and CD10 are helpful in MRD detection by flow cytometry. © 2018 John Wiley & Sons Ltd.

Comparison of procedures for correction of matrix interferences in the analysis of soils by ICP-OES with CCD detection

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

Sadler, D.A.; Sun, F.; Littlejohn, D.

1995-12-31

ICP-OES is a useful technique for multi-element analysis of soils. However, as a number of elements are present in relatively high concentrations, matrix interferences can occur and examples have been widely reported. The availability of CCD detectors has increased the opportunities for rapid multi-element, multi-wave-length determination of elemental concentrations in soils and other environmental samples. As the composition of soils from industrial sites can vary considerably, especially when taken from different pit horizons, procedures are required to assess the extent of interferences and correct the effects, on a simultaneous multi-element basis. In single element analysis, plasma operating conditions can sometimesmore » be varied to minimize or even remove multiplicative interferences. In simultaneous multi-element analysis, the scope for this approach may be limited, depending on the spectrochemical characteristics of the emitting analyte species. Matrix matching, by addition of major sample components to the analyte calibrant solutions, can be used to minimize inaccuracies. However, there are also limitations to this procedure, when the sample composition varies significantly. Multiplicative interference effects can also be assessed by a {open_quotes}single standard addition{close_quotes} of each analyte to the sample solution and the information obtained may be used to correct the analyte concentrations determined directly. Each of these approaches has been evaluated to ascertain the best procedure for multi-element analysis of industrial soils by ICP-OES with CCD detection at multiple wavelengths. Standard reference materials and field samples have been analyzed to illustrate the efficacy of each procedure.« less

Simultaneous detection of multiple biomarkers by means of SERS on polymer nanopillar gold arrays

NASA Astrophysics Data System (ADS)

Morasso, Carlo; Picciolini, Silvia; Mehn, Dora; Pellacani, Paola; Frangolho, Ana; Marchesini, Gerardo; Vanna, Renzo; Gualerzi, Alice; Bedoni, Marzia; Marabelli, Franco; Gramatica, Furio

2016-03-01

The detection of biomarkers by means of Surface Enhanced Raman Spectroscopy (SERS) is foreseen to became a very important tool in the clinical practice because of its excellent sensitivity and potential for the simultaneous detection of multiple biomarkers. In the present paper we describe how it was possible to build a sensor for the detection of genetic biomarkers involved in acute myeloid leukemia. The assay is based on the use of a specifically designed SERS substrate made of a 2D crystal structure of polymeric pillars embedded in a gold layer. This substrate is characterized by good enhancing properties coupled with an excellent homogeneity. The SERS substrate was conjugated with DNA probes complementary to a target sequence and used in a sandwich assay with gold nanoparticles labeled with a second DNA probe and a Raman reporter. The so developed assay allowed the detection of a leukemia biomarker (WT1 gene) and an housekeeping gene with low picomolar sensitivity. At last, we optimized the assay in order to tackle one of the main limitations of SERS based assay: the loss of signal that is observed when the Raman spectra are collected in liquid. Combining a preferential functionalization on the polymeric pillars with a different height of the polymer pillars from the gold layer the assay demonstrated its effectiveness even when measured in buffer.

Deep Whole-Genome Sequencing to Detect Mixed Infection of Mycobacterium tuberculosis

PubMed Central

Gan, Mingyu; Liu, Qingyun; Yang, Chongguang; Gao, Qian; Luo, Tao

2016-01-01

Mixed infection by multiple Mycobacterium tuberculosis (MTB) strains is associated with poor treatment outcome of tuberculosis (TB). Traditional genotyping methods have been used to detect mixed infections of MTB, however, their sensitivity and resolution are limited. Deep whole-genome sequencing (WGS) has been proved highly sensitive and discriminative for studying population heterogeneity of MTB. Here, we developed a phylogenetic-based method to detect MTB mixed infections using WGS data. We collected published WGS data of 782 global MTB strains from public database. We called homogeneous and heterogeneous single nucleotide variations (SNVs) of individual strains by mapping short reads to the ancestral MTB reference genome. We constructed a phylogenomic database based on 68,639 homogeneous SNVs of 652 MTB strains. Mixed infections were determined if multiple evolutionary paths were identified by mapping the SNVs of individual samples to the phylogenomic database. By simulation, our method could specifically detect mixed infections when the sequencing depth of minor strains was as low as 1× coverage, and when the genomic distance of two mixed strains was as small as 16 SNVs. By applying our methods to all 782 samples, we detected 47 mixed infections and 45 of them were caused by locally endemic strains. The results indicate that our method is highly sensitive and discriminative for identifying mixed infections from deep WGS data of MTB isolates. PMID:27391214

Comparison of a novel passive sampler to standard water-column sampling for organic contaminants associated with wastewater effluents entering a New Jersey stream

USGS Publications Warehouse

Alvarez, D.A.; Stackelberg, P.E.; Petty, J.D.; Huckins, J.N.; Furlong, E.T.; Zaugg, S.D.; Meyer, M.T.

2005-01-01

Four water samples collected using standard depth and width water-column sampling methodology were compared to an innovative passive, in situ, sampler (the polar organic chemical integrative sampler or POCIS) for the detection of 96 organic wastewater-related contaminants (OWCs) in a stream that receives agricultural, municipal, and industrial wastewaters. Thirty-two OWCs were identified in POCIS extracts whereas 9-24 were identified in individual water-column samples demonstrating the utility of POCIS for identifying contaminants whose occurrence are transient or whose concentrations are below routine analytical detection limits. Overall, 10 OWCs were identified exclusively in the POCIS extracts and only six solely identified in the water-column samples, however, repetitive water samples taken using the standard method during the POCIS deployment period required multiple trips to the sampling site and an increased number of samples to store, process, and analyze. Due to the greater number of OWCs detected in the POCIS extracts as compared to individual water-column samples, the ease of performing a single deployment as compared to collecting and processing multiple water samples, the greater mass of chemical residues sequestered, and the ability to detect chemicals which dissipate quickly, the passive sampling technique offers an efficient and effective alternative for detecting OWCs in our waterways for wastewater contaminants.

Automated visual inspection of brake shoe wear

NASA Astrophysics Data System (ADS)

Lu, Shengfang; Liu, Zhen; Nan, Guo; Zhang, Guangjun

2015-10-01

With the rapid development of high-speed railway, the automated fault inspection is necessary to ensure train's operation safety. Visual technology is paid more attention in trouble detection and maintenance. For a linear CCD camera, Image alignment is the first step in fault detection. To increase the speed of image processing, an improved scale invariant feature transform (SIFT) method is presented. The image is divided into multiple levels of different resolution. Then, we do not stop to extract the feature from the lowest resolution to the highest level until we get sufficient SIFT key points. At that level, the image is registered and aligned quickly. In the stage of inspection, we devote our efforts to finding the trouble of brake shoe, which is one of the key components in brake system on electrical multiple units train (EMU). Its pre-warning on wear limitation is very important in fault detection. In this paper, we propose an automatic inspection approach to detect the fault of brake shoe. Firstly, we use multi-resolution pyramid template matching technology to fast locate the brake shoe. Then, we employ Hough transform to detect the circles of bolts in brake region. Due to the rigid characteristic of structure, we can identify whether the brake shoe has a fault. The experiments demonstrate that the way we propose has a good performance, and can meet the need of practical applications.

The Novel Multiple Inner Primers-Loop-Mediated Isothermal Amplification (MIP-LAMP) for Rapid Detection and Differentiation of Listeria monocytogenes.

PubMed

Wang, Yi; Wang, Yan; Ma, Aijing; Li, Dongxun; Luo, Lijuan; Liu, Dongxin; Hu, Shoukui; Jin, Dong; Liu, Kai; Ye, Changyun

2015-12-03

Here, a novel model of loop-mediated isothermal amplification (LAMP), termed multiple inner primers-LAMP (MIP-LAMP), was devised and successfully applied to detect Listeria monocytogenes. A set of 10 specific MIP-LAMP primers, which recognized 14 different regions of target gene, was designed to target a sequence in the hlyA gene. The MIP-LAMP assay efficiently amplified the target element within 35 min at 63 °C and was evaluated for sensitivity and specificity. The templates were specially amplified in the presence of the genomic DNA from L. monocytogenes. The limit of detection (LoD) of MIP-LAMP assay was 62.5 fg/reaction using purified L. monocytogenes DNA. The LoD for DNA isolated from serial dilutions of L. monocytogenes cells in buffer and in milk corresponded to 2.4 CFU and 24 CFU, respectively. The amplified products were analyzed by real-time monitoring of changes in turbidity, and visualized by adding Loop Fluorescent Detection Reagent (FD), or as a ladder-like banding pattern on gel electrophoresis. A total of 48 pork samples were investigated for L. monocytogenes by the novel MIP-LAMP method, and the diagnostic accuracy was shown to be 100% when compared to the culture-biotechnical method. In conclusion, the MIP-LAMP methodology was demonstrated to be a reliable, sensitive and specific tool for rapid detection of L. monocytogenes strains.

[Arthroscopy-guided fracture management. Ankle joint and calcaneus].

PubMed

Schoepp, C; Rixen, D

2013-04-01

Arthroscopic fracture management of the ankle and calcaneus requires a differentiated approach. The aim is to minimize surgical soft tissue damage and to visualize anatomical fracture reduction arthroscopically. Moreover, additional cartilage damage can be detected and treated. The arthroscopic approach is limited by deep impressions of the joint surface needing cancellous bone grafting, by multiple fracture lines on the articular side and by high-grade soft tissue damage. An alternative to the minimally invasive arthroscopic approach is open arthroscopic reduction in conventional osteosynthesis. This facilitates correct assessment of surgical reduction of complex calcaneal fractures, otherwise remaining non-anatomical reduction might not be fluoroscopically detected during surgery.

Invited Review Article: Pump-probe microscopy.

PubMed

Fischer, Martin C; Wilson, Jesse W; Robles, Francisco E; Warren, Warren S

2016-03-01

Multiphoton microscopy has rapidly gained popularity in biomedical imaging and materials science because of its ability to provide three-dimensional images at high spatial and temporal resolution even in optically scattering environments. Currently the majority of commercial and home-built devices are based on two-photon fluorescence and harmonic generation contrast. These two contrast mechanisms are relatively easy to measure but can access only a limited range of endogenous targets. Recent developments in fast laser pulse generation, pulse shaping, and detection technology have made accessible a wide range of optical contrasts that utilize multiple pulses of different colors. Molecular excitation with multiple pulses offers a large number of adjustable parameters. For example, in two-pulse pump-probe microscopy, one can vary the wavelength of each excitation pulse, the detection wavelength, the timing between the excitation pulses, and the detection gating window after excitation. Such a large parameter space can provide much greater molecular specificity than existing single-color techniques and allow for structural and functional imaging without the need for exogenous dyes and labels, which might interfere with the system under study. In this review, we provide a tutorial overview, covering principles of pump-probe microscopy and experimental setup, challenges associated with signal detection and data processing, and an overview of applications.

Estimate of within population incremental selection through branch imbalance in lineage trees

PubMed Central

Liberman, Gilad; Benichou, Jennifer I.C.; Maman, Yaakov; Glanville, Jacob; Alter, Idan; Louzoun, Yoram

2016-01-01

Incremental selection within a population, defined as limited fitness changes following mutation, is an important aspect of many evolutionary processes. Strongly advantageous or deleterious mutations are detected using the synonymous to non-synonymous mutations ratio. However, there are currently no precise methods to estimate incremental selection. We here provide for the first time such a detailed method and show its precision in multiple cases of micro-evolution. The proposed method is a novel mixed lineage tree/sequence based method to detect within population selection as defined by the effect of mutations on the average number of offspring. Specifically, we propose to measure the log of the ratio between the number of leaves in lineage trees branches following synonymous and non-synonymous mutations. The method requires a high enough number of sequences, and a large enough number of independent mutations. It assumes that all mutations are independent events. It does not require of a baseline model and is practically not affected by sampling biases. We show the method's wide applicability by testing it on multiple cases of micro-evolution. We show that it can detect genes and inter-genic regions using the selection rate and detect selection pressures in viral proteins and in the immune response to pathogens. PMID:26586802

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

Fischer, Martin C., E-mail: Martin.Fischer@duke.edu; Wilson, Jesse W.; Robles, Francisco E.

Multiphoton microscopy has rapidly gained popularity in biomedical imaging and materials science because of its ability to provide three-dimensional images at high spatial and temporal resolution even in optically scattering environments. Currently the majority of commercial and home-built devices are based on two-photon fluorescence and harmonic generation contrast. These two contrast mechanisms are relatively easy to measure but can access only a limited range of endogenous targets. Recent developments in fast laser pulse generation, pulse shaping, and detection technology have made accessible a wide range of optical contrasts that utilize multiple pulses of different colors. Molecular excitation with multiple pulsesmore » offers a large number of adjustable parameters. For example, in two-pulse pump-probe microscopy, one can vary the wavelength of each excitation pulse, the detection wavelength, the timing between the excitation pulses, and the detection gating window after excitation. Such a large parameter space can provide much greater molecular specificity than existing single-color techniques and allow for structural and functional imaging without the need for exogenous dyes and labels, which might interfere with the system under study. In this review, we provide a tutorial overview, covering principles of pump-probe microscopy and experimental setup, challenges associated with signal detection and data processing, and an overview of applications.« less

Invited Review Article: Pump-probe microscopy

PubMed Central

Wilson, Jesse W.; Robles, Francisco E.; Warren, Warren S.

2016-01-01

Multiphoton microscopy has rapidly gained popularity in biomedical imaging and materials science because of its ability to provide three-dimensional images at high spatial and temporal resolution even in optically scattering environments. Currently the majority of commercial and home-built devices are based on two-photon fluorescence and harmonic generation contrast. These two contrast mechanisms are relatively easy to measure but can access only a limited range of endogenous targets. Recent developments in fast laser pulse generation, pulse shaping, and detection technology have made accessible a wide range of optical contrasts that utilize multiple pulses of different colors. Molecular excitation with multiple pulses offers a large number of adjustable parameters. For example, in two-pulse pump-probe microscopy, one can vary the wavelength of each excitation pulse, the detection wavelength, the timing between the excitation pulses, and the detection gating window after excitation. Such a large parameter space can provide much greater molecular specificity than existing single-color techniques and allow for structural and functional imaging without the need for exogenous dyes and labels, which might interfere with the system under study. In this review, we provide a tutorial overview, covering principles of pump-probe microscopy and experimental setup, challenges associated with signal detection and data processing, and an overview of applications. PMID:27036751

One Novel Multiple-Target Plasmid Reference Molecule Targeting Eight Genetically Modified Canola Events for Genetically Modified Canola Detection.

PubMed

Li, Zhuqing; Li, Xiang; Wang, Canhua; Song, Guiwen; Pi, Liqun; Zheng, Lan; Zhang, Dabing; Yang, Litao

2017-09-27

Multiple-target plasmid DNA reference materials have been generated and utilized as good substitutes of matrix-based reference materials in the analysis of genetically modified organisms (GMOs). Herein, we report the construction of one multiple-target plasmid reference molecule, pCAN, which harbors eight GM canola event-specific sequences (RF1, RF2, MS1, MS8, Topas 19/2, Oxy235, RT73, and T45) and a partial sequence of the canola endogenous reference gene PEP. The applicability of this plasmid reference material in qualitative and quantitative PCR assays of the eight GM canola events was evaluated, including the analysis of specificity, limit of detection (LOD), limit of quantification (LOQ), and performance of pCAN in the analysis of various canola samples, etc. The LODs are 15 copies for RF2, MS1, and RT73 assays using pCAN as the calibrator and 10 genome copies for the other events. The LOQ in each event-specific real-time PCR assay is 20 copies. In quantitative real-time PCR analysis, the PCR efficiencies of all event-specific and PEP assays are between 91% and 97%, and the squared regression coefficients (R 2 ) are all higher than 0.99. The quantification bias values varied from 0.47% to 20.68% with relative standard deviation (RSD) from 1.06% to 24.61% in the quantification of simulated samples. Furthermore, 10 practical canola samples sampled from imported shipments in the port of Shanghai, China, were analyzed employing pCAN as the calibrator, and the results were comparable with those assays using commercial certified materials as the calibrator. Concluding from these results, we believe that this newly developed pCAN plasmid is one good candidate for being a plasmid DNA reference material in the detection and quantification of the eight GM canola events in routine analysis.

Characterization of Harmonic Signal Acquisition with Parallel Dipole and Multipole Detectors

NASA Astrophysics Data System (ADS)

Park, Sung-Gun; Anderson, Gordon A.; Bruce, James E.

2018-04-01

Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) is a powerful instrument for the study of complex biological samples due to its high resolution and mass measurement accuracy. However, the relatively long signal acquisition periods needed to achieve high resolution can serve to limit applications of FTICR-MS. The use of multiple pairs of detector electrodes enables detection of harmonic frequencies present at integer multiples of the fundamental cyclotron frequency, and the obtained resolving power for a given acquisition period increases linearly with the order of harmonic signal. However, harmonic signal detection also increases spectral complexity and presents challenges for interpretation. In the present work, ICR cells with independent dipole and harmonic detection electrodes and preamplifiers are demonstrated. A benefit of this approach is the ability to independently acquire fundamental and multiple harmonic signals in parallel using the same ions under identical conditions, enabling direct comparison of achieved performance as parameters are varied. Spectra from harmonic signals showed generally higher resolving power than spectra acquired with fundamental signals and equal signal duration. In addition, the maximum observed signal to noise (S/N) ratio from harmonic signals exceeded that of fundamental signals by 50 to 100%. Finally, parallel detection of fundamental and harmonic signals enables deconvolution of overlapping harmonic signals since observed fundamental frequencies can be used to unambiguously calculate all possible harmonic frequencies. Thus, the present application of parallel fundamental and harmonic signal acquisition offers a general approach to improve utilization of harmonic signals to yield high-resolution spectra with decreased acquisition time. [Figure not available: see fulltext.

Improved Sensor Fault Detection, Isolation, and Mitigation Using Multiple Observers Approach

PubMed Central

Wang, Zheng; Anand, D. M.; Moyne, J.; Tilbury, D. M.

2017-01-01

Traditional Fault Detection and Isolation (FDI) methods analyze a residual signal to detect and isolate sensor faults. The residual signal is the difference between the sensor measurements and the estimated outputs of the system based on an observer. The traditional residual-based FDI methods, however, have some limitations. First, they require that the observer has reached its steady state. In addition, residual-based methods may not detect some sensor faults, such as faults on critical sensors that result in an unobservable system. Furthermore, the system may be in jeopardy if actions required for mitigating the impact of the faulty sensors are not taken before the faulty sensors are identified. The contribution of this paper is to propose three new methods to address these limitations. Faults that occur during the observers' transient state can be detected by analyzing the convergence rate of the estimation error. Open-loop observers, which do not rely on sensor information, are used to detect faults on critical sensors. By switching among different observers, we can potentially mitigate the impact of the faulty sensor during the FDI process. These three methods are systematically integrated with a previously developed residual-based method to provide an improved FDI and mitigation capability framework. The overall approach is validated mathematically, and the effectiveness of the overall approach is demonstrated through simulation on a 5-state suspension system. PMID:28924303

Advance in plasma SEPT9 gene methylation assay for colorectal cancer early detection

PubMed Central

Wang, Yu; Chen, Pei-Min; Liu, Rong-Bin

2018-01-01

This review article summarizes the research advances of the plasma-based SEPT9 gene methylation assay for the clinical detection of colorectal cancer and its limitations. Colorectal cancer is a common malignancy with a poor prognosis and a high mortality, for which early detection and diagnosis are particularly crucial for the high-risk groups. Increasing evidence supported that SEPT9 gene methylation is associated with the pathogenesis of colorectal cancer and that detecting the level of methylation of SEPT9 in the peripheral blood can be used for screening of colorectal cancer in susceptible populations. In recent years, the data obtained in clinical studies demonstrated that the SEPT9 gene methylation assay has a good diagnostic performance with regard to both sensitivity and specificity with the advantage of better acceptability, convenience and compliance with serological testing compared with fecal occult blood tests and carcinoembryonic antigen for colorectal cancer (CRC). Furthermore, the combination of multiple methods or markers has become a growing trend for CRC detection and screening. Nevertheless, the clinical availability of the methylated SEPT9 assay is still limited because of the large degree of sample heterogeneity caused by demographic characteristics, pathological features, comorbidities and/or technique selection. Another factor is the cost-effectiveness of colorectal cancer screening strategies that hinders its large-scale application. In addition, improvements in its accuracy in detecting adenomas and premalignant polyps are required. PMID:29375744

Advance in plasma SEPT9 gene methylation assay for colorectal cancer early detection.

PubMed

Wang, Yu; Chen, Pei-Min; Liu, Rong-Bin

2018-01-15

This review article summarizes the research advances of the plasma-based SEPT9 gene methylation assay for the clinical detection of colorectal cancer and its limitations. Colorectal cancer is a common malignancy with a poor prognosis and a high mortality, for which early detection and diagnosis are particularly crucial for the high-risk groups. Increasing evidence supported that SEPT9 gene methylation is associated with the pathogenesis of colorectal cancer and that detecting the level of methylation of SEPT9 in the peripheral blood can be used for screening of colorectal cancer in susceptible populations. In recent years, the data obtained in clinical studies demonstrated that the SEPT9 gene methylation assay has a good diagnostic performance with regard to both sensitivity and specificity with the advantage of better acceptability, convenience and compliance with serological testing compared with fecal occult blood tests and carcinoembryonic antigen for colorectal cancer (CRC). Furthermore, the combination of multiple methods or markers has become a growing trend for CRC detection and screening. Nevertheless, the clinical availability of the methylated SEPT9 assay is still limited because of the large degree of sample heterogeneity caused by demographic characteristics, pathological features, comorbidities and/or technique selection. Another factor is the cost-effectiveness of colorectal cancer screening strategies that hinders its large-scale application. In addition, improvements in its accuracy in detecting adenomas and premalignant polyps are required.

Ultrasensitive Electrochemical Detection of Glycoprotein Based on Boronate Affinity Sandwich Assay and Signal Amplification with Functionalized SiO2@Au Nanocomposites.

PubMed

You, Min; Yang, Shuai; Tang, Wanxin; Zhang, Fan; He, Pin-Gang

2017-04-26

Herein we propose a multiple signal amplification strategy designed for ultrasensitive electrochemical detection of glycoproteins. This approach introduces a new type of boronate-affinity sandwich assay (BASA), which was fabricated by using gold nanoparticles combined with reduced graphene oxide (AuNPs-GO) to modify sensing surface for accelerating electron transfer, the composite of molecularly imprinted polymer (MIP) including 4-vinylphenylboronic acid (VPBA) for specific capturing glycoproteins, and SiO 2 nanoparticles carried gold nanoparticles (SiO 2 @Au) labeled with 6-ferrocenylhexanethiol (FcHT) and 4-mercaptophenylboronic acid (MPBA) (SiO 2 @Au/FcHT/MPBA) as tracing tag for binding glycoprotein and generating electrochemical signal. As a sandwich-type sensing, the SiO 2 @Au/FcHT/MPBA was captured by glycoprotein on the surface of imprinting film for further electrochemical detection in 0.1 M PBS (pH 7.4). Using horseradish peroxidase (HRP) as a model glycoprotein, the proposed approach exhibited a wide linear range from 1 pg/mL to 100 ng/mL, with a low detection limit of 0.57 pg/mL. To the best of our knowledge, this is first report of a multiple signal amplification approach based on boronate-affinity molecularly imprinted polymer and SiO 2 @Au/FcHT/MPBA, exhibiting greatly enhanced sensitivity for glycoprotein detection. Furthermore, the newly constructed BASA based glycoprotein sensor demonstrated HRP detection in real sample, such as human serum, suggesting its promising prospects in clinical diagnostics.

A non-earthcentric approach to life detection

NASA Technical Reports Server (NTRS)

Conrad, P. G.; Nealson, K. H.

2001-01-01

The ultimate goal of a comprehensive life detection strategy is never to miss life when we encounter it. To accomplish this goal, we must define life in universal, that is, non-Earthcentric, measurable terms. Next, we must understand the nature of biosignatures observed from the measured parameters of life. And finally, we must have a clear idea of the end-member states for the search--what does life, past life, or no life look like (in terms of the measured parameters) at multiple spatial and temporal scales? If we can approach these problems both in the laboratory and in the field on Earth, then we have a chance of being able to detect life elsewhere in our solar system. What are the required limits of detection at each of those scales? What spatial, spectral, and temporal resolutions are necessary to detect life? These questions are actively being investigated in our group, and in this report, we present our strategy and approach to non-Earthcentric life detection.

Comparison of real-time PCR methods for the detection of Naegleria fowleri in surface water and sediment.

PubMed

Streby, Ashleigh; Mull, Bonnie J; Levy, Karen; Hill, Vincent R

2015-05-01

Naegleria fowleri is a thermophilic free-living ameba found in freshwater environments worldwide. It is the cause of a rare but potentially fatal disease in humans known as primary amebic meningoencephalitis. Established N. fowleri detection methods rely on conventional culture techniques and morphological examination followed by molecular testing. Multiple alternative real-time PCR assays have been published for rapid detection of Naegleria spp. and N. fowleri. Foursuch assays were evaluated for the detection of N. fowleri from surface water and sediment. The assays were compared for thermodynamic stability, analytical sensitivity and specificity, detection limits, humic acid inhibition effects, and performance with seeded environmental matrices. Twenty-one ameba isolates were included in the DNA panel used for analytical sensitivity and specificity analyses. N. fowleri genotypes I and III were used for method performance testing. Two of the real-time PCR assays were determined to yield similar performance data for specificity and sensitivity for detecting N. fowleri in environmental matrices.

Comparison of real-time PCR methods for the detection of Naegleria fowleri in surface water and sediment

PubMed Central

Streby, Ashleigh; Mull, Bonnie J.; Levy, Karen

2015-01-01

Naegleria fowleri is a thermophilic free-living ameba found in freshwater environments worldwide. It is the cause of a rare but potentially fatal disease in humans known as primary amebic meningoencephalitis. Established N. fowleri detection methods rely on conventional culture techniques and morphological examination followed by molecular testing. Multiple alternative real-time PCR assays have been published for rapid detection of Naegleria spp. and N. fowleri. Four such assays were evaluated for the detection of N. fowleri from surface water and sediment. The assays were compared for thermodynamic stability, analytical sensitivity and specificity, detection limits, humic acid inhibition effects, and performance with seeded environmental matrices. Twenty-one ameba isolates were included in the DNA panel used for analytical sensitivity and specificity analyses. N. fowleri genotypes I and III were used for method performance testing. Two of the real-time PCR assays were determined to yield similar performance data for specificity and sensitivity for detecting N. fowleri in environmental matrices. PMID:25855343

Taking Halo-Independent Dark Matter Methods Out of the Bin

DOE PAGES

Fox, Patrick J.; Kahn, Yonatan; McCullough, Matthew

2014-10-30

We develop a new halo-independent strategy for analyzing emerging DM hints, utilizing the method of extended maximum likelihood. This approach does not require the binning of events, making it uniquely suited to the analysis of emerging DM direct detection hints. It determines a preferred envelope, at a given confidence level, for the DM velocity integral which best fits the data using all available information and can be used even in the case of a single anomalous scattering event. All of the halo-independent information from a direct detection result may then be presented in a single plot, allowing simple comparisons betweenmore » multiple experiments. This results in the halo-independent analogue of the usual mass and cross-section plots found in typical direct detection analyses, where limit curves may be compared with best-fit regions in halo-space. The method is straightforward to implement, using already-established techniques, and its utility is demonstrated through the first unbinned halo-independent comparison of the three anomalous events observed in the CDMS-Si detector with recent limits from the LUX experiment.« less

Stellar Companions of Exoplanet Host Stars in K2

NASA Astrophysics Data System (ADS)

Matson, Rachel; Howell, Steve; Horch, Elliott; Everett, Mark

2018-01-01

Stellar multiplicity has significant implications for the detection and characterization of exoplanets. A stellar companion can mimic the signal of a transiting planet or distort the true planetary radii, leading to improper density estimates and over-predicting the occurrence rates of Earth-sized planets. Determining the fraction of exoplanet host stars that are also binaries allows us to better determine planetary characteristics as well as establish the relationship between binarity and planet formation. Using high-resolution speckle imaging to obtain diffraction limited images of K2 planet candidate host stars we detect stellar companions within one arcsec and up to six magnitudes fainter than the host star. By comparing our observed companion fraction to TRILEGAL star count simulations, and using the known detection limits of speckle imaging, we find the binary fraction of K2 planet host stars to be similar to that of Kepler host stars and solar-type field stars. Accounting for stellar companions in exoplanet studies is therefore essential for deriving true stellar and planetary properties as well as maximizing the returns for TESS and future exoplanet missions.

Analytical methods for multiresidue determination of sulfonamides and trimethoprim in meat and ground water samples by CE-MS and CE-MS/MS.

PubMed

Soto-Chinchilla, Jorge J; García-Campaña, Ana M; Gámiz-Gracia, Laura

2007-11-01

This paper presents two methods based on CZE-MS detection and CZE-MS/MS detection developed for the multiresidue determination of ten sulfonamides (sulfapyridine, sulfadoxin, sulfamethazine, sulfadimethoxine, sulfameter, sulfamerazine, sulfachlorpyridazine, sulfadiazine, sulfamethoxazole, and sulfamethizole) and a potentiator, trimethoprim (TMP), whose contents are regulated by the EU Council Regulation no. 2377/90 in animal edible tissues. Experimental designs were employed to optimize the electrospray conditions. MS/MS experiments using an IT as analyzer operating in multiple reaction monitoring (MRM) mode were carried out to achieve the minimum number of points according to the 2002/657/EC European Decision for unambiguous identification. The proposed procedures have been compared in terms of the performance characteristics and trueness. The limits of detection and quantification were in all cases lower than the maximum residue limits legislated for these compounds and the recoveries were satisfactory, being possible the application for their monitoring in foodstuff of animal origin and in environmental samples, allowing the determination of sulfonamides and TMP residues in meat and in superficial water in the low microg/L range.

A phantom design for assessment of detectability in PET imaging

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

Wollenweber, Scott D., E-mail: scott.wollenweber@g

2016-09-15

Purpose: The primary clinical role of positron emission tomography (PET) imaging is the detection of anomalous regions of {sup 18}F-FDG uptake, which are often indicative of malignant lesions. The goal of this work was to create a task-configurable fillable phantom for realistic measurements of detectability in PET imaging. Design goals included simplicity, adjustable feature size, realistic size and contrast levels, and inclusion of a lumpy (i.e., heterogeneous) background. Methods: The detection targets were hollow 3D-printed dodecahedral nylon features. The exostructure sphere-like features created voids in a background of small, solid non-porous plastic (acrylic) spheres inside a fillable tank. The featuresmore » filled at full concentration while the background concentration was reduced due to filling only between the solid spheres. Results: Multiple iterations of feature size and phantom construction were used to determine a configuration at the limit of detectability for a PET/CT system. A full-scale design used a 20 cm uniform cylinder (head-size) filled with a fixed pattern of features at a contrast of approximately 3:1. Known signal-present and signal-absent PET sub-images were extracted from multiple scans of the same phantom and with detectability in a challenging (i.e., useful) range. These images enabled calculation and comparison of the quantitative observer detectability metrics between scanner designs and image reconstruction methods. The phantom design has several advantages including filling simplicity, wall-less contrast features, the control of the detectability range via feature size, and a clinically realistic lumpy background. Conclusions: This phantom provides a practical method for testing and comparison of lesion detectability as a function of imaging system, acquisition parameters, and image reconstruction methods and parameters.« less

The AstraLux Multiplicity Survey: Extension to Late M-dwarfs

NASA Astrophysics Data System (ADS)

Janson, Markus; Bergfors, Carolina; Brandner, Wolfgang; Kudryavtseva, Natalia; Hormuth, Felix; Hippler, Stefan; Henning, Thomas

2014-07-01

The distribution of multiplicity among low-mass stars is a key issue to understanding the formation of stars and brown dwarfs, and recent surveys have yielded large enough samples of nearby low-mass stars to study this issue statistically to good accuracy. Previously, we have presented a multiplicity study of ~700 early/mid M-type stars observed with the AstraLux high-resolution Lucky Imaging cameras. Here, we extend the study of multiplicity in M-type stars through studying 286 nearby mid/late M-type stars, bridging the gap between our previous study and multiplicity studies of brown dwarfs. Most of the targets have been observed more than once, allowing us to assess common proper motion to confirm companionship. We detect 68 confirmed or probable companions in 66 systems, of which 41 were previously undiscovered. Detections are made down to the resolution limit of ~100 mas of the instrument. The raw multiplicity in the AstraLux sensitivity range is 17.9%, leading to a total multiplicity fraction of 21%-27% depending on the mass ratio distribution, which is consistent with being flat down to mass ratios of ~0.4, but cannot be stringently constrained below this value. The semi-major axis distribution is well represented by a log-normal function with μa = 0.78 and σa = 0.47, which is narrower and peaked at smaller separations than for a Sun-like sample. This is consistent with a steady decrease in average semi-major axis from the highest-mass binary stars to the brown dwarf binaries. Based on observations collected at the Centro Astronómico Hispano Alemán (CAHA) at Calar Alto, operated jointly by the Max-Planck Institute for Astronomy and the Instituto de Astrofísica de Andalucía (CSIC).

High-resolution, high-throughput imaging with a multibeam scanning electron microscope.

PubMed

Eberle, A L; Mikula, S; Schalek, R; Lichtman, J; Knothe Tate, M L; Zeidler, D

2015-08-01

Electron-electron interactions and detector bandwidth limit the maximal imaging speed of single-beam scanning electron microscopes. We use multiple electron beams in a single column and detect secondary electrons in parallel to increase the imaging speed by close to two orders of magnitude and demonstrate imaging for a variety of samples ranging from biological brain tissue to semiconductor wafers. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

Detection of Brain Reorganization in Pediatric Multiple Sclerosis Using Functional MRI

DTIC Science & Technology

2015-10-01

Page | 2 AWARD NUMBER: W81XWH-13-1-0464 TITLE: Detection of Brain Reorganization in Pediatric Multiple Sclerosis Using Functional MRI...Sep 2014 – 29 Sep 2015 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Detection of Brain Reorganization in Pediatric Multiple Sclerosis Using Functional...findings include: 1) detection of brain organization in a cohort of 24 pediatric onset multiple sclerosis patients (POMS) and 25 healthy controls

An integrated data model to estimate spatiotemporal occupancy, abundance, and colonization dynamics.

PubMed

Williams, Perry J; Hooten, Mevin B; Womble, Jamie N; Esslinger, George G; Bower, Michael R; Hefley, Trevor J

2017-02-01

Ecological invasions and colonizations occur dynamically through space and time. Estimating the distribution and abundance of colonizing species is critical for efficient management or conservation. We describe a statistical framework for simultaneously estimating spatiotemporal occupancy and abundance dynamics of a colonizing species. Our method accounts for several issues that are common when modeling spatiotemporal ecological data including multiple levels of detection probability, multiple data sources, and computational limitations that occur when making fine-scale inference over a large spatiotemporal domain. We apply the model to estimate the colonization dynamics of sea otters (Enhydra lutris) in Glacier Bay, in southeastern Alaska. © 2016 by the Ecological Society of America.

The HARPS search for southern extra-solar planets . XXXII. New multi-planet systems in the HARPS volume limited sample: a super-Earth and a Neptune in the habitable zone

NASA Astrophysics Data System (ADS)

Lo Curto, G.; Mayor, M.; Benz, W.; Bouchy, F.; Hébrard, G.; Lovis, C.; Moutou, C.; Naef, D.; Pepe, F.; Queloz, D.; Santos, N. C.; Segransan, D.; Udry, S.

2013-03-01

The vast diversity of planetary systems detected to date is defying our capability of understanding their formation and evolution. Well-defined volume-limited surveys are the best tool at our disposal to tackle the problem, via the acquisition of robust statistics of the orbital elements. We are using the HARPS spectrograph to conduct our survey of ≈850 nearby solar-type stars, and in the course of the past nine years we have monitored the radial velocity of HD 103774, HD 109271, and BD-061339. In this work we present the detection of five planets orbiting these stars, with msin (i) between 0.6 and 7 Neptune masses, four of which are in two multiple systems, comprising one super-Earth and one planet within the habitable zone of a late-type dwarf. Although for strategic reasons we chose efficiency over precision in this survey, we have the capability to detect planets down to the Neptune and super-Earth mass range as well as multiple systems, provided that enough data points are made available. Based on observations made with the HARPS instrument on the ESO 3.6 m telescope at La Silla (Chile), under the GTO program ID 072.C-0488 and the regular programs: 085.C-0019, 087.C-0831 and 089.C-0732. RV data are only available at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/551/A59

Direct sampling of chemical weapons in water by photoionization mass spectrometry.

PubMed

Syage, Jack A; Cai, Sheng-Suan; Li, Jianwei; Evans, Matthew D

2006-05-01

The vulnerability of water supplies to toxic contamination calls for fast and effective means for screening water samples for multiple threats. We describe the use of photoionization (PI) mass spectrometry (MS) for high-speed, high-throughput screening and molecular identification of chemical weapons (CW) threats and other hazardous compounds. The screening technology can detect a wide range of compounds at subacute concentrations with no sample preparation and a sampling cycle time of approximately 45 s. The technology was tested with CW agents VX, GA, GB, GD, GF, HD, HN1, and HN3, in addition to riot agents and precursors. All are sensitively detected and give simple PI mass spectra dominated by the parent ion. The target application of the PI MS method is as a routine, real-time early warning system for CW agents and other hazardous compounds in air and in water. In this work, we also present comprehensive measurements for water analysis and report on the system detection limits, linearity, quantitation accuracy, and false positive (FP) and false negative rates for concentrations at subacute levels. The latter data are presented in the form of receiver operating characteristic curves of the form of detection probability P(D) versus FP probability P(FP). These measurements were made using the CW surrogate compounds, DMMP, DEMP, DEEP, and DIMP. Method detection limits (3sigma) obtained using a capillary injection method yielded 1, 6, 3, and 2 ng/mL, respectively. These results were obtained using 1-microL injections of water samples without any preparation, corresponding to mass detection limits of 1, 6, 3, and 2 pg, respectively. The linear range was about 3-4 decades and the dynamic range about 4-5 decades. The relative standard deviations were generally <10% at CW subacute concentrations levels.

Limits of Spatial Attention in Three-Dimensional Space and Dual-task Driving Performance

PubMed Central

Andersen, George J.; Ni, Rui; Bian, Zheng; Kang, Julie

2010-01-01

The present study examined the limits of spatial attention while performing two driving relevant tasks that varied in depth. The first task was to maintain a fixed headway distance behind a lead vehicle that varied speed. The second task was to detect a light-change target in an array of lights located above the roadway. In Experiment 1 the light detection task required drivers to encode color and location. The results indicated that reaction time to detect a light-change target increased and accuracy decreased as a function of the horizontal location of the light-change target and as a function of the distance from the driver. In a second experiment the light change task was changed to a singleton search (detect the onset of a yellow light) and the workload of the car following task was systematically varied. The results of Experiment 2 indicated that RT increased as a function of task workload, the 2D position of the light-change target and the distance of the light-change target. A multiple regression analysis indicated that the effect of distance on light detection performance was not due to changes in the projected size of the light target. In Experiment 3 we found that the distance effect in detecting a light change could not be explained by the location of eye fixations. The results demonstrate that when drivers attend to a roadway scene attention is limited in three-dimensional space. These results have important implications for developing tests for assessing crash risk among drivers as well as the design of in vehicle technologies such as head-up displays. PMID:21094336

Development of a micromanipulation method for single cell isolation of prokaryotes and its application in food safety.

PubMed

Hohnadel, Marisa; Maumy, Myriam; Chollet, Renaud

2018-01-01

For nearly a century, conventional microbiological methods have been standard practice for detecting and identifying pathogens in food. Nevertheless, the microbiological safety of food has improved and various rapid methods have been developed to overcome the limitations of conventional methods. Alternative methods are expected to detect low cell numbers, since the presence in food of even a single cell of a pathogenic organism may be infectious. With respect to low population levels, the performance of a detection method is assessed by producing serial dilutions of a pure bacterial suspension to inoculate representative food matrices with highly diluted bacterial cells (fewer than 10 CFU/ml). The accuracy of data obtained by multiple dilution techniques is not certain and does not exclude some colonies arising from clumps of cells. Micromanipulation techniques to capture and isolate single cells from environmental samples were introduced more than 40 years ago. The main limitation of the current micromanipulation technique is still the low recovery rate for the growth of a single cell in culture medium. In this study, we describe a new single cell isolation method and demonstrate that it can be used successfully to grow various types of microorganism from picked individual cells. Tests with Gram-positive and Gram-negative organisms, including cocci, rods, aerobes, anaerobes, yeasts and molds showed growth recovery rates from 60% to 100% after micromanipulation. We also highlight the use of our method to evaluate and challenge the detection limits of standard detection methods in food samples contaminated by a single cell of Salmonella enterica.

Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma

PubMed Central

Addona, Terri A; Abbatiello, Susan E; Schilling, Birgit; Skates, Steven J; Mani, D R; Bunk, David M; Spiegelman, Clifford H; Zimmerman, Lisa J; Ham, Amy-Joan L; Keshishian, Hasmik; Hall, Steven C; Allen, Simon; Blackman, Ronald K; Borchers, Christoph H; Buck, Charles; Cardasis, Helene L; Cusack, Michael P; Dodder, Nathan G; Gibson, Bradford W; Held, Jason M; Hiltke, Tara; Jackson, Angela; Johansen, Eric B; Kinsinger, Christopher R; Li, Jing; Mesri, Mehdi; Neubert, Thomas A; Niles, Richard K; Pulsipher, Trenton C; Ransohoff, David; Rodriguez, Henry; Rudnick, Paul A; Smith, Derek; Tabb, David L; Tegeler, Tony J; Variyath, Asokan M; Vega-Montoto, Lorenzo J; Wahlander, Åsa; Waldemarson, Sofia; Wang, Mu; Whiteaker, Jeffrey R; Zhao, Lei; Anderson, N Leigh; Fisher, Susan J; Liebler, Daniel C; Paulovich, Amanda G; Regnier, Fred E; Tempst, Paul; Carr, Steven A

2010-01-01

Verification of candidate biomarkers relies upon specific, quantitative assays optimized for selective detection of target proteins, and is increasingly viewed as a critical step in the discovery pipeline that bridges unbiased biomarker discovery to preclinical validation. Although individual laboratories have demonstrated that multiple reaction monitoring (MRM) coupled with isotope dilution mass spectrometry can quantify candidate protein biomarkers in plasma, reproducibility and transferability of these assays between laboratories have not been demonstrated. We describe a multilaboratory study to assess reproducibility, recovery, linear dynamic range and limits of detection and quantification of multiplexed, MRM-based assays, conducted by NCI-CPTAC. Using common materials and standardized protocols, we demonstrate that these assays can be highly reproducible within and across laboratories and instrument platforms, and are sensitive to low µg/ml protein concentrations in unfractionated plasma. We provide data and benchmarks against which individual laboratories can compare their performance and evaluate new technologies for biomarker verification in plasma. PMID:19561596

Clinical update for the diagnosis and treatment of Clostridium difficile infection

PubMed Central

IV, Edward C Oldfield; III, Edward C Oldfield; Johnson, David A

2014-01-01

Clostridium difficile infection (CDI) presents a rapidly evolving challenge in the battle against hospital-acquired infections. Recent advances in CDI diagnosis and management include rapid changes in diagnostic approach with the introduction of newer tests, such as detection of glutamate dehydrogenase in stool and polymerase chain reaction to detect the gene for toxin production, which will soon revolutionize the diagnostic approach to CDI. New medications and multiple medical society guidelines have introduced changing concepts in the definitions of severity of CDI and the choice of therapeutic agents, while rapid expansion of data on the efficacy of fecal microbiota transplantation heralds a revolutionary change in the management of patients suffering multiple relapses of CDI. Through a comprehensive review of current medical literature, this article aims to offer an intensive review of the current state of CDI diagnosis, discuss the strengths and limitations of available laboratory tests, compare both current and future treatments options and offer recommendations for best practice strategies. PMID:24729930

Simultaneous screening for 238 drugs in blood by liquid chromatography-ion spray tandem mass spectrometry with multiple-reaction monitoring.

PubMed

Gergov, M; Ojanperä, I; Vuori, E

2003-09-25

A liquid chromatography-tandem mass spectrometry (LC-MS-MS) method is presented for the qualitative screening for 238 drugs in blood samples, which is considerably more than in previous methods. After a two-step liquid-liquid extraction and C(18) chromatography, the compounds were introduced into a triple quadrupole mass spectrometer equipped with a turbo ion spray ion source operating in the positive ionization mode. Identification was based on the compound's absolute retention time, protonated molecular ion, and one representative fragment ion obtained by multiple reaction monitoring (MRM) at an individually selected collision energy of 20, 35, or 50 eV. The limit of detection (LOD) for the majority of the compounds (80%) was < or = 0.05 mg/l, ranging from 0.002 mg/l (e.g., antihistamines) to 5 mg/l (acidic compounds), and for malathion it was 10 mg/l. The LOD values were sufficiently low to allow the majority of compounds to be detected at therapeutic concentrations in the blood.

Simultaneous quantification of Myelin Basic Protein and Tau proteins in cerebrospinal fluid and serum of Multiple Sclerosis patients using nanoimmunosensor.

PubMed

Derkus, Burak; Acar Bozkurt, Pinar; Tulu, Metin; Emregul, Kaan C; Yucesan, Canan; Emregul, Emel

2017-03-15

This study was aimed at the development of an immunosensor for the simultaneous quantification of Myelin Basic Protein (MBP) and Tau proteins in cerebrospinal fluid (CSF) and serum, obtained from Multiple Sclerosis (MS) patients. The newly developed GO/pPG/anti-MBP/anti-Tau nanoimmunosensor has been established by immobilization of MBP and Tau antibodies. The newly developed nanoimmunosensor was tested, optimized and characterized using differential pulse voltammetry (DPV) and electrochemical impedance spectroscopy (EIS). The developed nanoimmunosensor was seen to have detection limits of 0.30nM for MBP and 0.15nM for Tau proteins which were sufficient for the levels to be analysed in neuro-clinic. The clinical study performed using CSF and serum of MS patients showed that the designed nanoimmunosensor was capable of detecting the proteins properly, that were essentially proven by ELISA. Copyright © 2016 Elsevier B.V. All rights reserved.

An Inexpensive, Fast and Sensitive Quantitative Lateral Flow Magneto-Immunoassay for Total Prostate Specific Antigen

PubMed Central

Barnett, Jacqueline M.; Wraith, Patrick; Kiely, Janice; Persad, Raj; Hurley, Katrina; Hawkins, Peter; Luxton, Richard

2014-01-01

We describe the detection characteristics of a device the Resonant Coil Magnetometer (RCM) to quantify paramagnetic particles (PMPs) in immunochromatographic (lateral flow) assays. Lateral flow assays were developed using PMPs for the measurement of total prostate specific antigen (PSA) in serum samples. A detection limit of 0.8 ng/mL was achieved for total PSA using the RCM and is at clinically significant concentrations. Comparison of data obtained in a pilot study from the analysis of serum samples with commercially available immunoassays shows good agreement. The development of a quantitative magneto-immunoassay in lateral flow format for total PSA suggests the potential of the RCM to operate with many immunoassay formats. The RCM has the potential to be modified to quantify multiple analytes in this format. This research shows promise for the development of an inexpensive device capable of quantifying multiple analytes at the point-of-care using a magneto-immunoassay in lateral flow format. PMID:25587419

Identification Of Cells With A Compact Microscope Imaging System With Intelligent Controls

NASA Technical Reports Server (NTRS)

McDowell, Mark (Inventor)

2006-01-01

A Microscope Imaging System (CMIS) with intelligent controls is disclosed that provides techniques for scanning, identifying, detecting and tracking mic?oscopic changes in selected characteristics or features of various surfaces including, but not limited to, cells, spheres, and manufactured products subject to difficult-to-see imperfections. The practice of the present invention provides applications that include colloidal hard spheres experiments, biological cell detection for patch clamping, cell movement and tracking, as well as defect identification in products, such as semiconductor devices, where surface damage can be significant, but difficult to detect. The CMIS system is a machine vision system, which combines intelligent image processing with remote control capabilities and provides the ability to autofocus on a microscope sample, automatically scan an image, and perform machine vision analysis on multiple samples simultaneously.

Tracking of Cells with a Compact Microscope Imaging System with Intelligent Controls

NASA Technical Reports Server (NTRS)

McDowell, Mark (Inventor)

2007-01-01

A Microscope Imaging System (CMIS) with intelligent controls is disclosed that provides techniques for scanning, identifying, detecting and tracking microscopic changes in selected characteristics or features of various surfaces including, but not limited to, cells, spheres, and manufactured products subject to difficult-to-see imperfections. The practice of the present invention provides applications that include colloidal hard spheres experiments, biological cell detection for patch clamping, cell movement and tracking, as well as defect identification in products, such as semiconductor devices, where surface damage can be significant, but difficult to detect. The CMIS system is a machine vision system, which combines intelligent image processing with remote control capabilities and provides the ability to autofocus on a microscope sample, automatically scan an image, and perform machine vision analysis on multiple samples simultaneously

Tracking of cells with a compact microscope imaging system with intelligent controls

NASA Technical Reports Server (NTRS)

McDowell, Mark (Inventor)

2007-01-01

A Microscope Imaging System (CMIS) with intelligent controls is disclosed that provides techniques for scanning, identifying, detecting and tracking microscopic changes in selected characteristics or features of various surfaces including, but not limited to, cells, spheres, and manufactured products subject to difficult-to-see imperfections. The practice of the present invention provides applications that include colloidal hard spheres experiments, biological cell detection for patch clamping, cell movement and tracking, as well as defect identification in products, such as semiconductor devices, where surface damage can be significant, but difficult to detect. The CMIS system is a machine vision system, which combines intelligent image processing with remote control capabilities and provides the ability to auto-focus on a microscope sample, automatically scan an image, and perform machine vision analysis on multiple samples simultaneously.

Operation of a Cartesian Robotic System in a Compact Microscope with Intelligent Controls

NASA Technical Reports Server (NTRS)

McDowell, Mark (Inventor)

2006-01-01

A Microscope Imaging System (CMIS) with intelligent controls is disclosed that provides techniques for scanning, identifying, detecting and tracking microscopic changes in selected characteristics or features of various surfaces including, but not limited to, cells, spheres, and manufactured products subject to difficult-to-see imperfections. The practice of the present invention provides applications that include colloidal hard spheres experiments, biological cell detection for patch clamping, cell movement and tracking, as well as defect identification in products, such as semiconductor devices, where surface damage can be significant, but difficult to detect. The CMIS system is a machine vision system, which combines intelligent image processing with remote control capabilities and provides the ability to autofocus on a microscope sample, automatically scan an image, and perform machine vision analysis on multiple samples simultaneously.

A multiplex real-time polymerase chain reaction assay with two internal controls for the detection of Brucella species in tissues, blood, and feces from marine mammals.

PubMed

Sidor, Inga F; Dunn, J Lawrence; Tsongalis, Gregory J; Carlson, Jolene; Frasca, Salvatore

2013-01-01

Brucellosis has emerged as a disease of concern in marine mammals in the last 2 decades. Molecular detection techniques have the potential to address limitations of other methods for detecting infection with Brucella in these species. Presented herein is a real-time polymerase chain reaction (PCR) method targeting the Brucella genus-specific bcsp31 gene. The method also includes a target to a conserved region of the eukaryotic mitochondrial 16S ribosomal RNA gene to assess suitability of extracted DNA and a plasmid-based internal control to detect failure of PCR due to inhibition. This method was optimized and validated to detect Brucella spp. in multiple sample matrices, including fresh or frozen tissue, blood, and feces. The analytical limit of detection was low, with 95% amplification at 24 fg, or an estimated 7 bacterial genomic copies. When Brucella spp. were experimentally added to tissue or fecal homogenates, the assay detected an estimated 1-5 bacteria/µl. An experiment simulating tissue autolysis showed relative persistence of bacterial DNA compared to host mitochondrial DNA. When used to screen 1,658 field-collected marine mammal tissues in comparison to microbial culture, diagnostic sensitivity and specificity were 70.4% and 98.3%, respectively. In addition to amplification in fresh and frozen tissues, Brucella spp. were detected in feces and formalin-fixed, paraffin-embedded tissues from culture-positive animals. Results indicate the utility of this real-time PCR for the detection of Brucella spp. in marine species, which may have applications in surveillance or epidemiologic investigations.

CO J = 2-1 LINE EMISSION IN CLUSTER GALAXIES AT z {approx} 1: FUELING STAR FORMATION IN DENSE ENVIRONMENTS

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

Wagg, Jeff; Pope, Alexandra; Alberts, Stacey

We present observations of CO J = 2-1 line emission in infrared-luminous cluster galaxies at z {approx} 1 using the IRAM Plateau de Bure Interferometer. Our two primary targets are optically faint, dust-obscured galaxies (DOGs) found to lie within 2 Mpc of the centers of two massive (>10{sup 14} M{sub Sun }) galaxy clusters. CO line emission is not detected in either DOG. We calculate 3{sigma} upper limits to the CO J = 2-1 line luminosities, L'{sub CO} < 6.08 Multiplication-Sign 10{sup 9} and <6.63 Multiplication-Sign 10{sup 9} K km s{sup -1} pc{sup 2}. Assuming a CO-to-H{sub 2} conversion factormore » derived for ultraluminous infrared galaxies in the local universe, this translates to limits on the cold molecular gas mass of M{sub H{sub 2}}< 4.86 Multiplication-Sign 10{sup 9} M{sub Sun} and M{sub H{sub 2}}< 5.30 Multiplication-Sign 10{sup 9} M{sub Sun }. Both DOGs exhibit mid-infrared continuum emission that follows a power law, suggesting that an active galactic nucleus (AGN) contributes to the dust heating. As such, estimates of the star formation efficiencies in these DOGs are uncertain. A third cluster member with an infrared luminosity, L{sub IR} < 7.4 Multiplication-Sign 10{sup 11} L{sub Sun }, is serendipitously detected in CO J = 2-1 line emission in the field of one of the DOGs located roughly two virial radii away from the cluster center. The optical spectrum of this object suggests that it is likely an obscured AGN, and the measured CO line luminosity is L'{sub CO} = (1.94 {+-} 0.35) Multiplication-Sign 10{sup 10} K km s{sup -1} pc{sup 2}, which leads to an estimated cold molecular gas mass M{sub H{sub 2}}= (1.55{+-}0.28) Multiplication-Sign 10{sup 10} M{sub Sun }. A significant reservoir of molecular gas in a z {approx} 1 galaxy located away from the cluster center demonstrates that the fuel can exist to drive an increase in star formation and AGN activity at the outskirts of high-redshift clusters.« less

Multiple buoyancy driven flows in a vertical cylinder heated from below

NASA Technical Reports Server (NTRS)

Yamaguchi, Y.; Chang, C. J.; Brown, R. A.

1983-01-01

The structure of axisymmetric buoyancy-driven convection in a vertical cylinder heated from below is probed by finite element solution of the Boussinesq equations coupled with computed-implemented perturbation techniques for detecting and tracking multiple flows and for determining flow stability. Results are reported for fluids with Prandtl number of one and for cylinders with aspect ratio (Lambda) (defined as the height to radius of the cylinder) between 0.5 and 2.25. Extensive calculations of the neutral stability curve for the static solution and of the nonlinear motions along the bifurcating flow families show a continuous evolution of the primary cellular motion from a single toroidal cell to two and three cells nested radially in the cylinder, instead of the sharp transitions found for a cylinder with shear-free sidewalls. The smooth transitions in flow structure with Rayleigh number and lambda are explained by nonlinear connectivity between the first two bifurcating flow families formed either by a secondary bifurcation point for Lambda or = Lambda * approximately 0.80 or by a limit point for Lambda Lambda *. The transition between these two modes may be described by the theory of multiple limit point bifurcation.

Development and application of a real-time PCR assay for the detection and quantitation of lymphocystis disease virus.

PubMed

Ciulli, Sara; Pinheiro, Ana Cristina de Aguiar Saldana; Volpe, Enrico; Moscato, Michele; Jung, Tae Sung; Galeotti, Marco; Stellino, Sabrina; Farneti, Riccardo; Prosperi, Santino

2015-03-01

Lymphocystis disease virus (LCDV) is responsible for a chronic self-limiting disease that affects more than 125 teleosts. Viral isolation of LCDV is difficult, time-consuming and often ineffective; the development of a rapid and specific tool to detect and quantify LCDV is desirable for both diagnosis and pathogenic studies. In this study, a quantitative real-time PCR (qPCR) assay was developed using a Sybr-Green-based assay targeting a highly conserved region of the MCP gene. Primers were designed on a multiple alignment that included all known LCDV genotypes. The viral DNA segment was cloned within a plasmid to generate a standard curve. The limit of detection was as low as 2.6DNA copies/μl of plasmid and the qPCR was able to detect viral DNA from cell culture lysates and tissues at levels ten-times lower than conventional PCR. Both gilthead seabream and olive flounder LCDV has been amplified, and an in silico assay showed that LCDV of all genotypes can be amplified. LCDV was detected in target and non-target tissues of both diseased and asymptomatic fish. The LCDV qPCR assay developed in this study is highly sensitive, specific, reproducible and versatile for the detection and quantitation of Lymphocystivirus, and may also be used for asymptomatic carrier detection or pathogenesis studies of different LCDV strains. Copyright © 2014 Elsevier B.V. All rights reserved.

Multidimensional Extension of Multiple Indicators Multiple Causes Models to Detect DIF

ERIC Educational Resources Information Center

Lee, Soo; Bulut, Okan; Suh, Youngsuk

2017-01-01

A number of studies have found multiple indicators multiple causes (MIMIC) models to be an effective tool in detecting uniform differential item functioning (DIF) for individual items and item bundles. A recently developed MIMIC-interaction model is capable of detecting both uniform and nonuniform DIF in the unidimensional item response theory…

Sensitive Detection of Norovirus Using Phage Nanoparticle Reporters in Lateral-Flow Assay

PubMed Central

Hagström, Anna E. V.; Garvey, Gavin; Paterson, Andrew S.; Dhamane, Sagar; Adhikari, Meena; Estes, Mary K.; Strych, Ulrich; Kourentzi, Katerina; Atmar, Robert L.; Willson, Richard C.

2015-01-01

Noroviruses are recognized worldwide as the principal cause of acute, non-bacterial gastroenteritis, resulting in 19-21 million cases of disease every year in the United States. Noroviruses have a very low infectious dose, a short incubation period, high resistance to traditional disinfection techniques and multiple modes of transmission, making early, point-of-care detection essential for controlling the spread of the disease. The traditional diagnostic tools, electron microscopy, RT-PCR and ELISA require sophisticated and expensive instrumentation, and are considered too laborious and slow to be useful during severe outbreaks. In this paper we describe the development of a new, rapid and sensitive lateral-flow assay using labeled phage particles for the detection of the prototypical norovirus GI.1 (Norwalk), with a limit of detection of 107 virus-like particles per mL, one hundred-fold lower than a conventional gold nanoparticle lateral-flow assay using the same antibody pair. PMID:25978622

Simple Approaches to Minimally-Instrumented, Microfluidic-Based Point-of-Care Nucleic Acid Amplification Tests

PubMed Central

Mauk, Michael G.; Song, Jinzhao; Liu, Changchun; Bau, Haim H.

2018-01-01

Designs and applications of microfluidics-based devices for molecular diagnostics (Nucleic Acid Amplification Tests, NAATs) in infectious disease testing are reviewed, with emphasis on minimally instrumented, point-of-care (POC) tests for resource-limited settings. Microfluidic cartridges (‘chips’) that combine solid-phase nucleic acid extraction; isothermal enzymatic nucleic acid amplification; pre-stored, paraffin-encapsulated lyophilized reagents; and real-time or endpoint optical detection are described. These chips can be used with a companion module for separating plasma from blood through a combined sedimentation-filtration effect. Three reporter types: Fluorescence, colorimetric dyes, and bioluminescence; and a new paradigm for end-point detection based on a diffusion-reaction column are compared. Multiplexing (parallel amplification and detection of multiple targets) is demonstrated. Low-cost detection and added functionality (data analysis, control, communication) can be realized using a cellphone platform with the chip. Some related and similar-purposed approaches by others are surveyed. PMID:29495424

Air and Surface Sampling Method for Assessing Exposures to Quaternary Ammonium Compounds Using Liquid Chromatography Tandem Mass Spectrometry.

PubMed

LeBouf, Ryan F; Virji, Mohammed Abbas; Ranpara, Anand; Stefaniak, Aleksandr B

2017-07-01

This method was designed for sampling select quaternary ammonium (quat) compounds in air or on surfaces followed by analysis using ultraperformance liquid chromatography tandem mass spectrometry. Target quats were benzethonium chloride, didecyldimethylammonium bromide, benzyldimethyldodecylammonium chloride, benzyldimethyltetradecylammonium chloride, and benzyldimethylhexadecylammonium chloride. For air sampling, polytetrafluoroethylene (PTFE) filters are recommended for 15-min to 24-hour sampling. For surface sampling, Pro-wipe® 880 (PW) media was chosen. Samples were extracted in 60:40 acetonitrile:0.1% formic acid for 1 hour on an orbital shaker. Method detection limits range from 0.3 to 2 ng/ml depending on media and analyte. Matrix effects of media are minimized through the use of multiple reaction monitoring versus selected ion recording. Upper confidence limits on accuracy meet the National Institute for Occupational Safety and Health 25% criterion for PTFE and PW media for all analytes. Using PTFE and PW analyzed with multiple reaction monitoring, the method quantifies levels among the different quats compounds with high precision (<10% relative standard deviation) and low bias (<11%). The method is sensitive enough with very low method detection limits to capture quats on air sampling filters with only a 15-min sample duration with a maximum assessed storage time of 103 days before sample extraction. This method will support future exposure assessment and quantitative epidemiologic studies to explore exposure-response relationships and establish levels of quats exposures associated with adverse health effects. © The Author 2017. Published by Oxford University Press on behalf of the British Occupational Hygiene Society.

Sequencing sit-to-stand and upright posture for mobility limitation assessment: determination of the timing of the task phases from force platform data.

PubMed

Mazzà, Claudia; Zok, Mounir; Della Croce, Ugo

2005-06-01

The identification of quantitative tools to assess an individual's mobility limitation is a complex and challenging task. Several motor tasks have been designated as potential indicators of mobility limitation. In this study, a multiple motor task obtained by sequencing sit-to-stand and upright posture was used. Algorithms based on data obtained exclusively from a single force platform were developed to detect the timing of the motor task phases (sit-to-stand, preparation to the upright posture and upright posture). To test these algorithms, an experimental protocol inducing predictable changes in the acquired signals was designed. Twenty-two young, able-bodied subjects performed the task in four different conditions: self-selected natural and high speed with feet kept together, and self-selected natural and high speed with feet pelvis-width apart. The proposed algorithms effectively detected the timing of the task phases, the duration of which was sensitive to the four different experimental conditions. As expected, the duration of the sit-to-stand was sensitive to the speed of the task and not to the foot position, while the duration of the preparation to the upright posture was sensitive to foot position but not to speed. In addition to providing a simple and effective description of the execution of the motor task, the correct timing of the studied multiple task could facilitate the accurate determination of variables descriptive of the single isolated phases, allowing for a more thorough description of the motor task and therefore could contribute to the development of effective quantitative functional evaluation tests.

Cross-reactivity by botanicals used in dietary supplements and spices using the multiplex xMAP food allergen detection assay (xMAP FADA).

PubMed

Pedersen, Ronnie O; Nowatzke, William L; Cho, Chung Y; Oliver, Kerry G; Garber, Eric A E

2018-06-18

Food allergies affect some 15 million Americans. The only treatment for food allergies is a strict avoidance diet. To help ensure the reliability of food labels, analytical methods are employed; the most common being enzyme-linked immunosorbent assays (ELISAs). However, the commonly employed ELISAs are single analyte-specific and cannot distinguish between false positives due to cross-reactive homologous proteins; making the method of questionable utility for regulatory purposes when analyzing for unknown or multiple food allergens. Also, should the need arise to detect additional analytes, extensive research must be undertaken to develop new ELISAs. To address these and other limitations, a multiplex immunoassay, the xMAP® food allergen detection assay (xMAP FADA), was developed using 30 different antibodies against 14 different food allergens plus gluten. Besides incorporating two antibodies for the detection of most analytes, the xMAP FADA also relies on two different extraction protocols; providing multiple confirmatory end-points. Using the xMAP FADA, the cross-reactivities of 45 botanicals used in dietary supplements and spices commercially sold in the USA were assessed. Only a few displayed cross-reactivities with the antibodies in the xMAP FADA at levels exceeding 0.0001%. The utility of the xMAP FADA was exemplified by its ability to detect and distinguish between betel nut, saw palmetto, and acai which are in the same family as coconut. Other botanicals examined included allspice, amchur, anise seed, black pepper, caraway seed, cardamom, cayenne red pepper, sesame seed, poppy seed, white pepper, and wheat grass. The combination of direct antibody detection, multi-antibody profiling, high sensitivity, and a modular design made it possible for the xMAP FADA to distinguish between homologous antigens, provide multiple levels of built-in confirmatory analysis, and optimize the bead set cocktail to address specific needs.

Laser-Induced Fluorescence Emission (L.I.F.E.): searching for Mars organics with a UV-enhanced PanCam.

PubMed

Storrie-Lombardi, Michael C; Muller, Jan-Peter; Fisk, Martin R; Cousins, Claire; Sattler, Birgit; Griffiths, Andrew D; Coates, Andrew J

2009-12-01

The European Space Agency will launch the ExoMars mission in 2016 with a primary goal of surveying the martian subsurface for evidence of organic material. We have recently investigated the utility of including either a 365 nm light-emitting diode or a 375 nm laser light source in the ExoMars rover panoramic camera (PanCam). Such a modification would make it feasible to monitor rover drill cuttings optically for the fluorescence signatures of aromatic organic molecules and map the distribution of polycyclic aromatic hydrocarbons (PAHs) as a function of depth to the 2 m limit of the ExoMars drill. The technique described requires no sample preparation, does not consume irreplaceable resources, and would allow mission control to prioritize deployment of organic detection experiments that require sample destruction, expenditure of non-replaceable consumables, or both. We report here for the first time laser-induced fluorescence emission (L.I.F.E.) imaging detection limits for anthracene, pyrene, and perylene targets doped onto a Mars analog granular peridotite with a 375 nm Nichia laser diode in optically uncorrected wide-angle mode. Data were collected via the Beagle 2 PanCam backup filter wheel fitted with original blue (440 nm), green (530 nm), and red (670 nm) filters. All three PAH species can be detected with the PanCam green (530 nm) filter. Detection limits in the green band for signal-to-noise ratios (S/N) > 10 are 49 parts per million (ppm) for anthracene, 145 ppm for pyrene, and 20 ppm for perylene. The anthracene detection limit improves to 7 ppm with use of the PanCam blue filter. We discuss soil-dependent detection limit constraints; use of UV excitation with other rover cameras, which provides higher spatial resolution; and the advantages of focused and wide-angle laser modes. Finally, we discuss application of L.I.F.E. techniques at multiple wavelengths for exploration of Mars analog extreme environments on Earth, including Icelandic hydrothermally altered basalts and the ice-covered lakes and glaciers of Dronning Maud Land, Antarctica.

Individual and combined effects of multiple pathogens on Pacific treefrogs.

PubMed

Romansic, John M; Johnson, Pieter T J; Searle, Catherine L; Johnson, James E; Tunstall, Tate S; Han, Barbara A; Rohr, Jason R; Blaustein, Andrew R

2011-08-01

In nature, individual hosts often encounter multiple pathogens simultaneously, which can lead to additive, antagonistic, or synergistic effects on hosts. Synergistic effects on infection prevalence or severity could greatly affect host populations. However, ecologists and managers often overlook the influence of pathogen combinations on hosts. This is especially true in amphibian conservation, even though multiple pathogens coexist within amphibian populations, and several pathogens have been implicated in amphibian population declines and extinctions. Using an amphibian host, Pseudacris regilla (Pacific treefrog), we experimentally investigated interactive effects among three pathogens: the trematode Ribeiroia sp. (hereafter, Ribeiroia), the fungus Batrachochytrium dendrobatidis (hereafter, BD), and the water mold Achlya flagellata. We detected no effects of A. flagellata, but did find effects of Ribeiroia and BD that varied depending on context. Low doses of Ribeiroia caused relatively few malformations, while higher Ribeiroia doses caused numerous deformities dominated by missing and reduced limbs and limb elements. Exposure to low doses of BD accelerated larval host development, despite there being no detectable BD infections, while exposure to higher BD doses caused infection but did not alter developmental rate. Hosts exposed to both Ribeiroia and BD exhibited the highest mortality, although overall evidence of interactive effects of multiple pathogens was limited. We suggest further research on the influence of multi-pathogen assemblages on amphibians, particularly under a variety of ecological conditions and with a wider diversity of hosts and pathogens.

Membrane-based lateral flow immunochromatographic strip with nanoparticles as reporters for detection: A review.

PubMed

Huang, Xiaolin; Aguilar, Zoraida P; Xu, Hengyi; Lai, Weihua; Xiong, Yonghua

2016-01-15

Membrane-based lateral flow immunochromatographic strip (LFICS) is widely used in various fields because of its simplicity, rapidity (detection within 10min), and low cost. However, early designs of membrane-based LFICS for preliminary screening only provide qualitative ("yes/no" signal) or semi-quantitative results without quantitative information. These designs often suffer from low-signal intensity and poor sensitivity and are only capable of single analyte detection, not simultaneous multiple detections. The performance of existing techniques used for detection using LFICS has been considerably improved by incorporating different kinds of nanoparticles (NPs) as reporters. NPs can serve as alternative labels and improve analytical sensitivity or limit of detection of LFICS because of their unique properties, such as optical absorption, fluorescence spectra, and magnetic properties. The controlled manipulation of NPs allows simultaneous or multiple detections by using membrane-based LFICS. In this review, we discuss how colored (e.g., colloidal gold, carbon, and colloidal selenium NPs), luminescent (e.g., quantum dots, up-converting phosphor NPs, and dye-doped NPs), and magnetic NPs are integrated into membrane-based LFICS for the detection of target analytes. Gold NPs are also featured because of their wide applications. Different types and unique properties of NPs are briefly explained. This review focuses on examples of NP-based LFICS to illustrate novel concepts in various devices with potential applications as screening tools. This review also highlights the superiority of NP-based approaches over existing conventional strategies for clinical analysis, food safety, and environmental monitoring. This paper is concluded by a short section on future research trends regarding NP-based LFICS. Copyright © 2015 Elsevier B.V. All rights reserved.

Extracting Behaviorally Relevant Traits from Natural Stimuli: Benefits of Combinatorial Representations at the Accessory Olfactory Bulb

PubMed Central

Kahan, Anat; Ben-Shaul, Yoram

2016-01-01

For many animals, chemosensation is essential for guiding social behavior. However, because multiple factors can modulate levels of individual chemical cues, deriving information about other individuals via natural chemical stimuli involves considerable challenges. How social information is extracted despite these sources of variability is poorly understood. The vomeronasal system provides an excellent opportunity to study this topic due to its role in detecting socially relevant traits. Here, we focus on two such traits: a female mouse’s strain and reproductive state. In particular, we measure stimulus-induced neuronal activity in the accessory olfactory bulb (AOB) in response to various dilutions of urine, vaginal secretions, and saliva, from estrus and non-estrus female mice from two different strains. We first show that all tested secretions provide information about a female’s receptivity and genotype. Next, we investigate how these traits can be decoded from neuronal activity despite multiple sources of variability. We show that individual neurons are limited in their capacity to allow trait classification across multiple sources of variability. However, simple linear classifiers sampling neuronal activity from small neuronal ensembles can provide a substantial improvement over that attained with individual units. Furthermore, we show that some traits are more efficiently detected than others, and that particular secretions may be optimized for conveying information about specific traits. Across all tested stimulus sources, discrimination between strains is more accurate than discrimination of receptivity, and detection of receptivity is more accurate with vaginal secretions than with urine. Our findings highlight the challenges of chemosensory processing of natural stimuli, and suggest that downstream readout stages decode multiple behaviorally relevant traits by sampling information from distinct but overlapping populations of AOB neurons. PMID:26938460

Extracting Behaviorally Relevant Traits from Natural Stimuli: Benefits of Combinatorial Representations at the Accessory Olfactory Bulb.

PubMed

Kahan, Anat; Ben-Shaul, Yoram

2016-03-01

For many animals, chemosensation is essential for guiding social behavior. However, because multiple factors can modulate levels of individual chemical cues, deriving information about other individuals via natural chemical stimuli involves considerable challenges. How social information is extracted despite these sources of variability is poorly understood. The vomeronasal system provides an excellent opportunity to study this topic due to its role in detecting socially relevant traits. Here, we focus on two such traits: a female mouse's strain and reproductive state. In particular, we measure stimulus-induced neuronal activity in the accessory olfactory bulb (AOB) in response to various dilutions of urine, vaginal secretions, and saliva, from estrus and non-estrus female mice from two different strains. We first show that all tested secretions provide information about a female's receptivity and genotype. Next, we investigate how these traits can be decoded from neuronal activity despite multiple sources of variability. We show that individual neurons are limited in their capacity to allow trait classification across multiple sources of variability. However, simple linear classifiers sampling neuronal activity from small neuronal ensembles can provide a substantial improvement over that attained with individual units. Furthermore, we show that some traits are more efficiently detected than others, and that particular secretions may be optimized for conveying information about specific traits. Across all tested stimulus sources, discrimination between strains is more accurate than discrimination of receptivity, and detection of receptivity is more accurate with vaginal secretions than with urine. Our findings highlight the challenges of chemosensory processing of natural stimuli, and suggest that downstream readout stages decode multiple behaviorally relevant traits by sampling information from distinct but overlapping populations of AOB neurons.

Capillary electrophoresis with electrochemiluminescent detection for highly sensitive assay of genetically modified organisms.

PubMed

Guo, Longhua; Yang, Huanghao; Qiu, Bin; Xiao, Xueyang; Xue, Linlin; Kim, Donghwan; Chen, Guonan

2009-12-01

A capillary electrophoresis coupled with electrochemiluminescent detection system (CE-ECL) was developed for the detection of polymerase chain reaction (PCR) amplicons. The ECL luminophore, tris(1,10-phenanthroline) ruthenium(II) (Ru(phen)(3)(2+)), was labeled to the PCR primers before amplification. Ru(phen)(3)(2+) was then introduced to PCR amplicons by PCR amplification. Eventually, the PCR amplicons were separated and detected by the homemade CE-ECL system. The detection of a typical genetically modified organism (GMO), Roundup Ready Soy (RRS), was shown as an example to demonstrate the reliability of the proposed approach. Four pairs of primers were amplified by multiple PCR (MPCR) simultaneously, three of which were targeted on the specific sequence of exogenous genes of RRS, and another was targeted on the endogenous reference gene of soybean. Both the conditions for PCR amplification and CE-ECL separation and detection were investigated in detail. Results showed that, under the optimal conditions, the proposed method can accurately identifying RRS. The corresponding limit of detection (LOD) was below 0.01% with 35 PCR cycles.

Improved Statistical Methods Enable Greater Sensitivity in Rhythm Detection for Genome-Wide Data

PubMed Central

Hutchison, Alan L.; Maienschein-Cline, Mark; Chiang, Andrew H.; Tabei, S. M. Ali; Gudjonson, Herman; Bahroos, Neil; Allada, Ravi; Dinner, Aaron R.

2015-01-01

Robust methods for identifying patterns of expression in genome-wide data are important for generating hypotheses regarding gene function. To this end, several analytic methods have been developed for detecting periodic patterns. We improve one such method, JTK_CYCLE, by explicitly calculating the null distribution such that it accounts for multiple hypothesis testing and by including non-sinusoidal reference waveforms. We term this method empirical JTK_CYCLE with asymmetry search, and we compare its performance to JTK_CYCLE with Bonferroni and Benjamini-Hochberg multiple hypothesis testing correction, as well as to five other methods: cyclohedron test, address reduction, stable persistence, ANOVA, and F24. We find that ANOVA, F24, and JTK_CYCLE consistently outperform the other three methods when data are limited and noisy; empirical JTK_CYCLE with asymmetry search gives the greatest sensitivity while controlling for the false discovery rate. Our analysis also provides insight into experimental design and we find that, for a fixed number of samples, better sensitivity and specificity are achieved with higher numbers of replicates than with higher sampling density. Application of the methods to detecting circadian rhythms in a metadataset of microarrays that quantify time-dependent gene expression in whole heads of Drosophila melanogaster reveals annotations that are enriched among genes with highly asymmetric waveforms. These include a wide range of oxidation reduction and metabolic genes, as well as genes with transcripts that have multiple splice forms. PMID:25793520

Direct large volume injection ultra-high performance liquid chromatography-tandem mass spectrometry determination of artificial sweeteners sucralose and acesulfame in well water.

PubMed

Wu, Minghuo; Qian, Yichao; Boyd, Jessica M; Hrudey, Steve E; Le, X Chris; Li, Xing-Fang

2014-09-12

Acesulfame (ACE) and sucralose (SUC) have become recognized as ideal domestic wastewater contamination indicators. Liquid chromatography-electrospray ionization mass spectrometry (LC-ESI-MS) analysis is commonly used; however, the sensitivity of SUC is more than two orders of magnitude lower than that of ACE, limiting the routine monitoring of SUC. To address this issue, we examined the ESI behavior of both ACE and SUC under various conditions. ACE is ionic in aqueous solution and efficiently produces simple [M-H](-) ions, but SUC produces multiple adduct ions, limiting its sensitivity. The formic acid (FA) adducts of SUC [M+HCOO](-) are sensitively and reproducibly generated under the LC-MS conditions. When [M+HCOO](-) is used as the precursor ion for SUC detection, the sensitivity increases approximately 20-fold compared to when [M-H](-) is the precursor ion. To further improve the limit of detection (LOD), we integrated the large volume injection approach (500μL injection) with ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS), which reduced the method detection limit (MDL) to 0.2ng/L for ACE and 5ng/L for SUC. To demonstrate the applicability of this method, we analyzed 100 well water samples collected in Alberta. ACE was detected in 24 wells at concentrations of 1-1534ng/L and SUC in 8 wells at concentrations of 65-541ng/L. These results suggest that wastewater is the most likely source of ACE and SUC impacts in these wells, suggesting the need for monitoring the quality of domestic well water. Copyright © 2014 Elsevier B.V. All rights reserved.

A gold immunochromatographic assay for the rapid and simultaneous detection of fifteen β-lactams

NASA Astrophysics Data System (ADS)

Chen, Yanni; Wang, Yongwei; Liu, Liqiang; Wu, Xiaoling; Xu, Liguang; Kuang, Hua; Li, Aike; Xu, Chuanlai

2015-10-01

A novel gold immunochromatographic assay (GICA) based on anti-β-lactam receptors was innovatively developed that successfully allowed rapid and simultaneous detection of fifteen β-lactams in milk samples in 5-10 minutes. By replacing the antibodies used in traditional GICA with anti-β-lactam receptors, the difficulty in producing broad specific antibodies against β-lactams was overcome. Conjugates of ampicillin with BSA and goat anti-mouse immunoglobulin (IgG) were immobilized onto the test and control lines on the nitrocellulose membrane, respectively. Since goat anti-mouse IgG does not combine with receptors, negative serum from mice labelled with gold nanoparticles (GNP) was mixed with GNP-labelled receptors. Results were obtained within 20 min using a paper-based sensor. The utility of the assay was confirmed by the analysis of milk samples. The limits of detection (LOD) for amoxicillin, ampicillin, penicillin G, penicillin V, cloxacillin, dicloxacillin, nafcillin, oxacillin, cefaclor, ceftezole, cefotaxime, ceftiofur, cefoperazone, cefathiamidine, and cefepime were 0.25, 0.5, 0.5, 0.5, 1, 5, 5, 10, 25, 10, 100, 10, 5, 5, and 2 ng mL-1, respectively, which satisfies the maximum residue limits (MRL) set by the European Union (EU). In conclusion, our newly developed GICA-based anti-β-lactam receptor assay provides a rapid and effective method for one-site detection of multiple β-lactams in milk samples.A novel gold immunochromatographic assay (GICA) based on anti-β-lactam receptors was innovatively developed that successfully allowed rapid and simultaneous detection of fifteen β-lactams in milk samples in 5-10 minutes. By replacing the antibodies used in traditional GICA with anti-β-lactam receptors, the difficulty in producing broad specific antibodies against β-lactams was overcome. Conjugates of ampicillin with BSA and goat anti-mouse immunoglobulin (IgG) were immobilized onto the test and control lines on the nitrocellulose membrane, respectively. Since goat anti-mouse IgG does not combine with receptors, negative serum from mice labelled with gold nanoparticles (GNP) was mixed with GNP-labelled receptors. Results were obtained within 20 min using a paper-based sensor. The utility of the assay was confirmed by the analysis of milk samples. The limits of detection (LOD) for amoxicillin, ampicillin, penicillin G, penicillin V, cloxacillin, dicloxacillin, nafcillin, oxacillin, cefaclor, ceftezole, cefotaxime, ceftiofur, cefoperazone, cefathiamidine, and cefepime were 0.25, 0.5, 0.5, 0.5, 1, 5, 5, 10, 25, 10, 100, 10, 5, 5, and 2 ng mL-1, respectively, which satisfies the maximum residue limits (MRL) set by the European Union (EU). In conclusion, our newly developed GICA-based anti-β-lactam receptor assay provides a rapid and effective method for one-site detection of multiple β-lactams in milk samples. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr04987c

Unsupervised building detection from irregularly spaced LiDAR and aerial imagery

NASA Astrophysics Data System (ADS)

Shorter, Nicholas Sven

As more data sources containing 3-D information are becoming available, an increased interest in 3-D imaging has emerged. Among these is the 3-D reconstruction of buildings and other man-made structures. A necessary preprocessing step is the detection and isolation of individual buildings that subsequently can be reconstructed in 3-D using various methodologies. Applications for both building detection and reconstruction have commercial use for urban planning, network planning for mobile communication (cell phone tower placement), spatial analysis of air pollution and noise nuisances, microclimate investigations, geographical information systems, security services and change detection from areas affected by natural disasters. Building detection and reconstruction are also used in the military for automatic target recognition and in entertainment for virtual tourism. Previously proposed building detection and reconstruction algorithms solely utilized aerial imagery. With the advent of Light Detection and Ranging (LiDAR) systems providing elevation data, current algorithms explore using captured LiDAR data as an additional feasible source of information. Additional sources of information can lead to automating techniques (alleviating their need for manual user intervention) as well as increasing their capabilities and accuracy. Several building detection approaches surveyed in the open literature have fundamental weaknesses that hinder their use; such as requiring multiple data sets from different sensors, mandating certain operations to be carried out manually, and limited functionality to only being able to detect certain types of buildings. In this work, a building detection system is proposed and implemented which strives to overcome the limitations seen in existing techniques. The developed framework is flexible in that it can perform building detection from just LiDAR data (first or last return), or just nadir, color aerial imagery. If data from both LiDAR and aerial imagery are available, then the algorithm will use them both for improved accuracy. Additionally, the proposed approach does not employ severely limiting assumptions thus enabling the end user to apply the approach to a wider variety of different building types. The proposed approach is extensively tested using real data sets and it is also compared with other existing techniques. Experimental results are presented.

Detection of Atmospheric Methyl Mercaptan Using Wavelength Modulation Spectroscopy with Multicomponent Spectral Fitting

PubMed Central

Du, Zhenhui; Wan, Jiaxin; Li, Jinyi; Luo, Gang; Gao, Hong; Ma, Yiwen

2017-01-01

Detection of methyl mercaptan (CH3SH) is essential for environmental atmosphere assessment and exhaled-breath analysis. This paper presents a sensitive CH3SH sensor based on wavelength modulation spectroscopy (WMS) with a mid-infrared distributed feedback interband cascade laser (DFB-ICL). Multicomponent spectral fitting was used not only to enhance the sensitivity of the sensor but also to determine the concentration of interferents (atmospheric water and methane). The results showed that the uncertainties in the measurement of CH3SH, H2O, and CH4 were less than 1.2%, 1.7% and 2.0%, respectively, with an integration time of 10 s. The CH3SH detection limit was as low as 7.1 ppb with an integration time of 295 s. Overall, the reported sensor, boasting the merits of high sensitivity, can be used for atmospheric methyl mercaptan detection, as well as multiple components detection of methyl mercaptan, water, and methane, simultaneously. PMID:28212311

On-chip detection of non-classical light by scalable integration of single-photon detectors

PubMed Central

Najafi, Faraz; Mower, Jacob; Harris, Nicholas C.; Bellei, Francesco; Dane, Andrew; Lee, Catherine; Hu, Xiaolong; Kharel, Prashanta; Marsili, Francesco; Assefa, Solomon; Berggren, Karl K.; Englund, Dirk

2015-01-01

Photonic-integrated circuits have emerged as a scalable platform for complex quantum systems. A central goal is to integrate single-photon detectors to reduce optical losses, latency and wiring complexity associated with off-chip detectors. Superconducting nanowire single-photon detectors (SNSPDs) are particularly attractive because of high detection efficiency, sub-50-ps jitter and nanosecond-scale reset time. However, while single detectors have been incorporated into individual waveguides, the system detection efficiency of multiple SNSPDs in one photonic circuit—required for scalable quantum photonic circuits—has been limited to <0.2%. Here we introduce a micrometer-scale flip-chip process that enables scalable integration of SNSPDs on a range of photonic circuits. Ten low-jitter detectors are integrated on one circuit with 100% device yield. With an average system detection efficiency beyond 10%, and estimated on-chip detection efficiency of 14–52% for four detectors operated simultaneously, we demonstrate, to the best of our knowledge, the first on-chip photon correlation measurements of non-classical light. PMID:25575346

A rapid low-cost high-density DNA-based multi-detection test for routine inspection of meat species.

PubMed

Lin, Chun Chi; Fung, Lai Ling; Chan, Po Kwok; Lee, Cheuk Man; Chow, Kwok Fai; Cheng, Shuk Han

2014-02-01

The increasing occurrence of food frauds suggests that species identification should be part of food authentication. Current molecular-based species identification methods have their own limitations or drawbacks, such as relatively time-consuming experimental steps, expensive equipment and, in particular, these methods cannot identify mixed species in a single experiment. This project proposes an improved method involving PCR amplification of the COI gene and detection of species-specific sequences by hybridisation. Major innovative breakthrough lies in the detection of multiple species, including pork, beef, lamb, horse, cat, dog and mouse, from a mixed sample within a single experiment. The probes used are species-specific either in sole or mixed species samples. As little as 5 pg of DNA template in the PCR is detectable in the proposed method. By designing species-specific probes and adopting reverse dot blot hybridisation and flow-through hybridisation, a low-cost high-density DNA-based multi-detection test suitable for routine inspection of meat species was developed. © 2013.

Nucleic acid sequence detection using multiplexed oligonucleotide PCR

DOEpatents

Nolan, John P [Santa Fe, NM; White, P Scott [Los Alamos, NM

2006-12-26

Methods for rapidly detecting single or multiple sequence alleles in a sample nucleic acid are described. Provided are all of the oligonucleotide pairs capable of annealing specifically to a target allele and discriminating among possible sequences thereof, and ligating to each other to form an oligonucleotide complex when a particular sequence feature is present (or, alternatively, absent) in the sample nucleic acid. The design of each oligonucleotide pair permits the subsequent high-level PCR amplification of a specific amplicon when the oligonucleotide complex is formed, but not when the oligonucleotide complex is not formed. The presence or absence of the specific amplicon is used to detect the allele. Detection of the specific amplicon may be achieved using a variety of methods well known in the art, including without limitation, oligonucleotide capture onto DNA chips or microarrays, oligonucleotide capture onto beads or microspheres, electrophoresis, and mass spectrometry. Various labels and address-capture tags may be employed in the amplicon detection step of multiplexed assays, as further described herein.

Time-frequency analysis of band-limited EEG with BMFLC and Kalman filter for BCI applications

PubMed Central

2013-01-01

Background Time-Frequency analysis of electroencephalogram (EEG) during different mental tasks received significant attention. As EEG is non-stationary, time-frequency analysis is essential to analyze brain states during different mental tasks. Further, the time-frequency information of EEG signal can be used as a feature for classification in brain-computer interface (BCI) applications. Methods To accurately model the EEG, band-limited multiple Fourier linear combiner (BMFLC), a linear combination of truncated multiple Fourier series models is employed. A state-space model for BMFLC in combination with Kalman filter/smoother is developed to obtain accurate adaptive estimation. By virtue of construction, BMFLC with Kalman filter/smoother provides accurate time-frequency decomposition of the bandlimited signal. Results The proposed method is computationally fast and is suitable for real-time BCI applications. To evaluate the proposed algorithm, a comparison with short-time Fourier transform (STFT) and continuous wavelet transform (CWT) for both synthesized and real EEG data is performed in this paper. The proposed method is applied to BCI Competition data IV for ERD detection in comparison with existing methods. Conclusions Results show that the proposed algorithm can provide optimal time-frequency resolution as compared to STFT and CWT. For ERD detection, BMFLC-KF outperforms STFT and BMFLC-KS in real-time applicability with low computational requirement. PMID:24274109

Detection of radioactive particles offshore by γ-ray spectrometry Part I: Monte Carlo assessment of detection depth limits

NASA Astrophysics Data System (ADS)

Maučec, M.; de Meijer, R. J.; Rigollet, C.; Hendriks, P. H. G. M.; Jones, D. G.

2004-06-01

A joint research project between the British Geological Survey and Nuclear Geophysics Division of the Kernfysisch Versneller Instituut, Groningen, the Netherlands, was commissioned by the United Kingdom Atomic Energy Authority to establish the efficiency of a towed seabed γ-ray spectrometer for the detection of 137Cs-containing radioactive particles offshore Dounreay, Scotland. Using the MCNP code, a comprehensive Monte Carlo feasibility study was carried out to model various combinations of geological matrices, particle burial depth and lateral displacement, source activity and detector material. To validate the sampling and absolute normalisation procedures of MCNP for geometries including multiple (natural and induced) heterogeneous sources in environmental monitoring, a benchmark experiment was conducted. The study demonstrates the ability of seabed γ-ray spectrometry to locate radioactive particles offshore and to distinguish between γ count rate increases due to particles from those due to enhanced natural radioactivity. The information presented in this study will be beneficial for estimation of the inventory of 137Cs particles and their activity distribution and for the recovery of particles from the sea floor. In this paper, the Monte Carlo assessment of the detection limits is presented. The estimation of the required towing speed and acquisition times and their application to radioactive particle detection and discrimination offshore formed a supplementary part of this study.

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

Blom, Philip Stephen; Marcillo, Omar Eduardo; Euler, Garrett Gene

InfraPy is a Python-based analysis toolkit being development at LANL. The algorithms are intended for ground-based nuclear detonation detection applications to detect, locate, and characterize explosive sources using infrasonic observations. The implementation is usable as a stand-alone Python library or as a command line driven tool operating directly on a database. With multiple scientists working on the project, we've begun using a LANL git repository for collaborative development and version control. Current and planned work on InfraPy focuses on the development of new algorithms and propagation models. Collaboration with Southern Methodist University (SMU) has helped identify bugs and limitations ofmore » the algorithms. The current focus of usage development is focused on library imports and CLI.« less

Differential Multiphoton Laser Scanning Microscopy

PubMed Central

Field, Jeffrey J.; Sheetz, Kraig E.; Chandler, Eric V.; Hoover, Erich E.; Young, Michael D.; Ding, Shi-you; Sylvester, Anne W.; Kleinfeld, David; Squier, Jeff A.

2016-01-01

Multifocal multiphoton microscopy (MMM) in the biological and medical sciences has become an important tool for obtaining high resolution images at video rates. While current implementations of MMM achieve very high frame rates, they are limited in their applicability to essentially those biological samples that exhibit little or no scattering. In this paper, we report on a method for MMM in which imaging detection is not necessary (single element point detection is implemented), and is therefore fully compatible for use in imaging through scattering media. Further, we demonstrate that this method leads to a new type of MMM wherein it is possible to simultaneously obtain multiple images and view differences in excitation parameters in a single shot. PMID:27390511

Diagnostic Imaging of Reproductive Tract Disorders in Reptiles.

PubMed

Gumpenberger, Michaela

2017-05-01

Diagnostic imaging of the reproductive tract in reptiles is used for gender determination, evaluation of breeding status, detection of pathologic changes, and supervising treatment. Whole-body radiographs provide an overview and support detection of mineralized egg shells. Sonography is used to evaluate follicles, nonmineralized eggs, and the salpinx in all reptiles. Computed tomography is able to overcome imaging limitations in chelonian species. This article provides detailed information about the performance of different imaging techniques. Multiple images demonstrate the physiologic appearance of the male and female reproductive tract in various reptile species and pathologic changes. Advantages and disadvantages of radiography, sonography, and computed tomography are described. Copyright © 2016 Elsevier Inc. All rights reserved.

[Development of poliovirus infection in laboratory animals of different species].

PubMed

Koroleva, G A; Lashkevich, V A; Voroshilova, M K

1975-01-01

The capacity of vaccine and virulent strains of poliomyelitis virus to multiply in laboratory animals of different species was studied. Virus reproduction was judged by formation of photoresistant virus progeny in response to inoculation of the animals with photosensitized virus. Multiplication of virulent poliomyelitis virus strains observed in the majority of animal species examined (monkeys, newborn and adult cotton rats, newborn and adult white mice, chickens, chick embryos) resulted in active formation of photoresistant virus population and in some cases was accompanied by clinical symptoms of the disease. Multiplication of vaccine strains was observed in a smaller number of animal species and was limited, as a rule. Among non-primate animals, newborn cotton rats were most susceptible to poliovirus infection. Newborn guinea pigs were the only species of laboratory animals in which no multiplication of any of the six strains under study could be detected.

Dual Contrast - Magnetic Resonance Fingerprinting (DC-MRF): A Platform for Simultaneous Quantification of Multiple MRI Contrast Agents.

PubMed

Anderson, Christian E; Donnola, Shannon B; Jiang, Yun; Batesole, Joshua; Darrah, Rebecca; Drumm, Mitchell L; Brady-Kalnay, Susann M; Steinmetz, Nicole F; Yu, Xin; Griswold, Mark A; Flask, Chris A

2017-08-16

Injectable Magnetic Resonance Imaging (MRI) contrast agents have been widely used to provide critical assessments of disease for both clinical and basic science imaging research studies. The scope of available MRI contrast agents has expanded over the years with the emergence of molecular imaging contrast agents specifically targeted to biological markers. Unfortunately, synergistic application of more than a single molecular contrast agent has been limited by MRI's ability to only dynamically measure a single agent at a time. In this study, a new Dual Contrast - Magnetic Resonance Fingerprinting (DC - MRF) methodology is described that can detect and independently quantify the local concentration of multiple MRI contrast agents following simultaneous administration. This "multi-color" MRI methodology provides the opportunity to monitor multiple molecular species simultaneously and provides a practical, quantitative imaging framework for the eventual clinical translation of molecular imaging contrast agents.

UFLC-ESI-MS/MS analysis of multiple mycotoxins in medicinal and edible Areca catechu.

PubMed

Liu, Hongmei; Luo, Jiaoyang; Kong, Weijun; Liu, Qiutao; Hu, Yichen; Yang, Meihua

2016-05-01

A robust, sensitive and reliable ultra fast liquid chromatography combined with electrospray ionization tandem mass spectrometry (UFLC-ESI-MS/MS) was optimized and validated for simultaneous identification and quantification of eleven mycotoxins in medicinal and edible Areca catechu, based on one-step extraction without any further clean-up. Separation and quantification were performed in both positive and negative modes under multiple reaction monitoring (MRM) in a single run with zearalanone (ZAN) as internal standard. The chromatographic conditions and MS/MS parameters were carefully optimized. Matrix-matched calibration was recommended to reduce matrix effects and improve accuracy, showing good linearity within wide concentration ranges. Limits of quantification (LOQ) were lower than 50 μg kg(-1), while limits of detection (LOD) were in the range of 0.1-20 μg kg(-1). The accuracy of the developed method was validated for recoveries, ranging from 85% to 115% with relative standard deviation (RSD) ≤14.87% at low level, from 75% to 119% with RSD ≤ 14.43% at medium level and from 61% to 120% with RSD ≤ 13.18% at high level, respectively. Finally, the developed multi-mycotoxin method was applied for screening of these mycotoxins in 24 commercial samples. Only aflatoxin B2 and zearalenone were found in 2 samples. This is the first report on the application of UFLC-ESI(+/-)-MS/MS for multi-class mycotoxins in A. catechu. The developed method with many advantages of simple pretreatment, rapid determination and high sensitivity is a proposed candidate for large-scale detection and quantification of multiple mycotoxins in other complex matrixes. Copyright © 2016 Elsevier Ltd. All rights reserved.

A dynamical approach in exploring the unknown mass in the Solar system using pulsar timing arrays

NASA Astrophysics Data System (ADS)

Guo, Y. J.; Lee, K. J.; Caballero, R. N.

2018-04-01

The error in the Solar system ephemeris will lead to dipolar correlations in the residuals of pulsar timing array for widely separated pulsars. In this paper, we utilize such correlated signals, and construct a Bayesian data-analysis framework to detect the unknown mass in the Solar system and to measure the orbital parameters. The algorithm is designed to calculate the waveform of the induced pulsar-timing residuals due to the unmodelled objects following the Keplerian orbits in the Solar system. The algorithm incorporates a Bayesian-analysis suit used to simultaneously analyse the pulsar-timing data of multiple pulsars to search for coherent waveforms, evaluate the detection significance of unknown objects, and to measure their parameters. When the object is not detectable, our algorithm can be used to place upper limits on the mass. The algorithm is verified using simulated data sets, and cross-checked with analytical calculations. We also investigate the capability of future pulsar-timing-array experiments in detecting the unknown objects. We expect that the future pulsar-timing data can limit the unknown massive objects in the Solar system to be lighter than 10-11-10-12 M⊙, or measure the mass of Jovian system to a fractional precision of 10-8-10-9.

Novel and remarkable enhanced-fluorescence system based on gold nanoclusters for detection of tetracycline.

PubMed

Yang, Xiaoming; Zhu, Shanshan; Dou, Yao; Zhuo, Yan; Luo, Yawen; Feng, Yuanjiao

2014-05-01

Tetracycline and Eu(3+), while coexisting, usually appear as a complex by chelating. This complex shows low fluorescence intensity, leading to its limitation of analytical goals. Gold nanoclusters (AuNCs), emerging as novel nano-material, are attracting increasing attentions in multiple fields. Herein, gold nanoclusters first function as a fluorescence-enhanced reagent rather than a conventional fluorescent-probe, and a dramatic enhanced-fluorescence system was built based on Eu(3+)-Tetracycline complex (EuTC) by introducing gold nanoclusters. Simultaneously, three types of gold nanoclusters were employed for exploring various conditions likely affecting the system, which demonstrate that no other gold nanoclusters than DNA-templated gold nanoclusters enormously caused fluorescence-enhancement of EuTC. Moreover, this enhanced-fluorescence system permitted available detection of tetracycline (TC) in a linear range of 0.01-5 μM, with a detection limit of 4 nM at a signal-to-noise ratio of 3. Significantly, the practicality of this method for detection of TC in human urine and milk samples was validated, demonstrating its advantages of simplicity, sensitivity and low cost. Interestingly, this system described here is probably promising for kinds of applications based on its dramatically enhanced-fluorescence. © 2013 Published by Elsevier B.V.

Robust experimental design for optimizing the microbial inhibitor test for penicillin detection in milk.

PubMed

Nagel, O G; Molina, M P; Basílico, J C; Zapata, M L; Althaus, R L

2009-06-01

To use experimental design techniques and a multiple logistic regression model to optimize a microbiological inhibition test with dichotomous response for the detection of Penicillin G in milk. A 2(3) x 2(2) robust experimental design with two replications was used. The effects of three control factors (V: culture medium volume, S: spore concentration of Geobacillus stearothermophilus, I: indicator concentration), two noise factors (Dt: diffusion time, Ip: incubation period) and their interactions were studied. The V, S, Dt, Ip factors and V x S, V x Ip, S x Ip interactions showed significant effects. The use of 100 microl culture medium volume, 2 x 10(5) spores ml(-1), 60 min diffusion time and 3 h incubation period is recommended. In these elaboration conditions, the penicillin detection limit was of 3.9 microg l(-1), similar to the maximum residue limit (MRL). Of the two noise factors studied, the incubation period can be controlled by means of the culture medium volume and spore concentration. We were able to optimize bioassays of dichotomous response using an experimental design and logistic regression model for the detection of residues at the level of MRL, aiding in the avoidance of health problems in the consumer.

SERS Assay for Copper(II) Ions Based on Dual Hot-Spot Model Coupling with MarR Protein: New Cu2+-Specific Biorecognition Element.

PubMed

Wang, Yulong; Su, Zhenhe; Wang, Limin; Dong, Jinbo; Xue, Juanjuan; Yu, Jiao; Wang, Yuan; Hua, Xiude; Wang, Minghua; Zhang, Cunzheng; Liu, Fengquan

2017-06-20

We have developed a rapid and ultrasensitive surface-enhanced Raman scattering (SERS) assay for Cu 2+ detection using the multiple antibiotic resistance regulator (MarR) as specific bridging molecules in a SERS hot-spot model. In the assay, Cu 2+ induces formation of MarR tetramers, which provide Au nanoparticle (NP)-AuNP bridges, resulting in the formation of SERS hot spots. 4-Mercaptobenzoic acid (4-MBA) was used as a Raman reporter. The addition of Cu 2+ increased the Raman intensity of 4-MBA. Use of a dual hot-spot signal-amplification strategy based on AuNP-AgNP heterodimers combined through antigen-antibody reactions increased the sensitivity of the sensing platform by 50-fold. The proposed method gave a linear response for Cu 2+ detection in the range of 0.5-1000 nM, with a detection limit of 0.18 nM, which is 5 orders of magnitude lower than the U.S. Environmental Protection Agency limit for Cu 2+ in drinking water (20 μM). In addition, all analyses can be completed in less than 15 min. The high sensitivity, high specificity, and rapid detection capacity of the SERS assay therefore provide a combined advantage over current assays.

A physics investigation of deadtime losses in neutron counting at low rates with Cf252

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

Evans, Louise G; Croft, Stephen

2009-01-01

{sup 252}Cf spontaneous fission sources are used for the characterization of neutron counters and the determination of calibration parameters; including both neutron coincidence counting (NCC) and neutron multiplicity deadtime (DT) parameters. Even at low event rates, temporally-correlated neutron counting using {sup 252}Cf suffers a deadtime effect. Meaning that in contrast to counting a random neutron source (e.g. AmLi to a close approximation), DT losses do not vanish in the low rate limit. This is because neutrons are emitted from spontaneous fission events in time-correlated 'bursts', and are detected over a short period commensurate with their lifetime in the detector (characterizedmore » by the system die-away time, {tau}). Thus, even when detected neutron events from different spontaneous fissions are unlikely to overlap in time, neutron events within the detected 'burst' are subject to intrinsic DT losses. Intrinsic DT losses for dilute Pu will be lower since the multiplicity distribution is softer, but real items also experience self-multiplication which can increase the 'size' of the bursts. Traditional NCC DT correction methods do not include the intrinsic (within burst) losses. We have proposed new forms of the traditional NCC Singles and Doubles DT correction factors. In this work, we apply Monte Carlo neutron pulse train analysis to investigate the functional form of the deadtime correction factors for an updating deadtime. Modeling is based on a high efficiency {sup 3}He neutron counter with short die-away time, representing an ideal {sup 3}He based detection system. The physics of dead time losses at low rates is explored and presented. It is observed that new forms are applicable and offer more accurate correction than the traditional forms.« less

Highly sensitive microfluidic paper-based photoelectrochemical sensing platform based on reversible photo-oxidation products and morphology-preferable multi-plate ZnO nanoflowers.

PubMed

Kong, Qingkun; Wang, Yanhu; Zhang, Lina; Xu, Caixia; Yu, Jinghua

2018-07-01

A microfluidic paper-based analytical device (μPAD) was simply constructed for highly sensitive detection of L-glutamic acid and L-cysteine. The μPAD featured with two functional zones on one strip of paper achieved by preferable multi-plate ZnO nanoflowers (ZnO NFs) and molecularly imprinting polymer (MIP) membranes. The as-designed μPAD was established based on the inherent relation between the photo-oxidation products and photoelectrochemical (PEC) performance with the highly sensitive detection of biomolecules. The ZnO NFs were utilized to produce photo-oxidation products by driving the reaction between ferrocenemethanol and photogenerated holes under ultraviolet light. The photo-oxidation products easily flowed to MIP membranes along the hydrophilic channel via capillary action. MIP membranes as the receptors specifically recognized the analytes as well as decreased the electron loss by blocking the reduction reaction between electrons and photo-oxidation products. The PEC response was obtained in the processes of electrons transfer and exhibited the direct relationships corresponding to the concentrations of target analytes. The μPAD showed the detection limits toward L-glutamic acid and L-cysteine as low as 9.6 pM and 24 pM, respectively. Moreover, it is interesting to point out that ZnO NFs nanostructure shows superior PEC signal compared with those of ZnO nanospheres, nanosheets, and nanorod arrays. In current work, photo-oxidation products are utilized to achieve highly sensitive PEC detection for biomolecules under ultraviolet light as well as avoid the effects of multiple modifications in the same region on the reproducibility, which is beneficial for opening up rich possibility for designing more efficient analytical strategy. Copyright © 2018 Elsevier B.V. All rights reserved.

Sensitive immunoassay detection of multiple environmental chemicals on protein microarrays using DNA/dye conjugate as a fluorescent label.

PubMed

Fan, Ziyan; Keum, Young Soo; Li, Qing X; Shelver, Weilin L; Guo, Liang-Hong

2012-05-01

Indirect competitive immunoassays were developed on protein microarrays for the sensitive and simultaneous detection of multiple environmental chemicals in one sample. In this assay, a DNA/SYTOX Orange conjugate was employed as an antibody label to increase the fluorescence signal and sensitivity of the immunoassays. Epoxy-modified glass slides were selected as the substrate for the production of 4 × 4 coating antigen microarrays. With this signal-enhancing system, competition curves for 17β-estradiol (E2), benzo[a]pyrene (BaP) and 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) were obtained individually on the protein microarray. The IC(50) and calculated limit of detection (LOD) are 0.32 μg L(-1) and 0.022 μg L(-1) for E2, 37.2 μg L(-1) and 24.5 μg L(-1) for BaP, and 31.6 μg L(-1) and 2.8 μg L(-1) for BDE-47, respectively. LOD of E2 is 14-fold lower than the value reported in a previous study using Cy3 labeled antibody (Du et al., Clin. Chem, 2005, 51, 368-375). The results of the microarray immunoassay were within 15% of chromatographic analysis for all three pollutants in spiked river water samples, thus verifying the immunoassay. Simultaneous detection of E2, BaP and BDE-47 in one sample was demonstrated. There was no cross-reaction in the immunoassay between these three environmental chemicals. These results suggest that microarray-based immunoassays with DNA/dye conjugate labels are useful tools for the rapid, sensitive, and high throughput screening of multiple environmental contaminants.

Label-Free Fluorescent DNA Dendrimers for microRNA Detection Based On Nonlinear Hybridization Chain Reaction-Mediated Multiple G-Quadruplex with Low Background Signal.

PubMed

Xue, Qingwang; Liu, Chunxue; Li, Xia; Dai, Li; Wang, Huaisheng

2018-04-18

Various fluorescent sensing systems for miRNA detection have been developed, but they mostly contain enzymatic amplification reactions and label procedures. The strict reaction conditions of tool enzymes and the high cost of labeling limit their potential applications, especially in complex biological matrices. Here, we have addressed the difficult problems and report a strategy for label-free fluorescent DNA dendrimers based on enzyme-free nonlinear hybridization chain reaction (HCR)-mediated multiple G-quadruplex for simple, sensitive, and selective detection of miRNAs with low-background signal. In the strategy, a split G-quadruplex (3:1) sequence is ingeniously designed at both ends of two double-stranded DNAs, which is exploited as building blocks for nonlinear HCR assembly, thereby acquiring a low background signal. A hairpin switch probe (HSP) was employed as recognition and transduction element. Upon sensing the target miRNA, the nonlinear HCR assembly of two blocks (blocks-A and blocks-B) was initiated with the help of two single-stranded DNA assistants, resulting in chain-branching growth of DNA dendrimers with multiple G-quadruplex incorporation. With the zinc(II)-protoporphyrin IX (ZnPPIX) selectively intercalated into the multiple G-quadruplexes, fluorescent DNA dendrimers were obtained, leading to an exponential fluorescence intensity increase. Benefiting from excellent performances of nonlinear HCR and low background signal, this strategy possesses the characteristics of a simplified reaction operation process, as well as high sensitivity. Moreover, the proposed fluorescent sensing strategy also shows preferable selectivity, and can be implemented without modified DNA blocks. Importantly, the strategy has also been tested for miRNA quantification with high confidence in breast cancer cells. Thus, this proposed strategy for label-free fluorescent DNA dendrimers based on a nonlinear HCR-mediated multiple G-quadruplex will be turned into an alternative approach for simple, sensitive, and selective miRNA quantification.

Multiple Cross Displacement Amplification Coupled With Nanoparticles-Based Lateral Flow Biosensor for Detection of Staphylococcus aureus and Identification of Methicillin-Resistant S. aureus.

PubMed

Wang, Yi; Yan, Weiqiang; Fu, Shanshan; Hu, Shoukui; Wang, Yan; Xu, Jianguo; Ye, Changyun

2018-01-01

Staphylococcus aureus ( S. aureus ), including methicillin-resistant S. aureus (MRSA), is one of the most important human pathogens, which is responsible for bacteremia, soft-tissue infections, and food poisoning. Hence, multiple cross displacement amplification (MCDA) is employed to detect all S. aureus strains, and differentiates MRSA from methicillin-sensitive S. aureus . Multiplex MCDA (m-MCDA), which targets the nuc gene ( S. aureus -specific gene) and mecA gene (encoding penicillin-binding protein-2'), could detect S. aureus strains and identify MRSA within 85 min. Detection of the m-MCDA products is achieved using disposable lateral flow biosensors. A total of 58 strains, including various species of Gram-positive and Gram-negative strains, are used for evaluating and optimizing m-MCDA assays. The optimal amplification condition is found to be 63°C for 40 min, with detection limits at 100 fg DNA/reaction for nuc and mecA genes in the pure cultures, and 10 CFU/tube for nuc and mecA genes in the blood samples. The analytical specificity of m-MCDA assay is of 100%, and no cross-reactions to non- S. aureus strains are produced according to the specificity testing. Particularly, two additional components, including AUDG enzyme and dUTP, are added into the m-MCDA amplification mixtures, which are used for eliminating the unwanted results arising from carryover contamination. Thus, the m-MCDA technique appears to be a simple, rapid, sensitive, and reliable assay to detect all S. aureus strains, and identify MRSA infection for appropriate antibiotic therapy.

A multiple reaction monitoring (MRM) method to detect Bcr-Abl kinase activity in CML using a peptide biosensor.

PubMed

Yang, Tzu-Yi; Eissler, Christie L; Hall, Mark C; Parker, Laurie L

2013-01-01

The protein kinase Bcr-Abl plays a major role in the pathogenesis of chronic myelogenous leukemia (CML), and is the target of the breakthrough drug imatinib (Gleevec™). While most patients respond well to imatinib, approximately 30% never achieve remission or develop resistance within 1-5 years of starting imatinib treatment. Evidence from clinical studies suggests that achieving at least 50% inhibition of a patient's Bcr-Abl kinase activity (relative to their level at diagnosis) is associated with improved patient outcomes, including reduced occurrence of resistance and longer maintenance of remission. Accordingly, sensitive assays for detecting Bcr-Abl kinase activity compatible with small amounts of patient material are desirable as potential companion diagnostics for imatinib. Here we report the detection of Bcr-Abl activity and inhibition by imatinib in the human CML cell line K562 using a cell-penetrating peptide biosensor and multiple reaction monitoring (MRM) on a triple quadrupole mass spectrometer. MRM enabled reproducible, selective detection of the peptide biosensor at fmol levels from aliquots of cell lysate equivalent to ~15,000 cells. This degree of sensitivity will facilitate the miniaturization of the entire assay procedure down to cell numbers approaching 15,000, making it practical for translational applications in patient cells in which the limited amount of available patient material often presents a major challenge.

A Multiple Reaction Monitoring (MRM) Method to Detect Bcr-Abl Kinase Activity in CML Using a Peptide Biosensor

PubMed Central

Yang, Tzu-Yi; Eissler, Christie L.; Hall, Mark C.; Parker, Laurie L.

2013-01-01

The protein kinase Bcr-Abl plays a major role in the pathogenesis of chronic myelogenous leukemia (CML), and is the target of the breakthrough drug imatinib (Gleevec™). While most patients respond well to imatinib, approximately 30% never achieve remission or develop resistance within 1–5 years of starting imatinib treatment. Evidence from clinical studies suggests that achieving at least 50% inhibition of a patient’s Bcr-Abl kinase activity (relative to their level at diagnosis) is associated with improved patient outcomes, including reduced occurrence of resistance and longer maintenance of remission. Accordingly, sensitive assays for detecting Bcr-Abl kinase activity compatible with small amounts of patient material are desirable as potential companion diagnostics for imatinib. Here we report the detection of Bcr-Abl activity and inhibition by imatinib in the human CML cell line K562 using a cell-penetrating peptide biosensor and multiple reaction monitoring (MRM) on a triple quadrupole mass spectrometer. MRM enabled reproducible, selective detection of the peptide biosensor at fmol levels from aliquots of cell lysate equivalent to ∼15,000 cells. This degree of sensitivity will facilitate the miniaturization of the entire assay procedure down to cell numbers approaching 15,000, making it practical for translational applications in patient cells in which the limited amount of available patient material often presents a major challenge. PMID:23437189

ExScalibur: A High-Performance Cloud-Enabled Suite for Whole Exome Germline and Somatic Mutation Identification.

PubMed

Bao, Riyue; Hernandez, Kyle; Huang, Lei; Kang, Wenjun; Bartom, Elizabeth; Onel, Kenan; Volchenboum, Samuel; Andrade, Jorge

2015-01-01

Whole exome sequencing has facilitated the discovery of causal genetic variants associated with human diseases at deep coverage and low cost. In particular, the detection of somatic mutations from tumor/normal pairs has provided insights into the cancer genome. Although there is an abundance of publicly-available software for the detection of germline and somatic variants, concordance is generally limited among variant callers and alignment algorithms. Successful integration of variants detected by multiple methods requires in-depth knowledge of the software, access to high-performance computing resources, and advanced programming techniques. We present ExScalibur, a set of fully automated, highly scalable and modulated pipelines for whole exome data analysis. The suite integrates multiple alignment and variant calling algorithms for the accurate detection of germline and somatic mutations with close to 99% sensitivity and specificity. ExScalibur implements streamlined execution of analytical modules, real-time monitoring of pipeline progress, robust handling of errors and intuitive documentation that allows for increased reproducibility and sharing of results and workflows. It runs on local computers, high-performance computing clusters and cloud environments. In addition, we provide a data analysis report utility to facilitate visualization of the results that offers interactive exploration of quality control files, read alignment and variant calls, assisting downstream customization of potential disease-causing mutations. ExScalibur is open-source and is also available as a public image on Amazon cloud.

Millimeter wave sensor for monitoring effluents

DOEpatents

Gopalsami, Nachappa; Bakhtiari, Sasan; Raptis, Apostolos C.; Dieckman, Stephen L.

1995-01-01

A millimeter-wave sensor for detecting and measuring effluents from processing plants either remotely or on-site includes a high frequency signal source for transmitting frequency-modulated continuous waves in the millimeter or submillimeter range with a wide sweep capability and a computer-controlled detector for detecting a plurality of species of effluents on a real time basis. A high resolution spectrum of an effluent, or effluents, is generated by a deconvolution of the measured spectra resulting in a narrowing of the line widths by 2 or 3 orders of magnitude as compared with the pressure broadened spectra detected at atmospheric pressure for improved spectral specificity and measurement sensitivity. The sensor is particularly adapted for remote monitoring such as where access is limited or sensor cost restricts multiple sensors as well as for large area monitoring under nearly all weather conditions.

Comparison of 16-Channel Laser Photoreceivers for Topographic Mapping

NASA Technical Reports Server (NTRS)

Krainak, Michael A.; Yang, Guangning; Sun, XiaoIi; Lu, Wei; Bai, Xiaogang; Yuan, Ping; McDonald, Paul; Boisvert, Joseph; Woo, Robyn; Wan, Kam;

Microfluidics-Based PCR for Fusion Transcript Detection.

PubMed

Chen, Hui

2016-01-01

The microfluidic technology allows the production of network of submillimeter-size fluidic channels and reservoirs in a variety of material systems. The microfluidic-based polymerase chain reaction (PCR) allows automated multiplexing of multiple samples and multiple assays simultaneously within a network of microfluidic channels and chambers that are co-ordinated in controlled fashion by the valves. The individual PCR reaction is performed in nanoliter volume, which allows testing on samples with limited DNA and RNA. The microfluidics devices are used in various types of PCR such as digital PCR and single molecular emulsion PCR for genotyping, gene expression, and miRNA expression. In this chapter, the use of a microfluidics-based PCR for simultaneous screening of 14 known fusion transcripts in patients with leukemia is described.

2D-DIGE in Proteomics.

PubMed

Pasquali, Matias; Serchi, Tommaso; Planchon, Sebastien; Renaut, Jenny

2017-01-01

The two-dimensional difference gel electrophoresis method is a valuable approach for proteomics. The method, using cyanine fluorescent dyes, allows the co-migration of multiple protein samples in the same gel and their simultaneous detection, thus reducing experimental and analytical time. 2D-DIGE, compared to traditional post-staining 2D-PAGE protocols (e.g., colloidal Coomassie or silver nitrate), provides faster and more reliable gel matching, limiting the impact of gel to gel variation, and allows also a good dynamic range for quantitative comparisons. By the use of internal standards, it is possible to normalize for experimental variations in spot intensities and gel patterns. Here we describe the experimental steps we follow in our routine 2D-DIGE procedure that we then apply to multiple biological questions.

Microfabricated capillary electrophoresis chip and method for simultaneously detecting multiple redox labels

DOEpatents

Mathies, Richard A.; Singhal, Pankaj; Xie, Jin; Glazer, Alexander N.

2002-01-01

This invention relates to a microfabricated capillary electrophoresis chip for detecting multiple redox-active labels simultaneously using a matrix coding scheme and to a method of selectively labeling analytes for simultaneous electrochemical detection of multiple label-analyte conjugates after electrophoretic or chromatographic separation.

CARMENES input catalogue of M dwarfs. II. High-resolution imaging with FastCam

NASA Astrophysics Data System (ADS)

Cortés-Contreras, M.; Béjar, V. J. S.; Caballero, J. A.; Gauza, B.; Montes, D.; Alonso-Floriano, F. J.; Jeffers, S. V.; Morales, J. C.; Reiners, A.; Ribas, I.; Schöfer, P.; Quirrenbach, A.; Amado, P. J.; Mundt, R.; Seifert, W.

2017-01-01

Aims: We search for low-mass companions of M dwarfs and characterize their multiplicity fraction with the purpose of helping in the selection of the most appropriate targets for the CARMENES exoplanet survey. Methods: We obtained high-resolution images in the I band with the lucky imaging instrument FastCam at the 1.5 m Telescopio Carlos Sánchez for 490 mid- to late-M dwarfs. For all the detected binaries, we measured angular separations, position angles, and magnitude differences in the I band. We also calculated the masses of each individual component and estimated orbital periods, using the available magnitude and colour relations for M dwarfs and our own MJ-spectral type and mass-MI relations. To avoid biases in our sample selection, we built a volume-limited sample of M0.0-M5.0 dwarfs that is complete up to 86% within 14 pc. Results: From the 490 observed stars, we detected 80 companions in 76 systems, of which 30 are new discoveries. Another six companion candidates require additional astrometry to confirm physical binding. The multiplicity fraction in our observed sample is 16.7 ± 2.0%. The bias-corrected multiplicity fraction in our volume-limited sample is 19.5 ± 2.3% for angular separations of 0.2 to 5.0 arcsec (1.4-65.6 au), with a peak in the distribution of the projected physical separations at 2.5-7.5 au. For M0.0-M3.5 V primaries, our search is sensitive to mass ratios higher than 0.3 and there is a higher density of pairs with mass ratios over 0.8 compared to those at lower mass ratios. Binaries with projected physical separations shorter than 50 au also tend to be of equal mass. For 26 of our systems, we estimated orbital periods shorter than 50 a, 10 of which are presented here for the first time. We measured variations in angular separation and position angle that are due to orbital motions in 17 of these systems. The contribution of binaries and multiples with angular separations shorter than 0.2 arcsec, longer than 5.0 arcsec, and of spectroscopic binaries identified from previous searches, although not complete, may increase the multiplicity fraction of M dwarfs in our volume-limited sample to at least 36%. Tables A.1-A.6 are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/597/A47

Multiple animal studies for medical chemical defense program in soldier/patient decontamination and drug development on task 85-17: Validation of an analytical method for the detection of soman (GD), mustard (HD), tabun (GA), and VX in wastewater samples. Final report, 13 October 1985-1 January 1989

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

Joiner, R.L.; Hayes, L.; Rust, W.

1989-05-01

The following report summarizes the development and validation of an analytical method for the analyses of soman (GD), mustard (HD), VX, and tabun (GA) in wastewater. The need for an analytical method that can detect GD, HD, VX, and GA with the necessary sensitivity (< 20 parts per billion (PPB))and selectivity is essential to Medical Research and Evaluation Facility (MREF) operations. The analytical data were generated using liquid-liquid extraction of the wastewater, with the extract being concentrated and analyzed by gas chromatography (GC) methods. The sample preparation and analyses methods were developed in support of ongoing activities within the MREF.more » We have documented the precision and accuracy of the analytical method through an expected working calibration range (3.0 to 60 ppb). The analytical method was statistically evaluated over a range of concentrations to establish a detection limit and quantitation limit for the method. Whenever the true concentration is 8.5 ppb or above, the probability is at least 99.9 percent that the measured concentration will be ppb or above. Thus, 6 ppb could be used as a lower reliability limit for detecting concentrations in excess of 8.5 ppb. In summary, the proposed sample extraction and analyses methods are suitable for quantitative analyses to determine the presence of GD, HD, VX, and GA in wastewater samples. Our findings indicate that we can detect any of these chemical surety materiel (CSM) in water at or below the established U.S. Army Surgeon General's safety levels in drinking water.« less

Convenient, inexpensive quantification of elemental sulfur by simultaneous in situ reduction and colorimetric detection.

PubMed

Kwasniewski, Misha T; Allison, Rachel B; Wilcox, Wayne F; Sacks, Gavin L

2011-10-03

Rapid, inexpensive, and convenient methods for quantifying elemental sulfur (S(0)) with low or sub-μgg(-1) limits of detection would be useful for a range of applications where S(0) can act as a precursor for noxious off-aromas, e.g., S(0) in pesticide residues on winegrapes or as a contaminant in drywall. However, existing quantification methods rely on toxic reagents, expensive and cumbersome equipment, or demonstrate poor selectivity. We have developed and optimized an inexpensive, rapid method (∼15 min per sample) for quantifying S(0) in complex matrices. Following dispersion of the sample in PEG-400 and buffering, S(0) is quantitatively reduced to H(2)S in situ by dithiothreitol and simultaneously quantified by commercially available colorimetric H(2)S detection tubes. By employing multiple tubes, the method demonstrated linearity from 0.03 to 100 μg S(0) g(-1) for a 5 g sample (R(2)=0.994, mean CV=6.4%), and the methodological detection limit was 0.01 μg S(0) g(-1). Interferences from sulfite or sulfate were not observed. Mean recovery of an S(0) containing sulfur fungicide in grape macerate was 84.7% with a mean CV of 10.4%. Mean recovery of S(0) in a colloidal sulfur preparation from a drywall matrix was 106.6% with a mean CV of 6.9%. Comparable methodological detection limits, sensitivity, and recoveries were achieved in grape juice, grape macerate and with 1g drywall samples, indicating that the methodology should be robust across a range of complex matrices. Copyright © 2011 Elsevier B.V. All rights reserved.

Human exposure to Bisphenol A and liver health status: Quantification of urinary and circulating levels by LC-MS/MS.

PubMed

Nicolucci, Carla; Errico, Sonia; Federico, Alessandro; Dallio, Marcello; Loguercio, Carmelina; Diano, Nadia

2017-06-05

A selective and highly sensitive analytical methodology for determination of Bisphenol A in human plasma was developed and validated. The method was based on selective liquid/solid extraction, combined with liquid chromatography-electrospray ionization tandem mass spectrometry in the multiple reaction monitoring mode and negative ionization. The linearity of the detector response was verified in human plasma over the concentration range 0.100-200ngmL -1 . The detection limit was 0.03ngmL -1 and the quantification limit was 0.100ngmL -1 . The analytical features of the proposed in-house validated method were satisfactory: precision was <10% and recoveries were around 84-104%. The matrix effect was studied and compensated using deuterated labeled standard. The applicability of the proposed method was demonstrated analyzing human plasma samples from individuals affected by non-alcoholic fatty liver disease. Bisphenol A was detected above the detection limit in all samples. The data show a persistence of unconjugated Bisphenol A levels in plasma and indicate a chronic Bisphenol A exposure of the target organ, suggesting an association between liver health status and Bisphenol A exposure. The results from our study are valuable for further investigation with large sample size and longitudinal study designs, necessary to confirm the observed association. Copyright © 2017 Elsevier B.V. All rights reserved.

CO EMISSION IN OPTICALLY OBSCURED (TYPE-2) QUASARS AT REDSHIFTS z Almost-Equal-To 0.1-0.4

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

Krips, M.; Neri, R.; Cox, P., E-mail: krips@iram.fr, E-mail: neri@iram.fr, E-mail: cox@iram.fr

We present a search for CO emission in a sample of 10 type-2 quasar host galaxies with redshifts of z Almost-Equal-To 0.1-0.4. We detect CO(J = 1-0) line emission with {>=}5{sigma} in the velocity integrated intensity maps of five sources. A sixth source shows a tentative detection at the {approx}4.5{sigma} level of its CO(J = 1-0) line emission. The CO emission of all six sources is spatially coincident with the position at optical, infrared, or radio wavelengths. The spectroscopic redshifts derived from the CO(J = 1-0) line are very close to the photometric ones for all five detections except formore » the tentative detection for which we find a much larger discrepancy. We derive gas masses of {approx}(2-16) Multiplication-Sign 10{sup 9} M{sub Sun} for the CO emission in the six detected sources, while we constrain the gas masses to upper limits of M{sub gas} {<=} 8 Multiplication-Sign 10{sup 9} M{sub Sun} for the four non-detections. These values are of the order or slightly lower than those derived for type-1 quasars. The line profiles of the CO(J = 1-0) emission are rather narrow ({approx}<300 km s{sup -1}) and single peaked, unveiling no typical signatures for current or recent merger activity, and are comparable to that of type-1 quasars. However, at least one of the observed sources shows a tidal-tail-like emission in the optical that is indicative of an ongoing or past merging event. We also address the problem of detecting spurious {approx}5{sigma} emission peaks within the field of view.« less

Multiplex Droplet Digital PCR Quantification of Recurrent Somatic Mutations in Diffuse Large B-Cell and Follicular Lymphoma.

PubMed

Alcaide, Miguel; Yu, Stephen; Bushell, Kevin; Fornika, Daniel; Nielsen, Julie S; Nelson, Brad H; Mann, Koren K; Assouline, Sarit; Johnson, Nathalie A; Morin, Ryan D

2016-09-01

A plethora of options to detect mutations in tumor-derived DNA currently exist but each suffers limitations in analytical sensitivity, cost, or scalability. Droplet digital PCR (ddPCR) is an appealing technology for detecting the presence of specific mutations based on a priori knowledge and can be applied to tumor biopsies, including formalin-fixed paraffin embedded (FFPE) tissues. More recently, ddPCR has gained popularity in its utility in quantifying circulating tumor DNA. We have developed a suite of novel ddPCR assays for detecting recurrent mutations that are prevalent in common B-cell non-Hodgkin lymphomas (NHLs), including diffuse large B-cell lymphoma, follicular lymphoma, and lymphoplasmacytic lymphoma. These assays allowed the differentiation and counting of mutant and wild-type molecules using one single hydrolysis probe. We also implemented multiplexing that allowed the simultaneous detection of distinct mutations and an "inverted" ddPCR assay design, based on employing probes matching wild-type alleles, capable of detecting the presence of multiple single nucleotide polymorphisms. The assays successfully detected and quantified somatic mutations commonly affecting enhancer of zeste 2 polycomb repressive complex 2 subunit (EZH2) (Y641) and signal transducer and activator of transcription 6 (STAT6) (D419) hotspots in fresh tumor, FFPE, and liquid biopsies. The "inverted" ddPCR approach effectively reported any single nucleotide variant affecting either of these 2 hotspots as well. Finally, we could effectively multiplex hydrolysis probes targeting 2 additional lymphoma-related hotspots: myeloid differentiation primary response 88 (MYD88; L265P) and cyclin D3 (CCND3; I290R). Our suite of ddPCR assays provides sufficient analytical sensitivity and specificity for either the invasive or noninvasive detection of multiple recurrent somatic mutations in B-cell NHLs. © 2016 American Association for Clinical Chemistry.

Rapid and Sensitive Detection of Vibrio parahaemolyticus and Vibrio vulnificus by Multiple Endonuclease Restriction Real-Time Loop-Mediated Isothermal Amplification Technique.

PubMed

Wang, Yi; Li, Dongxun; Wang, Yan; Li, Kewei; Ye, Changyun

2016-01-19

Vibrio parahaemolyticus and Vibrio vulnificus are two marine seafood-borne pathogens causing severe illnesses in humans and aquatic animals. In this study, a recently developed novel multiple endonuclease restriction real-time loop-mediated isothermal amplification technology (MERT-LAMP) were successfully developed and evaluated for simultaneous detection of V. parahaemolyticus and V. vulnificus strains in only a single reaction. Two MERT-LAMP primer sets were designed to specifically target toxR gene of V. parahaemolyticus and rpoS gene of V. vulnificus. The MERT-LAMP reactions were conducted at 62 °C, and the positive results were produced in as short as 19 min with the genomic DNA templates extracted from the V. parahaemolyticus and V. vulnificus strains. The two target pathogens present in the same sample could be simultaneously detected and correctly differentiated based on distinct fluorescence curves in a real-time format. The sensitivity of MERT-LAMP assay was 250 fg and 125 fg DNA per reaction with genomic templates of V. parahaemolyticus and V. vulnificus strains, which was in conformity with conventional LAMP detection. Compared with PCR-based techniques, the MERT-LAMP technology was 100- and 10-fold more sensitive than that of PCR and qPCR methods. Moreover, the limit of detection of MERT-LAMP approach for V. parahaemolyticus isolates and V. vulnificus isolates detection in artificially-contaminated oyster samples was 92 CFU and 83 CFU per reaction. In conclusion, the MERT-LAMP assay presented here was a rapid, specific, and sensitive tool for the detection of V. parahaemolyticus and V. vulnificus, and could be adopted for simultaneous screening of V. parahaemolyticus and V. vulnificus in a wide variety of samples.

The association between cecal insertion time and colorectal neoplasm detection

PubMed Central

2013-01-01

Background Information on the impact of cecal insertion time on colorectal neoplasm detection is limited. Our objective was to determine the association between cecal insertion time and colorectal neoplasm detection rate in colonoscopy screening. Methods We performed a cross-sectional study of 12,679 consecutive subjects aged 40–79 years undergoing screening colonoscopy in routine health check-ups at the Center for Health Promotion of the Samsung Medical Center from December 2007 to June 2009. Fixed effects logistic regression conditioning on colonoscopist was used to eliminate confounding due to differences in technical ability and other characteristics across colonoscopists. Results The mean cecal insertion time was 5.9 (SD, 4.4 minutes). We identified 4,249 (33.5%) participants with colorectal neoplasms, of whom 1,956 had small single adenomas (<5 mm), 595 had medium single adenomas (5–9 mm), and 1,699 had multiple adenomas or advanced colorectal neoplasms. The overall rates of colorectal neoplasm detection by quartiles of cecal insertion time were 36.8%, 33.4%, 32.7%, and 31.0%, respectively (p trend <0.001).The odds for small single colorectal adenoma detection was 16% lower (adjusted OR 0.84; 95% CI 0.71 to 0.99) in the fourth compared to the first quartile of insertion time (p trend 0.005). Insertion time was not associated with the detection rate of single adenomas ≥5 mm, multiple adenomas or advanced colorectal neoplasms. Conclusion Shorter insertion times were associated with increased rates of detection of small colorectal adenomas <5 mm. Cecal insertion time may be clinically relevant as missed small colorectal adenomas may progress to more advanced lesions. PMID:23915303

Supporting secure programming in web applications through interactive static analysis.

PubMed

Zhu, Jun; Xie, Jing; Lipford, Heather Richter; Chu, Bill

2014-07-01

Many security incidents are caused by software developers' failure to adhere to secure programming practices. Static analysis tools have been used to detect software vulnerabilities. However, their wide usage by developers is limited by the special training required to write rules customized to application-specific logic. Our approach is interactive static analysis, to integrate static analysis into Integrated Development Environment (IDE) and provide in-situ secure programming support to help developers prevent vulnerabilities during code construction. No additional training is required nor are there any assumptions on ways programs are built. Our work is motivated in part by the observation that many vulnerabilities are introduced due to failure to practice secure programming by knowledgeable developers. We implemented a prototype interactive static analysis tool as a plug-in for Java in Eclipse. Our technical evaluation of our prototype detected multiple zero-day vulnerabilities in a large open source project. Our evaluations also suggest that false positives may be limited to a very small class of use cases.

Supporting secure programming in web applications through interactive static analysis

PubMed Central

Zhu, Jun; Xie, Jing; Lipford, Heather Richter; Chu, Bill

2013-01-01

Many security incidents are caused by software developers’ failure to adhere to secure programming practices. Static analysis tools have been used to detect software vulnerabilities. However, their wide usage by developers is limited by the special training required to write rules customized to application-specific logic. Our approach is interactive static analysis, to integrate static analysis into Integrated Development Environment (IDE) and provide in-situ secure programming support to help developers prevent vulnerabilities during code construction. No additional training is required nor are there any assumptions on ways programs are built. Our work is motivated in part by the observation that many vulnerabilities are introduced due to failure to practice secure programming by knowledgeable developers. We implemented a prototype interactive static analysis tool as a plug-in for Java in Eclipse. Our technical evaluation of our prototype detected multiple zero-day vulnerabilities in a large open source project. Our evaluations also suggest that false positives may be limited to a very small class of use cases. PMID:25685513

Co-immobilization of multiple enzymes by metal coordinated nucleotide hydrogel nanofibers: improved stability and an enzyme cascade for glucose detection.

PubMed

Liang, Hao; Jiang, Shuhui; Yuan, Qipeng; Li, Guofeng; Wang, Feng; Zhang, Zijie; Liu, Juewen

2016-03-21

Preserving enzyme activity and promoting synergistic activity via co-localization of multiple enzymes are key topics in bionanotechnology, materials science, and analytical chemistry. This study reports a facile method for co-immobilizing multiple enzymes in metal coordinated hydrogel nanofibers. Specifically, four types of protein enzymes, including glucose oxidase, Candida rugosa lipase, α-amylase, and horseradish peroxidase, were respectively encapsulated in a gel nanofiber made of Zn(2+) and adenosine monophosphate (AMP) with a simple mixing step. Most enzymes achieved quantitative loading and retained full activity. At the same time, the entrapped enzymes were more stable against temperature variation (by 7.5 °C), protease attack, extreme pH (by 2-fold), and organic solvents. After storing for 15 days, the entrapped enzyme still retained 70% activity while the free enzyme nearly completely lost its activity. Compared to nanoparticles formed with AMP and lanthanide ions, the nanofiber gels allowed much higher enzyme activity. Finally, a highly sensitive and selective biosensor for glucose was prepared using the gel nanofiber to co-immobilize glucose oxidase and horseradish peroxidase for an enzyme cascade system. A detection limit of 0.3 μM glucose with excellent selectivity was achieved. This work indicates that metal coordinated materials using nucleotides are highly useful for interfacing with biomolecules.

Long-Term Occupancy Trends in a Data-Poor Dugong Population in the Andaman and Nicobar Archipelago

PubMed Central

D’Souza, Elrika; Patankar, Vardhan; Arthur, Rohan; Alcoverro, Teresa; Kelkar, Nachiket

2013-01-01

Prioritizing efforts for conserving rare and threatened species with limited past data and lacking population estimates is predicated on robust assessments of their occupancy rates. This is particularly challenging for elusive, long-lived and wide-ranging marine mammals. In this paper we estimate trends in long-term (over 50years) occupancy, persistence and extinction of a vulnerable and data-poor dugong (Dugong dugon) population across multiple seagrass meadows in the Andaman and Nicobar archipelago (India). For this we use hierarchical Bayesian dynamic occupancy models accounting for false negatives (detection probability<1), persistence and extinction, to two datasets: a) fragmentary long-term occurrence records from multiple sources (1959–2004, n = 40 locations), and b) systematic detection/non-detection data from current surveys (2010–2012, n = 57). Dugong occupancy across the archipelago declined by 60% (from 0.45 to 0.18) over the last 20 years and present distribution was largely restricted to sheltered bays and channels with seagrass meadows dominated by Halophila and Halodule sp. Dugongs were not found in patchy meadows with low seagrass cover. In general, seagrass habitat availability was not limiting for dugong occupancy, suggesting that anthropogenic factors such as entanglement in gillnets and direct hunting may have led to local extinction of dugongs from locations where extensive seagrass meadows still thrive. Effective management of these remnant dugong populations will require a multi-pronged approach, involving 1) protection of areas where dugongs still persist, 2) monitoring of seagrass habitats that dugongs could recolonize, 3) reducing gillnet use in areas used by dugongs, and 4) engaging with indigenous/settler communities to reduce impacts of hunting. PMID:24143180

Cost effectiveness of the addition of a comprehensive CT scan to the abdomen and pelvis for the detection of cancer after unprovoked venous thromboembolism.

PubMed

Coyle, Kathryn; Carrier, Marc; Lazo-Langner, Alejandro; Shivakumar, Sudeep; Zarychanski, Ryan; Tagalakis, Vicky; Solymoss, Susan; Routhier, Nathalie; Douketis, James; Coyle, Douglas

2017-03-01

Unprovoked venous thromboembolism (VTE) can be the first manifestation of cancer. It is unclear if extensive screening for occult cancer including a comprehensive computed tomography (CT) scan of the abdomen/pelvis is cost-effective in this patient population. To assess the health care related costs, number of missed cancer cases and health related utility values of a limited screening strategy with and without the addition of a comprehensive CT scan of the abdomen/pelvis and to identify to what extent testing should be done in these circumstances to allow early detection of occult cancers. Cost effectiveness analysis using data that was collected alongside the SOME randomized controlled trial which compared an extensive occult cancer screening including a CT of the abdomen/pelvis to a more limited screening strategy in patients with a first unprovoked VTE, was used for the current analyses. Analyses were conducted with a one-year time horizon from a Canadian health care perspective. Primary analysis was based on complete cases, with sensitivity analysis using appropriate multiple imputation methods to account for missing data. Data from a total of 854 patients with a first unprovoked VTE were included in these analyses. The addition of a comprehensive CT scan was associated with higher costs ($551 CDN) with no improvement in utility values or number of missed cancers. Results were consistent when adopting multiple imputation methods. The addition of a comprehensive CT scan of the abdomen/pelvis for the screening of occult cancer in patients with unprovoked VTE is not cost effective, as it is both more costly and not more effective in detecting occult cancer. Copyright © 2017 Elsevier Ltd. All rights reserved.

A Facile Stable-Isotope Dilution Method for Determination of Sphingosine Phosphate Lyase Activity

PubMed Central

Suh, Jung H.; Eltanawy, Abeer; Rangan, Apoorva; Saba, Julie D.

2015-01-01

A new technique for quantifying sphingosine phosphate lyase activity in biological samples is described. In this procedure, 2-hydrazinoquinoline is used to convert (2E)-hexadecenal into the corresponding hydrazone derivative to improve ionization efficiency and selectivity of detection. Combined utilization of liquid chromatographic separation and multiple reaction monitoring-mass spectrometry allows for simultaneous quantification of the substrate S1P and product (2E)-hexadecenal. Incorporation of (2E)-d5-hexadecenal as an internal standard improves detection accuracy and precision. A simple one-step derivatization procedure eliminates the need for further extractions. Limits of quantification for (2E)-hexadecenal and sphingosine-1-phosphate are 100 and 50 fmol, respectively. The assay displays a wide dynamic detection range useful for detection of low basal sphingosine phosphate lyase activity in wild type cells, SPL-overexpressing cell lines, and wild type mouse tissues. Compared to current methods, the capacity for simultaneous detection of sphingosine-1-phosphate and (2E)-hexadecenal greatly improves the accuracy of results and shows excellent sensitivity and specificity for sphingosine phosphate lyase activity detection. PMID:26408264

Graphene nano-ink biosensor arrays on a microfluidic paper for multiplexed detection of metabolites.

PubMed

Labroo, Pratima; Cui, Yue

2014-02-27

The development of a miniaturized and low-cost platform for the highly sensitive, selective and rapid detection of multiplexed metabolites is of great interest for healthcare, pharmaceuticals, food science, and environmental monitoring. Graphene is a delicate single-layer, two-dimensional network of carbon atoms with extraordinary electrical sensing capability. Microfluidic paper with printing technique is a low cost matrix. Here, we demonstrated the development of graphene-ink based biosensor arrays on a microfluidic paper for the multiplexed detection of different metabolites, such as glucose, lactate, xanthine and cholesterol. Our results show that the graphene biosensor arrays can detect multiple metabolites on a microfluidic paper sensitively, rapidly and simultaneously. The device exhibits a fast measuring time of less than 2 min, a low detection limit of 0.3 μM, and a dynamic detection range of 0.3-15 μM. The process is simple and inexpensive to operate and requires a low consumption of sample volume. We anticipate that these results could open exciting opportunities for a variety of applications. Copyright © 2014 Elsevier B.V. All rights reserved.

Cross-subtype Detection of HIV-1 Using Reverse Transcription and Recombinase Polymerase Amplification

PubMed Central

Lillis, Lorraine; Lehman, Dara A.; Siverson, Joshua B.; Weis, Julie; Cantera, Jason; Parker, Mathew; Piepenburg, Olaf; Overbaugh, Julie; Boyle, David S.

2016-01-01

A low complexity diagnostic test that rapidly and reliably detects HIV infection in infants at the point of care could facilitate early treatment, improving outcomes. However, many infant HIV diagnostics can only be performed in laboratory settings. Recombinase polymerase amplification (RPA) is an isothermal amplification technology that can rapidly amplify proviral DNA from multiple subtypes of HIV-1 in under twenty minutes without complex equipment. In this study we added reverse transcription (RT) to RPA to allow detection of both HIV-1 RNA and DNA. We show that this RT-RPA HIV-1 assay has a limit of detection of 10 to 30 copies of an exact sequence matched DNA or RNA, respectively. In addition, at 100 copies of RNA or DNA, the assay detected 171 of 175 (97.7 %) sequence variants that represent all the major subtypes and recombinant forms of HIV-1 Groups M and O. This data suggests that the application of RT-RPA for the combined detection of HIV-1 viral RNA and proviral DNA may prove a highly sensitive tool for rapid and accurate diagnosis of infant HIV. PMID:26821087

Speciation analysis of arsenic in biological matrices by automated hydride generation-cryotrapping-atomic absorption spectrometry with multiple microflame quartz tube atomizer (multiatomizer)

PubMed Central

Hernández-Zavala, Araceli; Matoušek, Tomáš; Drobná, Zuzana; Paul, David S.; Walton, Felecia; Adair, Blakely M.; Jiří, Dědina; Thomas, David J.

2008-01-01

Analyses of arsenic (As) species in tissues and body fluids of individuals chronically exposed to inorganic arsenic (iAs) provide essential information about the exposure level and pattern of iAs metabolism. We have previously described an oxidation state-specific analysis of As species in biological matrices by hydride-generation atomic absorption spectrometry (HG-AAS), using cryotrapping (CT) for preconcentration and separation of arsines. To improve performance and detection limits of the method, HG and CT steps are automated and a conventional flame-in-tube atomizer replaced with a recently developed multiple microflame quartz tube atomizer (multiatomizer). In this system, arsines from AsIII-species are generated in a mixture of Tris-HCl (pH 6) and sodium borohydride. For generation of arsines from both AsIII- and AsV-species, samples are pretreated with L-cysteine. Under these conditions, dimethylthioarsinic acid, a newly described metabolite of iAs, does not interfere significantly with detection and quantification of methylated trivalent arsenicals. Analytical performance of the automated HG-CT-AAS was characterized by analyses of cultured cells and mouse tissues that contained mono- and dimethylated metabolites of iAs. The capacity to detect methylated AsIII- and AsV-species was verified, using an in vitro methylation system containing recombinant rat arsenic (+3 oxidation state) methyltransferase and cultured rat hepatocytes treated with iAs. Compared with the previous HG-CT-AAS design, detection limits for iAs and its metabolites have improved significantly with the current system, ranging from 8 to 20 pg. Recoveries of As were between 78 and 117%. The precision of the method was better than 5% for all biological matrices examined. Thus, the automated HG-CT-AAS system provides an effective and sensitive tool for analysis of all major human metabolites of iAs in complex biological matrices. PMID:18677417

DISENTANGLING CONFUSED STARS AT THE GALACTIC CENTER WITH LONG-BASELINE INFRARED INTERFEROMETRY

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

Stone, Jordan M.; Eisner, J. A.; Monnier, J. D.

2012-08-01

We present simulations of Keck Interferometer ASTRA and VLTI GRAVITY observations of mock star fields in orbit within {approx}50 mas of Sgr A*. Dual-field phase referencing techniques, as implemented on ASTRA and planned for GRAVITY, will provide the sensitivity to observe Sgr A* with long-baseline infrared interferometers. Our results show an improvement in the confusion noise limit over current astrometric surveys, opening a window to study stellar sources in the region. Since the Keck Interferometer has only a single baseline, the improvement in the confusion limit depends on source position angles. The GRAVITY instrument will yield a more compact andmore » symmetric point-spread function, providing an improvement in confusion noise which will not depend as strongly on position angle. Our Keck results show the ability to characterize the star field as containing zero, few, or many bright stellar sources. We are also able to detect and track a source down to m{sub K} {approx} 18 through the least confused regions of our field of view at a precision of {approx}200 {mu}as along the baseline direction. This level of precision improves with source brightness. Our GRAVITY results show the potential to detect and track multiple sources in the field. GRAVITY will perform {approx}10 {mu}as astrometry on an m{sub K} = 16.3 source and {approx}200 {mu}as astrometry on an m{sub K} = 18.8 source in 6 hr of monitoring a crowded field. Monitoring the orbits of several stars will provide the ability to distinguish between multiple post-Newtonian orbital effects, including those due to an extended mass distribution around Sgr A* and to low-order general relativistic effects. ASTRA and GRAVITY both have the potential to detect and monitor sources very close to Sgr A*. Early characterizations of the field by ASTRA, including the possibility of a precise source detection, could provide valuable information for future GRAVITY implementation and observation.« less

Genetic testing for patients with renal disease: procedures, pitfalls, and ethical considerations.

PubMed

Korf, B R

1999-07-01

The Human Genome Project is rapidly producing insights into the molecular basis of human genetic disorders. The most immediate clinical benefit is the advent of new diagnostic methods. Molecular diagnostic tools are available for several genetic renal disorders and are in development for many more. Two general approaches to molecular diagnosis are linkage-based testing and direct mutation detection. The former is used when the gene has not been cloned but has been mapped in relation to polymorphic loci. Linkage-based testing is also helpful when a large diversity of mutations makes direct detection difficult. Limitations include the need to study multiple family members, the need for informative polymorphisms, and genetic heterogeneity. Direct mutation detection is limited by genetic heterogeneity and the need to distinguish nonpathogenic allelic variants from pathogenic mutations. Molecular testing raises a number of complex ethical issues, including those associated with prenatal or presymptomatic diagnosis. In addition, there are concerns about informed consent, privacy, genetic discrimination, and technology transfer for newly developed tests. Health professionals need to be aware of the technical and ethical implications of these new methods of testing, as well as the complexities in test interpretation, as molecular approaches are increasingly integrated into medical practice.

Ultrasensitive measurement of microcantilever displacement below the shot-noise limit

DOE PAGES

Pooser, Raphael C.; Lawrie, Benjamin J.

2015-04-23

The displacement of micro-electro-mechanical-systems (MEMs) cantilevers is used to measure a variety of phe- nomena in devices ranging from force microscopes for single spin detection[1] to biochemical sensors[2] to un- cooled thermal imaging systems[3]. The displacement readout is often performed optically with segmented de- tectors or interference measurements. Until recently, var- ious noise sources have limited the minimum detectable displacement in MEMs systems, but it is now possible to minimize all other sources[4] so that the noise level of the coherent light eld, called the shot noise limit (SNL), becomes the dominant source. Light sources dis- playing quantum-enhanced statistics belowmore » this limit are available[5, 6], with applications in gravitational wave astronomy[7] and bioimaging[8], but direct displacement measurements of MEMS cantilevers below the SNL have been impossible until now. Here, we demonstrate the rst direct measurement of a MEMs cantilever displace- ment with sub-SNL sensitivity, thus enabling ultratrace sensing, imaging, and microscopy applications. By com- bining multi-spatial-mode quantum light sources with a simple dierential measurement, we show that sub-SNL MEMs displacement sensitivity is highly accessible com- pared to previous eorts that measured the displacement of macroscopic mirrors with very distinct spatial struc- tures crafted with multiple optical parametric ampliers and locking loops[9]. We apply this technique to a com- mercially available microcantilever in order to detect dis- placements 60% below the SNL at frequencies where the microcantilever is shot-noise-limited. These results sup- port a new class of quantum MEMS sensor whose ulti- mate signal to noise ratio is determined by the correla- tions possible in quantum optics systems.« less

Ultrasensitive measurement of microcantilever displacement below the shot-noise limit

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

Pooser, Raphael C.; Lawrie, Benjamin J.

The displacement of micro-electro-mechanical-systems (MEMs) cantilevers is used to measure a variety of phe- nomena in devices ranging from force microscopes for single spin detection[1] to biochemical sensors[2] to un- cooled thermal imaging systems[3]. The displacement readout is often performed optically with segmented de- tectors or interference measurements. Until recently, var- ious noise sources have limited the minimum detectable displacement in MEMs systems, but it is now possible to minimize all other sources[4] so that the noise level of the coherent light eld, called the shot noise limit (SNL), becomes the dominant source. Light sources dis- playing quantum-enhanced statistics belowmore » this limit are available[5, 6], with applications in gravitational wave astronomy[7] and bioimaging[8], but direct displacement measurements of MEMS cantilevers below the SNL have been impossible until now. Here, we demonstrate the rst direct measurement of a MEMs cantilever displace- ment with sub-SNL sensitivity, thus enabling ultratrace sensing, imaging, and microscopy applications. By com- bining multi-spatial-mode quantum light sources with a simple dierential measurement, we show that sub-SNL MEMs displacement sensitivity is highly accessible com- pared to previous eorts that measured the displacement of macroscopic mirrors with very distinct spatial struc- tures crafted with multiple optical parametric ampliers and locking loops[9]. We apply this technique to a com- mercially available microcantilever in order to detect dis- placements 60% below the SNL at frequencies where the microcantilever is shot-noise-limited. These results sup- port a new class of quantum MEMS sensor whose ulti- mate signal to noise ratio is determined by the correla- tions possible in quantum optics systems.« less

Methods and apparatus using commutative error detection values for fault isolation in multiple node computers

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

Almasi, Gheorghe; Blumrich, Matthias Augustin; Chen, Dong

Methods and apparatus perform fault isolation in multiple node computing systems using commutative error detection values for--example, checksums--to identify and to isolate faulty nodes. When information associated with a reproducible portion of a computer program is injected into a network by a node, a commutative error detection value is calculated. At intervals, node fault detection apparatus associated with the multiple node computer system retrieve commutative error detection values associated with the node and stores them in memory. When the computer program is executed again by the multiple node computer system, new commutative error detection values are created and stored inmore » memory. The node fault detection apparatus identifies faulty nodes by comparing commutative error detection values associated with reproducible portions of the application program generated by a particular node from different runs of the application program. Differences in values indicate a possible faulty node.« less

Pulsed Multiple Reaction Monitoring Approach to Enhancing Sensitivity of a Tandem Quadrupole Mass Spectrometer

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

Belov, Mikhail E.; Prasad, Satendra; Prior, David C.

2011-02-23

Liquid chromatography (LC)-triple quadrupole mass spectrometers operating in a Multiple Reaction Monitoring (MRM) mode are increasingly used for quantitative analysis of low abundance analytes in highly complex biochemical matrices. After development and selection of optimum MRM transition, sensitivity and data quality limitations are largely related to mass spectral peak interferences from sample or matrix constituents and statistical limitations at low number of ions reaching the detector. Herein, we report a new approach to enhancing MRM sensitivity by converting the continuous stream of ions from the ion source into a pulsed ion beam through the use of an Ion Funnel Trapmore » (IFT). Evaluation of the pulsed MRM approach was performed with a tryptic digest of Shewanella oneidensis strain MR-1 spiked with several reference peptides. The sensitivity improvement observed with the IFT coupled to the triple quadrupole instrument is based on several unique features. First, ion accumulation in the radio frequency (RF) ion trap facilitates improved droplet desolvation, which is manifested in the reduced background ion noise at the detector. Second, signal amplitude for a given transition is enhanced because of an order-of-magnitude increase in the ion charge density per unit time compared to a continuous mode of operation. Third, signal detection at the full duty cycle is obtained, as the trap use eliminates dead times between transitions, which are inevitable with continuous ion streams. In comparison with the conventional approach, the pulsed MRM signals showed up to 5-fold enhanced peak amplitude and 2-3 fold reduced chemical background, resulting in an improvement in the limit of detection (LOD) by a factor of ~ 4 to ~ 8.« less

The Need for Cervical Cancer Control in HIV-Positive and HIV-Negative Women from Romania by Primary Prevention and by Early Detection Using Clinically Validated HPV/DNA Tests.

PubMed

Ursu, Ramona Gabriela; Onofriescu, Mircea; Luca, Alexandru; Prisecariu, Liviu Jany; Sălceanu, Silvia Olivia; Nemescu, Dragoş; Iancu, Luminiţa Smaranda

2015-01-01

In Romania, a country with no organized national surveillance program regarding cervical cancer, the early diagnosis of HPV (Human Papilloma Virus) infections is a major requirement, especially in HIV-infected women. The objective of this study was to determine the HPV prevalence and type distribution in young HIV-positive women and to assess the difference in the risk factors for developing cervical cancer compared to those of HIV-negative women. We conducted one cross-sectional cohort study from June 2013-September 2014, including 1,032 women: 992 HIV- women who were 36.5 years old (limits: 17 ÷ 84) and 40 HIV + women who were 22.9 years old (limits: 17 ÷ 30) with iatrogenic HIV infected. We detected HPV types with the Linear Array HPV Genotyping test (Roche, Romania). DNA/HPV was detected in 18/40 (45%) of the HIV+ patients and in 350/992 (35.2%) of the HIV- patients (OR = 1.5, 95%CI 0.76÷2.96). After age adjustment, the overall HPV prevalence was 51.6% in HIV+ versus 63.2% in HIV- women aged under 25, and 22.2% in HPV+ versus 47.2% in HIV- women aged 25-34. We detect HIV being a risk factor for acquiring multiple HPV type infections (OR = 2.30, 95% CI 0.88÷5.97). The eight most common HPV types (high-risk, and low-risk) for women below age 30, HIV+ / - were: HPV 16, 18, 31, 51, 58, 68, and 6 and 82 respectively. To assess the risk factors of HIV-positive women for acquiring HPV infection, we analyzed the CD4/μL, ARN/HIV copies/μL, the age group, the number of sexual partners, smoking, and the type of HPV infection (single versus multiple infections). We found that the number of sexual partners and smoking are statistically significant risk factors. Even though there are no significant differences regarding the prevalence of HPV infection in HIV + versus HIV - patients, multiple infections were more frequent in the first group. In our study group young HIV-infected patients under HAART therapy, high number of sexual partners (more than 3) and smoking were detected to be risk factors. Future organized screening for HPV infection using sensitive and specific methods are necessary at the national level in Romania.

Capacity of optical communications over a lossy bosonic channel with a receiver employing the most general coherent electro-optic feedback control

NASA Astrophysics Data System (ADS)

Chung, Hye Won; Guha, Saikat; Zheng, Lizhong

2017-07-01

We study the problem of designing optical receivers to discriminate between multiple coherent states using coherent processing receivers—i.e., one that uses arbitrary coherent feedback control and quantum-noise-limited direct detection—which was shown by Dolinar to achieve the minimum error probability in discriminating any two coherent states. We first derive and reinterpret Dolinar's binary-hypothesis minimum-probability-of-error receiver as the one that optimizes the information efficiency at each time instant, based on recursive Bayesian updates within the receiver. Using this viewpoint, we propose a natural generalization of Dolinar's receiver design to discriminate M coherent states, each of which could now be a codeword, i.e., a sequence of N coherent states, each drawn from a modulation alphabet. We analyze the channel capacity of the pure-loss optical channel with a general coherent-processing receiver in the low-photon number regime and compare it with the capacity achievable with direct detection and the Holevo limit (achieving the latter would require a quantum joint-detection receiver). We show compelling evidence that despite the optimal performance of Dolinar's receiver for the binary coherent-state hypothesis test (either in error probability or mutual information), the asymptotic communication rate achievable by such a coherent-processing receiver is only as good as direct detection. This suggests that in the infinitely long codeword limit, all potential benefits of coherent processing at the receiver can be obtained by designing a good code and direct detection, with no feedback within the receiver.

Measuring electrically charged particle fluxes in space using a fiber optic loop sensor

NASA Technical Reports Server (NTRS)

1992-01-01

The purpose of this program was to demonstrate the potential of a fiber optic loop sensor for the measurement of electrically charged particle fluxes in space. The key elements of the sensor are a multiple turn loop of low birefringence, single mode fiber, with a laser diode light source, and a low noise optical receiver. The optical receiver is designed to be shot noise limited, with this being the limiting sensitivity factor for the sensor. The sensing element is the fiber optic loop. Under a magnetic field from an electric current flowing along the axis of the loop, there is a non-vanishing line integral along the fiber optic loop. This causes a net birefringence producing two states of polarization whose phase difference is correlated to magnetic field strength and thus, current in the optical receiver electronic processing. The objectives in this program were to develop a prototype laser diode powered fiber optic sensor. The performance specification of a minimum detectable current density of 1 (mu)amp/sq m-(radical)Hz, should be at the shot noise limit of the detection electronics. OPTRA has successfully built and tested a 3.2 m diameter loop with 137 turns of low birefringence optical fiber and achieved a minimum detectable current density of 5.4 x 10(exp-5) amps/(radical)Hz. If laboratory space considerations were not an issue, with the length of optical fiber available to us, we would have achieved a minimum detectable current density of 4 x 10(exp -7) amps/(radical)Hz.

A Combination of Extreme Environmental Conditions Favor the Prevalence of Endospore-Forming Firmicutes

PubMed Central

Filippidou, Sevasti; Wunderlin, Tina; Junier, Thomas; Jeanneret, Nicole; Dorador, Cristina; Molina, Veronica; Johnson, David R.; Junier, Pilar

2016-01-01

Environmental conditions unsuitable for microbial growth are the rule rather than the exception in most habitats. In response to this, microorganisms have developed various strategies to withstand environmental conditions that limit active growth. Endospore-forming Firmicutes (EFF) deploy a myriad of survival strategies in order to resist adverse conditions. Like many bacterial groups, they can form biofilms and detect nutrient scarcity through chemotaxis. Moreover, within this paraphyletic group of Firmicutes, ecophysiological optima are diverse. Nonetheless, a response to adversity that delimits this group is the formation of wet-heat resistant spores. These strategies are energetically demanding and therefore might affect the biological success of EFF. Therefore, we hypothesize that abundance and diversity of EFF should be maximized in those environments in which the benefits of these survival strategies offsets the energetic cost. In order to address this hypothesis, geothermal and mineral springs and drillings were selected because in these environments of steep physicochemical gradients, diversified survival strategies may become a successful strategy.We collected 71 samples from geothermal and mineral environments characterized by none (null), single or multiple limiting environmental factors (temperature, pH, UV radiation, and specific mineral composition). To measure success, we quantified EFF gene copy numbers (GCN; spo0A gene) in relation to total bacterial GCN (16S rRNA gene), as well as the contribution of EFF to community composition. The quantification showed that relative GCN for EFF reached up to 20% at sites characterized by multiple limiting environmental factors, whereas it corresponded to less than 1% at sites with one or no limiting environmental factor. Pyrosequencing of the 16S rRNA gene supports a higher contribution of EFF at sites with multiple limiting factors. Community composition suggested a combination of phylotypes for which active growth could be expected, and phylotypes that are most likely in the state of endospores, in all the sites. In summary, our results suggest that diversified survival strategies, including sporulation and metabolic adaptations, explain the biological success of EFF in geothermal and natural springs, and that multiple extreme environmental factors favor the prevalence of EFF. PMID:27857706

A Combination of Extreme Environmental Conditions Favor the Prevalence of Endospore-Forming Firmicutes.

PubMed

Filippidou, Sevasti; Wunderlin, Tina; Junier, Thomas; Jeanneret, Nicole; Dorador, Cristina; Molina, Veronica; Johnson, David R; Junier, Pilar

2016-01-01

Environmental conditions unsuitable for microbial growth are the rule rather than the exception in most habitats. In response to this, microorganisms have developed various strategies to withstand environmental conditions that limit active growth. Endospore-forming Firmicutes (EFF) deploy a myriad of survival strategies in order to resist adverse conditions. Like many bacterial groups, they can form biofilms and detect nutrient scarcity through chemotaxis. Moreover, within this paraphyletic group of Firmicutes, ecophysiological optima are diverse. Nonetheless, a response to adversity that delimits this group is the formation of wet-heat resistant spores. These strategies are energetically demanding and therefore might affect the biological success of EFF. Therefore, we hypothesize that abundance and diversity of EFF should be maximized in those environments in which the benefits of these survival strategies offsets the energetic cost. In order to address this hypothesis, geothermal and mineral springs and drillings were selected because in these environments of steep physicochemical gradients, diversified survival strategies may become a successful strategy.We collected 71 samples from geothermal and mineral environments characterized by none (null), single or multiple limiting environmental factors (temperature, pH, UV radiation, and specific mineral composition). To measure success, we quantified EFF gene copy numbers (GCN; spo0A gene) in relation to total bacterial GCN (16S rRNA gene), as well as the contribution of EFF to community composition. The quantification showed that relative GCN for EFF reached up to 20% at sites characterized by multiple limiting environmental factors, whereas it corresponded to less than 1% at sites with one or no limiting environmental factor. Pyrosequencing of the 16S rRNA gene supports a higher contribution of EFF at sites with multiple limiting factors. Community composition suggested a combination of phylotypes for which active growth could be expected, and phylotypes that are most likely in the state of endospores, in all the sites. In summary, our results suggest that diversified survival strategies, including sporulation and metabolic adaptations, explain the biological success of EFF in geothermal and natural springs, and that multiple extreme environmental factors favor the prevalence of EFF.

High Data Rate Quantum Cryptography

NASA Astrophysics Data System (ADS)

Kwiat, Paul; Christensen, Bradley; McCusker, Kevin; Kumor, Daniel; Gauthier, Daniel

2015-05-01

While quantum key distribution (QKD) systems are now commercially available, the data rate is a limiting factor for some desired applications (e.g., secure video transmission). Most QKD systems receive at most a single random bit per detection event, causing the data rate to be limited by the saturation of the single-photon detectors. Recent experiments have begun to explore using larger degree of freedoms, i.e., temporal or spatial qubits, to optimize the data rate. Here, we continue this exploration using entanglement in multiple degrees of freedom. That is, we use simultaneous temporal and polarization entanglement to reach up to 8.3 bits of randomness per coincident detection. Due to current technology, we are unable to fully secure the temporal degree of freedom against all possible future attacks; however, by assuming a technologically-limited eavesdropper, we are able to obtain 23.4 MB/s secure key rate across an optical table, after error reconciliation and privacy amplification. In this talk, we will describe our high-rate QKD experiment, with a short discussion on our work towards extending this system to ship-to-ship and ship-to-shore communication, aiming to secure the temporal degree of freedom and to implement a 30-km free-space link over a marine environment.

Stability Limits of Circumbinary Planets: Is There a Pile-up in the Kepler CBPs?

NASA Astrophysics Data System (ADS)

Quarles, B.; Satyal, S.; Kostov, V.; Kaib, N.; Haghighipour, N.

2018-04-01

The stability limit for circumbinary planets (CBPs) is not well defined and can depend on initial parameters defining either the planetary orbit and/or the inner binary orbit. We expand on the work of Holman & Wiegert (1999) to develop numerical tools for quick, easy, and accurate determination of the stability limit. The results of our simulations, as well as our numerical tools, are available to the community through Zenodo and GitHub, respectively. We employ a grid interpolation method based on ∼150 million full N-body simulations of initially circular, coplanar systems and compare to the nine known Kepler CBP systems. Using a formalism from planet packing studies, we find that 55% of the Kepler CBP systems allow for an additional equal-mass planet to potentially exist on an interior orbit relative to the observed planet. Therefore, we do not find strong evidence for a pile-up in the Kepler CBP systems and more detections are needed to adequately characterize the formation mechanisms for the CBP population. Observations from the Transiting Exoplanet Survey Satellite are expected to substantially increase the number of detections using the unique geometry of CBP systems, where multiple transits can occur during a single conjunction.

A Novel Method for Remote Depth Estimation of Buried Radioactive Contamination.

PubMed

Ukaegbu, Ikechukwu Kevin; Gamage, Kelum A A

2018-02-08

Existing remote radioactive contamination depth estimation methods for buried radioactive wastes are either limited to less than 2 cm or are based on empirical models that require foreknowledge of the maximum penetrable depth of the contamination. These severely limits their usefulness in some real life subsurface contamination scenarios. Therefore, this work presents a novel remote depth estimation method that is based on an approximate three-dimensional linear attenuation model that exploits the benefits of using multiple measurements obtained from the surface of the material in which the contamination is buried using a radiation detector. Simulation results showed that the proposed method is able to detect the depth of caesium-137 and cobalt-60 contamination buried up to 40 cm in both sand and concrete. Furthermore, results from experiments show that the method is able to detect the depth of caesium-137 contamination buried up to 12 cm in sand. The lower maximum depth recorded in the experiment is due to limitations in the detector and the low activity of the caesium-137 source used. Nevertheless, both results demonstrate the superior capability of the proposed method compared to existing methods.

Limits of linearity and detection for some drugs of abuse.

PubMed

Needleman, S B; Romberg, R W

1990-01-01

The limits of linearity (LOL) and detection (LOD) are important factors in establishing the reliability of an analytical procedure for accurately assaying drug concentrations in urine specimens. Multiple analyses of analyte over an extended range of concentrations provide a measure of the ability of the analytical procedure to correctly identify known quantities of drug in a biofluid matrix. Each of the seven drugs of abuse gives linear analytical responses from concentrations at or near their LOD to concentrations several-fold higher than those generally encountered in the drug screening laboratory. The upper LOL exceeds the Department of Navy (DON) cutoff values by factors of approximately 2 to 160. The LOD varies from 0.4 to 5.0% of the DON cutoff value for each drug. The limit of quantitation (LOQ) is calculated as the LOD + 7 SD. The range for LOL is greater for drugs analyzed with deuterated internal standards compared with those using conventional internal standards. For THC acid, cocaine, PCP, and morphine, LOLs are 8 to 160-fold greater than the defined cutoff concentrations. For the other drugs, the LOL's are only 2 to 4-fold greater than the defined cutoff concentrations.

New directions in diagnostic evaluation of insect allergy.

PubMed

Golden, David B K

2014-08-01

Diagnosis of insect sting allergy and prediction of risk of sting anaphylaxis are often difficult because tests for venom-specific IgE antibodies have a limited positive predictive value and do not reliably predict the severity of sting reactions. Component-resolved diagnosis using recombinant venom allergens has shown promise in improving the specificity of diagnostic testing for insect sting allergy. Basophil activation tests have been explored as more sensitive assays for identification of patients with insect allergy and for prediction of clinical outcomes. Measurement of mast cell mediators reflects the underlying risk for more severe reactions and limited clinical response to treatment. Measurement of IgE to recombinant venom allergens can distinguish cross-sensitization from dual sensitization to honeybee and vespid venoms, thus helping to limit venom immunotherapy to a single venom instead of multiple venoms in many patients. Basophil activation tests can detect venom allergy in patients who show no detectable venom-specific IgE in standard diagnostic tests and can predict increased risk of systemic reactions to venom immunotherapy, and to stings during and after stopping venom immunotherapy. The risk of severe or fatal anaphylaxis to stings can also be predicted by measurement of baseline serum tryptase or other mast cell mediators.

A Novel Method for Remote Depth Estimation of Buried Radioactive Contamination

PubMed Central

2018-01-01

Existing remote radioactive contamination depth estimation methods for buried radioactive wastes are either limited to less than 2 cm or are based on empirical models that require foreknowledge of the maximum penetrable depth of the contamination. These severely limits their usefulness in some real life subsurface contamination scenarios. Therefore, this work presents a novel remote depth estimation method that is based on an approximate three-dimensional linear attenuation model that exploits the benefits of using multiple measurements obtained from the surface of the material in which the contamination is buried using a radiation detector. Simulation results showed that the proposed method is able to detect the depth of caesium-137 and cobalt-60 contamination buried up to 40 cm in both sand and concrete. Furthermore, results from experiments show that the method is able to detect the depth of caesium-137 contamination buried up to 12 cm in sand. The lower maximum depth recorded in the experiment is due to limitations in the detector and the low activity of the caesium-137 source used. Nevertheless, both results demonstrate the superior capability of the proposed method compared to existing methods. PMID:29419759

Simultaneous detection of multiple chemical residues in milk using broad-specifity antibodies in a hybrid immunosorbent assay

USDA-ARS?s Scientific Manuscript database

The wide array of applications using quantum dots (QDs) for detection of multiple analytes reflects the versatility of the technology. In this study, a novel immunoassay using 2 types of sensors (QDs and an enzyme) were simultaneously used for detecting multiple structurally different low-molecular...

Optimizing plasmonic nanoantennas via coordinated multiple coupling

NASA Astrophysics Data System (ADS)

Lin, Linhan; Zheng, Yuebing

2015-10-01

Plasmonic nanoantennas, which can efficiently convert light from free space into sub-wavelength scale with the local field enhancement, are fundamental building blocks for nanophotonic systems. Predominant design methods, which exploit a single type of near- or far-field coupling in pairs or arrays of plasmonic nanostructures, have limited the tunability of spectral response and the local field enhancement. To overcome this limit, we are developing a general strategy towards exploiting the coordinated effects of multiple coupling. Using Au bowtie nanoantenna arrays with metal-insulator-metal configuration as examples, we numerically demonstrate that coordinated design and implementation of various optical coupling effects leads to both the increased tunability in the spectral response and the significantly enhanced electromagnetic field. Furthermore, we design and analyze a refractive index sensor with an ultra-high figure-of-merit (254), a high signal-to-noise ratio and a wide working range of refractive indices, and a narrow-band near-infrared plasmonic absorber with 100% absorption efficiency, high quality factor of up to 114 and a wide range of tunable wavelength from 800 nm to 1,500 nm. The plasmonic nanoantennas that exploit coordinated multiple coupling will benefit a broad range of applications, including label-free bio-chemical detection, reflective filter, optical trapping, hot-electron generation, and heat-assisted magnetic recording.

Proteomics goes forensic: Detection and mapping of blood signatures in fingermarks.

PubMed

Deininger, Lisa; Patel, Ekta; Clench, Malcolm R; Sears, Vaughn; Sammon, Chris; Francese, Simona

2016-06-01

A bottom up in situ proteomic method has been developed enabling the mapping of multiple blood signatures on the intact ridges of blood fingermarks by Matrix Assisted Laser Desorption Mass Spectrometry Imaging (MALDI-MSI). This method, at a proof of concept stage, builds upon recently published work demonstrating the opportunity to profile and identify multiple blood signatures in bloodstains via a bottom up proteomic approach. The present protocol addresses the limitation of the previously developed profiling method with respect to destructivity; destructivity should be avoided for evidence such as blood fingermarks, where the ridge detail must be preserved in order to provide the associative link between the biometric information and the events of bloodshed. Using a blood mark reference model, trypsin concentration and spraying conditions have been optimised within the technical constraints of the depositor eventually employed; the application of MALDI-MSI and Ion Mobility MS have enabled the detection, confirmation and visualisation of blood signatures directly onto the ridge pattern. These results are to be considered a first insight into a method eventually informing investigations (and judicial debates) of violent crimes in which the reliable and non-destructive detection and mapping of blood in fingermarks is paramount to reconstruct the events of bloodshed. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Track Everything: Limiting Prior Knowledge in Online Multi-Object Recognition.

PubMed

Wong, Sebastien C; Stamatescu, Victor; Gatt, Adam; Kearney, David; Lee, Ivan; McDonnell, Mark D

2017-10-01

This paper addresses the problem of online tracking and classification of multiple objects in an image sequence. Our proposed solution is to first track all objects in the scene without relying on object-specific prior knowledge, which in other systems can take the form of hand-crafted features or user-based track initialization. We then classify the tracked objects with a fast-learning image classifier, that is based on a shallow convolutional neural network architecture and demonstrate that object recognition improves when this is combined with object state information from the tracking algorithm. We argue that by transferring the use of prior knowledge from the detection and tracking stages to the classification stage, we can design a robust, general purpose object recognition system with the ability to detect and track a variety of object types. We describe our biologically inspired implementation, which adaptively learns the shape and motion of tracked objects, and apply it to the Neovision2 Tower benchmark data set, which contains multiple object types. An experimental evaluation demonstrates that our approach is competitive with the state-of-the-art video object recognition systems that do make use of object-specific prior knowledge in detection and tracking, while providing additional practical advantages by virtue of its generality.

Universal surface-enhanced Raman scattering amplification detector for ultrasensitive detection of multiple target analytes.

PubMed

Zheng, Jing; Hu, Yaping; Bai, Junhui; Ma, Cheng; Li, Jishan; Li, Yinhui; Shi, Muling; Tan, Weihong; Yang, Ronghua

2014-02-18

Up to now, the successful fabrication of efficient hot-spot substrates for surface-enhanced Raman scattering (SERS) remains an unsolved problem. To address this issue, we describe herein a universal aptamer-based SERS biodetection approach that uses a single-stranded DNA as a universal trigger (UT) to induce SERS-active hot-spot formation, allowing, in turn, detection of a broad range of targets. More specifically, interaction between the aptamer probe and its target perturbs a triple-helix aptamer/UT structure in a manner that activates a hybridization chain reaction (HCR) among three short DNA building blocks that self-assemble into a long DNA polymer. The SERS-active hot-spots are formed by conjugating 4-aminobenzenethiol (4-ABT)-encoded gold nanoparticles with the DNA polymer through a specific Au-S bond. As proof-of-principle, we used this approach to quantify multiple target analytes, including thrombin, adenosine, and CEM cancer cells, achieving lowest limit of detection values of 18 pM, 1.5 nM, and 10 cells/mL, respectively. As a universal SERS detector, this prototype can be applied to many other target analytes through the use of suitable DNA-functional partners, thus inspiring new designs and applications of SERS for bioanalysis.

Raman gas sensing of modified Ag nanoparticle SERS

NASA Astrophysics Data System (ADS)

Myoung, NoSoung; Yoo, Hyung Keun; Hwang, In-Wook

2014-03-01

Recent progress in modified Surface Enhanced Raman Scattering (SERS) using Ag nanoparticles makes them promising optical technique for direct gas sensing of interest. However, SERS has been shown to provide sub ppb level detection of the compounds in the vapor phase. The major problem with the sensitivity scaling-up was in the development of fabrication technology for stability and reproducibility of SERS substrates. We report an optimization of 1-propanethiol coated multiple Ag nanoparticle layers on SiO2 substrate as well as new records of real-time, simultaneous vapor phase detection of toluene and 1-2 dichlorobenzene by the radiation of fiber optic coupled 785 nm diode laser and spectrograph. Multiple depositions of Ag NPs were loaded on SiO2 and soaked in 1-propanethiol solution for 24 hours to modify the surface into hydrophobic due to the characteristics of vapor phase of our interests. Raman bands at 1003 cm-1 and 1130 cm-1 for toluene and 12DCB, respectively were compared to 1089 cm-1 and each gas concentration in 1000 mL flask were calculated as a function of each vapor phase ratio. The saturation of toluene and 12DCB were limited only by 800 ppm and the detectable range was 0.6-800 ppm.

Environmental acoustic cues guide the biosonar attention of a highly specialised echolocator.

PubMed

Lattenkamp, Ella Z; Kaiser, Samuel; Kaučič, Rožle; Großmann, Martina; Koselj, Klemen; Goerlitz, Holger R

2018-04-23

Sensory systems experience a trade-off between maximizing the detail and amount of sampled information. This trade-off is particularly pronounced in sensory systems that are highly specialised for a single task and thus experience limitations in other tasks. We hypothesised that combining sensory input from multiple streams of information may resolve this trade-off and improve detection and sensing reliability. Specifically, we predicted that perceptive limitations experienced by animals reliant on specialised active echolocation can be compensated for by the phylogenetically older and less specialised process of passive hearing. We tested this hypothesis in greater horseshoe bats, which possess morphological and neural specialisations allowing them to identify fluttering prey in dense vegetation using echolocation only. At the same time, their echolocation system is both spatially and temporally severely limited. Here, we show that greater horseshoe bats employ passive hearing to initially detect and localise prey-generated and other environmental sounds, and then raise vocalisation level and concentrate the scanning movements of their sonar beam on the sound source for further investigation with echolocation. These specialised echolocators thus supplement echo-acoustic information with environmental acoustic cues, enlarging perceived space beyond their biosonar range. Contrary to our predictions, we did not find consistent preferences for prey-related acoustic stimuli, indicating the use of passive acoustic cues also for detection of non-prey objects. Our findings suggest that even specialised echolocators exploit a wide range of environmental information, and that phylogenetically older sensory systems can support the evolution of sensory specialisations by compensating for their limitations. © 2018. Published by The Company of Biologists Ltd.

Impedance biosensor for the rapid detection of Listeria spp. based on aptamer functionalized Pt-interdigitated microelectrodes array

NASA Astrophysics Data System (ADS)

Sidhu, R.; Rong, Y.; Vanegas, D. C.; Claussen, J.; McLamore, E. S.; Gomes, C.

2016-05-01

Listeria monocytogenes is one of the most common causes of food illness deaths worldwide, with multiple outbreaks in the United States alone. Current methods to detect foodborne pathogens are laborious and can take several hours to days to produce results. Thus, faster techniques are needed to detect bacteria within the same reliability level as traditional techniques. This study reports on a rapid, accurate, and sensitive aptamer biosensor device for Listeria spp. detection based on platinum interdigitated array microelectrodes (Pt-IDEs). Pt-IDEs with different geometric electrode gaps were fabricated by lithographic techniques and characterized by cyclic voltammetric (CV), electrochemical impedance spectroscopy (EIS), and potential amperometry (DCPA) measurements of reversible redox species. Based on these results, 50 μm Pt-IDE was chosen to further functionalize with a Listeria monocytogenes DNA aptamer selective to the cell surface protein internalin A, via metal-thiol self-assembly at the 5' end of the 47-mer's. EIS analysis was used to detect Listeria spp. without the need for label amplification and pre-concentration steps. The optimized aptamer concentration of 800 nM was selected to capture the bacteria through internalin A binding and the aptamer hairpin structure near the 3' end. The aptasensor was capable of detecting a wide range of bacteria concentration from 10 to 106 CFU/mL at lower detection limit of 5.39 +/- 0.21 CFU/mL with sensitivity of 268.1 +/- 25.40 (Ohms/log [CFU/mL]) in 17 min. The aptamer based biosensor offers a portable, rapid and sensitive alternative for food safety applications with one of the lowest detection limits reported to date.

Tropospheric dry layers in the tropical western Pacific: comparisons of GPS radio occultation with multiple data sets

NASA Astrophysics Data System (ADS)

Rieckh, Therese; Anthes, Richard; Randel, William; Ho, Shu-Peng; Foelsche, Ulrich

2017-03-01

We use GPS radio occultation (RO) data to investigate the structure and temporal behavior of extremely dry, high-ozone tropospheric air in the tropical western Pacific during the 6-week period of the CONTRAST (CONvective TRansport of Active Species in the Tropics) experiment (January and February 2014). Our analyses are aimed at testing whether the RO method is capable of detecting these extremely dry layers and evaluating comparisons with in situ measurements, satellite observations, and model analyses. We use multiple data sources as comparisons, including CONTRAST research aircraft profiles, radiosonde profiles, AIRS (Atmospheric Infrared Sounder) satellite retrievals, and profiles extracted from the ERA (ERA-Interim reanalysis) and the GFS (US National Weather Service Global Forecast System) analyses, as well as MTSAT-2 satellite images. The independent and complementary radiosonde, aircraft, and RO data provide high vertical resolution observations of the dry layers. However, they all have limitations. The coverage of the radiosonde data is limited by having only a single station in this oceanic region; the aircraft data are limited in their temporal and spatial coverage; and the RO data are limited in their number and horizontal resolution over this period. However, nearby observations from the three types of data are highly consistent with each other and with the lower-vertical-resolution AIRS profiles. They are also consistent with the ERA and GFS data. We show that the RO data, used here for the first time to study this phenomenon, contribute significant information on the water vapor content and are capable of detecting layers in the tropics and subtropics with extremely low humidity (less than 10 %), independent of the retrieval used to extract moisture information. Our results also verify the quality of the ERA and GFS data sets, giving confidence to the reanalyses and their use in diagnosing the full four-dimensional structure of the dry layers.

Simple and effective label-free capillary electrophoretic analysis of sugars by complexation using quinoline boronic acids.

PubMed

Kubo, Takuya; Kanemori, Koichi; Kusumoto, Risa; Kawai, Takayuki; Sueyoshi, Kenji; Naito, Toyohiro; Otsuka, Koji

2015-01-01

An effective separation and detection procedure for sugars by capillary electrophoresis (CE) using a complexation between quinolineboronic acid (QBA) and multiple hydroxyl structure of sugar alcohol is reported. We investigated the variation of fluorescence spectra of a variety of QBAs with sorbitol at a wide range of pH conditions and then found that 5-isoQBA strongly enhanced the fluorescence intensity by the complexation at basic pH conditions. The other sugar alcohols having multiple hydroxyls also revealed the enhancement of the fluorescence intensity with 5-isoQBA, whereas the alternation of the intensity was not found in the sugars such as glucose. After optimization of the 5-isoQBA concentration and pH of the buffered solution in CE analysis, 6 sugar alcohols were successfully separated in the order based on the formation constants with 5-isoQBA, which were calculated from the variation of the fluorescence intensity with each sugar alcohol and 5-isoQBA. Furthermore, the limits of detection for sorbitol and xylitol by the CE method were estimated at 15 and 27 μM, respectively.

DSPCP: A Data Scalable Approach for Identifying Relationships in Parallel Coordinates.

PubMed

Nguyen, Hoa; Rosen, Paul

2018-03-01

Parallel coordinates plots (PCPs) are a well-studied technique for exploring multi-attribute datasets. In many situations, users find them a flexible method to analyze and interact with data. Unfortunately, using PCPs becomes challenging as the number of data items grows large or multiple trends within the data mix in the visualization. The resulting overdraw can obscure important features. A number of modifications to PCPs have been proposed, including using color, opacity, smooth curves, frequency, density, and animation to mitigate this problem. However, these modified PCPs tend to have their own limitations in the kinds of relationships they emphasize. We propose a new data scalable design for representing and exploring data relationships in PCPs. The approach exploits the point/line duality property of PCPs and a local linear assumption of data to extract and represent relationship summarizations. This approach simultaneously shows relationships in the data and the consistency of those relationships. Our approach supports various visualization tasks, including mixed linear and nonlinear pattern identification, noise detection, and outlier detection, all in large data. We demonstrate these tasks on multiple synthetic and real-world datasets.

III-V strain layer superlattice based band engineered avalanche photodiodes (Presentation Recording)

NASA Astrophysics Data System (ADS)

Ghosh, Sid

2015-08-01

Laser detection and ranging (LADAR)-based systems operating in the Near Infrared (NIR) and Short Wave Infrared (SWIR) have become popular optical sensors for remote sensing, medical, and environmental applications. Sophisticated laser-based radar and weapon systems used for long-range military and astronomical applications need to detect, recognize, and track a variety of targets under a wide spectrum of atmospheric conditions. Infrared APDs play an important role in LADAR systems by integrating the detection and gain stages in a single device. Robust silicon-APDs are limited to visible and very near infrared region (< 1 um), while InGaAs works well up to wavelengths of about 1.5um. Si APDs have low multiplication or excess noise but are limited to below 1um due very poor quantum efficiency above 0.8um. InGaAs and Ge APDs operate up to wavelengths of 1.5um but have poor multiplication or excess noise due to a low impact ionization coefficient ratio between electrons and holes. For the past several decades HgCdTe has been traditionally used in longer wavelength (> 3um) infrared photon detection applications. Recently, various research groups (including Ghosh et. al.) have reported SWIR and MWIR HgCdTe APDs on CdZnTe and Si substrates. However, HgCdTe APDs suffer from low breakdown fields due to material defects, and excess noise increases significantly at high electric fields. During the past decade, InAs/GaSb Strain Layer Superlattice (SLS) material system has emerged as a potential material for the entire infrared spectrum because of relatively easier growth, comparable absorption coefficients, lower tunneling currents and longer Auger lifetimes resulting in enhanced detectivities (D*). Band engineering in type II SLS allows us to engineer avalanche properties of electrons and holes. This is a great advantage over bulk InGaAs and HgCdTe APDs where engineering avalanche properties is not possible. The talk will discuss the evolution of superlattice based avalanche photodiodes and some of the recent results on the work being done at Raytheon on SWIR avalanche photodiodes.

The Evolution of the Multiplicity of Embedded Protostars. I. Sample Properties and Binary Detections

NASA Astrophysics Data System (ADS)

Connelley, Michael S.; Reipurth, Bo; Tokunaga, Alan T.

2008-06-01

We present the observational results of a near-infrared survey of a large sample of Class I protostars designed to determine the Class I binary separation distribution from ~100 AU to ~5000 AU. We have selected targets from a new sample of 267 nearby candidate Class I objects. This sample is well understood, consists of mostly Class I young stellar objects (YSOs) within 1 kpc, has targets selected from the whole sky, and is not biased by previous studies of star formation. We have observed 189 Class I YSOs north of δ = -40° at the H, K, and L' bands, with a median angular resolution of 0farcs33 at L'. We determine our detection limit for close binary companions by observing artificial binaries. We choose a contrast limit and an outer detection limit to minimize contamination and to ensure that a candidate companion is gravitationally bound. Our survey uses observations at the L' rather than the K band for the detection of binary companions since there is less scattered light and better seeing at L'. This paper presents the positions of our targets, the near-IR photometry of sources detected in our fields at L', as well as the observed properties of the 89 detected companions (73 of which are newly discovered). Although we have chosen contrast and separation limits to minimize contamination, we expect that there are about six stars identified as binary companions that are due to contamination. Finder charts at L' for each field are shown to facilitate future studies of these objects. The Infrared Telescope Facility is operated by the University of Hawaii under Cooperative Agreement no. NCC 5-538 with the National Aeronautics and Space Administration, Science Mission Directorate, Planetary Astronomy Program. The United Kingdom Infrared Telescope is operated by the Joint Astronomy Centre on behalf of the Science and Technology Facilities Council of the U.K. Based in part on data collected at the Subaru Telescope, which is operated by the National Astronomical Observatory of Japan.

Multitarget, quantitative nanoplasmonic electrical field-enhanced resonating device (NE2RD) for diagnostics.

PubMed

Inci, Fatih; Filippini, Chiara; Baday, Murat; Ozen, Mehmet Ozgun; Calamak, Semih; Durmus, Naside Gozde; Wang, ShuQi; Hanhauser, Emily; Hobbs, Kristen S; Juillard, Franceline; Kuang, Ping Ping; Vetter, Michael L; Carocci, Margot; Yamamoto, Hidemi S; Takagi, Yuko; Yildiz, Umit Hakan; Akin, Demir; Wesemann, Duane R; Singhal, Amit; Yang, Priscilla L; Nibert, Max L; Fichorova, Raina N; Lau, Daryl T-Y; Henrich, Timothy J; Kaye, Kenneth M; Schachter, Steven C; Kuritzkes, Daniel R; Steinmetz, Lars M; Gambhir, Sanjiv S; Davis, Ronald W; Demirci, Utkan

2015-08-11

Recent advances in biosensing technologies present great potential for medical diagnostics, thus improving clinical decisions. However, creating a label-free general sensing platform capable of detecting multiple biotargets in various clinical specimens over a wide dynamic range, without lengthy sample-processing steps, remains a considerable challenge. In practice, these barriers prevent broad applications in clinics and at patients' homes. Here, we demonstrate the nanoplasmonic electrical field-enhanced resonating device (NE(2)RD), which addresses all these impediments on a single platform. The NE(2)RD employs an immunodetection assay to capture biotargets, and precisely measures spectral color changes by their wavelength and extinction intensity shifts in nanoparticles without prior sample labeling or preprocessing. We present through multiple examples, a label-free, quantitative, portable, multitarget platform by rapidly detecting various protein biomarkers, drugs, protein allergens, bacteria, eukaryotic cells, and distinct viruses. The linear dynamic range of NE(2)RD is five orders of magnitude broader than ELISA, with a sensitivity down to 400 fg/mL This range and sensitivity are achieved by self-assembling gold nanoparticles to generate hot spots on a 3D-oriented substrate for ultrasensitive measurements. We demonstrate that this precise platform handles multiple clinical samples such as whole blood, serum, and saliva without sample preprocessing under diverse conditions of temperature, pH, and ionic strength. The NE(2)RD's broad dynamic range, detection limit, and portability integrated with a disposable fluidic chip have broad applications, potentially enabling the transition toward precision medicine at the point-of-care or primary care settings and at patients' homes.

Time-resolved non-sequential ray-tracing modelling of non-line-of-sight picosecond pulse LIDAR

NASA Astrophysics Data System (ADS)

Sroka, Adam; Chan, Susan; Warburton, Ryan; Gariepy, Genevieve; Henderson, Robert; Leach, Jonathan; Faccio, Daniele; Lee, Stephen T.

2016-05-01

The ability to detect motion and to track a moving object that is hidden around a corner or behind a wall provides a crucial advantage when physically going around the obstacle is impossible or dangerous. One recently demonstrated approach to achieving this goal makes use of non-line-of-sight picosecond pulse laser ranging. This approach has recently become interesting due to the availability of single-photon avalanche diode (SPAD) receivers with picosecond time resolution. We present a time-resolved non-sequential ray-tracing model and its application to indirect line-of-sight detection of moving targets. The model makes use of the Zemax optical design programme's capabilities in stray light analysis where it traces large numbers of rays through multiple random scattering events in a 3D non-sequential environment. Our model then reconstructs the generated multi-segment ray paths and adds temporal analysis. Validation of this model against experimental results is shown. We then exercise the model to explore the limits placed on system design by available laser sources and detectors. In particular we detail the requirements on the laser's pulse energy, duration and repetition rate, and on the receiver's temporal response and sensitivity. These are discussed in terms of the resulting implications for achievable range, resolution and measurement time while retaining eye-safety with this technique. Finally, the model is used to examine potential extensions to the experimental system that may allow for increased localisation of the position of the detected moving object, such as the inclusion of multiple detectors and/or multiple emitters.

Threat assessment and sensor management in a modular architecture

NASA Astrophysics Data System (ADS)

Page, S. F.; Oldfield, J. P.; Islip, S.; Benfold, B.; Brandon, R.; Thomas, P. A.; Stubbins, D. J.

2016-10-01

Many existing asset/area protection systems, for example those deployed to protect critical national infrastructure, are comprised of multiple sensors such as EO/IR, radar, and Perimeter Intrusion Detection Systems (PIDS), loosely integrated with a central Command and Control (C2) system. Whilst some sensors provide automatic event detection and C2 systems commonly provide rudimentary multi-sensor rule based alerting, the performance of such systems is limited by the lack of deep integration and autonomy. As a result, these systems have a high degree of operator burden. To address these challenges, an architectural concept termed "SAPIENT" was conceived. SAPIENT is based on multiple Autonomous Sensor Modules (ASMs) connected to a High-Level Decision Making Module (HLDMM) that provides data fusion, situational awareness, alerting, and sensor management capability. The aim of the SAPIENT concept is to allow for the creation of a surveillance system, in a modular plug-and-play manner, that provides high levels of autonomy, threat detection performance, and reduced operator burden. This paper considers the challenges associated with developing an HLDMM aligned with the SAPIENT concept, through the discussion of the design of a realised HLDMM. Particular focus is drawn to how high levels of system level performance can be achieved whilst retaining modularity and flexibility. A number of key aspects of our HLDMM are presented, including an integrated threat assessment and sensor management framework, threat sequence matching, and ASM trust modelling. The results of real-world testing of the HLDMM, in conjunction with multiple Laser, Radar, and EO/IR sensors, in representative semi-urban environments, are discussed.

Multitarget, quantitative nanoplasmonic electrical field-enhanced resonating device (NE2RD) for diagnostics

PubMed Central

Inci, Fatih; Filippini, Chiara; Ozen, Mehmet Ozgun; Calamak, Semih; Durmus, Naside Gozde; Wang, ShuQi; Hanhauser, Emily; Hobbs, Kristen S.; Juillard, Franceline; Kuang, Ping Ping; Vetter, Michael L.; Carocci, Margot; Yamamoto, Hidemi S.; Takagi, Yuko; Yildiz, Umit Hakan; Akin, Demir; Wesemann, Duane R.; Singhal, Amit; Yang, Priscilla L.; Nibert, Max L.; Fichorova, Raina N.; Lau, Daryl T.-Y.; Henrich, Timothy J.; Kaye, Kenneth M.; Schachter, Steven C.; Kuritzkes, Daniel R.; Steinmetz, Lars M.; Gambhir, Sanjiv S.; Davis, Ronald W.; Demirci, Utkan

2015-01-01

Recent advances in biosensing technologies present great potential for medical diagnostics, thus improving clinical decisions. However, creating a label-free general sensing platform capable of detecting multiple biotargets in various clinical specimens over a wide dynamic range, without lengthy sample-processing steps, remains a considerable challenge. In practice, these barriers prevent broad applications in clinics and at patients’ homes. Here, we demonstrate the nanoplasmonic electrical field-enhanced resonating device (NE2RD), which addresses all these impediments on a single platform. The NE2RD employs an immunodetection assay to capture biotargets, and precisely measures spectral color changes by their wavelength and extinction intensity shifts in nanoparticles without prior sample labeling or preprocessing. We present through multiple examples, a label-free, quantitative, portable, multitarget platform by rapidly detecting various protein biomarkers, drugs, protein allergens, bacteria, eukaryotic cells, and distinct viruses. The linear dynamic range of NE2RD is five orders of magnitude broader than ELISA, with a sensitivity down to 400 fg/mL This range and sensitivity are achieved by self-assembling gold nanoparticles to generate hot spots on a 3D-oriented substrate for ultrasensitive measurements. We demonstrate that this precise platform handles multiple clinical samples such as whole blood, serum, and saliva without sample preprocessing under diverse conditions of temperature, pH, and ionic strength. The NE2RD’s broad dynamic range, detection limit, and portability integrated with a disposable fluidic chip have broad applications, potentially enabling the transition toward precision medicine at the point-of-care or primary care settings and at patients’ homes. PMID:26195743

Real-time multiplexed digital cavity-enhanced spectroscopy

DOE PAGES

Boyson, Toby K.; Dagdigian, Paul J.; Pavey, Karl D.; ...

2015-10-01

Cavity-enhanced spectroscopy is a sensitive optical absorption technique but one where the practical applications have been limited to studying small wavelength ranges. In addition, this Letter shows that wideband operation can be achieved by combining techniques usually reserved for the communications community with that of cavity-enhanced spectroscopy, producing a multiplexed real-time cavity-enhanced spectrometer. We use multiple collinear laser sources operating asynchronously and simultaneously while being detected on a single photodetector. This is synonymous with radio frequency (RF) cellular systems in which signals are detected on a single antenna but decoded uniquely. Here, we demonstrate results with spectra of methyl salicylatemore » and show parts-per-billion per root hertz sensitivity measured in real-time.« less

Detection of multiple blood feeding in Aedes aegypti (Diptera: Culicidae) during a single gonotrophic cycle using a histologic technique.

PubMed

Scott, T W; Clark, G G; Lorenz, L H; Amerasinghe, P H; Reiter, P; Edman, J D

1993-01-01

We evaluated a histologic technique for its usefulness in detecting multiple blood feeding by Aedes aegypti (L.) in a single gonotrophic cycle. To standardize the procedure, we carried out a laboratory study in which 166 mosquitoes imbibed two blood meals at known intervals. Eighty percent (78/98) of the multiple meals were detected when the interval between meals was from 1 to < to = 24 h and the time from the second meal to fixation ranged from 0 to 12 hr. At intervals outside this range, only 34% (23/68) of the multiple meals were detected. Overall, 61% (101/166) of the double meals were detected. Examination of 96 engorged Ae. aegypti collected by aspiration from inside houses in San Juan, Puerto Rico, indicated that 50% had imbibed multiple meals. Most wild-caught mosquitoes took their last meal the day before capture, and most multiple feeders fed twice on consecutive days. A dark line of digested blood, or heme, around the first meal and a physical separation between meals were the most useful histologic parameters for detecting multiple feeding in wild Ae. aegypti. An association of multiple feeding with advanced stages of oocyte development suggests that, at the time of collection, most Ae. aegypti from the study site had fed twice in each gonotrophic cycle. We conclude that, although it is labor intensive, histologic examination is an appropriate technique for a longitudinal, community-wide survey of multiple feeding by Ae. aegypti.

Detection of latent bloodstains beneath painted surfaces using reflected infrared photography.

PubMed

Farrar, Andrew; Porter, Glenn; Renshaw, Adrian

2012-09-01

Bloodstain evidence is a highly valued form of physical evidence commonly found at scenes involving violent crimes. However, painting over bloodstains will often conceal this type of evidence. There is limited research in the scientific literature that describes methods of detecting painted-over bloodstains. This project employed a modified digital single-lens reflex camera to investigate the effectiveness of infrared (IR) photography in detecting latent bloodstain evidence beneath a layer or multiple layers of paint. A qualitative evaluation was completed by comparing images taken of a series of samples using both IR and standard (visible light) photography. Further quantitative image analysis was used to verify the findings. Results from this project indicate that bloodstain evidence can be detected beneath up to six layers of paint using reflected IR; however, the results vary depending on the characteristics of the paint. This technique provides crime scene specialists with a new field method to assist in locating, visualizing, and documenting painted-over bloodstain evidence. © 2012 American Academy of Forensic Sciences.

Mechanism of fat taste perception: Association with diet and obesity.

PubMed

Liu, Dongli; Archer, Nicholas; Duesing, Konsta; Hannan, Garry; Keast, Russell

2016-07-01

Energy homeostasis plays a significant role in food consumption and body weight regulation with fat intake being an area of particular interest due to its palatability and high energy density. Increasing evidence from humans and animal studies indicate the existence of a taste modality responsive to fat via its breakdown product fatty acids. These studies implicate multiple candidate receptors and ion channels for fatty acid taste detection, indicating a complex peripheral physiology that is currently not well understood. Additionally, a limited number of studies suggest a reduced ability to detect fatty acids is associated with obesity and a diet high in fat reduces an individual's ability to detect fatty acids. To support this, genetic variants within candidate fatty acid receptors are also associated with obesity reduced ability to detect fatty acids. Understanding oral peripheral fatty acid transduction mechanisms and the association with fat consumption may provide the basis of novel approaches to control development of obesity. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

DEVELOPMENT OF A METHOD FOR THE OBSERVATION OF LIGHTNING IN PROTOPLANETARY DISKS USING ION LINES

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

Muranushi, Takayuki; Akiyama, Eiji; Inutsuka, Shu-ichiro

2015-12-20

In this paper, we propose observational methods for detecting lightning in protoplanetary disks. We do so by calculating the critical electric field strength in the lightning matrix gas (LMG), the parts of the disk where the electric field is strong enough to cause lightning. That electric field accelerates multiple positive ion species to characteristic terminal velocities. In this paper, we present three distinct discharge models with corresponding critical electric fields. We simulate the position–velocity diagrams and the integrated emission maps for the models. We calculate the measure-of-sensitivity values for detection of the models and for distinguishing between the models. Atmore » the distance of TW Hya (54 pc), LMG that occupies 2π in azimuth and has 25 AU < r < 50 AU is detectable at 1200σ to 4000σ. The lower limits of the radii of 5σ-detectable LMG clumps are between 1.6 AU and 5.3 AU, depending on the models.« less

An integrated approach for identifying wrongly labelled samples when performing classification in microarray data.

PubMed

Leung, Yuk Yee; Chang, Chun Qi; Hung, Yeung Sam

2012-01-01

Using hybrid approach for gene selection and classification is common as results obtained are generally better than performing the two tasks independently. Yet, for some microarray datasets, both classification accuracy and stability of gene sets obtained still have rooms for improvement. This may be due to the presence of samples with wrong class labels (i.e. outliers). Outlier detection algorithms proposed so far are either not suitable for microarray data, or only solve the outlier detection problem on their own. We tackle the outlier detection problem based on a previously proposed Multiple-Filter-Multiple-Wrapper (MFMW) model, which was demonstrated to yield promising results when compared to other hybrid approaches (Leung and Hung, 2010). To incorporate outlier detection and overcome limitations of the existing MFMW model, three new features are introduced in our proposed MFMW-outlier approach: 1) an unbiased external Leave-One-Out Cross-Validation framework is developed to replace internal cross-validation in the previous MFMW model; 2) wrongly labeled samples are identified within the MFMW-outlier model; and 3) a stable set of genes is selected using an L1-norm SVM that removes any redundant genes present. Six binary-class microarray datasets were tested. Comparing with outlier detection studies on the same datasets, MFMW-outlier could detect all the outliers found in the original paper (for which the data was provided for analysis), and the genes selected after outlier removal were proven to have biological relevance. We also compared MFMW-outlier with PRAPIV (Zhang et al., 2006) based on same synthetic datasets. MFMW-outlier gave better average precision and recall values on three different settings. Lastly, artificially flipped microarray datasets were created by removing our detected outliers and flipping some of the remaining samples' labels. Almost all the 'wrong' (artificially flipped) samples were detected, suggesting that MFMW-outlier was sufficiently powerful to detect outliers in high-dimensional microarray datasets.

Addressing the targeting range of the ABILHAND-56 in relapsing-remitting multiple sclerosis: A mixed methods psychometric study.

PubMed

Cleanthous, Sophie; Strzok, Sara; Pompilus, Farrah; Cano, Stefan; Marquis, Patrick; Cohan, Stanley; Goldman, Myla D; Kresa-Reahl, Kiren; Petrillo, Jennifer; Castrillo-Viguera, Carmen; Cadavid, Diego; Chen, Shih-Yin

2018-01-01

ABILHAND, a manual ability patient-reported outcome instrument originally developed for stroke patients, has been used in multiple sclerosis clinical trials; however, psychometric analyses indicated the measure's limited measurement range and precision in higher-functioning multiple sclerosis patients. The purpose of this study was to identify candidate items to expand the measurement range of the ABILHAND-56, thus improving its ability to detect differences in manual ability in higher-functioning multiple sclerosis patients. A step-wise mixed methods design strategy was used, comprising two waves of patient interviews, a combination of qualitative (concept elicitation and cognitive debriefing) and quantitative (Rasch measurement theory) analytic techniques, and consultation interviews with three clinical neurologists specializing in multiple sclerosis. Original ABILHAND was well understood in this context of use. Eighty-two new manual ability concepts were identified. Draft supplementary items were generated and refined with patient and neurologist input. Rasch measurement theory psychometric analysis indicated supplementary items improved targeting to higher-functioning multiple sclerosis patients and measurement precision. The final pool of Early Multiple Sclerosis Manual Ability items comprises 20 items. The synthesis of qualitative and quantitative methods used in this study improves the ABILHAND content validity to more effectively identify manual ability changes in early multiple sclerosis and potentially help determine treatment effect in higher-functioning patients in clinical trials.

Finding Kuiper Belt Objects Below the Detection Limit

NASA Astrophysics Data System (ADS)

Whidden, Peter; Kalmbach, Bryce; Bektesevic, Dino; Connolly, Andrew; Jones, Lynne; Smotherman, Hayden; Becker, Andrew

2018-01-01

We demonstrate a novel approach for uncovering the signatures of moving objects (e.g. Kuiper Belt Objects) below the detection thresholds of single astronomical images. To do so, we will employ a matched filter moving at specific rates of proposed orbits through a time-domain dataset. This is analogous to the better-known "shift-and-stack" method; however it uses neither direct shifting nor stacking of the image pixels. Instead of resampling the raw pixels to create an image stack, we will instead integrate the object detection probabilities across multiple single-epoch images to accrue support for a proposed orbit. The filtering kernel provides a measure of the probability that an object is present along a given orbit, and enables the user to make principled decisions about when the search has been successful, and when it may be terminated. The results we present here utilize GPUs to speed up the search by two orders of magnitudes over CPU implementations.

Practical photon number detection with electric field-modulated silicon avalanche photodiodes.

PubMed

Thomas, O; Yuan, Z L; Shields, A J

2012-01-24

Low-noise single-photon detection is a prerequisite for quantum information processing using photonic qubits. In particular, detectors that are able to accurately resolve the number of photons in an incident light pulse will find application in functions such as quantum teleportation and linear optics quantum computing. More generally, such a detector will allow the advantages of quantum light detection to be extended to stronger optical signals, permitting optical measurements limited only by fluctuations in the photon number of the source. Here we demonstrate a practical high-speed device, which allows the signals arising from multiple photon-induced avalanches to be precisely discriminated. We use a type of silicon avalanche photodiode in which the lateral electric field profile is strongly modulated in order to realize a spatially multiplexed detector. Clearly discerned multiphoton signals are obtained by applying sub-nanosecond voltage gates in order to restrict the detector current.

Nanoporous-Gold-Based Electrode Morphology Libraries for Investigating Structure-Property Relationships in Nucleic Acid Based Electrochemical Biosensors.

PubMed

Matharu, Zimple; Daggumati, Pallavi; Wang, Ling; Dorofeeva, Tatiana S; Li, Zidong; Seker, Erkin

2017-04-19

Nanoporous gold (np-Au) electrode coatings significantly enhance the performance of electrochemical nucleic acid biosensors because of their three-dimensional nanoscale network, high electrical conductivity, facile surface functionalization, and biocompatibility. Contrary to planar electrodes, the np-Au electrodes also exhibit sensitive detection in the presence of common biofouling media due to their porous structure. However, the pore size of the nanomatrix plays a critical role in dictating the extent of biomolecular capture and transport. Small pores perform better in the case of target detection in complex samples by filtering out the large nonspecific proteins. On the other hand, larger pores increase the accessibility of target nucleic acids in the nanoporous structure, enhancing the detection limits of the sensor at the expense of more interference from biofouling molecules. Here, we report a microfabricated np-Au multiple electrode array that displays a range of electrode morphologies on the same chip for identifying feature sizes that reduce the nonspecific adsorption of proteins but facilitate the permeation of target DNA molecules into the pores. We demonstrate the utility of the electrode morphology library in studying DNA functionalization and target detection in complex biological media with a special emphasis on revealing ranges of electrode morphologies that mutually enhance the limit of detection and biofouling resilience. We expect this technique to assist in the development of high-performance biosensors for point-of-care diagnostics and facilitate studies on the electrode structure-property relationships in potential applications ranging from neural electrodes to catalysts.

Multiplexed detection of mycotoxins in foods with a regenerable array.

PubMed

Ngundi, Miriam M; Shriver-Lake, Lisa C; Moore, Martin H; Ligler, Frances S; Taitt, Chris R

2006-12-01

The occurrence of different mycotoxins in cereal products calls for the development of a rapid, sensitive, and reliable detection method that is capable of analyzing samples for multiple toxins simultaneously. In this study, we report the development and application of a multiplexed competitive assay for the simultaneous detection of ochratoxin A (OTA) and deoxynivalenol (DON) in spiked barley, cornmeal, and wheat, as well as in naturally contaminated maize samples. Fluoroimmunoassays were performed with the Naval Research Laboratory array biosensor, by both a manual and an automated version of the system. This system employs evanescent-wave fluorescence excitation to probe binding events as they occur on the surface of a waveguide. Methanolic extracts of the samples were diluted threefold with buffer containing a mixture of fluorescent antibodies and were then passed over the arrays of mycotoxins immobilized on a waveguide. Fluorescent signals of the surface-bound antibody-antigen complexes decreased with increasing concentrations of free mycotoxins in the extract. After sample analysis was completed, surfaces were regenerated with 6 M guanidine hydrochloride in 50 mM glycine, pH 2.0. The limits of detection determined by the manual biosensor system were as follows: 1, 180, and 65 ng/g for DON and 1, 60, and 85 ng/g for OTA in cornmeal, wheat, and barley, respectively. The limits of detection in cornmeal determined with the automated array biosensor were 15 and 150 ng/g for OTA and DON, respectively.

Comparison of LIDAR system performance for alternative single-mode receiver architectures: modeling and experimental validation

NASA Astrophysics Data System (ADS)

Toliver, Paul; Ozdur, Ibrahim; Agarwal, Anjali; Woodward, T. K.

2013-05-01

In this paper, we describe a detailed performance comparison of alternative single-pixel, single-mode LIDAR architectures including (i) linear-mode APD-based direct-detection, (ii) optically-preamplified PIN receiver, (iii) PINbased coherent-detection, and (iv) Geiger-mode single-photon-APD counting. Such a comparison is useful when considering next-generation LIDAR on a chip, which would allow one to leverage extensive waveguide-based structures and processing elements developed for telecom and apply them to small form-factor sensing applications. Models of four LIDAR transmit and receive systems are described in detail, which include not only the dominant sources of receiver noise commonly assumed in each of the four detection limits, but also additional noise terms present in realistic implementations. These receiver models are validated through the analysis of detection statistics collected from an experimental LIDAR testbed. The receiver is reconfigurable into four modes of operation, while transmit waveforms and channel characteristics are held constant. The use of a diffuse hard target highlights the importance of including speckle noise terms in the overall system analysis. All measurements are done at 1550 nm, which offers multiple system advantages including less stringent eye safety requirements and compatibility with available telecom components, optical amplification, and photonic integration. Ultimately, the experimentally-validated detection statistics can be used as part of an end-to-end system model for projecting rate, range, and resolution performance limits and tradeoffs of alternative integrated LIDAR architectures.

Rapid and Highly Sensitive Detection of Dopamine Using Conjugated Oxaborole-Based Polymer and Glycopolymer Systems.

PubMed

Jiang, Keren; Wang, Yinan; Thakur, Garima; Kotsuchibashi, Yohei; Naicker, Selvaraj; Narain, Ravin; Thundat, Thomas

2017-05-10

A conjugated polymer interface consisting of an oxaborole containing polymer and a glycopolymer was used for achieving very high selectivity in dopamine (DA) detection. The optimum binding affinity between the polymers promotes the selectivity to DA through a displacement mechanism while remaining unaffected by other structurally related analogs and saccharide derivatives. Real-time detection of DA with very high selectivity and sensitivity has been demonstrated by immobilizing the polymer conjugates on surface plasmon resonance (SPR) and microcantilever (MCL) sensor platforms. Using the conjugated polymer sensing layer, the SPR biosensor was capable of detecting DA in the concentration range of 1 × 10 -9 to 1 × 10 -4 mol L -1 , whereas the MCL sensor showed a limit of detection (LOD) of 5 × 10 -11 mol L -1 . We find that the sensing mechanism is based on DA-induced reversible swelling of the conjugated polymer layer and this allows regeneration and reuse of the sensor multiple times. Also, we conclude that SPR is a suitable sensor platform for DA in-line detection at clinical level considering the detection time and stability, whereas MCL can achieve a much lower LOD.

Analysis of Android Device-Based Solutions for Fall Detection

PubMed Central

Casilari, Eduardo; Luque, Rafael; Morón, María-José

2015-01-01

Falls are a major cause of health and psychological problems as well as hospitalization costs among older adults. Thus, the investigation on automatic Fall Detection Systems (FDSs) has received special attention from the research community during the last decade. In this area, the widespread popularity, decreasing price, computing capabilities, built-in sensors and multiplicity of wireless interfaces of Android-based devices (especially smartphones) have fostered the adoption of this technology to deploy wearable and inexpensive architectures for fall detection. This paper presents a critical and thorough analysis of those existing fall detection systems that are based on Android devices. The review systematically classifies and compares the proposals of the literature taking into account different criteria such as the system architecture, the employed sensors, the detection algorithm or the response in case of a fall alarms. The study emphasizes the analysis of the evaluation methods that are employed to assess the effectiveness of the detection process. The review reveals the complete lack of a reference framework to validate and compare the proposals. In addition, the study also shows that most research works do not evaluate the actual applicability of the Android devices (with limited battery and computing resources) to fall detection solutions. PMID:26213928

Passive IR polarization sensors: a new technology for mine detection

NASA Astrophysics Data System (ADS)

Barbour, Blair A.; Jones, Michael W.; Barnes, Howard B.; Lewis, Charles P.

1998-09-01

The problem of mine and minefield detection continues to provide a significant challenge to sensor systems. Although the various sensor technologies (infrared, ground penetrating radar, etc.) may excel in certain situations there does not exist a single sensor technology that can adequately detect mines in all conditions such as time of day, weather, buried or surface laid, etc. A truly robust mine detection system will likely require the fusion of data from multiple sensor technologies. The performance of these systems, however, will ultimately depend on the performance of the individual sensors. Infrared (IR) polarimetry is a new and innovative sensor technology that adds substantial capabilities to the detection of mines. IR polarimetry improves on basic IR imaging by providing improved spatial resolution of the target, an inherent ability to suppress clutter, and the capability for zero (Delta) T imaging. Nichols Research Corporation (Nichols) is currently evaluating the effectiveness of IR polarization for mine detection. This study is partially funded by the U.S. Army Night Vision & Electronic Sensors Directorate (NVESD). The goal of the study is to demonstrate, through phenomenology studies and limited field trials, that IR polarizaton outperforms conventional IR imaging in the mine detection arena.

Analysis of Android Device-Based Solutions for Fall Detection.

PubMed

Casilari, Eduardo; Luque, Rafael; Morón, María-José

2015-07-23

Falls are a major cause of health and psychological problems as well as hospitalization costs among older adults. Thus, the investigation on automatic Fall Detection Systems (FDSs) has received special attention from the research community during the last decade. In this area, the widespread popularity, decreasing price, computing capabilities, built-in sensors and multiplicity of wireless interfaces of Android-based devices (especially smartphones) have fostered the adoption of this technology to deploy wearable and inexpensive architectures for fall detection. This paper presents a critical and thorough analysis of those existing fall detection systems that are based on Android devices. The review systematically classifies and compares the proposals of the literature taking into account different criteria such as the system architecture, the employed sensors, the detection algorithm or the response in case of a fall alarms. The study emphasizes the analysis of the evaluation methods that are employed to assess the effectiveness of the detection process. The review reveals the complete lack of a reference framework to validate and compare the proposals. In addition, the study also shows that most research works do not evaluate the actual applicability of the Android devices (with limited battery and computing resources) to fall detection solutions.

Aptamer-based microfluidic beads array sensor for simultaneous detection of multiple analytes employing multienzyme-linked nanoparticle amplification and quantum dots labels.

PubMed

Zhang, He; Hu, Xinjiang; Fu, Xin

2014-07-15

This study reports the development of an aptamer-mediated microfluidic beads-based sensor for multiple analytes detection and quantification using multienzyme-linked nanoparticle amplification and quantum dots labels. Adenosine and cocaine were selected as the model analytes to validate the assay design based on strand displacement induced by target-aptamer complex. Microbeads functionalized with the aptamers and modified electron rich proteins were arrayed within a microfluidic channel and were connected with the horseradish peroxidases (HRP) and capture DNA probe derivative gold nanoparticles (AuNPs) via hybridization. The conformational transition of aptamer induced by target-aptamer complex contributes to the displacement of functionalized AuNPs and decreases the fluorescence signal of microbeads. In this approach, increased binding events of HRP on each nanosphere and enhanced mass transport capability inherent from microfluidics are integrated for enhancing the detection sensitivity of analytes. Based on the dual signal amplification strategy, the developed aptamer-based microfluidic bead array sensor could discriminate as low as 0.1 pM of adenosine and 0.5 pM cocaine, and showed a 500-fold increase in detection limit of adenosine compared to the off-chip test. The results proved the microfluidic-based method was a rapid and efficient system for aptamer-based targets assays (adenosine (0.1 pM) and cocaine (0.5 pM)), requiring only minimal (microliter) reagent use. This work demonstrated the successful application of aptamer-based microfluidic beads array sensor for detection of important molecules in biomedical fields. Copyright © 2014 Elsevier B.V. All rights reserved.

Highly sensitive photoelectrochemical biosensor for kinase activity detection and inhibition based on the surface defect recognition and multiple signal amplification of metal-organic frameworks.

PubMed

Wang, Zonghua; Yan, Zhiyong; Wang, Feng; Cai, Jibao; Guo, Lei; Su, Jiakun; Liu, Yang

2017-11-15

A turn-on photoelectrochemical (PEC) biosensor based on the surface defect recognition and multiple signal amplification of metal-organic frameworks (MOFs) was proposed for highly sensitive protein kinase activity analysis and inhibitor evaluation. In this strategy, based on the phosphorylation reaction in the presence of protein kinase A (PKA), the Zr-based metal-organic frameworks (UiO-66) accommodated with [Ru(bpy) 3 ] 2+ photoactive dyes in the pores were linked to the phosphorylated kemptide modified TiO 2 /ITO electrode through the chelation between the Zr 4+ defects on the surface of UiO-66 and the phosphate groups in kemptide. Under visible light irradiation, the excited electrons from [Ru(bpy) 3 ] 2+ adsorbed in the pores of UiO-66 injected into the TiO 2 conduction band to generate photocurrent, which could be utilized for protein kinase activities detection. The large surface area and high porosities of UiO-66 facilitated a large number of [Ru(bpy) 3 ] 2+ that increased the photocurrent significantly, and afforded a highly sensitive PEC analysis of kinase activity. The detection limit of the as-proposed PEC biosensor was 0.0049UmL -1 (S/N!=!3). The biosensor was also applied for quantitative kinase inhibitor evaluation and PKA activities detection in MCF-7 cell lysates. The developed visible-light PEC biosensor provides a simple detection procedure and a cost-effective manner for PKA activity assays, and shows great potential in clinical diagnosis and drug discoveries. Copyright © 2017 Elsevier B.V. All rights reserved.

Broad attention to multiple individual objects may facilitate change detection with complex auditory scenes.

PubMed

Irsik, Vanessa C; Vanden Bosch der Nederlanden, Christina M; Snyder, Joel S

2016-11-01

Attention and other processing constraints limit the perception of objects in complex scenes, which has been studied extensively in the visual sense. We used a change deafness paradigm to examine how attention to particular objects helps and hurts the ability to notice changes within complex auditory scenes. In a counterbalanced design, we examined how cueing attention to particular objects affected performance in an auditory change-detection task through the use of valid or invalid cues and trials without cues (Experiment 1). We further examined how successful encoding predicted change-detection performance using an object-encoding task and we addressed whether performing the object-encoding task along with the change-detection task affected performance overall (Experiment 2). Participants had more error for invalid compared to valid and uncued trials, but this effect was reduced in Experiment 2 compared to Experiment 1. When the object-encoding task was present, listeners who completed the uncued condition first had less overall error than those who completed the cued condition first. All participants showed less change deafness when they successfully encoded change-relevant compared to irrelevant objects during valid and uncued trials. However, only participants who completed the uncued condition first also showed this effect during invalid cue trials, suggesting a broader scope of attention. These findings provide converging evidence that attention to change-relevant objects is crucial for successful detection of acoustic changes and that encouraging broad attention to multiple objects is the best way to reduce change deafness. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

THE USE OF MULTIPLE DISPLACEMENT AMPLIFICATION TO INCREASE THE DETECTION AND GENOTYPING OF TRYPANOSOMA SPECIES SAMPLES IMMOBILISED ON FTA FILTERS

PubMed Central

MORRISON, LIAM J.; McCORMACK, GILLIAN; SWEENEY, LINDSAY; LIKEUFACK, ANNE C. L.; TRUC, PHILIPPE; TURNER, C. MICHAEL; TAIT, ANDY; MacLEOD, ANNETTE

2007-01-01

Whole genome amplification methods are a recently developed tool for amplifying DNA from limited template. We report its application in trypanosome infections, characterised by low parasitaemias. Multiple Displacement Amplification (MDA) amplifies DNA with a simple in vitro step, and was evaluated on mouse blood samples on FTA filter cards with known numbers of Trypanosoma brucei parasites. The data showed a twenty-fold increase in the number of PCRs possible per sample, using primers diagnostic for the multi-copy ribosomal ITS region or 177 bp repeats, and a twenty-fold increase in sensitivity over nested PCR against a single copy microsatellite. Using MDA for microsatellite genotyping caused allele dropout at low DNA concentrations, which was overcome by pooling multiple MDA reactions. The validity of using MDA was established with samples from Human African Trypanosomiasis patients. The use of MDA allows maximal use of finite DNA samples and may prove a valuable tool in studies where multiple reactions are necessary, such as population genetic analyses. PMID:17556624

Development and evaluation of a real-time fluorogenic loop-mediated isothermal amplification assay integrated on a microfluidic disc chip (on-chip LAMP) for rapid and simultaneous detection of ten pathogenic bacteria in aquatic animals.

PubMed

Zhou, Qian-Jin; Wang, Lei; Chen, Jiong; Wang, Rui-Na; Shi, Yu-Hong; Li, Chang-Hong; Zhang, De-Min; Yan, Xiao-Jun; Zhang, Yan-Jun

2014-09-01

Rapid, low-cost, and user-friendly strategies are urgently needed for early disease diagnosis and timely treatment, particularly for on-site screening of pathogens in aquaculture. In this study, we successfully developed a real-time fluorogenic loop-mediated isothermal amplification assay integrated on a microfluidic disc chip (on-chip LAMP), which was capable of simultaneously detecting 10 pathogenic bacteria in aquatic animals, i.e., Nocardia seriolae, Pseudomonas putida, Streptococcus iniae, Vibrio alginolyticus, Vibrio anguillarum, Vibrio fluvialis, Vibrio harveyi, Vibrio parahaemolyticus, Vibrio rotiferianus, and Vibrio vulnificus. The assay provided a nearly-automated approach, with only a single pipetting step per chip for sample dispensing. This technique could achieve limits of detection (LOD) ranging from 0.40 to 6.42pg per 1.414μL reaction in less than 30 min. The robust reproducibility was demonstrated by a little variation among duplications for each bacterium with the coefficient of variation (CV) for time to positive (Tp) value less than 0.10. The clinical sensitivity and specificity of this on-chip LAMP assay in detecting field samples were 96.2% and 93.8% by comparison with conventional microbiological methods. Compared with other well-known techniques, on-chip LAMP assay provides low sample and reagent consumption, ease-of-use, accelerated analysis, multiple bacteria and on-site detection, and high reproducibility, indicating that such a technique would be applicable for on-site detection and routine monitoring of multiple pathogens in aquaculture. Copyright © 2014 Elsevier B.V. All rights reserved.

Critical analysis of dual-chamber implantable cardioverter-defibrillator arrhythmia detection : results and technical considerations.

PubMed

Wilkoff, B L; Kühlkamp, V; Volosin, K; Ellenbogen, K; Waldecker, B; Kacet, S; Gillberg, J M; DeSouza, C M

2001-01-23

One of the perceived benefits of dual-chamber implantable cardioverter-defibrillators (ICDs) is the reduction in inappropriate therapy due to new detection algorithms. It was the purpose of the present investigation to propose methods to minimize bias during such comparisons and to report the arrhythmia detection clinical results of the PR Logic dual-chamber detection algorithm in the GEM DR ICD in the context of these methods. Between November 1997 and October 1998, 933 patients received the GEM DR ICD in this prospective multicenter study. A total of 4856 sustained arrhythmia episodes (n=311) with stored electrogram and marker channel were classified by the investigators; 3488 episodes (n=232) were ventricular tachycardia (VT)/ventricular fibrillation (VF), and 1368 episodes (n=149) were supraventricular tachycardia (SVT). The overall detection results were corrected for multiple episodes within a patient with the generalized estimating equations (GEE) method with an exchangeable correlation structure between episodes. The relative sensitivity for detection of sustained VT and/or VF was 100.0% (3488 of 3488, n=232; 95% CI 98.3% to 100%), the VT/VF positive predictivity was 88.4% uncorrected (3488 of 3945, n=278) and 78.1% corrected (95% CI 73.3% to 82.3%) with the GEE method, and the SVT positive predictivity was 100.0% (911 of 911, n=101; 95% CI 96% to 100%). A structured approach to analysis limits the bias inherent in the evaluation of tachycardia discrimination algorithms through the use of relative VT/VF sensitivity, VT/VF positive predictivity, and SVT positive predictivity along with corrections for multiple tachycardia episodes in a single patient.

Evaluation of Targeted Next-Generation Sequencing for Detection of Bovine Pathogens in Clinical Samples.

PubMed

Anis, Eman; Hawkins, Ian K; Ilha, Marcia R S; Woldemeskel, Moges W; Saliki, Jeremiah T; Wilkes, Rebecca P

2018-07-01

The laboratory diagnosis of infectious diseases, especially those caused by mixed infections, is challenging. Routinely, it requires submission of multiple samples to separate laboratories. Advances in next-generation sequencing (NGS) have provided the opportunity for development of a comprehensive method to identify infectious agents. This study describes the use of target-specific primers for PCR-mediated amplification with the NGS technology in which pathogen genomic regions of interest are enriched and selectively sequenced from clinical samples. In the study, 198 primers were designed to target 43 common bovine and small-ruminant bacterial, fungal, viral, and parasitic pathogens, and a bioinformatics tool was specifically constructed for the detection of targeted pathogens. The primers were confirmed to detect the intended pathogens by testing reference strains and isolates. The method was then validated using 60 clinical samples (including tissues, feces, and milk) that were also tested with other routine diagnostic techniques. The detection limits of the targeted NGS method were evaluated using 10 representative pathogens that were also tested by quantitative PCR (qPCR), and the NGS method was able to detect the organisms from samples with qPCR threshold cycle ( C T ) values in the 30s. The method was successful for the detection of multiple pathogens in the clinical samples, including some additional pathogens missed by the routine techniques because the specific tests needed for the particular organisms were not performed. The results demonstrate the feasibility of the approach and indicate that it is possible to incorporate NGS as a diagnostic tool in a cost-effective manner into a veterinary diagnostic laboratory. Copyright © 2018 Anis et al.

The multiplicity of T Tauri stars in the star forming regions Taurus-Auriga and Ophiuchus-Scorpius: A 2.2 micron speckle imaging survey

NASA Technical Reports Server (NTRS)

Ghez, A. M.; Neugebauer, G.; Matthews, K.

1993-01-01

We present the results of a magnitude limited (K less than = 8.5 mag) speckle imaging survey of 69 T Tauri stars in the star forming regions Taurus-Auriga and Ophiuchus-Scorpius. Thirty-three companion stars were found with separations ranging from 0.07 sec to 2.5 sec, nine are new detections. This survey reveals a distinction between the classical T Tauri stars (CTTS) and the weak-lined T Tauri stars (WTTS) based on the binary star frequency as a function of separation: the WTTS binary star distribution is enhanced at the closer separations (less than 50 AU) relative to the CTTS binary star distribution. We suggest that the nearby companion stars shorten the accretion time scale in multiple star systems, thereby accounting for the presence of WTTS that are coeval with many CTTS. The binary star frequency in the projected linear separation range 16 to 252 AU for T Tauri stars (60 (+/- 17)%) is a factor of 4 greater than that of the solar-type main-sequence stars (16(+/- 3)%). Given the limited separation range of this survey, the rate at which binaries are detected suggests that most, if not all, T Tauri stars have companions. We propose that the observed overabundance of companions of T Tauri stars is an evolutionary effect, in which triple and higher order T Tauri stars are disrupted by close encounters with another star or system of stars.

Evidence for unlimited capacity processing of simple features in visual cortex

PubMed Central

White, Alex L.; Runeson, Erik; Palmer, John; Ernst, Zachary R.; Boynton, Geoffrey M.

2017-01-01

Performance in many visual tasks is impaired when observers attempt to divide spatial attention across multiple visual field locations. Correspondingly, neuronal response magnitudes in visual cortex are often reduced during divided compared with focused spatial attention. This suggests that early visual cortex is the site of capacity limits, where finite processing resources must be divided among attended stimuli. However, behavioral research demonstrates that not all visual tasks suffer such capacity limits: The costs of divided attention are minimal when the task and stimulus are simple, such as when searching for a target defined by orientation or contrast. To date, however, every neuroimaging study of divided attention has used more complex tasks and found large reductions in response magnitude. We bridged that gap by using functional magnetic resonance imaging to measure responses in the human visual cortex during simple feature detection. The first experiment used a visual search task: Observers detected a low-contrast Gabor patch within one or four potentially relevant locations. The second experiment used a dual-task design, in which observers made independent judgments of Gabor presence in patches of dynamic noise at two locations. In both experiments, blood-oxygen level–dependent (BOLD) signals in the retinotopic cortex were significantly lower for ignored than attended stimuli. However, when observers divided attention between multiple stimuli, BOLD signals were not reliably reduced and behavioral performance was unimpaired. These results suggest that processing of simple features in early visual cortex has unlimited capacity. PMID:28654964

Comparison of culture and a multiplex probe PCR for identifying Mycoplasma species in bovine milk, semen and swab samples

PubMed Central

Parker, Alysia M.; House, John K.; Hazelton, Mark S.; Bosward, Katrina L.; Sheehy, Paul A.

2017-01-01

Mycoplasma spp. are a major cause of mastitis, arthritis and pneumonia in cattle, and have been associated with reproductive disorders in cows. While culture is the traditional method of identification the use of PCR has become more common. Several investigators have developed PCR protocols to detect M. bovis in milk, yet few studies have evaluated other sample types or other important Mycoplasma species. Therefore the objective of this study was to develop a multiplex PCR assay to detect M. bovis, M. californicum and M. bovigenitalium, and evaluate its analytical performance against traditional culture of bovine milk, semen and swab samples. The PCR specificity was determined and the limit of detection evaluated in spiked milk, semen and swabs. The PCR was then compared to culture on 474 field samples from individual milk, bulk tank milk (BTM), semen and swab (vaginal, preputial, nose and eye) samples. Specificity analysis produced appropriate amplification for all M. bovis, M. californicum and M. bovigenitalium isolates. Amplification was not seen for any of the other Mollicutes or eubacterial isolates. The limit of detection of the PCR was best in milk, followed by semen and swabs. When all three Mycoplasma species were present in a sample, the limit of detection increased. When comparing culture and PCR, overall there was no significant difference in the proportion of culture and PCR positive samples. Culture could detect significantly more positive swab samples. No significant differences were identified for semen, individual milk or BTM samples. PCR identified five samples with two species present. Culture followed by 16S-23S rRNA sequencing did not enable identification of more than one species. Therefore, the superior method for identification of M. bovis, M. californicum and M. bovigenitalium may be dependent on the sample type being analysed, and whether the identification of multiple target species is required. PMID:28264012

Combined array CGH plus SNP genome analyses in a single assay for optimized clinical testing

PubMed Central

Wiszniewska, Joanna; Bi, Weimin; Shaw, Chad; Stankiewicz, Pawel; Kang, Sung-Hae L; Pursley, Amber N; Lalani, Seema; Hixson, Patricia; Gambin, Tomasz; Tsai, Chun-hui; Bock, Hans-Georg; Descartes, Maria; Probst, Frank J; Scaglia, Fernando; Beaudet, Arthur L; Lupski, James R; Eng, Christine; Wai Cheung, Sau; Bacino, Carlos; Patel, Ankita

2014-01-01

In clinical diagnostics, both array comparative genomic hybridization (array CGH) and single nucleotide polymorphism (SNP) genotyping have proven to be powerful genomic technologies utilized for the evaluation of developmental delay, multiple congenital anomalies, and neuropsychiatric disorders. Differences in the ability to resolve genomic changes between these arrays may constitute an implementation challenge for clinicians: which platform (SNP vs array CGH) might best detect the underlying genetic cause for the disease in the patient? While only SNP arrays enable the detection of copy number neutral regions of absence of heterozygosity (AOH), they have limited ability to detect single-exon copy number variants (CNVs) due to the distribution of SNPs across the genome. To provide comprehensive clinical testing for both CNVs and copy-neutral AOH, we enhanced our custom-designed high-resolution oligonucleotide array that has exon-targeted coverage of 1860 genes with 60 000 SNP probes, referred to as Chromosomal Microarray Analysis – Comprehensive (CMA-COMP). Of the 3240 cases evaluated by this array, clinically significant CNVs were detected in 445 cases including 21 cases with exonic events. In addition, 162 cases (5.0%) showed at least one AOH region >10 Mb. We demonstrate that even though this array has a lower density of SNP probes than other commercially available SNP arrays, it reliably detected AOH events >10 Mb as well as exonic CNVs beyond the detection limitations of SNP genotyping. Thus, combining SNP probes and exon-targeted array CGH into one platform provides clinically useful genetic screening in an efficient manner. PMID:23695279

Fluorescent Dye-doped Sol-gel Sensor for Highly Sensitive Carbon Dioxide Gas Detection below Atmospheric Concentrations

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

Dansby-Sparks, Royce N.; Jin, Jun; Mechery, Shelly J

2009-01-01

Optical fluorescence sol-gel sensors have been developed for the detection of carbon dioxide gas in the 0.03?30% range with a detection limit of 0.008% (or 80 ppm) and a quantitation limit of 0.02% (or 200 ppm) CO{sub 2}. Sol?gels were spin-coated on glass slides to create an organically modified silica-doped matrix with the 1-hydroxypyrene-3,6,8-trisulfonate (HPTS) fluorescent indicator. The luminescence intensity of the HPTS indicator (513 nm) is quenched by CO{sub 2}, which protonates the anionic form of HPTS. An ion pair technique was used to incorporate the lipophilic dye into the hydrophilic sol?gel matrix. TiO{sub 2} particles (<5 {mu}m diameter)more » were added to induce Mie scattering and increase the incident light interaction with the sensing film, thus increasing the signal-to-noise ratio. Moisture-proof overcoatings have been used to maintain a constant level of water inside the sensor films. The optical sensors are inexpensive to prepare and can be easily coupled to fiber optics for remote sensing capabilities. A fiber-optic bundle was used for the gas detection and shown to work as part of a multianalyte platform for simultaneous detection of multiple analytes. The studies reported here resulted in the development of sol?gel optical fluorescent sensors for CO{sub 2} gas with sensitivity below that in the atmosphere (ca. 387 ppm). These sensors are a complementary approach to current FT-IR measurements for real-time carbon dioxide detection in environmental applications.« less

Digital breast tomosynthesis for detecting multifocal and multicentric breast cancer: influence of acquisition geometry on model observer performance in breast phantom images

NASA Astrophysics Data System (ADS)

Wen, Gezheng; Park, Subok; Markey, Mia K.

2017-03-01

Multifocal and multicentric breast cancer (MFMC), i.e., the presence of two or more tumor foci within the same breast, has an immense clinical impact on treatment planning and survival outcomes. Detecting multiple breast tumors is challenging as MFMC breast cancer is relatively uncommon, and human observers do not know the number or locations of tumors a priori. Digital breast tomosynthesis (DBT), in which an x-ray beam sweeps over a limited angular range across the breast, has the potential to improve the detection of multiple tumors.1, 2 However, prior efforts to optimize DBT image quality only considered unifocal breast cancers (e.g.,3-9), so the recommended geometries may not necessarily yield images that are informative for the task of detecting MFMC. Hence, the goal of this study is to employ a 3D multi-lesion (ml) channelized-Hotelling observer (CHO) to identify optimal DBT acquisition geometries for MFMC. Digital breast phantoms and simulated DBT scanners of different geometries (e.g., wide or narrow arc scans, different number of projections in each scan) were used to generate image data for the simulation study. Multiple 3D synthetic lesions were inserted into different breast regions to simulate MF cases and MC cases. 3D partial least squares (PLS) channels, and 3D Laguerre-Gauss (LG) channels were estimated to capture discriminant information and correlations among signals in locally varying anatomical backgrounds, enabling the model observer to make both image-level and location-specific detection decisions. The 3D ml-CHO with PLS channels outperformed that with LG channels in this study. The simulated MC cases and MC cases were not equally difficult for the ml-CHO to detect across the different simulated DBT geometries considered in this analysis. Also, the results suggest that the optimal design of DBT may vary as the task of clinical interest changes, e.g., a geometry that is better for finding at least one lesion may be worse for counting the number of lesions.

rmpM genosensor for detection of human brain bacterial meningitis in cerebrospinal fluid.

PubMed

Dash, Sandip Kumar; Sharma, Minakshi; Khare, Shashi; Kumar, Ashok

2013-09-01

Human brain bacterial meningitis is a life-threatening disease caused mainly by Neisseria meningitidis, lead to damage of the outer membrane covering (meninges) of brain or even death. The usual methods of diagnosis are either time-consuming or have some limitations. The specific rmpM (reduction-modifiable protein M) virulent gene based genosensor is more sensitive, specific, and can detect N. meningitidis directly from the patient cerebrospinal fluid in 30 min including 1-min response time. 5'-Thiol-labeled single-stranded DNA (ssDNA) probe was immobilized onto screen-printed gold electrode (SPGE) and hybridized with denatured (95 °C) single-stranded genomic DNA (ssG-DNA) for 10 min at 25 °C. The electrochemical response was measured by cyclic voltammetry, differential pulse voltammetry (DPV) and electrochemical impedance using redox indicators. The sensitivity of the genosensor was 9.5087 (μA/cm(2))/ng with DPV and limit of detection was 3 ng/6 μL ssG-DNA. The immobilization of the ssDNA probe and hybridization with ssG-DNA from N. meningitidis was characterized by atomic force microscopy and Fourier transform infrared spectroscopy. The rmpM genosensor was stable for 6 months at 4 °C with 10 % loss in initial DPV current. The advantage of rmpM genosensor is to detect bacterial meningitis simultaneously in multiple patients using SPGE array during an outbreak of the disease.

Spatio-temporal Hotelling observer for signal detection from image sequences

PubMed Central

Caucci, Luca; Barrett, Harrison H.; Rodríguez, Jeffrey J.

2010-01-01

Detection of signals in noisy images is necessary in many applications, including astronomy and medical imaging. The optimal linear observer for performing a detection task, called the Hotelling observer in the medical literature, can be regarded as a generalization of the familiar prewhitening matched filter. Performance on the detection task is limited by randomness in the image data, which stems from randomness in the object, randomness in the imaging system, and randomness in the detector outputs due to photon and readout noise, and the Hotelling observer accounts for all of these effects in an optimal way. If multiple temporal frames of images are acquired, the resulting data set is a spatio-temporal random process, and the Hotelling observer becomes a spatio-temporal linear operator. This paper discusses the theory of the spatio-temporal Hotelling observer and estimation of the required spatio-temporal covariance matrices. It also presents a parallel implementation of the observer on a cluster of Sony PLAYSTATION 3 gaming consoles. As an example, we consider the use of the spatio-temporal Hotelling observer for exoplanet detection. PMID:19550494

Spatio-temporal Hotelling observer for signal detection from image sequences.

PubMed

Caucci, Luca; Barrett, Harrison H; Rodriguez, Jeffrey J

2009-06-22

Detection of signals in noisy images is necessary in many applications, including astronomy and medical imaging. The optimal linear observer for performing a detection task, called the Hotelling observer in the medical literature, can be regarded as a generalization of the familiar prewhitening matched filter. Performance on the detection task is limited by randomness in the image data, which stems from randomness in the object, randomness in the imaging system, and randomness in the detector outputs due to photon and readout noise, and the Hotelling observer accounts for all of these effects in an optimal way. If multiple temporal frames of images are acquired, the resulting data set is a spatio-temporal random process, and the Hotelling observer becomes a spatio-temporal linear operator. This paper discusses the theory of the spatio-temporal Hotelling observer and estimation of the required spatio-temporal covariance matrices. It also presents a parallel implementation of the observer on a cluster of Sony PLAYSTATION 3 gaming consoles. As an example, we consider the use of the spatio-temporal Hotelling observer for exoplanet detection.

Direct duplex real-time loop mediated isothermal amplification assay for the simultaneous detection of cow and goat species origin of milk and yogurt products for field use.

PubMed

Kim, Mi-Ju; Kim, Hae-Yeong

2018-04-25

A multiple loop-mediated isothermal amplification (LAMP) method was developed to detect cow and goat milk in the field using a portable fluorescence device. For rapid on-site detection, this duplex LAMP assay was used in combination with direct amplification, without DNA extraction. The cow- and goat-specific LAMP primer sets were designed based on the mitochondrial cytochrome b gene, and showed specificity against 13 other animal species in the reactions. The sensitivity of the duplex LAMP assay for cow and goat was 0.1 and 1 pg, respectively. The detection limit for both target species in milk mixtures was 2%. This assay successfully amplified and identified the two target species in 24 samples of commercial milk and yogurt products, with 30 min sampling-to-result analysis time. Therefore, this direct duplex real-time LAMP assay is useful for on-site simultaneous detection of cow and goat milk in commercial products, a capability needed to confirm accurate labeling. Copyright © 2017 Elsevier Ltd. All rights reserved.

Silver-dendrimer nanocomposites as oligonucleotide labels for electrochemical stripping detection of DNA hybridization.

PubMed

Jin, Xin; Zhou, Ling; Zhu, Bo; Jiang, Xue; Zhu, Ningning

2018-06-01

Silver-dendrimer nanocomposites were synthesized and used as oligonucleotide labels for electrochemical stripping detection of DNA hybridization. The synthesized silver-dendrimer nanocomposites were characterized by UV-vis spectrophotometry, X-ray photoelectron spectroscopy (XPS) and transmission electron microscopy (TEM). Ratios of silver/dendrimer were optimized in order to obtain stable nanocomposites with maximal silver loading in the interior of a polymeric shell. The silver-dendrimer nanocomposites were attached to sequence-known DNA probes specific to colitoxin, and used to detect probe hybridization by dissolution of the silver nanoparticles in the interior of dendrimer in a diluted nitric acid, followed by measurement of Ag + ions by anodic stripping voltammetry (ASV). Use of differential pulse voltammetry for the stripping step, along with optimization of the ASV conditions, enabled a detection limit of 0.78 pM. The present strategy, in combination with dendrimer-encapsulated copper labeled oligonucleotides probe reported previously, could potentially be used to detect single or multiple DNA targets in one sample. Copyright © 2018 Elsevier B.V. All rights reserved.

Identification of limit cycles in multi-nonlinearity, multiple path systems

NASA Technical Reports Server (NTRS)

Mitchell, J. R.; Barron, O. L.

1979-01-01

A method of analysis which identifies limit cycles in autonomous systems with multiple nonlinearities and multiple forward paths is presented. The FORTRAN code for implementing the Harmonic Balance Algorithm is reported. The FORTRAN code is used to identify limit cycles in multiple path and nonlinearity systems while retaining the effects of several harmonic components.

Medical chart validation of an algorithm for identifying multiple sclerosis relapse in healthcare claims.

PubMed

Chastek, Benjamin J; Oleen-Burkey, Merrikay; Lopez-Bresnahan, Maria V

2010-01-01

Relapse is a common measure of disease activity in relapsing-remitting multiple sclerosis (MS). The objective of this study was to test the content validity of an operational algorithm for detecting relapse in claims data. A claims-based relapse detection algorithm was tested by comparing its detection rate over a 1-year period with relapses identified based on medical chart review. According to the algorithm, MS patients in a US healthcare claims database who had either (1) a primary claim for MS during hospitalization or (2) a corticosteroid claim following a MS-related outpatient visit were designated as having a relapse. Patient charts were examined for explicit indication of relapse or care suggestive of relapse. Positive and negative predictive values were calculated. Medical charts were reviewed for 300 MS patients, half of whom had a relapse according to the algorithm. The claims-based criteria correctly classified 67.3% of patients with relapses (positive predictive value) and 70.0% of patients without relapses (negative predictive value; kappa 0.373: p < 0.001). Alternative algorithms did not improve on the predictive value of the operational algorithm. Limitations of the algorithm include lack of differentiation between relapsing-remitting MS and other types, and that it does not incorporate measures of function and disability. The claims-based algorithm appeared to successfully detect moderate-to-severe MS relapse. This validated definition can be applied to future claims-based MS studies.

ExScalibur: A High-Performance Cloud-Enabled Suite for Whole Exome Germline and Somatic Mutation Identification

PubMed Central

Huang, Lei; Kang, Wenjun; Bartom, Elizabeth; Onel, Kenan; Volchenboum, Samuel; Andrade, Jorge

2015-01-01

Whole exome sequencing has facilitated the discovery of causal genetic variants associated with human diseases at deep coverage and low cost. In particular, the detection of somatic mutations from tumor/normal pairs has provided insights into the cancer genome. Although there is an abundance of publicly-available software for the detection of germline and somatic variants, concordance is generally limited among variant callers and alignment algorithms. Successful integration of variants detected by multiple methods requires in-depth knowledge of the software, access to high-performance computing resources, and advanced programming techniques. We present ExScalibur, a set of fully automated, highly scalable and modulated pipelines for whole exome data analysis. The suite integrates multiple alignment and variant calling algorithms for the accurate detection of germline and somatic mutations with close to 99% sensitivity and specificity. ExScalibur implements streamlined execution of analytical modules, real-time monitoring of pipeline progress, robust handling of errors and intuitive documentation that allows for increased reproducibility and sharing of results and workflows. It runs on local computers, high-performance computing clusters and cloud environments. In addition, we provide a data analysis report utility to facilitate visualization of the results that offers interactive exploration of quality control files, read alignment and variant calls, assisting downstream customization of potential disease-causing mutations. ExScalibur is open-source and is also available as a public image on Amazon cloud. PMID:26271043

Microbleed detection using automated segmentation (MIDAS): a new method applicable to standard clinical MR images.

PubMed

Seghier, Mohamed L; Kolanko, Magdalena A; Leff, Alexander P; Jäger, Hans R; Gregoire, Simone M; Werring, David J

2011-03-23

Cerebral microbleeds, visible on gradient-recalled echo (GRE) T2* MRI, have generated increasing interest as an imaging marker of small vessel diseases, with relevance for intracerebral bleeding risk or brain dysfunction. Manual rating methods have limited reliability and are time-consuming. We developed a new method for microbleed detection using automated segmentation (MIDAS) and compared it with a validated visual rating system. In thirty consecutive stroke service patients, standard GRE T2* images were acquired and manually rated for microbleeds by a trained observer. After spatially normalizing each patient's GRE T2* images into a standard stereotaxic space, the automated microbleed detection algorithm (MIDAS) identified cerebral microbleeds by explicitly incorporating an "extra" tissue class for abnormal voxels within a unified segmentation-normalization model. The agreement between manual and automated methods was assessed using the intraclass correlation coefficient (ICC) and Kappa statistic. We found that MIDAS had generally moderate to good agreement with the manual reference method for the presence of lobar microbleeds (Kappa = 0.43, improved to 0.65 after manual exclusion of obvious artefacts). Agreement for the number of microbleeds was very good for lobar regions: (ICC = 0.71, improved to ICC = 0.87). MIDAS successfully detected all patients with multiple (≥2) lobar microbleeds. MIDAS can identify microbleeds on standard MR datasets, and with an additional rapid editing step shows good agreement with a validated visual rating system. MIDAS may be useful in screening for multiple lobar microbleeds.

Analysing the impact of multiple stressors in aquatic biomonitoring data: A 'cookbook' with applications in R.

PubMed

Feld, Christian K; Segurado, Pedro; Gutiérrez-Cánovas, Cayetano

2016-12-15

Multiple stressors threaten biodiversity and ecosystem integrity, imposing new challenges to ecosystem management and restoration. Ecosystem managers are required to address and mitigate the impact of multiple stressors, yet the knowledge required to disentangle multiple-stressor effects is still incomplete. Experimental studies have advanced the understanding of single and combined stressor effects, but there is a lack of a robust analytical framework, to address the impact of multiple stressors based on monitoring data. Since 2000, the monitoring of Europe's waters has resulted in a vast amount of biological and environmental (stressor) data of about 120,000 water bodies. For many reasons, this data is rarely exploited in the multiple-stressor context, probably because of its rather heterogeneous nature: stressors vary and are mixed with broad-scale proxies of environmental stress (e.g. land cover), missing values and zero-inflated data limit the application of statistical methods and biological indicators are often aggregated (e.g. taxon richness) and do not respond stressor-specific. Here, we present a 'cookbook' to analyse the biological response to multiple stressors using data from biomonitoring schemes. Our 'cookbook' includes guidance for the analytical process and the interpretation of results. The 'cookbook' is accompanied by scripts, which allow the user to run a stepwise analysis based on his/her own data in R, an open-source language and environment for statistical computing and graphics. Using simulated and real data, we show that the recommended procedure is capable of identifying stressor hierarchy (importance) and interaction in large datasets. We recommend a minimum number of 150 independent observations and a minimum stressor gradient length of 75% (of the most relevant stressor's gradient in nature), to be able to reliably rank the stressor's importance, detect relevant interactions and estimate their standardised effect size. We conclude with a brief discussion of the advantages and limitations of this protocol. Copyright © 2016 Elsevier B.V. All rights reserved.

Detection and spatial distribution of multiple-contaminants in agro-ecological Mediterranean wetlands (Marjal de Pego-Oliva, Spain)

NASA Astrophysics Data System (ADS)

Pascual-Aguilar, Juan Antonio; Andreu, Vicente; Gimeno-García, Eugenia; Picó, Yolanda; Masia, Ana

2015-04-01

Socio economic activities are more and more producing amounts (in quantity and quality) of non desirable chemical substances (contaminants) that can be found in open air environments. As many of these products persist and may also circulate among environmental compartments, the cumulative incidence of such multiple contaminants combination may be a cause of treat that should not exists taking only in consideration concentrations of each contaminant individually because the number and the type of compounds are not known, as well as their cumulative and interaction effects. Thus prior to any further work analyzing the environmental risk of multiple contaminants their identification and level of concentration is required. In this work the potential presence of multiple contaminants of anthropogenic origin in a protected agro-ecological Mediterranean wetland is studied: the Pego-Oliva Marsh Natural Park (Valencian Community, Spain), which is characterized by a long history of human pressures, such as marsh transformation for agricultural uses. Two major groups of relevant pollutants have been targeted according o two distinct environmental matrices: seven heavy metals in soils (Cd, Co, Cr, Cu, Ni, Pb and Zn) and fourteen emerging contaminants /drugs of abuse in surface waters of the natural lagoon, rivers and artificial irrigation networks (6-ACMOR, AMP, BECG, COC, ECGME, HER, KET, MAMP, MDA, MDMA, MET, MOR, THC, THC-COOH). The wetland was divided in nine representative zones with different types of land cover and land use. For soils, 24 samples were collected and for waters 33 taking in consideration the spatial representativeness of the above mention nine environments. Spatial analysis applying Geographical Information Systems to determine areas with greater incidence of both types of contaminants were also performed. With regard to heavy metals, Zn showed values under the detection limits in all samples, the remainder metals appeared in concentrations surpassing the WHO and EU limits for drinking waters, and all except Pb exceed the limits established for irrigation waters. For drugs of abuse 3,4-Methylenedioxymethamphe-tamine, ketamine, morphine, benzoylecgonine, cocaine,methadone, 6-acetylmorphine and nor-9-carboxy-tetrahydro-cannabinol were detected. The mean concentrations were 0.62, 21.33, 1.30, 1.92, 2.25, 0.32, 0.04 and 0.07 ng l, respectively. Almost all samples had at least one substance. In the natural park a spatial trend in the number of contaminants and concentrations can be identified. Such pattern is more evident when analyzing heavy metals in soils. The presence of multiple contaminants is greater in agriculture fields devoted to citrus farming with decreasing intensities for rice fields and natural areas. Connectivity between urban, agriculture and natural lands produced by water flows may be part of the processes that introduce contaminants in the marsh land. Acknowledgements This work was supported by the Spanish Ministry of Science and Innovation through the project CONSOLIDER-INGENIO 2010 (CSD2009) and by the Ministry and the European Regional Development Fund (ERDF) (projects CGL2011-29703-C02-00, CGL2011-29703-C02-01, CGL2011-29703-C02-02).

Rapid Microarray Detection of DNA and Proteins in Microliter Volumes with SPR Imaging Measurements

PubMed Central

Seefeld, Ting Hu; Zhou, Wen-Juan; Corn, Robert M.

2011-01-01

A four chamber microfluidic biochip is fabricated for the rapid detection of multiple proteins and nucleic acids from microliter volume samples with the technique of surface plasmon resonance imaging (SPRI). The 18 mm × 18 mm biochip consists of four 3 μL microfluidic chambers attached to an SF10 glass substrate, each of which contains three individually addressable SPRI gold thin film microarray elements. The twelve element (4 × 3) SPRI microarray consists of gold thin film spots (1 mm2 area; 45 nm thickness) each in individually addressable 0.5 μL volume microchannels. Microarrays of single-stranded DNA and RNA (ssDNA and ssRNA respectively) are fabricated by either chemical and/or enzymatic attachment reactions in these microchannels; the SPRI microarrays are then used to detect femtomole amounts (nanomolar concentrations) of DNA and proteins (single stranded DNA binding protein and thrombin via aptamer-protein bioaffinity interactions). Microarrays of ssRNA microarray elements were also used for the ultrasensitive detection of zeptomole amounts (femtomolar concentrations) of DNA via the technique of RNase H-amplified SPRI. Enzymatic removal of ssRNA from the surface due to the hybridization adsorption of target ssDNA is detected as a reflectivity decrease in the SPR imaging measurements. The observed reflectivity loss was proportional to the log of the target ssDNA concentration with a detection limit of 10 fM or 30 zeptomoles (18,000 molecules). This enzymatic amplified ssDNA detection method is not limited by diffusion of ssDNA to the interface, and thus is extremely fast, requiring only 200 seconds in the microliter volume format. PMID:21488682

Point-of-care detection and real-time monitoring of intravenously delivered drugs via tubing with an integrated SERS sensor

NASA Astrophysics Data System (ADS)

Wu, Hsin-Yu; Cunningham, Brian T.

2014-04-01

We demonstrate an approach for detection, identification, and kinetic monitoring of drugs flowing within tubing, through the use of a plasmonic nanodome array (PNA) surface. The PNA structures are fabricated using a low-cost nanoreplica molding process upon a flexible plastic substrate that is subsequently integrated with a flow cell that connects in series with ordinary intravenous (IV) drug delivery tubing. To investigate the potential clinical applications for point-of-care detection and real-time monitoring, we perform SERS detection of ten pharmaceutical compounds (hydrocodone, levorphanol, morphine, oxycodone, methadone, phenobarbital, dopamine, diltiazem, promethazine, and mitoxantrone). We demonstrate dose-dependent SERS signal magnitude, resulting in detection limits (ng ml-1) well below typical administered dosages (mg ml-1). Further, we show that the detected drugs are not permanently attached to the PNA surface, and thus our approach is capable of performing continuous monitoring of drug delivery as materials flow through IV tubing that is connected in series with the sensor. Finally, we demonstrate the potential co-detection of multiple drugs when they are mixed together, and show excellent reproducibility and stability of SERS measurements for periods extending at least five days. The capabilities reported here demonstrate the potential to use PNA SERS surfaces for enhancing the safety of IV drug delivery.We demonstrate an approach for detection, identification, and kinetic monitoring of drugs flowing within tubing, through the use of a plasmonic nanodome array (PNA) surface. The PNA structures are fabricated using a low-cost nanoreplica molding process upon a flexible plastic substrate that is subsequently integrated with a flow cell that connects in series with ordinary intravenous (IV) drug delivery tubing. To investigate the potential clinical applications for point-of-care detection and real-time monitoring, we perform SERS detection of ten pharmaceutical compounds (hydrocodone, levorphanol, morphine, oxycodone, methadone, phenobarbital, dopamine, diltiazem, promethazine, and mitoxantrone). We demonstrate dose-dependent SERS signal magnitude, resulting in detection limits (ng ml-1) well below typical administered dosages (mg ml-1). Further, we show that the detected drugs are not permanently attached to the PNA surface, and thus our approach is capable of performing continuous monitoring of drug delivery as materials flow through IV tubing that is connected in series with the sensor. Finally, we demonstrate the potential co-detection of multiple drugs when they are mixed together, and show excellent reproducibility and stability of SERS measurements for periods extending at least five days. The capabilities reported here demonstrate the potential to use PNA SERS surfaces for enhancing the safety of IV drug delivery. Electronic supplementary information (ESI) available: Fabrication of PNA substrates, fabrication details of the flow cell, details of FDTD simulation, characterization of the scattering volume, and detection of diltiazem diluted in DI water and PBS. See DOI: 10.1039/c4nr00027g

Methods for the preparation and analysis of solids and suspended solids for total mercury

USGS Publications Warehouse

Olund, Shane D.; DeWild, John F.; Olson, Mark L.; Tate, Michael T.

2004-01-01

The methods documented in this report are utilized by the Wisconsin District Mercury Lab for analysis of total mercury in solids (soils and sediments) and suspended solids (isolated on filters). Separate procedures are required for the different sample types. For solids, samples are prepared by room-temperature acid digestion and oxidation with aqua regia. The samples are brought up to volume with a 5 percent bromine monochloride solution to ensure complete oxidation and heated at 50?C in an oven overnight. Samples are then analyzed with an automated flow injection system incorporating a cold vapor atomic fluorescence spectrometer. A method detection limit of 0.3 ng of mercury per digestion bomb was established using multiple analyses of an environmental sample. Based on the range of masses processed, the minimum sample reporting limit varies from 0.6 ng/g to 6 ng/g. Suspended solids samples are oxidized with a 5 percent bromine monochloride solution and held at 50?C in an oven for 5 days. The samples are then analyzed with an automated flow injection system incorporating a cold vapor atomic fluorescence spectrometer. Using a certified reference material as a surrogate for an environmental sample, a method detection limit of 0.059 ng of mercury per filter was established. The minimum sample reporting limit varies from 0.059 ng/L to 1.18 ng/L, depending on the volume of water filtered.

Development of a rapid, sensitive TaqMan real-time RT-PCR assay for the detection of Rose rosette virus using multiple gene targets.

PubMed

Babu, Binoy; Jeyaprakash, Ayyamperumal; Jones, Debra; Schubert, Timothy S; Baker, Carlye; Washburn, Brian K; Miller, Steven H; Poduch, Kristina; Knox, Gary W; Ochoa-Corona, Francisco M; Paret, Mathews L

2016-09-01

Rose rosette virus (RRV), belonging to the genus Emaravirus, is a highly destructive pathogen that causes rose rosette disease. The disease is a major concern for the rose industry in the U.S. due to the lack of highly sensitive methods for early detection of RRV. This is critical, as early identification of the infected plants and eradication is necessary in minimizing the risks associated with the spread of the disease. A highly reliable, specific and sensitive detection assay is thus required to test and confirm the presence of RRV in suspected plant samples. In this study a TaqMan real-time reverse transcription-polymerase chain reaction (RT-PCR) assay was developed for the detection of RRV from infected roses, utilizing multiple gene targets. Four pairs of primers and probes; two of them (RRV_2-1 and RRV_2-2) based on the consensus sequences of the glycoprotein gene (RNA2) and the other two (RRV_3-2 and RRV_3-5) based on the nucleocapsid gene (RNA3) were designed. The specificity of the primers and probes was evaluated against other representative viruses infecting roses, belonging to the genera Alfamovirus, Cucumovirus, Ilarvirus, Nepovirus, Tobamovirus, and Tospovirus and one Emaravirus (Wheat mosaic virus). Dilution assays using the in vitro transcripts (spiked with total RNA from healthy plants, and non-spiked) showed that all the primers and probes are highly sensitive in consistently detecting RRV with a detection limit of 1 fg. Testing of the infected plants over a period of time (three times in monthly intervals) indicated high reproducibility, with the primer/probe RRV_3-5 showing 100% positive detection, while RRV_2-1, RRV_2-2 and RRV_3-2 showed 90% positive detection. The developed real-time RT-PCR assay is reliable, highly sensitive, and can be easily used in diagnostic laboratories for testing and confirmation of RRV. Copyright © 2016 Elsevier B.V. All rights reserved.

Evaluation of blood and muscle tissues for molecular detection and characterization of hematozoa infections in northern pintails (Anas acuta) wintering in California

USGS Publications Warehouse

Ramey, Andy M.; Schmutz, Joel A.; Fleskes, Joseph P.; Yabsley, Michael J.

2013-01-01

Information on the molecular detection of hematozoa from different tissue types and multiple years would be useful to inform sample collection efforts and interpret results of meta-analyses or investigations spanning multiple seasons. In this study, we tested blood and muscle tissue collected from northern pintails (Anas acuta) during autumn and winter of different years to evaluate prevalence and genetic diversity ofLeucocytozoon, Haemoproteus, and Plasmodium infections in this abundant waterfowl species of the Central Valley of California. We first compared results for paired blood and wing muscle samples to assess the utility of different tissue types for molecular investigations of haemosporidian parasites. Second, we explored inter-annual variability of hematozoa infection in Central Valley northern pintails and investigated possible effects of age, sex, and sub-region of sample collection on estimated parasite detection probability and prevalence. We found limited evidence for differences between tissue types in detection probability and prevalence ofLeucocytozoon, Haemoproteus, and Plasmodium parasites, which supports the utility of both sample types for obtaining information on hematozoan infections. However, we detected 11 haemosporidian mtDNA cyt bhaplotypes in blood samples vs. six in wing muscle tissue collected during the same sample year suggesting an advantage to using blood samples for investigations of genetic diversity. Estimated prevalence ofLeucocytozoon parasites was greater during 2006–2007 as compared to 2011–2012 and four unique haemosporidian mtDNA cyt b haplotypes were detected in the former sample year but not in the latter. Seven of 15 mtDNA cyt b haplotypes detected in northern pintails had 100% identity with previously reported hematozoa lineages detected in waterfowl (Haemoproteus and Leucocytozoon) or other avian taxa (Plasmodium) providing support for lack of host specificity for some parasite lineages.

The Chandra Source Catalog 2.0

NASA Astrophysics Data System (ADS)

Evans, Ian N.; Allen, Christopher E.; Anderson, Craig S.; Budynkiewicz, Jamie A.; Burke, Douglas; Chen, Judy C.; Civano, Francesca Maria; D'Abrusco, Raffaele; Doe, Stephen M.; Evans, Janet D.; Fabbiano, Giuseppina; Gibbs, Danny G., II; Glotfelty, Kenny J.; Graessle, Dale E.; Grier, John D.; Hain, Roger; Hall, Diane M.; Harbo, Peter N.; Houck, John C.; Lauer, Jennifer L.; Laurino, Omar; Lee, Nicholas P.; Martínez-Galarza, Juan Rafael; McCollough, Michael L.; McDowell, Jonathan C.; McLaughlin, Warren; Miller, Joseph; Morgan, Douglas L.; Mossman, Amy E.; Nguyen, Dan T.; Nichols, Joy S.; Nowak, Michael A.; Paxson, Charles; Plummer, David A.; Primini, Francis Anthony; Rots, Arnold H.; Siemiginowska, Aneta; Sundheim, Beth A.; Tibbetts, Michael; Van Stone, David W.; Zografou, Panagoula

2018-01-01

The current version of the Chandra Source Catalog (CSC) continues to be well utilized by the astronomical community. Usage over the past year has continued to average more than 15,000 searches per month. Version 1.1 of the CSC, released in 2010, includes properties and data for 158,071 detections, corresponding to 106,586 distinct X-ray sources on the sky. The second major release of the catalog, CSC 2.0, will be made available to the user community in early 2018, and preliminary lists of detections and sources are available now. Release 2.0 will roughly triple the size of the current version of the catalog to an estimated 375,000 detections, corresponding to ~315,000 unique X-ray sources. Compared to release 1.1, the limiting sensitivity for compact sources in CSC 2.0 is significantly enhanced. This improvement is achieved by using a two-stage approach that involves stacking (co-adding) multiple observations of the same field prior to source detection, and then using an improved source detection approach that enables us to detect point source down to ~5 net counts on-axis for exposures shorter than ~15 ks. In addition to enhanced source detection capabilities, improvements to the Bayesian aperture photometry code included in release 2.0 provides robust photometric probability density functions (PDFs) in crowded fields even for low count detections. All post-aperture photometry properties (e.g., hardness ratios, source variability) work directly from the PDFs in release 2.0. CSC 2.0 also adds a Bayesian Blocks analysis of the multi-band aperture photometry PDFs to identify multiple observations of the same source that have similar photometric properties, and therefore can be analyzed simultaneously to improve S/N.We briefly describe these and other updates that significantly enhance the scientific utility of CSC 2.0 when compared to the earlier catalog release.This work has been supported by NASA under contract NAS 8-03060 to the Smithsonian Astrophysical Observatory for operation of the Chandra X-ray Center.

DETECTION OF FAST RADIO TRANSIENTS WITH MULTIPLE STATIONS: A CASE STUDY USING THE VERY LONG BASELINE ARRAY

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

Thompson, David R.; Wagstaff, Kiri L.; Majid, Walid A.

2011-07-10

Recent investigations reveal an important new class of transient radio phenomena that occur on submillisecond timescales. Often, transient surveys' data volumes are too large to archive exhaustively. Instead, an online automatic system must excise impulsive interference and detect candidate events in real time. This work presents a case study using data from multiple geographically distributed stations to perform simultaneous interference excision and transient detection. We present several algorithms that incorporate dedispersed data from multiple sites, and report experiments with a commensal real-time transient detection system on the Very Long Baseline Array. We test the system using observations of pulsar B0329+54.more » The multiple-station algorithms enhanced sensitivity for detection of individual pulses. These strategies could improve detection performance for a future generation of geographically distributed arrays such as the Australian Square Kilometre Array Pathfinder and the Square Kilometre Array.« less

Attention to Attributes and Objects in Working Memory

PubMed Central

Cowan, Nelson; Blume, Christopher L.; Saults, J. Scott

2013-01-01

It has been debated on the basis of change-detection procedures whether visual working memory is limited by the number of objects, task-relevant attributes within those objects, or bindings between attributes. This debate, however, has been hampered by several limitations, including the use of conditions that vary between studies and the absence of appropriate mathematical models to estimate the number of items in working memory in different stimulus conditions. We re-examined working memory limits in two experiments with a wide array of conditions involving color and shape attributes, relying on a set of new models to fit various stimulus situations. In Experiment 2, a new procedure allowed identical retrieval conditions across different conditions of attention at encoding. The results show that multiple attributes compete for attention, but that retaining the binding between attributes is accomplished only by retaining the attributes themselves. We propose a theoretical account in which a fixed object capacity limit contains within it the possibility of the incomplete retention of object attributes, depending on the direction of attention. PMID:22905929

Co-immobilization of multiple enzymes by metal coordinated nucleotide hydrogel nanofibers: improved stability and an enzyme cascade for glucose detection

NASA Astrophysics Data System (ADS)

Liang, Hao; Jiang, Shuhui; Yuan, Qipeng; Li, Guofeng; Wang, Feng; Zhang, Zijie; Liu, Juewen

2016-03-01

Preserving enzyme activity and promoting synergistic activity via co-localization of multiple enzymes are key topics in bionanotechnology, materials science, and analytical chemistry. This study reports a facile method for co-immobilizing multiple enzymes in metal coordinated hydrogel nanofibers. Specifically, four types of protein enzymes, including glucose oxidase, Candida rugosa lipase, α-amylase, and horseradish peroxidase, were respectively encapsulated in a gel nanofiber made of Zn2+ and adenosine monophosphate (AMP) with a simple mixing step. Most enzymes achieved quantitative loading and retained full activity. At the same time, the entrapped enzymes were more stable against temperature variation (by 7.5 °C), protease attack, extreme pH (by 2-fold), and organic solvents. After storing for 15 days, the entrapped enzyme still retained 70% activity while the free enzyme nearly completely lost its activity. Compared to nanoparticles formed with AMP and lanthanide ions, the nanofiber gels allowed much higher enzyme activity. Finally, a highly sensitive and selective biosensor for glucose was prepared using the gel nanofiber to co-immobilize glucose oxidase and horseradish peroxidase for an enzyme cascade system. A detection limit of 0.3 μM glucose with excellent selectivity was achieved. This work indicates that metal coordinated materials using nucleotides are highly useful for interfacing with biomolecules.Preserving enzyme activity and promoting synergistic activity via co-localization of multiple enzymes are key topics in bionanotechnology, materials science, and analytical chemistry. This study reports a facile method for co-immobilizing multiple enzymes in metal coordinated hydrogel nanofibers. Specifically, four types of protein enzymes, including glucose oxidase, Candida rugosa lipase, α-amylase, and horseradish peroxidase, were respectively encapsulated in a gel nanofiber made of Zn2+ and adenosine monophosphate (AMP) with a simple mixing step. Most enzymes achieved quantitative loading and retained full activity. At the same time, the entrapped enzymes were more stable against temperature variation (by 7.5 °C), protease attack, extreme pH (by 2-fold), and organic solvents. After storing for 15 days, the entrapped enzyme still retained 70% activity while the free enzyme nearly completely lost its activity. Compared to nanoparticles formed with AMP and lanthanide ions, the nanofiber gels allowed much higher enzyme activity. Finally, a highly sensitive and selective biosensor for glucose was prepared using the gel nanofiber to co-immobilize glucose oxidase and horseradish peroxidase for an enzyme cascade system. A detection limit of 0.3 μM glucose with excellent selectivity was achieved. This work indicates that metal coordinated materials using nucleotides are highly useful for interfacing with biomolecules. Electronic supplementary information (ESI) available: Additional methods, IR and XRD spectroscopy, enzyme loading capacity, enzyme kinetic parameters, and enzyme stability data. See DOI: 10.1039/c5nr08734a

Method of analyzing multiple sample simultaneously by detecting absorption and systems for use in such a method

DOEpatents

Yeung, Edward S.; Gong, Xiaoyi

2004-09-07

The present invention provides a method of analyzing multiple samples simultaneously by absorption detection. The method comprises: (i) providing a planar array of multiple containers, each of which contains a sample comprising at least one absorbing species, (ii) irradiating the planar array of multiple containers with a light source and (iii) detecting absorption of light with a detetion means that is in line with the light source at a distance of at leaat about 10 times a cross-sectional distance of a container in the planar array of multiple containers. The absorption of light by a sample indicates the presence of an absorbing species in it. The method can further comprise: (iv) measuring the amount of absorption of light detected in (iii) indicating the amount of the absorbing species in the sample. Also provided by the present invention is a system for use in the abov metho.The system comprises; (i) a light source comrnpising or consisting essentially of at leaat one wavelength of light, the absorption of which is to be detected, (ii) a planar array of multiple containers, and (iii) a detection means that is in line with the light source and is positioned in line with and parallel to the planar array of multiple contiainers at a distance of at least about 10 times a cross-sectional distance of a container.

Current and Emerging Therapies in Multiple Sclerosis: Implications for the Radiologist, Part 1-Mechanisms, Efficacy, and Safety.

PubMed

McNamara, C; Sugrue, G; Murray, B; MacMahon, P J

2017-09-01

Imaging for the diagnosis and follow-up of patients with suspected or confirmed multiple sclerosis is a common scenario for many general radiologists and subspecialty neuroradiologists. The field of MS therapeutics has rapidly evolved with multiple new agents now being used in routine clinical practice. To provide an informed opinion in discussions concerning newer MS agents, radiologists must have a working understanding of the strengths and limitations of the various novel therapies. The role of imaging in MS has advanced beyond monitoring and surveillance of disease activity to include treatment complications. An understanding of the new generation of MS drugs in conjunction with the key role that MR imaging plays in the detection of disease progression, opportunistic infections, and drug-related adverse events is of vital importance to the radiologist and clinical physician alike. Radiologists are in a unique position to detect many of the described complications well in advance of clinical symptoms. Part 1 of this review outlines recent developments in the treatment of MS and discusses the published clinical data on the efficacy and safety of the currently approved and emerging therapies in this condition as they apply to the radiologist. Part 2 will cover pharmacovigilance and the role the neuroradiologist plays in monitoring patients for signs of opportunistic infection and/or disease progression. © 2017 by American Journal of Neuroradiology.

Summary of the Effort to Use Active-induced Time Correlation Techniques to Measure the Enrichment of HEU

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

McConchie, Seth M.; Crye, Jason Michael; Pena, Kirsten

2015-09-30

This document summarizes the effort to use active-induced time correlation techniques to measure the enrichment of bulk quantities of enriched uranium. In summary, these techniques use an external source to initiate fission chains, and the time distribution of the detected fission chain neutrons is sensitive to the fissile material enrichment. The number of neutrons emitted from a chain is driven by the multiplication of the item, and the enrichment is closely coupled to the multiplication of the item. As the enrichment increases (decreases), the multiplication increases (decreases) if the geometry is held constant. The time distribution of fission chain neutronsmore » is a complex function of the enrichment and material configuration. The enrichment contributes to the probability of a subsequent fission in a chain via the likelihood of fissioning on an even-numbered isotope versus an odd-numbered isotope. The material configuration contributes to the same probability via solid angle effects for neutrons inducing subsequent fissions and the presence of any moderating material. To simplify the ability to accurately measure the enrichment, an associated particle imaging (API) D-T neutron generator and an array of plastic scintillators are used to simultaneously image the item and detect the fission chain neutrons. The image is used to significantly limit the space of enrichment and material configuration and enable the enrichment to be determined unambiguously.« less

Rapid and simultaneous detection of Mycobacterium tuberculosis complex and Beijing/W genotype in sputum by an optimized DNA extraction protocol and a novel multiplex real-time PCR.

PubMed

Leung, Eric T Y; Zheng, L; Wong, Rity Y K; Chan, Edward W C; Au, T K; Chan, Raphael C Y; Lui, Grace; Lee, Nelson; Ip, Margaret

2011-07-01

Rapid diagnosis and genotyping of Mycobacterium tuberculosis by molecular methods are often limited by the amount and purity of DNA extracted from body fluids. In this study, we evaluated 12 DNA extraction methods and developed a highly sensitive protocol for mycobacterial DNA extraction directly from sputa using surface-coated magnetic particles. We have also developed a novel multiplex real-time PCR for simultaneous identification of M. tuberculosis complex and the Beijing/W genotype (a hypervirulent sublineage of M. tuberculosis) by using multiple fluorogenic probes targeting both the M. tuberculosis IS6110 and the Rv0927c-pstS3 intergenic region. With reference strains and clinical isolates, our real-time PCR accurately identified 20 non-Beijing/W and 20 Beijing/W M. tuberculosis strains from 17 different species of nontuberculosis Mycobacterium (NTM). Further assessment of our DNA extraction protocol and real-time PCR with 335 nonduplicate sputum specimens correctly identified all 74 M. tuberculosis culture-positive specimens. In addition, 15 culture-negative specimens from patients with confirmed tuberculosis were also identified. No cross-reactivity was detected with NTM specimens (n = 31). The detection limit of the assay is 10 M. tuberculosis bacilli, as determined by endpoint dilution analysis. In conclusion, an optimized DNA extraction protocol coupled with a novel multiprobe multiplex real-time PCR for the direct detection of M. tuberculosis, including Beijing/W M. tuberculosis, was found to confer high sensitivity and specificity. The combined procedure has the potential to compensate for the drawbacks of conventional mycobacterial culture in routine clinical laboratory setting, such as the lengthy incubation period and the limitation to viable organisms.

Technical note: Simultaneous carotenoid and vitamin analysis of milk from total mixed ration-fed cows optimized for xanthophyll detection.

PubMed

Stout, M A; Benoist, D M; Drake, M A

2018-06-01

Concentrations of retinol, α-tocopherol, and major carotenoids in dairy products are often determined simultaneously by liquid chromatography. These compounds have different polarity and solubility; thus, extracting them simultaneously can be difficult and inefficient. In milks with low carotenoid concentrations, the xanthophylls lutein and zeaxanthin may not be completely resolved using common extraction techniques. A simplified method was developed to optimize extraction efficiency and the limit of detection and limit of quantification (LoQ) of lutein and zeaxanthin in bovine milk without decreasing sensitivity to other vitamins or carotenoids. The developed method evaluates lutein, zeaxanthin, β-carotene, retinol, and α-tocopherol simultaneously by ultra-high performance liquid chromatography-photodiode array detection. Common saponification temperatures (40-60°C) and concentrations of KOH in water (10-50% KOH wt/vol) were evaluated. Multiple solvents were evaluated for optimal xanthophyll extraction (diethyl ether, dichloromethane, hexane, and tetrahydrofuran) following saponification. The limit of detection and LoQ were defined as 3:1 and 10:1 signal-to-noise ratio, respectively. All experiments were performed in triplicate. The optimal saponification procedure was a concentration of 25% KOH at either 40 or 50°C. Saponified extracts solubilized in solutions containing diethyl ether had greater concentrations of lutein- than hexane- or tetrahydrofuran-based solutions, with peak areas above LoQ values. The solution containing diethyl ether solubilized similar concentrations of retinol, α-tocopherol, and β-carotene when compared with other solutions. The proposed optimized method allows for the simultaneous determination of carotenoids from milk with increased lutein and zeaxanthin sensitivity without sacrificing recovery of retinol, α-tocopherol, and β-carotene. Copyright © 2018 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Demonstration of a rapidly-swept external cavity quantum cascade laser for atmospheric sensing applications

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

Brumfield, Brian E.; Taubman, Matthew S.; Phillips, Mark C.

2016-07-01

The application of quantum cascade lasers (QCLs) in atmospheric science for trace detection of gases has been demonstrated using sensors in point or remote sensing configurations. Many of these systems utilize single narrowly-tunable (~10 cm-1) distributed feedback (DFB-) QCLs that limit simultaneous detection to a restricted number of small chemical species like H2O or N2O. The narrow wavelength range of DFB-QCLs precludes accurate quantification of large chemical species with broad rotationally-unresolved vibrational spectra, such as volatile organic compounds, that play an important role in the chemistry of the atmosphere. External-cavity (EC-) QCL systems are available that offer tuning ranges >100more » cm-1, making them excellent IR sources for measuring multiple small and large chemical species in the atmosphere. While the broad wavelength coverage afforded by an EC system enables measurements of large chemical species, most commercial systems can only be swept over their entire wavelength range at less than 10 Hz. This prohibits broadband simultaneous measurements of multiple chemicals in plumes from natural or industrial sources where turbulence and/or chemical reactivity are resulting in rapid changes in chemical composition on sub-1s timescales. At Pacific Northwest National Laboratory we have developed rapidly-swept EC-QCL technology that acquires broadband absorption spectra (~100 cm-1) on ms timescales. The spectral resolution of this system has enabled simultaneous measurement of narrow rotationally-resolved atmospherically-broadened lines from small chemical species, while offering the broad tuning range needed to measure broadband spectral features from multiple large chemical species. In this talk the application of this technology for open-path atmospheric measurements will be discussed based on results from laboratory measurements with simulated plumes of chemicals. The performance offered by the system for simultaneous detection of multiple chemical species will be presented.« less

Demonstration of a Rapidly-Swept External Cavity Quantum Cascade Laser for Atmospheric Sensing Applications

NASA Astrophysics Data System (ADS)

Brumfield, Brian E.; Taubman, Matthew S.; Phillips, Mark C.; Suter, Jonathan D.

2016-06-01

The application of quantum cascade lasers (QCLs) in atmospheric science for trace detection of gases has been demonstrated using sensors in point or remote sensing configurations. Many of these systems utilize single narrowly-tunable (˜10 wn) distributed feedback (DFB-) QCLs that limit simultaneous detection to a restricted number of small chemical species like H2O or N2O. The narrow wavelength range of DFB-QCLs precludes accurate quantification of large chemical species with broad rotationally-unresolved vibrational spectra, such as volatile organic compounds, that play an important role in the chemistry of the atmosphere. External-cavity (EC-) QCL systems are available that offer tuning ranges greater than 100 wn, making them excellent IR sources for measuring multiple small and large chemical species in the atmosphere. While the broad wavelength coverage afforded by an EC system enables measurements of large chemical species, most commercial systems can only be swept over their entire wavelength range at less than 10 Hz. This prohibits broadband simultaneous measurements of multiple chemicals in plumes from natural or industrial sources where turbulence and/or chemical reactivity are resulting in rapid changes in chemical composition on sub-1s timescales. At Pacific Northwest National Laboratory we have developed rapidly-swept EC-QCL technology that acquires broadband absorption spectra (˜100 wn) on ms timescales. The spectral resolution of this system has enabled simultaneous measurement of narrow rotationally-resolved atmospherically-broadened lines from small chemical species, while offering the broad tuning range needed to measure broadband spectral features from multiple large chemical species. In this talk the application of this technology for open-path atmospheric measurements will be discussed based on results from laboratory measurements with simulated plumes of chemicals. The performance offered by the system for simultaneous detection of multiple chemical species will be presented. The Pacific Northwest National Laboratory is operated for the U.S. Department of Energy (DOE) by the Battelle Memorial Institute under Contract No. DE-AC05-76RL01830.

High-density fiber-optic DNA random microsphere array.

PubMed

Ferguson, J A; Steemers, F J; Walt, D R

2000-11-15

A high-density fiber-optic DNA microarray sensor was developed to monitor multiple DNA sequences in parallel. Microarrays were prepared by randomly distributing DNA probe-functionalized 3.1-microm-diameter microspheres in an array of wells etched in a 500-microm-diameter optical imaging fiber. Registration of the microspheres was performed using an optical encoding scheme and a custom-built imaging system. Hybridization was visualized using fluorescent-labeled DNA targets with a detection limit of 10 fM. Hybridization times of seconds are required for nanomolar target concentrations, and analysis is performed in minutes.

Liquid chromatographic determination of florfenicol in the plasma of multiple species of fish

USGS Publications Warehouse

Vue, C.; Schmidt, L.J.; Stehly, G.R.; Gingerich, W.H.

2002-01-01

A simple method was developed for determining florfenicol concentration in a small volume (250 mul) of plasma from five phylogenetically diverse species of freshwater fish. Florfenicol was isolated from the plasma matrix through C-18 solid-phase extraction and quantified by reversed-phase high-performance liquid chromatography with UV detection. The accuracy (84-104%), precision (%RSDless than or equal to8), and sensitivity (quantitation limit <30 ng/ml) of the method indicate its usefulness for conducting pharmacokinetic studies on a variety of freshwater fish. Published by Elsevier Science B.V.

Detection of ESBL among ampc producing enterobacteriaceae using inhibitor-based method

PubMed Central

Bakthavatchalu, Sasirekha; Shakthivel, Uma; Mishra, Tannu

2013-01-01

Introduction The occurrence of multiple β-lactamases among bacteria only limits the therapeutic options but also poses a challenge. A study using boronic acid (BA), an AmpC enzyme inhibitor, was designed to detect the combined expression of AmpC β-lactamases and extended-spectrum β-lactamases (ESBLs) in bacterial isolates further different phenotypic methods are compared to detect ESBL and AmpC. Methods A total of 259 clinical isolates of Enterobacteriaceae were isolated and screened for ESBL production by (i) CLSI double-disk diffusion method (ii) cefepime- clavulanic acid method (iii) boronic disk potentiation method. AmpC production was detected using cefoxitin alone and in combination with boronic acid and confirmation was done by three dimensional disk methods. Isolates were also subjected to detailed antibiotic susceptibility test. Results Among 259 isolates, 20.46% were coproducers of ESBL and AmpC, 26.45% were ESBL and 5.40% were AmpC. All of the 53 AmpC and ESBL coproducers were accurately detected by boronic acid disk potentiation method. Conclusion The BA disk test using Clinical and Laboratory Standards Institute methodology is simple and very efficient method that accurately detects the isolates that harbor both AmpCs and ESBLs. PMID:23504148

Clinical evaluation of a new single-tube multiplex reverse transcription PCR assay for simultaneous detection of 11 respiratory viruses, Mycoplasma pneumoniae and Chlamydia in hospitalized children with acute respiratory infections.

PubMed

Zhao, Meng-Chuan; Li, Gui-Xia; Zhang, Dan; Zhou, Hang-Yu; Wang, Hao; Yang, Shuo; Wang, Le; Feng, Zhi-Shan; Ma, Xue-Jun

2017-06-01

Respiratory Pathogen 13 Detection Kit (13× kit) is able to simultaneously detect 11 respiratory viruses, Mycoplasma pneumoniae (MP) and Chlamydia in a single reaction. Using 572 Nasopharyngeal aspirates collected from hospitalized children, the clinical performance of 13× kit for detecting 11 respiratory viruses was evaluated in comparison with a routinely used 2-tube multiplex reverse transcription PCR assay (2-tube assay) at provincial Centers for Disease Control and Prevention in China. The clinical performance of 13× kit for detecting MP and Chlamydia was evaluated by commercial real-time quantitative PCR (qPCR) kits or sequencing. For tested viruses, the assay concordance was 95.98% and the kappa coefficient was 0.89. All the MP and Chlamydia positive samples detected by 13× kit were confirmed as true positives. The utilization of the 13× kit in clinical settings will be helpful for doctors to assess clinical outcome according to virus type or multiple infections, and to limit the use of antibiotics. Copyright © 2017 Elsevier Inc. All rights reserved.

Cross-subtype detection of HIV-1 using reverse transcription and recombinase polymerase amplification.

PubMed

Lillis, Lorraine; Lehman, Dara A; Siverson, Joshua B; Weis, Julie; Cantera, Jason; Parker, Mathew; Piepenburg, Olaf; Overbaugh, Julie; Boyle, David S

2016-04-01

A low complexity diagnostic test that rapidly and reliably detects HIV infection in infants at the point of care could facilitate early treatment, improving outcomes. However, many infant HIV diagnostics can only be performed in laboratory settings. Recombinase polymerase amplification (RPA) is an isothermal amplification technology that can rapidly amplify proviral DNA from multiple subtypes of HIV-1 in under twenty minutes without complex equipment. In this study we added reverse transcription (RT) to RPA to allow detection of both HIV-1 RNA and DNA. We show that this RT-RPA HIV-1 assay has a limit of detection of 10-30 copies of an exact sequence matched DNA or RNA, respectively. In addition, at 100 copies of RNA or DNA, the assay detected 171 of 175 (97.7%) sequence variants that represent all the major subtypes and recombinant forms of HIV-1 Groups M and O. This data suggests that the application of RT-RPA for the combined detection of HIV-1 viral RNA and proviral DNA may prove a highly sensitive tool for rapid and accurate diagnosis of infant HIV. Copyright © 2016 Elsevier B.V. All rights reserved.

Recent mycotoxin survey data and advanced mycotoxin detection techniques reported from China: a review.

PubMed

Selvaraj, Jonathan Nimal; Wang, Yan; Zhou, Lu; Zhao, Yueju; Xing, Fuguo; Dai, Xiaofeng; Liu, Yang

2015-01-01

Mycotoxin contamination in agro-food systems has been a serious concern over the last few decades in China, where the Ministry of Health has set maximum limits for mycotoxins in different agro-products. Overall survey data show that aflatoxin contamination in infant cereals, edible oils, raw milk, ginger and its related products are far below Chinese regulatory limits. The absence of aflatoxin M1 contamination in infant milk powders indicates a high standard of control. Aflatoxins in liquorice roots and lotus seeds have been reported for the first time. For deoxynivalenol, high levels were found in wheat grown in the Yangtze Delta region, which is more prone to rainfall, supporting Fusarium infection. The emerging mycotoxins beauvericins and enniatins have been reported in the medicinal herbs in China. Ochratoxin A in wine was below the European Union regulatory limits, but fumonisins in maize need to be monitored and future regulatory control considered. Overall from all the survey data analysed in this review, it can be concluded that 92% of the samples analysed had mycotoxin levels below the Chinese regulatory limits. In terms of detection techniques in recent years, immuno-based assays have been developed largely due to their excellent sensitivity and ease of use. Assays targeting multiple mycotoxins like aflatoxins, ochratoxin A, zearalenone and deoxynivalenol have been reported using microarrays and suspension arrays targeting in particular maize, rice and peanuts. Aptamer-based assays against ochratoxin A and aflatoxins B1 and B2 have been developed involving fluorescence detection; and surface plasmon resonance immunosensors have been developed targeting wine, maize, wheat, wild rye, hay and peanut oil with high sensitivity (> 0.025 ng l(-1)). Commercialisation of these technologies is much needed for wider usage in the coming years.

Development of Multi-Field of view-Multiple-Scattering-Polarization Lidar ： analysis of angular resolved backscattered signals

NASA Astrophysics Data System (ADS)

Makino, T.; Okamoto, H.; Sato, K.; Tanaka, K.; Nishizawa, T.; Sugimoto, N.; Matsui, I.; Jin, Y.; Uchiyama, A.; Kudo, R.

2014-12-01

We have developed a new type of ground-based lidar, Multi-Field of view-Multiple-Scattering-Polarization Lidar (MFMSPL), to analyze multiple scattering contribution due to low-level clouds. One issue of the ground based lidar is the limitation of optical thickness of about 3 due to the strong attenuation in the lidar signals so that only the cloud bottom part can be observed. In order to overcome the problem, we have proposed the MFMSPL that has been designed to observe similar degree of multiple scattering contribution expected from space-borne lidar CALIOP on CALIPSO satellite. The system consists of eight detectors; four telescopes for parallel channels and four for perpendicular channels. The four pairs of telescope have been mounted with four different off-beam angles, ranging from -5 to 35mrad, where the angle is defined as the one between the direction of laser beam and the direction of telescope. Consequently, similar large foot print (100m) as CALIOP can be achieved in the MFMSPL observations when the altitude of clouds is located at about 1km. The use of multi-field of views enables to measure depolarization ratio from optically thick clouds. The outer receivers attached with larger angles generally detect backscattered signals from clouds located at upper altitudes due to the enhanced multiple scattering compared with the inner receiver that detects signals only from cloud bottom portions. Therefore the information of cloud microphysics from optically thicker regions is expected by the MFMSPL observations compared with the conventional lidar with small FOV. The MFMSPL have been continuously operated in Tsukuba, Japan since June 2014.Initial analyses have indicated expected performances from the theoretical estimation by backward Monte-Carlo simulations. The depolarization ratio from deeper part of the clouds detected by the receiver with large off-beam angle showed much larger values than those from the one with small angle. The calibration procedures and summary of initial observations will be presented. The observed data obtained by the MFMSPL will be used to develop and evaluate the retrieval algorithms for cloud microphysics applied to the CALIOP data.

Task-based optimization of flip angle for fibrosis detection in T1-weighted MRI of liver

PubMed Central

Brand, Jonathan F.; Furenlid, Lars R.; Altbach, Maria I.; Galons, Jean-Philippe; Bhattacharyya, Achyut; Sharma, Puneet; Bhattacharyya, Tulshi; Bilgin, Ali; Martin, Diego R.

2016-01-01

Abstract. Chronic liver disease is a worldwide health problem, and hepatic fibrosis (HF) is one of the hallmarks of the disease. The current reference standard for diagnosing HF is biopsy followed by pathologist examination; however, this is limited by sampling error and carries a risk of complications. Pathology diagnosis of HF is based on textural change in the liver as a lobular collagen network that develops within portal triads. The scale of collagen lobules is characteristically in the order of 1 to 5 mm, which approximates the resolution limit of in vivo gadolinium-enhanced magnetic resonance imaging in the delayed phase. We use MRI of formalin-fixed human ex vivo liver samples as phantoms that mimic the textural contrast of in vivo Gd-MRI. We have developed a local texture analysis that is applied to phantom images, and the results are used to train model observers to detect HF. The performance of the observer is assessed with the area-under-the-receiver–operator-characteristic curve (AUROC) as the figure-of-merit. To optimize the MRI pulse sequence, phantoms were scanned with multiple times at a range of flip angles. The flip angle that was associated with the highest AUROC was chosen as optimal for the task of detecting HF. PMID:27446971

Determination of statins by gas chromatography - EI/MRM - Tandem mass spectrometry: fermentation of pine samples with Pleurotus ostreatus.

PubMed

Sirén, Heli; Kaijanen, Laura; Kaartinen, Sini; Väre, Monna; Riikonen, Päivi; Jernström, Eeva

2014-06-01

Statins were separated and quantified with gas chromatography-mass spectrometry (GC-EI-MS/MS) using total ion monitoring (TIC) and multiple reactions monitoring (MRM). The MRM method in statins determination has a novelty value, since there are no previous studies on their simultaneous analysis in environmental or plant samples. The method development and optimization was challenging due to the physicochemical similarities of the silylated lovastatin, simvastatin, pravastatin, fluvastatin, and atorvastatin. The results showed that the use of MRM decreased their detection and quantification limits by factors of 2-10 compared to that obtained in TIC monitoring. The concentration calibration was made between 247.5ng/L and 9900ng/L. Limits of detection and quantification were between 50ng/L (lovastatin)-500ng/L (pravastatin) and 250ng/L (lovastatin)-1000ng/L (pravastatin), respectively. Based on the MRM results, the wood bark and phloem samples contained lovastatin, lovastatin-lactone, simvastatin, simvastatin-lactone, and pravastatin. Their concentrations were 250-3000μg/L, i.e. 4.2-50mg/kg in phloem and bark. However, they were not detected in fluids made with Pleurotus ostreatus fermentation of wood core. Copyright © 2014 Elsevier B.V. All rights reserved.

Microarrays--new possibilities for detecting biological factors hazardous for humans and animals, and for use in environmental protection.

PubMed

Mirski, Tomasz; Bartoszcze, Michał; Bielawska-Drózd, Agata; Gryko, Romuald; Kocik, Janusz; Niemcewicz, Marcin; Chomiczewski, Krzysztof

2016-01-01

Both the known biological agents that cause infectious diseases, as well as modified (ABF-Advanced Biological Factors) or new, emerging agents pose a significant diagnostic problem using previously applied methods, both classical, as well as based on molecular biology methods. The latter, such as PCR and real-time PCR, have significant limitations, both quantitative (low capacity), and qualitative (limited number of targets). The article discusses the results of studies on using the microarray method for the identification of viruses (e.g. Orthopoxvirus group, noroviruses, influenza A and B viruses, rhino- and enteroviruses responsible for the FRI (Febrile Respiratory Illness), European bunyaviruses, and SARS-causing viruses), and bacteria (Mycobacterium spp., Yersinia spp., Campylobacter spp., Streptococcus pneumoniae, Salmonella typhi, Salmonella enterica, Staphylococcus aureus, Neisseria meningitidis, Clostridium difficile , Helicobacter pylori), including multiple antibiotic-resistant strains. The method allows for the serotyping and genotyping of bacteria, and is useful in the diagnosis of genetically modified agents. It allows the testing of thousands of genes in one experiment. In addition to diagnosis, it is applicable for gene expression studies, analysis of the function of genes, microorganisms virulence, and allows the detection of even single mutations. The possibility of its operational application in epidemiological surveillance, and in the detection of disease outbreak agents is demonstrated.

Hyperspectral wide gap second derivative analysis for in vivo detection of cervical intraepithelial neoplasia

NASA Astrophysics Data System (ADS)

Zheng, Wenli; Wang, Chaojian; Chang, Shufang; Zhang, Shiwu; Xu, Ronald X.

2015-12-01

Hyperspectral reflectance imaging technique has been used for in vivo detection of cervical intraepithelial neoplasia. However, the clinical outcome of this technique is suboptimal owing to multiple limitations such as nonuniform illumination, high-cost and bulky setup, and time-consuming data acquisition and processing. To overcome these limitations, we acquired the hyperspectral data cube in a wavelength ranging from 600 to 800 nm and processed it by a wide gap second derivative analysis method. This method effectively reduced the image artifacts caused by nonuniform illumination and background absorption. Furthermore, with second derivative analysis, only three specific wavelengths (620, 696, and 772 nm) are needed for tissue classification with optimal separability. Clinical feasibility of the proposed image analysis and classification method was tested in a clinical trial where cervical hyperspectral images from three patients were used for classification analysis. Our proposed method successfully classified the cervix tissue into three categories of normal, inflammation and high-grade lesion. These classification results were coincident with those by an experienced gynecology oncologist after applying acetic acid. Our preliminary clinical study has demonstrated the technical feasibility for in vivo and noninvasive detection of cervical neoplasia without acetic acid. Further clinical research is needed in order to establish a large-scale diagnostic database and optimize the tissue classification technique.

Hyperspectral wide gap second derivative analysis for in vivo detection of cervical intraepithelial neoplasia.

PubMed

Zheng, Wenli; Wang, Chaojian; Chang, Shufang; Zhang, Shiwu; Xu, Ronald X

2015-12-01

Hyperspectral reflectance imaging technique has been used for in vivo detection of cervical intraepithelial neoplasia. However, the clinical outcome of this technique is suboptimal owing to multiple limitations such as nonuniform illumination, high-cost and bulky setup, and time-consuming data acquisition and processing. To overcome these limitations, we acquired the hyperspectral data cube in a wavelength ranging from 600 to 800 nm and processed it by a wide gap second derivative analysis method. This method effectively reduced the image artifacts caused by nonuniform illumination and background absorption. Furthermore, with second derivative analysis, only three specific wavelengths (620, 696, and 772 nm) are needed for tissue classification with optimal separability. Clinical feasibility of the proposed image analysis and classification method was tested in a clinical trial where cervical hyperspectral images from three patients were used for classification analysis. Our proposed method successfully classified the cervix tissue into three categories of normal, inflammation and high-grade lesion. These classification results were coincident with those by an experienced gynecology oncologist after applying acetic acid. Our preliminary clinical study has demonstrated the technical feasibility for in vivo and noninvasive detection of cervical neoplasia without acetic acid. Further clinical research is needed in order to establish a large-scale diagnostic database and optimize the tissue classification technique.

Handheld microwave bomb-detecting imaging system

NASA Astrophysics Data System (ADS)

Gorwara, Ashok; Molchanov, Pavlo

2017-05-01

Proposed novel imaging technique will provide all weather high-resolution imaging and recognition capability for RF/Microwave signals with good penetration through highly scattered media: fog, snow, dust, smoke, even foliage, camouflage, walls and ground. Image resolution in proposed imaging system is not limited by diffraction and will be determined by processor and sampling frequency. Proposed imaging system can simultaneously cover wide field of view, detect multiple targets and can be multi-frequency, multi-function. Directional antennas in imaging system can be close positioned and installed in cell phone size handheld device, on small aircraft or distributed around protected border or object. Non-scanning monopulse system allows dramatically decrease in transmitting power and at the same time provides increased imaging range by integrating 2-3 orders more signals than regular scanning imaging systems.

Network Intrusion Detection and Visualization using Aggregations in a Cyber Security Data Warehouse

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

Czejdo, Bogdan; Ferragut, Erik M; Goodall, John R

2012-01-01

The challenge of achieving situational understanding is a limiting factor in effective, timely, and adaptive cyber-security analysis. Anomaly detection fills a critical role in network assessment and trend analysis, both of which underlie the establishment of comprehensive situational understanding. To that end, we propose a cyber security data warehouse implemented as a hierarchical graph of aggregations that captures anomalies at multiple scales. Each node of our pro-posed graph is a summarization table of cyber event aggregations, and the edges are aggregation operators. The cyber security data warehouse enables domain experts to quickly traverse a multi-scale aggregation space systematically. We describemore » the architecture of a test bed system and a summary of results on the IEEE VAST 2012 Cyber Forensics data.« less

A model-based analysis of extinction ratio effects on phase-OTDR distributed acoustic sensing system performance

NASA Astrophysics Data System (ADS)

Aktas, Metin; Maral, Hakan; Akgun, Toygar

2018-02-01

Extinction ratio is an inherent limiting factor that has a direct effect on the detection performance of phase-OTDR based distributed acoustics sensing systems. In this work we present a model based analysis of Rayleigh scattering to simulate the effects of extinction ratio on the received signal under varying signal acquisition scenarios and system parameters. These signal acquisition scenarios are constructed to represent typically observed cases such as multiple vibration sources cluttered around the target vibration source to be detected, continuous wave light sources with center frequency drift, varying fiber optic cable lengths and varying ADC bit resolutions. Results show that an insufficient ER can result in high optical noise floor and effectively hide the effects of elaborate system improvement efforts.

Detecting and Attributing the Effects of Climate Change on the Distributions of Snake Species Over the Past 50 Years.

PubMed

Wu, Jianguo

2016-01-01

It is unclear whether the distributions of snakes have changed in association with climate change over the past years. We detected the distribution changes of snakes over the past 50 years and determined whether the changes could be attributed to recent climate change in China. Long-term records of the distribution of nine snake species in China, grey relationship analysis, fuzzy sets classification techniques, the consistency index, and attributed methods were used. Over the past 50 years, the distributions of snake species have changed in multiple directions, primarily shifting northwards, and most of the changes were related to the thermal index. Driven by climatic factors over the past 50 years, the distribution boundary and distribution centers of some species changed with the fluctuations. The observed and predicted changes in distribution were highly consistent for some snake species. The changes in the northern limits of distributions of nearly half of the species, as well as the southern and eastern limits, and the distribution centers of some snake species can be attributed to climate change.

[Oligonucleotide derivatives in the nucleic acid hybridization analysis. II. Isothermal signal amplification in process of DNA analysis by minisequencing].

PubMed

Dmitrienko, E V; Khomiakova, E A; Pyshnaia; Bragin, A G; Vedernikov, V E; Pyshnyĭ, D V

2010-01-01

The isothermal amplification of reporter signal via limited probe extension (minisequencing) upon hybridization of nucleic acids has been studied. The intensity of reporter signal has been shown to increase due to enzymatic labeling of multiple probes upon consecutive hybridization with one DNA template both in homophase and heterophase assays using various kinds of detection signal: radioisotope label, fluorescent label, and enzyme-linked assay. The kinetic scheme of the process has been proposed and kinetic parameters for each step have been determined. The signal intensity has been shown to correlate with physicochemical characteristics of both complexes: probe/DNA and product/DNA. The maximum intensity has been observed at minimal difference between the thermodynamic stability of these complexes, provided the reaction temperature has been adjusted near their melting temperature values; rising or lowering the reaction temperature reduces the amount of reporting product. The signal intensity has been shown to decrease significantly upon hybridization with the DNA template containing single-nucleotide mismatches. Limited probe extension assay is useful not only for detection of DNA template but also for its quantitative characterization.

Detection and quantification of cocaine and benzoylecgonine in meconium using solid phase extraction and UPLC/MS/MS.

PubMed

Gunn, Josh; Kriger, Scott; Terrell, Andrea R

2010-01-01

The simultaneous determination and quantification of cocaine and its major metabolite, benzoylecgonine, in meconium using UPLC-MS/MS is described. Ultra-performance liquid chromatography (UPLC) is an emerging analytical technique which draws upon the principles of chromatography to run separations at higher flow rates for increased speed, while simultaneously achieving superior resolution and sensitivity. Extraction of cocaine and benzoylecgonine from the homogenized meconium matrix was achieved with a preliminary protein precipitation or protein 'crash' employing cold acetonitrile, followed by a mixed mode solid phase extraction (SPE). Following elution from the SPE cartridge, eluents were dried down under nitrogen, reconstituted in 200 microL of DI water:acetonitrile (ACN) (75:25), and injected onto the UPLC/MS/MS for analysis. The increased speed and separation efficiency afforded by UPLC, allowed for the separation and subsequent quantification of both analytes in less than 2 min. Analytes were quantified using multiple reaction monitoring (MRM) and six-point calibration curves constructed in negative blood. Limits of detection for both analytes were 3 ng/g and the lower limit of quantitation (LLOQ) was 30 ng/g.

Integrated fiber optical receiver reducing the gap to the quantum limit.

PubMed

Zimmermann, Horst; Steindl, Bernhard; Hofbauer, Michael; Enne, Reinhard

2017-06-01

Experimental results of a single-photon avalanche diode (SPAD) based optical fiber receiver integrated in 0.35 µm PIN-photodiode CMOS technology are presented. To cope with the parasitic effects of SPADs an array of four receivers is implemented. The SPADs consist of a multiplication zone and a separate thick absorption zone to achieve a high photon detection probability (PDP). In addition cascoded quenchers allow to use a quenching voltage of twice the usual supply voltage, i.e. 6.6 V instead of 3.3 V, in order to increase the PDP further. Measurements result in sensitivities of -55.7 dBm at a data rate of 50 Mbit/s and -51.6 dBm at 100 Mbit/s for a wavelength of 635 nm and a bit-error ratio of 2 × 10 -3 , which is sufficient to perform error correction. These sensitivities are better than those of linear-mode APD receivers integrated in the same CMOS technology. These results are a major advance towards direct detection optical receivers working close to the quantum limit.

Liquid to liquid extraction and liquid chromatography-tandem mass spectrometry determination of hainanmycin in feed.

PubMed

Wang, Ze Ping; Shen, Jian Zhong; Linhardt, Robert J; Jiang, Hui; Cheng, Lin Li

2017-03-01

Hainanmycin is a new veterinary polyether antibiotic and has few sensitive analytical method in present days. In this study, a liquid chromatography-tandem mass spectrometry (LC-MS/MS) relying on multiple reaction monitoring (MRM) detection was developed for analysis of hainanmycin in animal feed. Feed samples were extracted with ethyl acetate and purified by two steps of liquid-liquid extraction (LLE) to get rid of water solvable matrix and lipids one by one. The final simple was analyzed by LC-MS/MS. The LC mobile phase was composed of 0.1% aqueous formic acid and 0.1% formic acidified acetonitrile by gradient elution. Average recoveries ranged from 74.22% to 87.85%, as determined by spiking with 2.0 (LOQ) ∼2500μgkg -1 of hainanmycin. The inter-day and intra-day coefficient of variation was 9.21% to 11.77% and 7.67% to 13.49%, respectively. The limit of detection (LOD) and the limit of quantitation (LOQ) were 0.36μgkg -1 and 2.0μgkg -1 , respectively. Copyright © 2016. Published by Elsevier B.V.

[Comparison between rapid detection method of enzyme substrate technique and multiple-tube fermentation technique in water coliform bacteria detection].

PubMed

Sun, Zong-ke; Wu, Rong; Ding, Pei; Xue, Jin-Rong

2006-07-01

To compare between rapid detection method of enzyme substrate technique and multiple-tube fermentation technique in water coliform bacteria detection. Using inoculated and real water samples to compare the equivalence and false positive rate between two methods. Results demonstrate that enzyme substrate technique shows equivalence with multiple-tube fermentation technique (P = 0.059), false positive rate between the two methods has no statistical difference. It is suggested that enzyme substrate technique can be used as a standard method for water microbiological safety evaluation.

Validity, invariance and responsiveness of a self-report measure of functional limitations and disability in multiple sclerosis.

PubMed

Motl, Robert W; McAuley, Edward; Suh, Yoojin

2010-01-01

This study examined the structural and external aspects of score validity for the abbreviated Late Life-Function and Disability Inventory (LL-FDI) as well as its longitudinal measurement invariance and responsiveness in individuals with multiple sclerosis (MS). The sample included 292 individuals with MS who completed a battery of questionnaires on two occasions separated by 6 months. The battery included the abbreviated LL-FDI along with measures of mobility disability; neurological impairments; symptoms of fatigue, anxiety, depression and pain; health status; and quality of life. The data were analysed using Analysis of Moment Structures (AMOS) and Statistical Package for the Social Sciences (SPSS), versions 16.0. Confirmatory factor analysis supported the structural validity and longitudinal measurement invariance of the disability and functional limitations components of the abbreviated LL-FDI. MANOVA and bivariate correlations supported the external aspects of score validity based on differences in mean scores as a function of clinical MS course (relapsing vs. progressive) and level of mobility disability (mild vs. moderate mobility disability) and associations with measures of neurological impairments, symptoms, health status and QOL, respectively. ANOVA established the responsiveness (i.e., sensitivity for reflecting clinically important differences in health status across time) of the functional limitations and disability components of the abbreviated LL-FDI for detecting changes in mobility disability across 6-months. Such findings provide a new option for the measurement of functional limitations and disability using the abbreviated LL-FDI in persons with MS.

Rapid limit tests for metal impurities in pharmaceutical materials by X-ray fluorescence spectroscopy using wavelet transform filtering.

PubMed

Arzhantsev, Sergey; Li, Xiang; Kauffman, John F

2011-02-01

We introduce a new method for analysis of X-ray fluorescence (XRF) spectra based on continuous wavelet transform filters, and the method is applied to the determination of toxic metals in pharmaceutical materials using hand-held XRF spectrometers. The method uses the continuous wavelet transform to filter the signal and noise components of the spectrum. We present a limit test that compares the wavelet domain signal-to-noise ratios at the energies of the elements of interest to an empirically determined signal-to-noise decision threshold. The limit test is advantageous because it does not require the user to measure calibration samples prior to measurement, though system suitability tests are still recommended. The limit test was evaluated in a collaborative study that involved five different hand-held XRF spectrometers used by multiple analysts in six separate laboratories across the United States. In total, more than 1200 measurements were performed. The detection limits estimated for arsenic, lead, mercury, and chromium were 8, 14, 20, and 150 μg/g, respectively.

THE ABSENCE OF RADIO EMISSION FROM THE GLOBULAR CLUSTER G1

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

Miller-Jones, J. C. A.; Wrobel, J. M.; Sivakoff, G. R.

2012-08-10

The detections of both X-ray and radio emission from the cluster G1 in M31 have provided strong support for existing dynamical evidence for an intermediate-mass black hole (IMBH) of mass (1.8 {+-} 0.5) Multiplication-Sign 10{sup 4} M{sub Sun} at the cluster center. However, given the relatively low significance and astrometric accuracy of the radio detection, and the non-simultaneity of the X-ray and radio measurements, this identification required further confirmation. Here we present deep, high angular resolution, strictly simultaneous X-ray and radio observations of G1. While the X-ray emission (L{sub X} = 1.74{sup +0.53}{sub -0.44} Multiplication-Sign 10{sup 36} (d/750 kpc){sup 2}more » erg s{sup -1} in the 0.5-10 keV band) remained fully consistent with previous observations, we detected no radio emission from the cluster center down to a 3{sigma} upper limit of 4.7 {mu}Jy beam{sup -1}. Our favored explanation for the previous radio detection is flaring activity from a black hole low-mass X-ray binary (LMXB). We performed a new regression of the 'Fundamental Plane' of black hole activity, valid for determining black hole mass from radio and X-ray observations of sub-Eddington black holes, finding log M{sub BH} = (1.638 {+-} 0.070)log L{sub R} - (1.136 {+-} 0.077)log L{sub X} - (6.863 {+-} 0.790), with an empirically determined uncertainty of 0.44 dex. This constrains the mass of the X-ray source in G1, if a black hole, to be <9.7 Multiplication-Sign 10{sup 3} M{sub Sun} at 95% confidence, suggesting that it is a persistent LMXB. This annuls what was previously the most convincing evidence from radiation for an IMBH in the Local Group, though the evidence for an IMBH in G1 from velocity dispersion measurements remains unaffected by these results.« less

Firewalls Prevent Systemic Dissemination of Vectors Derived from Human Adenovirus Type 5 and Suppress Production of Transgene-Encoded Antigen in a Murine Model of Oral Vaccination

PubMed Central

Revaud, Julien; Unterfinger, Yves; Rol, Nicolas; Suleman, Muhammad; Shaw, Julia; Galea, Sandra; Gavard, Françoise; Lacour, Sandrine A.; Coulpier, Muriel; Versillé, Nicolas; Havenga, Menzo; Klonjkowski, Bernard; Zanella, Gina; Biacchesi, Stéphane; Cordonnier, Nathalie; Corthésy, Blaise; Ben Arous, Juliette; Richardson, Jennifer P.

2018-01-01

To define the bottlenecks that restrict antigen expression after oral administration of viral-vectored vaccines, we tracked vectors derived from the human adenovirus type 5 at whole body, tissue, and cellular scales throughout the digestive tract in a murine model of oral delivery. After intragastric administration of vectors encoding firefly luciferase or a model antigen, detectable levels of transgene-encoded protein or mRNA were confined to the intestine, and restricted to delimited anatomical zones. Expression of luciferase in the form of multiple small bioluminescent foci in the distal ileum, cecum, and proximal colon suggested multiple crossing points. Many foci were unassociated with visible Peyer's patches, implying that transduced cells lay in proximity to villous rather than follicle-associated epithelium, as supported by detection of transgene-encoded antigen in villous epithelial cells. Transgene-encoded mRNA but not protein was readily detected in Peyer's patches, suggesting that post-transcriptional regulation of viral gene expression might limit expression of transgene-encoded antigen in this tissue. To characterize the pathways by which the vector crossed the intestinal epithelium and encountered sentinel cells, a fluorescent-labeled vector was administered to mice by the intragastric route or inoculated into ligated intestinal loops comprising a Peyer's patch. The vector adhered selectively to microfold cells in the follicle-associated epithelium, and, after translocation to the subepithelial dome region, was captured by phagocytes that expressed CD11c and lysozyme. In conclusion, although a large number of crossing events took place throughout the intestine within and without Peyer's patches, multiple firewalls prevented systemic dissemination of vector and suppressed production of transgene-encoded protein in Peyer's patches. PMID:29423380

Simulation of a method to directly image exoplanets around multiple stars systems

NASA Astrophysics Data System (ADS)

Thomas, Sandrine J.; Bendek, Eduardo; Belikov, Ruslan

2014-08-01

Direct imaging of extra-solar planets has now become a reality, especially with the deployment and commissioning of the first generation of specialized ground-based instruments such as the GPI, SPHERE, P1640 and SCExAO. These systems will allow detection of planets 107 times fainter than their host star. For space- based missions, such as EXCEDE, EXO-C, EXO-S, WFIRST/AFTA, different teams have shown in laboratories contrasts reaching 10-10 within a few diffraction limits from the star using a combination of a coronagraph to suppress light coming from the host star and a wavefront control system. These demonstrations use a de- formable mirror (DM) to remove residual starlight (speckles) created by the imperfections of telescope. However, all these current and future systems focus on detecting faint planets around a single host star or unresolved bi- naries/multiples, while several targets or planet candidates are located around nearby binary stars such as our neighbor star Alpha Centauri. Until now, it has been thought that removing the light of a companion star is impossible with current technology, excluding binary star systems from target lists of direct imaging missions. Direct imaging around binaries/multiple systems at a level of contrast allowing Earth-like planet detection is challenging because the region of interest, where a dark zone is essential, is contaminated by the light coming from the hosts star companion. We propose a method to simultaneously correct aberrations and diffraction of light coming from the target star as well as its companion star in order to reveal planets orbiting the target star. This method works even if the companion star is outside the control region of the DM (beyond its half-Nyquist frequency), by taking advantage of aliasing effects.

A multitask clustering approach for single-cell RNA-seq analysis in Recessive Dystrophic Epidermolysis Bullosa

PubMed Central

Petegrosso, Raphael; Tolar, Jakub

2018-01-01

Single-cell RNA sequencing (scRNA-seq) has been widely applied to discover new cell types by detecting sub-populations in a heterogeneous group of cells. Since scRNA-seq experiments have lower read coverage/tag counts and introduce more technical biases compared to bulk RNA-seq experiments, the limited number of sampled cells combined with the experimental biases and other dataset specific variations presents a challenge to cross-dataset analysis and discovery of relevant biological variations across multiple cell populations. In this paper, we introduce a method of variance-driven multitask clustering of single-cell RNA-seq data (scVDMC) that utilizes multiple single-cell populations from biological replicates or different samples. scVDMC clusters single cells in multiple scRNA-seq experiments of similar cell types and markers but varying expression patterns such that the scRNA-seq data are better integrated than typical pooled analyses which only increase the sample size. By controlling the variance among the cell clusters within each dataset and across all the datasets, scVDMC detects cell sub-populations in each individual experiment with shared cell-type markers but varying cluster centers among all the experiments. Applied to two real scRNA-seq datasets with several replicates and one large-scale droplet-based dataset on three patient samples, scVDMC more accurately detected cell populations and known cell markers than pooled clustering and other recently proposed scRNA-seq clustering methods. In the case study applied to in-house Recessive Dystrophic Epidermolysis Bullosa (RDEB) scRNA-seq data, scVDMC revealed several new cell types and unknown markers validated by flow cytometry. MATLAB/Octave code available at https://github.com/kuanglab/scVDMC. PMID:29630593

ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences.

PubMed

Bonizzoni, Paola; Rizzi, Raffaella; Pesole, Graziano

2005-10-05

Currently available methods to predict splice sites are mainly based on the independent and progressive alignment of transcript data (mostly ESTs) to the genomic sequence. Apart from often being computationally expensive, this approach is vulnerable to several problems--hence the need to develop novel strategies. We propose a method, based on a novel multiple genome-EST alignment algorithm, for the detection of splice sites. To avoid limitations of splice sites prediction (mainly, over-predictions) due to independent single EST alignments to the genomic sequence our approach performs a multiple alignment of transcript data to the genomic sequence based on the combined analysis of all available data. We recast the problem of predicting constitutive and alternative splicing as an optimization problem, where the optimal multiple transcript alignment minimizes the number of exons and hence of splice site observations. We have implemented a splice site predictor based on this algorithm in the software tool ASPIC (Alternative Splicing PredICtion). It is distinguished from other methods based on BLAST-like tools by the incorporation of entirely new ad hoc procedures for accurate and computationally efficient transcript alignment and adopts dynamic programming for the refinement of intron boundaries. ASPIC also provides the minimal set of non-mergeable transcript isoforms compatible with the detected splicing events. The ASPIC web resource is dynamically interconnected with the Ensembl and Unigene databases and also implements an upload facility. Extensive bench marking shows that ASPIC outperforms other existing methods in the detection of novel splicing isoforms and in the minimization of over-predictions. ASPIC also requires a lower computation time for processing a single gene and an EST cluster. The ASPIC web resource is available at http://aspic.algo.disco.unimib.it/aspic-devel/.

Study on the Spatial Resolution of Single and Multiple Coincidences Compton Camera

NASA Astrophysics Data System (ADS)

Andreyev, Andriy; Sitek, Arkadiusz; Celler, Anna

2012-10-01

In this paper we study the image resolution that can be obtained from the Multiple Coincidences Compton Camera (MCCC). The principle of MCCC is based on a simultaneous acquisition of several gamma-rays emitted in cascade from a single nucleus. Contrary to a standard Compton camera, MCCC can theoretically provide the exact location of a radioactive source (based only on the identification of the intersection point of three cones created by a single decay), without complicated tomographic reconstruction. However, practical implementation of the MCCC approach encounters several problems, such as low detection sensitivities result in very low probability of coincident triple gamma-ray detection, which is necessary for the source localization. It is also important to evaluate how the detection uncertainties (finite energy and spatial resolution) influence identification of the intersection of three cones, thus the resulting image quality. In this study we investigate how the spatial resolution of the reconstructed images using the triple-cone reconstruction (TCR) approach compares to images reconstructed from the same data using standard iterative method based on single-cone. Results show, that FWHM for the point source reconstructed with TCR was 20-30% higher than the one obtained from the standard iterative reconstruction based on expectation maximization (EM) algorithm and conventional single-cone Compton imaging. Finite energy and spatial resolutions of the MCCC detectors lead to errors in conical surfaces definitions (“thick” conical surfaces) which only amplify in image reconstruction when intersection of three cones is being sought. Our investigations show that, in spite of being conceptually appealing, the identification of triple cone intersection constitutes yet another restriction of the multiple coincidence approach which limits the image resolution that can be obtained with MCCC and TCR algorithm.

The absolute threshold of cone vision

PubMed Central

Koeing, Darran; Hofer, Heidi

2013-01-01

We report measurements of the absolute threshold of cone vision, which has been previously underestimated due to sub-optimal conditions or overly strict subjective response criteria. We avoided these limitations by using optimized stimuli and experimental conditions while having subjects respond within a rating scale framework. Small (1′ fwhm), brief (34 msec), monochromatic (550 nm) stimuli were foveally presented at multiple intensities in dark-adapted retina for 5 subjects. For comparison, 4 subjects underwent similar testing with rod-optimized stimuli. Cone absolute threshold, that is, the minimum light energy for which subjects were just able to detect a visual stimulus with any response criterion, was 203 ± 38 photons at the cornea, ∼0.47 log units lower than previously reported. Two-alternative forced-choice measurements in a subset of subjects yielded consistent results. Cone thresholds were less responsive to criterion changes than rod thresholds, suggesting a limit to the stimulus information recoverable from the cone mosaic in addition to the limit imposed by Poisson noise. Results were consistent with expectations for detection in the face of stimulus uncertainty. We discuss implications of these findings for modeling the first stages of human cone vision and interpreting psychophysical data acquired with adaptive optics at the spatial scale of the receptor mosaic. PMID:21270115

Lesion classification using clinical and visual data fusion by multiple kernel learning

NASA Astrophysics Data System (ADS)

Kisilev, Pavel; Hashoul, Sharbell; Walach, Eugene; Tzadok, Asaf

2014-03-01

To overcome operator dependency and to increase diagnosis accuracy in breast ultrasound (US), a lot of effort has been devoted to developing computer-aided diagnosis (CAD) systems for breast cancer detection and classification. Unfortunately, the efficacy of such CAD systems is limited since they rely on correct automatic lesions detection and localization, and on robustness of features computed based on the detected areas. In this paper we propose a new approach to boost the performance of a Machine Learning based CAD system, by combining visual and clinical data from patient files. We compute a set of visual features from breast ultrasound images, and construct the textual descriptor of patients by extracting relevant keywords from patients' clinical data files. We then use the Multiple Kernel Learning (MKL) framework to train SVM based classifier to discriminate between benign and malignant cases. We investigate different types of data fusion methods, namely, early, late, and intermediate (MKL-based) fusion. Our database consists of 408 patient cases, each containing US images, textual description of complaints and symptoms filled by physicians, and confirmed diagnoses. We show experimentally that the proposed MKL-based approach is superior to other classification methods. Even though the clinical data is very sparse and noisy, its MKL-based fusion with visual features yields significant improvement of the classification accuracy, as compared to the image features only based classifier.

Poly(dimethylsiloxane) microchip-based immunoassay with multiple reaction zones: Toward on-chip multiplex detection platform

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

Shao, Guocheng; Wang, Jun; Li, Zhaohui

2011-09-20

In this work, a poly(dimethylsiloxane) (PDMS) microchip-based immuno-sensing platform with integrated pneumatic micro valves is described. The microchip was fabricated with multiple layer soft lithography technology. By controlling the activation status of corresponding valves, reagent flows in the microchannel network can be well manipulated so that immuno-reactions only take place at designated reaction zones (DRZs). Four DRZs are included in the prototype microchip. Since these DRZs are all isolated from each other by micro valves, cross contamination is prevented. Using the inner surface of the all-PDMS microchannel as immunoassay substrate, on-chip sandwich format solid phase immunoassay was performed to demonstratemore » the feasibility of this immuno-sensing platform. Mouse IgG and fluorescein isothiocyanate (FITC) were used as the model analyte and the signal reporter respectively. Only 10 ul sample is needed for the assay and low detection limit of 5 ng/ml (≈33 pM) was achieved though low-cost polyclonal antibodies were used in our experiment for feasibility study only. The encouraging results from mouse IgG immunoassay proved the feasibility of our microchip design. With slight modification of the assay protocol, the same chip design can be used for multi-target detection and can provide a simple, cost-effective and integrated microchip solution for multiplex immunoassay applications.« less

Surface-Enhanced Raman Scattering-Based Immunoassay Technologies for Detection of Disease Biomarkers

PubMed Central

Smolsky, Joseph; Kaur, Sukhwinder; Hayashi, Chihiro; Batra, Surinder K.; Krasnoslobodtsev, Alexey V.

2017-01-01

Detection of biomarkers is of vital importance in disease detection, management, and monitoring of therapeutic efficacy. Extensive efforts have been devoted to the development of novel diagnostic methods that detect and quantify biomarkers with higher sensitivity and reliability, contributing to better disease diagnosis and prognosis. When it comes to such devastating diseases as cancer, these novel powerful methods allow for disease staging as well as detection of cancer at very early stages. Over the past decade, there have been some advances in the development of platforms for biomarker detection of diseases. The main focus has recently shifted to the development of simple and reliable diagnostic tests that are inexpensive, accurate, and can follow a patient’s disease progression and therapy response. The individualized approach in biomarker detection has been also emphasized with detection of multiple biomarkers in body fluids such as blood and urine. This review article covers the developments in Surface-Enhanced Raman Scattering (SERS) and related technologies with the primary focus on immunoassays. Limitations and advantages of the SERS-based immunoassay platform are discussed. The article thoroughly describes all components of the SERS immunoassay and highlights the superior capabilities of SERS readout strategy such as high sensitivity and simultaneous detection of a multitude of biomarkers. Finally, it introduces recently developed strategies for in vivo biomarker detection using SERS. PMID:28085088

Interfacial nano-mixing in a miniaturised platform enables signal enhancement and in situ detection of cancer biomarkers.

PubMed

Wuethrich, Alain; Sina, Abu Ali Ibn; Ahmed, Mostak; Lin, Ting-Yun; Carrascosa, Laura G; Trau, Matt

2018-06-14

Interfacial biosensing performs the detection of biomolecules at the bare-metal interface for disease diagnosis by comparing how biological species derived from patients and healthy individuals interact with bare metal surfaces. This technique retrieves clinicopathological information without complex surface functionalisation which is a major limitation of conventional techniques. However, it is still challenging to detect subtle molecular changes by interfacial biosensing, and the detection often requires prolonged sensing times due to the slow diffusion process of the biomolecules towards the sensor surface. Herein, we report on a novel strategy for interfacial biosensing which involves in situ electrochemical detection under the action of an electric field-induced nanoscopic flow at nanometre distance to the sensing surface. This nanomixing significantly increases target adsorption, reduces sensing time, and enables the detection of small molecular changes with enhanced sensitivity. Using a multiplex electrochemical microdevice that enables nanomixing and in situ label-free electrochemical detection, we demonstrate the detection of multiple cancer biomarkers on the same device. We present data for the detection of aberrant phosphorylation in the EGFR protein and hypermethylation in the EN1 gene region. Our method significantly shortens the assay period (from 40 min and 20 min to 3 minutes for protein and DNA, respectively), increases the sensitivity by up to two orders of magnitude, and improves detection specificity.

Detection limit of intragenic deletions with targeted array comparative genomic hybridization

PubMed Central

2013-01-01

Background Pathogenic mutations range from single nucleotide changes to deletions or duplications that encompass a single exon to several genes. The use of gene-centric high-density array comparative genomic hybridization (aCGH) has revolutionized the detection of intragenic copy number variations. We implemented an exon-centric design of high-resolution aCGH to detect single- and multi-exon deletions and duplications in a large set of genes using the OGT 60 K and 180 K arrays. Here we describe the molecular characterization and breakpoint mapping of deletions at the smaller end of the detectable range in several genes using aCGH. Results The method initially implemented to detect single to multiple exon deletions, was able to detect deletions much smaller than anticipated. The selected deletions we describe vary in size, ranging from over 2 kb to as small as 12 base pairs. The smallest of these deletions are only detectable after careful manual review during data analysis. Suspected deletions smaller than the detection size for which the method was optimized, were rigorously followed up and confirmed with PCR-based investigations to uncover the true detection size limit of intragenic deletions with this technology. False-positive deletion calls often demonstrated single nucleotide changes or an insertion causing lower hybridization of probes demonstrating the sensitivity of aCGH. Conclusions With optimizing aCGH design and careful review process, aCGH can uncover intragenic deletions as small as dozen bases. These data provide insight that will help optimize probe coverage in array design and illustrate the true assay sensitivity. Mapping of the breakpoints confirms smaller deletions and contributes to the understanding of the mechanism behind these events. Our knowledge of the mutation spectra of several genes can be expected to change as previously unrecognized intragenic deletions are uncovered. PMID:24304607

(Sub)millimetre interferometric imaging of a sample of COSMOS/AzTEC submillimetre galaxies. I. Multiwavelength identifications and redshift distribution

NASA Astrophysics Data System (ADS)

Miettinen, O.; Smolčić, V.; Novak, M.; Aravena, M.; Karim, A.; Masters, D.; Riechers, D. A.; Bussmann, R. S.; McCracken, H. J.; Ilbert, O.; Bertoldi, F.; Capak, P.; Feruglio, C.; Halliday, C.; Kartaltepe, J. S.; Navarrete, F.; Salvato, M.; Sanders, D.; Schinnerer, E.; Sheth, K.

2015-05-01

We used the Plateau de Bure Interferometer (PdBI) to map a sample of 15 submillimetre galaxies (SMGs) in the COSMOS field at the wavelength of 1.3 mm. The target SMGs were originally discovered in the James Clerk Maxwell Telescope (JCMT)/AzTEC 1.1 mm continuum survey at S/N1.1 mm = 4-4.5. This paper presents, for the first time, interferometric millimetre-wavelength observations of these sources. The angular resolution of our observations, 1''&dotbelow;8, allowed us to accurately determine the positions of the target SMGs. Using a detection threshold of S/N1.3 mm> 4.5 regardless of multiwavelength counterpart association, and 4